Using CUDA within Spark / boosting linear algebra

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Re: Using CUDA within Spark / boosting linear algebra

fommil
John, I have to disagree with you there. Dense matrices come up a lot in
industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <[hidden email]> wrote:

>  I mentioned this earlier in the thread, but I'll put it out again. Dense
> BLAS are not very important for most machine learning workloads: at least
> for non-image workloads in industry (and for image processing you would
> probably want a deep learning/SGD solution with convolution kernels). e.g.
> it was only relevant for 1/7 of our recent benchmarks, which should be a
> reasonable sample. What really matters is sparse BLAS performance. BIDMat
> is still an order of magnitude faster there. Those kernels are only in
> BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.
>
> Its also the case that the overall performance of an algorithm is
> determined by the slowest kernel, not the fastest. If the goal is to get
> closer to BIDMach's performance on typical problems, you need to make sure
> that every kernel goes at comparable speed. So the real question is how
> much faster MLLib routines do on a complete problem with/without GPU
> acceleration. For BIDMach, its close to a factor of 10. But that required
> running entirely on the GPU, and making sure every kernel is close to its
> limit.
>
> -John
>
> If you think nvblas would be helpful, you should try it in some end-to-end
> benchmarks.
> On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
>
> Yeah, much more reasonable - nice to know that we can get full GPU
> performance from breeze/netlib-java - meaning there's no compelling
> performance reason to switch out our current linear algebra library (at
> least as far as this benchmark is concerned).
>
>  Instead, it looks like a user guide for configuring Spark/MLlib to use
> the right BLAS library will get us most of the way there. Or, would it make
> sense to finally ship openblas compiled for some common platforms (64-bit
> linux, windows, mac) directly with Spark - hopefully eliminating the jblas
> warnings once and for all for most users? (Licensing is BSD) Or am I
> missing something?
>
> On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
> [hidden email]> wrote:
>
>> As everyone suggested, the results were too good to be true, so I
>> double-checked them. It turns that nvblas did not do multiplication due to
>> parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My
>> previously posted results with nvblas are matrices copying only. The
>> default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I
>> handpicked other values that worked. As a result, netlib+nvblas is on par
>> with BIDMat-cuda. As promised, I am going to post a how-to for nvblas
>> configuration.
>>
>>
>> https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
>>
>>
>>
>> -----Original Message-----
>> From: Ulanov, Alexander
>> Sent: Wednesday, March 25, 2015 2:31 PM
>> To: Sam Halliday
>>  Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R.
>> Sparks; jfcanny
>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>
>> Hi again,
>>
>> I finally managed to use nvblas within Spark+netlib-java. It has
>> exceptional performance for big matrices with Double, faster than
>> BIDMat-cuda with Float. But for smaller matrices, if you will copy them
>> to/from GPU, OpenBlas or MKL might be a better choice. This correlates with
>> original nvblas presentation on GPU conf 2013 (slide 21):
>> http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf
>>
>> My results:
>>
>> https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
>>
>> Just in case, these tests are not for generalization of performance of
>> different libraries. I just want to pick a library that does at best dense
>> matrices multiplication for my task.
>>
>> P.S. My previous issue with nvblas was the following: it has Fortran blas
>> functions, at the same time netlib-java uses C cblas functions. So, one
>> needs cblas shared library to use nvblas through netlib-java. Fedora does
>> not have cblas (but Debian and Ubuntu have), so I needed to compile it. I
>> could not use cblas from Atlas or Openblas because they link to their
>> implementation and not to Fortran blas.
>>
>> Best regards, Alexander
>>
>> -----Original Message-----
>> From: Ulanov, Alexander
>> Sent: Tuesday, March 24, 2015 6:57 PM
>> To: Sam Halliday
>> Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>
>> Hi,
>>
>> I am trying to use nvblas with netlib-java from Spark. nvblas functions
>> should replace current blas functions calls after executing LD_PRELOAD as
>> suggested in http://docs.nvidia.com/cuda/nvblas/#Usage without any
>> changes to netlib-java. It seems to work for simple Java example, but I
>> cannot make it work with Spark. I run the following:
>> export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
>> env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell
>> --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
>>
>> +-----------------------------------------------------------------------------+
>> | Processes:                                                       GPU
>> Memory |
>> |  GPU       PID  Type  Process name                               Usage
>>     |
>>
>> |=============================================================================|
>> |    0      8873    C   bash
>> 39MiB |
>> |    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java
>> 39MiB |
>>
>> +-----------------------------------------------------------------------------+
>>
>> In Spark shell I do matrix multiplication and see the following:
>> 15/03/25 06:48:01 INFO JniLoader: successfully loaded
>> /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
>> So I am sure that netlib-native is loaded and cblas supposedly used.
>> However, matrix multiplication does executes on CPU since I see 16% of CPU
>> used and 0% of GPU used. I also checked different matrix sizes, from
>> 100x100 to 12000x12000
>>
>> Could you suggest might the LD_PRELOAD not affect Spark shell?
>>
>> Best regards, Alexander
>>
>>
>>
>> From: Sam Halliday [mailto:[hidden email]]
>> Sent: Monday, March 09, 2015 6:01 PM
>> To: Ulanov, Alexander
>> Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>
>>
>> Thanks so much for following up on this!
>>
>> Hmm, I wonder if we should have a concerted effort to chart performance
>> on various pieces of hardware...
>> On 9 Mar 2015 21:08, "Ulanov, Alexander" <[hidden email]<mailto:
>> [hidden email]>> wrote:
>> Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the
>> comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the
>> support of Double in the current source code), did the test with BIDMat and
>> CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.
>>
>>
>> https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
>>
>> Best regards, Alexander
>>
>> -----Original Message-----
>> From: Sam Halliday [mailto:[hidden email]<mailto:
>> [hidden email]>]
>> Sent: Tuesday, March 03, 2015 1:54 PM
>> To: Xiangrui Meng; Joseph Bradley
>> Cc: Evan R. Sparks; Ulanov, Alexander; [hidden email]<mailto:
>> [hidden email]>
>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>
>> BTW, is anybody on this list going to the London Meetup in a few weeks?
>>
>>
>> https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community
>>
>> Would be nice to meet other people working on the guts of Spark! :-)
>>
>>
>> Xiangrui Meng <[hidden email]<mailto:[hidden email]>> writes:
>>
>> > Hey Alexander,
>> >
>> > I don't quite understand the part where netlib-cublas is about 20x
>> > slower than netlib-openblas. What is the overhead of using a GPU BLAS
>> > with netlib-java?
>> >
>> > CC'ed Sam, the author of netlib-java.
>> >
>> > Best,
>> > Xiangrui
>> >
>> > On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <[hidden email]
>> <mailto:[hidden email]>> wrote:
>> >> Better documentation for linking would be very helpful!  Here's a JIRA:
>> >> https://issues.apache.org/jira/browse/SPARK-6019
>> >>
>> >>
>> >> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> >> <[hidden email]<mailto:[hidden email]>>
>> >> wrote:
>> >>
>> >>> Thanks for compiling all the data and running these benchmarks,
>> >>> Alex. The big takeaways here can be seen with this chart:
>> >>>
>> >>> https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>> >>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>> >>>
>> >>> 1) A properly configured GPU matrix multiply implementation (e.g.
>> >>> BIDMat+GPU) can provide substantial (but less than an order of
>> >>> BIDMat+magnitude)
>> >>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>> >>> netlib-java+openblas-compiled).
>> >>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>> >>> worse than a well-tuned CPU implementation, particularly for larger
>> matrices.
>> >>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>> >>> basically agrees with the authors own benchmarks (
>> >>> https://github.com/fommil/netlib-java)
>> >>>
>> >>> I think that most of our users are in a situation where using GPUs
>> >>> may not be practical - although we could consider having a good GPU
>> >>> backend available as an option. However, *ALL* users of MLlib could
>> >>> benefit (potentially tremendously) from using a well-tuned CPU-based
>> >>> BLAS implementation. Perhaps we should consider updating the mllib
>> >>> guide with a more complete section for enabling high performance
>> >>> binaries on OSX and Linux? Or better, figure out a way for the
>> >>> system to fetch these automatically.
>> >>>
>> >>> - Evan
>> >>>
>> >>>
>> >>>
>> >>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>> >>> [hidden email]<mailto:[hidden email]>> wrote:
>> >>>
>> >>>> Just to summarize this thread, I was finally able to make all
>> >>>> performance comparisons that we discussed. It turns out that:
>> >>>> BIDMat-cublas>>BIDMat
>> >>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>> >>>> =netlib-cublas>netlib-blas>f2jblas
>> >>>>
>> >>>> Below is the link to the spreadsheet with full results.
>> >>>>
>> >>>> https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>> >>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>> >>>>
>> >>>> One thing still needs exploration: does BIDMat-cublas perform
>> >>>> copying to/from machine’s RAM?
>> >>>>
>> >>>> -----Original Message-----
>> >>>> From: Ulanov, Alexander
>> >>>> Sent: Tuesday, February 10, 2015 2:12 PM
>> >>>> To: Evan R. Sparks
>> >>>> Cc: Joseph Bradley;
>> >>>> [hidden email]<mailto:[hidden email]>
>> >>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>> >>>> the original one discusses slightly different topic. I was able to
>> >>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>> >>>> statically linked inside a 60MB library.
>> >>>>
>> >>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>> >>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>> >>>>
>> +-----------------------------------------------------------------------+
>> >>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>> >>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>> >>>> |1,638475459 |
>> >>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>> >>>> 1569,233228 |
>> >>>>
>> >>>> It turn out that pre-compiled MKL is faster than precompiled
>> >>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>> >>>> locally compiled openblas and cuda.
>> >>>>
>> >>>> Alexander
>> >>>>
>> >>>> From: Evan R. Sparks
>> >>>> [mailto:[hidden email]<mailto:[hidden email]>]
>> >>>> Sent: Monday, February 09, 2015 6:06 PM
>> >>>> To: Ulanov, Alexander
>> >>>> Cc: Joseph Bradley;
>> >>>> [hidden email]<mailto:[hidden email]>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> Great - perhaps we can move this discussion off-list and onto a
>> >>>> JIRA ticket? (Here's one:
>> >>>> https://issues.apache.org/jira/browse/SPARK-5705)
>> >>>>
>> >>>> It seems like this is going to be somewhat exploratory for a while
>> >>>> (and there's probably only a handful of us who really care about
>> >>>> fast linear
>> >>>> algebra!)
>> >>>>
>> >>>> - Evan
>> >>>>
>> >>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>> wrote:
>> >>>> Hi Evan,
>> >>>>
>> >>>> Thank you for explanation and useful link. I am going to build
>> >>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>> >>>>
>> >>>> Do I understand correctly that BIDMat binaries contain statically
>> >>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>> >>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>> >>>> wonder if it is OK because Intel sells this library. Nevertheless,
>> >>>> it seems that in my case precompiled MKL BLAS performs better than
>> >>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed
>> to be on par with JNI overheads.
>> >>>>
>> >>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>> >>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>> >>>> Halliday
>> >>>> (Netlib-java) interested to compare their libraries.
>> >>>>
>> >>>> Best regards, Alexander
>> >>>>
>> >>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>]
>> >>>> Sent: Friday, February 06, 2015 5:58 PM
>> >>>>
>> >>>> To: Ulanov, Alexander
>> >>>> Cc: Joseph Bradley;
>> >>>> [hidden email]<mailto:[hidden email]><mailto:dev@spark.
>> >>>> apache.org<mailto:[hidden email]>>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> I would build OpenBLAS yourself, since good BLAS performance comes
>> >>>> from getting cache sizes, etc. set up correctly for your particular
>> >>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>> >>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>> >>>> quickly and yields performance competitive with MKL.
>> >>>>
>> >>>> To make sure the right library is getting used, you have to make
>> >>>> sure it's first on the search path - export
>> >>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>> >>>>
>> >>>> For some examples of getting netlib-java setup on an ec2 node and
>> >>>> some example benchmarking code we ran a while back, see:
>> >>>> https://github.com/shivaram/matrix-bench
>> >>>>
>> >>>> In particular - build-openblas-ec2.sh shows you how to build the
>> >>>> library and set up symlinks correctly, and scala/run-netlib.sh
>> >>>> shows you how to get the path setup and get that library picked up
>> by netlib-java.
>> >>>>
>> >>>> In this way - you could probably get cuBLAS set up to be used by
>> >>>> netlib-java as well.
>> >>>>
>> >>>> - Evan
>> >>>>
>> >>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>> wrote:
>> >>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>> >>>> force loading the right blas? For netlib, I there are few JVM
>> >>>> flags, such as
>> >>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>> >>>> so I can force it to use Java implementation. Not sure I understand
>> how to force use a specific blas (not specific wrapper for blas).
>> >>>>
>> >>>> Btw. I have installed openblas (yum install openblas), so I suppose
>> >>>> that netlib is using it.
>> >>>>
>> >>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>]
>> >>>> Sent: Friday, February 06, 2015 5:19 PM
>> >>>> To: Ulanov, Alexander
>> >>>> Cc: Joseph Bradley;
>> >>>> [hidden email]<mailto:[hidden email]><mailto:dev@spark.
>> >>>> apache.org<mailto:[hidden email]>>
>> >>>>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> Getting breeze to pick up the right blas library is critical for
>> >>>> performance. I recommend using OpenBLAS (or MKL, if you already have
>> it).
>> >>>> It might make sense to force BIDMat to use the same underlying BLAS
>> >>>> library as well.
>> >>>>
>> >>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>> wrote:
>> >>>> Hi Evan, Joseph
>> >>>>
>> >>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>> >>>> faster than netlib-java+breeze (sorry for weird table formatting):
>> >>>>
>> >>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>> >>>> |native_system_linux_x86-64|
>> >>>> Breeze+Netlib-java f2jblas |
>> >>>>
>> +-----------------------------------------------------------------------+
>> >>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>> >>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>> >>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>> >>>> ||
>> >>>>
>> >>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>> >>>> 19 Linux, Scala 2.11.
>> >>>>
>> >>>> Later I will make tests with Cuda. I need to install new Cuda
>> >>>> version for this purpose.
>> >>>>
>> >>>> Do you have any ideas why breeze-netlib with native blas is so much
>> >>>> slower than BIDMat MKL?
>> >>>>
>> >>>> Best regards, Alexander
>> >>>>
>> >>>> From: Joseph Bradley [mailto:[hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>]
>> >>>> Sent: Thursday, February 05, 2015 5:29 PM
>> >>>> To: Ulanov, Alexander
>> >>>> Cc: Evan R. Sparks;
>> >>>> [hidden email]<mailto:[hidden email]><mailto:dev@spark.
>> >>>> apache.org<mailto:[hidden email]>>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> Hi Alexander,
>> >>>>
>> >>>> Using GPUs with Spark would be very exciting.  Small comment:
>> >>>> Concerning your question earlier about keeping data stored on the
>> >>>> GPU rather than having to move it between main memory and GPU
>> >>>> memory on each iteration, I would guess this would be critical to
>> >>>> getting good performance.  If you could do multiple local
>> >>>> iterations before aggregating results, then the cost of data
>> >>>> movement to the GPU could be amortized (and I believe that is done
>> >>>> in practice).  Having Spark be aware of the GPU and using it as
>> another part of memory sounds like a much bigger undertaking.
>> >>>>
>> >>>> Joseph
>> >>>>
>> >>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>> wrote:
>> >>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>> >>>> John Canny and I am really inspired by his talk and comparisons with
>> Spark MLlib.
>> >>>>
>> >>>> I am very interested to find out what will be better within Spark:
>> >>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>> >>>> fair way to benchmark them? Currently I do benchmarks on artificial
>> >>>> neural networks in batch mode. While it is not a “pure” test of
>> >>>> linear algebra, it involves some other things that are essential to
>> machine learning.
>> >>>>
>> >>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>]
>> >>>> Sent: Thursday, February 05, 2015 1:29 PM
>> >>>> To: Ulanov, Alexander
>> >>>> Cc:
>> >>>> [hidden email]<mailto:[hidden email]><mailto:dev@spark.
>> >>>> apache.org<mailto:[hidden email]>>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>> >>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>> >>>> netlib-java+data
>> >>>> layout and fewer levels of indirection - it's definitely a
>> >>>> worthwhile experiment to run. The main speedups I've seen from
>> >>>> using it come from highly optimized GPU code for linear algebra. I
>> >>>> know that in the past Canny has gone as far as to write custom GPU
>> >>>> kernels for performance-critical regions of code.[1]
>> >>>>
>> >>>> BIDMach is highly optimized for single node performance or
>> >>>> performance on small clusters.[2] Once data doesn't fit easily in
>> >>>> GPU memory (or can be batched in that way) the performance tends to
>> >>>> fall off. Canny argues for hardware/software codesign and as such
>> >>>> prefers machine configurations that are quite different than what
>> >>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and
>> 4 GPUs.
>> >>>>
>> >>>> In contrast, MLlib was designed for horizontal scalability on
>> >>>> commodity clusters and works best on very big datasets - order of
>> terabytes.
>> >>>>
>> >>>> For the most part, these projects developed concurrently to address
>> >>>> slightly different use cases. That said, there may be bits of
>> >>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>> >>>> careful about maintaining cross-language compatibility for our Java
>> >>>> and Python-users, though.
>> >>>>
>> >>>> - Evan
>> >>>>
>> >>>> [1] - http://arxiv.org/abs/1409.5402 [2] -
>> >>>> http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>> >>>>
>> >>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>><mailto:
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>>> wrote:
>> >>>> Hi Evan,
>> >>>>
>> >>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>> >>>> you know what makes them faster than netlib-java?
>> >>>>
>> >>>> The same group has BIDMach library that implements machine
>> >>>> learning. For some examples they use Caffe convolutional neural
>> >>>> network library owned by another group in Berkeley. Could you
>> >>>> elaborate on how these all might be connected with Spark Mllib? If
>> >>>> you take BIDMat for linear algebra why don’t you take BIDMach for
>> optimization and learning?
>> >>>>
>> >>>> Best regards, Alexander
>> >>>>
>> >>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>><mailto:
>> [hidden email]<mailto:[hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>>]
>> >>>> Sent: Thursday, February 05, 2015 12:09 PM
>> >>>> To: Ulanov, Alexander
>> >>>> Cc: [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>><mailto:
>> >>>> [hidden email]<mailto:[hidden email]><mailto:dev@spark.
>> >>>> apache.org<mailto:[hidden email]>>>
>> >>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>> >>>>
>> >>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>> >>>> blas in many cases.
>> >>>>
>> >>>> You might consider taking a look at the codepaths that BIDMat (
>> >>>> https://github.com/BIDData/BIDMat) takes and comparing them to
>> >>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>> >>>> optimizing to make this work really fast from Scala. I've run it on
>> >>>> my laptop and compared to MKL and in certain cases it's 10x faster
>> at matrix multiply.
>> >>>> There are a lot of layers of indirection here and you really want
>> >>>> to avoid data copying as much as possible.
>> >>>>
>> >>>> We could also consider swapping out BIDMat for Breeze, but that
>> >>>> would be a big project and if we can figure out how to get
>> >>>> breeze+cublas to comparable performance that would be a big win.
>> >>>>
>> >>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>><mailto:
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> [hidden email]<mailto:[hidden email]>>>> wrote:
>> >>>> Dear Spark developers,
>> >>>>
>> >>>> I am exploring how to make linear algebra operations faster within
>> Spark.
>> >>>> One way of doing this is to use Scala Breeze library that is
>> >>>> bundled with Spark. For matrix operations, it employs Netlib-java
>> >>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>> >>>> and LAPACK native binaries if they are available on the worker
>> >>>> node. It also has its own optimized Java implementation of BLAS. It
>> >>>> is worth mentioning, that native binaries provide better performance
>> only for BLAS level 3, i.e.
>> >>>> matrix-matrix operations or general matrix multiplication (GEMM).
>> >>>> This is confirmed by GEMM test on Netlib-java page
>> >>>> https://github.com/fommil/netlib-java. I also confirmed it with my
>> >>>> experiments with training of artificial neural network
>> >>>> https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>> >>>> However, I would like to boost performance more.
>> >>>>
>> >>>> GPU is supposed to work fast with linear algebra and there is
>> >>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>> >>>> server with Nvidia GPU and I was able to do the following. I linked
>> >>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>> >>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>> >>>> performance measurements with regards to artificial neural network
>> >>>> batch learning in Spark MLlib that involves matrix-matrix
>> >>>> multiplications. It turns out that for matrices of size less than
>> >>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>> >>>> slower for bigger matrices. It worth mentioning that it is was not a
>> test for ONLY multiplication since there are other operations involved.
>> >>>> One of the reasons for slowdown might be the overhead of copying
>> >>>> the matrices from computer memory to graphic card memory and back.
>> >>>>
>> >>>> So, few questions:
>> >>>> 1) Do these results with CUDA make sense?
>> >>>> 2) If the problem is with copy overhead, are there any libraries
>> >>>> that allow to force intermediate results to stay in graphic card
>> >>>> memory thus removing the overhead?
>> >>>> 3) Any other options to speed-up linear algebra in Spark?
>> >>>>
>> >>>> Thank you, Alexander
>> >>>>
>> >>>> -------------------------------------------------------------------
>> >>>> -- To unsubscribe, e-mail: [hidden email]<mailto:
>> [hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]
>> >>>> e.org>><mailto:[hidden email]<mailto:dev-unsubscribe@sp
>> >>>> ark.apac> he.org<http://he.org>
>> >>>> <mailto:[hidden email]<mailto:dev-unsubscribe@spa
>> >>>> rk.apache.org>>> For additional commands, e-mail:
>> >>>> [hidden email]<mailto:[hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>><mailto:
>> [hidden email]<mailto:[hidden email]><mailto:
>> >>>> [hidden email]<mailto:[hidden email]>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>
>>
>> --
>> Best regards,
>> Sam
>>
>
>
>
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Re: Using CUDA within Spark / boosting linear algebra

Sean Owen
In reply to this post by Evan R. Sparks
The license issue is with libgfortran, rather than OpenBLAS.

(FWIW I am going through the motions to get OpenBLAS set up by default
on CDH in the near future, and the hard part is just handling
libgfortran.)

On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
> Alright Sam - you are the expert here. If the GPL issues are unavoidable,
> that's fine - what is the exact bit of code that is GPL?
>
> The suggestion to use OpenBLAS is not to say it's the best option, but that
> it's a *free, reasonable default* for many users - keep in mind the most
> common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
> Additionally, for many of the problems we're targeting, this reasonable
> default can provide a 1-2 orders of magnitude improvement in performance
> over the f2jblas implementation that netlib-java falls back on.

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Re: Using CUDA within Spark / boosting linear algebra

Xiangrui Meng
Hi Alex,

Since it is non-trivial to make nvblas work with netlib-java, it would
be great if you can send the instructions to netlib-java as part of
the README. Hopefully we don't need to modify netlib-java code to use
nvblas.

Best,
Xiangrui

On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:

> The license issue is with libgfortran, rather than OpenBLAS.
>
> (FWIW I am going through the motions to get OpenBLAS set up by default
> on CDH in the near future, and the hard part is just handling
> libgfortran.)
>
> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
>> Alright Sam - you are the expert here. If the GPL issues are unavoidable,
>> that's fine - what is the exact bit of code that is GPL?
>>
>> The suggestion to use OpenBLAS is not to say it's the best option, but that
>> it's a *free, reasonable default* for many users - keep in mind the most
>> common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
>> Additionally, for many of the problems we're targeting, this reasonable
>> default can provide a 1-2 orders of magnitude improvement in performance
>> over the f2jblas implementation that netlib-java falls back on.
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email]
> For additional commands, e-mail: [hidden email]
>

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RE: Using CUDA within Spark / boosting linear algebra

Ulanov, Alexander
Hi Sam,

What is the best way to do it? Should I clone netlib-java, edit readme.md and make a PR?

Best regards, Alexander


-----Original Message-----
From: Xiangrui Meng [mailto:[hidden email]]
Sent: Monday, March 30, 2015 2:43 PM
To: Sean Owen
Cc: Evan R. Sparks; Sam Halliday; [hidden email]; Ulanov, Alexander; jfcanny
Subject: Re: Using CUDA within Spark / boosting linear algebra

Hi Alex,

Since it is non-trivial to make nvblas work with netlib-java, it would be great if you can send the instructions to netlib-java as part of the README. Hopefully we don't need to modify netlib-java code to use nvblas.

Best,
Xiangrui

On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:

> The license issue is with libgfortran, rather than OpenBLAS.
>
> (FWIW I am going through the motions to get OpenBLAS set up by default
> on CDH in the near future, and the hard part is just handling
> libgfortran.)
>
> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
>> Alright Sam - you are the expert here. If the GPL issues are
>> unavoidable, that's fine - what is the exact bit of code that is GPL?
>>
>> The suggestion to use OpenBLAS is not to say it's the best option,
>> but that it's a *free, reasonable default* for many users - keep in
>> mind the most common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
>> Additionally, for many of the problems we're targeting, this
>> reasonable default can provide a 1-2 orders of magnitude improvement
>> in performance over the f2jblas implementation that netlib-java falls back on.
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email] For
> additional commands, e-mail: [hidden email]
>

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RE: Using CUDA within Spark / boosting linear algebra

Ulanov, Alexander
In reply to this post by Xiangrui Meng
FYI, I've added instructions to Netlib-java wiki, Sam added the link to them from the project's readme.md
https://github.com/fommil/netlib-java/wiki/NVBLAS

Best regards, Alexander
-----Original Message-----
From: Xiangrui Meng [mailto:[hidden email]]
Sent: Monday, March 30, 2015 2:43 PM
To: Sean Owen
Cc: Evan R. Sparks; Sam Halliday; [hidden email]; Ulanov, Alexander; jfcanny
Subject: Re: Using CUDA within Spark / boosting linear algebra

Hi Alex,

Since it is non-trivial to make nvblas work with netlib-java, it would be great if you can send the instructions to netlib-java as part of the README. Hopefully we don't need to modify netlib-java code to use nvblas.

Best,
Xiangrui

On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:

> The license issue is with libgfortran, rather than OpenBLAS.
>
> (FWIW I am going through the motions to get OpenBLAS set up by default
> on CDH in the near future, and the hard part is just handling
> libgfortran.)
>
> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
>> Alright Sam - you are the expert here. If the GPL issues are
>> unavoidable, that's fine - what is the exact bit of code that is GPL?
>>
>> The suggestion to use OpenBLAS is not to say it's the best option,
>> but that it's a *free, reasonable default* for many users - keep in
>> mind the most common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
>> Additionally, for many of the problems we're targeting, this
>> reasonable default can provide a 1-2 orders of magnitude improvement
>> in performance over the f2jblas implementation that netlib-java falls back on.
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email] For
> additional commands, e-mail: [hidden email]
>

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Re: Using CUDA within Spark / boosting linear algebra

Xiangrui Meng
This is great! Thanks! -Xiangrui

On Wed, Apr 1, 2015 at 12:11 PM, Ulanov, Alexander
<[hidden email]> wrote:

> FYI, I've added instructions to Netlib-java wiki, Sam added the link to them from the project's readme.md
> https://github.com/fommil/netlib-java/wiki/NVBLAS
>
> Best regards, Alexander
> -----Original Message-----
> From: Xiangrui Meng [mailto:[hidden email]]
> Sent: Monday, March 30, 2015 2:43 PM
> To: Sean Owen
> Cc: Evan R. Sparks; Sam Halliday; [hidden email]; Ulanov, Alexander; jfcanny
> Subject: Re: Using CUDA within Spark / boosting linear algebra
>
> Hi Alex,
>
> Since it is non-trivial to make nvblas work with netlib-java, it would be great if you can send the instructions to netlib-java as part of the README. Hopefully we don't need to modify netlib-java code to use nvblas.
>
> Best,
> Xiangrui
>
> On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:
>> The license issue is with libgfortran, rather than OpenBLAS.
>>
>> (FWIW I am going through the motions to get OpenBLAS set up by default
>> on CDH in the near future, and the hard part is just handling
>> libgfortran.)
>>
>> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
>>> Alright Sam - you are the expert here. If the GPL issues are
>>> unavoidable, that's fine - what is the exact bit of code that is GPL?
>>>
>>> The suggestion to use OpenBLAS is not to say it's the best option,
>>> but that it's a *free, reasonable default* for many users - keep in
>>> mind the most common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
>>> Additionally, for many of the problems we're targeting, this
>>> reasonable default can provide a 1-2 orders of magnitude improvement
>>> in performance over the f2jblas implementation that netlib-java falls back on.
>>
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: [hidden email] For
>> additional commands, e-mail: [hidden email]
>>

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Re: Using CUDA within Spark / boosting linear algebra

Evan R. Sparks
Yeah, thanks Alex!

On Thu, Apr 2, 2015 at 5:05 PM, Xiangrui Meng <[hidden email]> wrote:

> This is great! Thanks! -Xiangrui
>
> On Wed, Apr 1, 2015 at 12:11 PM, Ulanov, Alexander
> <[hidden email]> wrote:
> > FYI, I've added instructions to Netlib-java wiki, Sam added the link to
> them from the project's readme.md
> > https://github.com/fommil/netlib-java/wiki/NVBLAS
> >
> > Best regards, Alexander
> > -----Original Message-----
> > From: Xiangrui Meng [mailto:[hidden email]]
> > Sent: Monday, March 30, 2015 2:43 PM
> > To: Sean Owen
> > Cc: Evan R. Sparks; Sam Halliday; [hidden email]; Ulanov,
> Alexander; jfcanny
> > Subject: Re: Using CUDA within Spark / boosting linear algebra
> >
> > Hi Alex,
> >
> > Since it is non-trivial to make nvblas work with netlib-java, it would
> be great if you can send the instructions to netlib-java as part of the
> README. Hopefully we don't need to modify netlib-java code to use nvblas.
> >
> > Best,
> > Xiangrui
> >
> > On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:
> >> The license issue is with libgfortran, rather than OpenBLAS.
> >>
> >> (FWIW I am going through the motions to get OpenBLAS set up by default
> >> on CDH in the near future, and the hard part is just handling
> >> libgfortran.)
> >>
> >> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]>
> wrote:
> >>> Alright Sam - you are the expert here. If the GPL issues are
> >>> unavoidable, that's fine - what is the exact bit of code that is GPL?
> >>>
> >>> The suggestion to use OpenBLAS is not to say it's the best option,
> >>> but that it's a *free, reasonable default* for many users - keep in
> >>> mind the most common deployment for Spark/MLlib is on 64-bit linux on
> EC2[1].
> >>> Additionally, for many of the problems we're targeting, this
> >>> reasonable default can provide a 1-2 orders of magnitude improvement
> >>> in performance over the f2jblas implementation that netlib-java falls
> back on.
> >>
> >> ---------------------------------------------------------------------
> >> To unsubscribe, e-mail: [hidden email] For
> >> additional commands, e-mail: [hidden email]
> >>
>
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RE: Using CUDA within Spark / boosting linear algebra

Ulanov, Alexander
In reply to this post by Ulanov, Alexander
Hi,

There is a major update on the benchmarks. I've performed them on a newer hardware with 2 CPUs and 3 GPUs. The latter can be used by NVBLAS for parallelizing matrix-matrix multiplication. Results are in the same spreadsheet as previously:
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Previous results are on the separate sheet of the same document. I have also created a github page with benchmark source code and few explanatory comments:
https://github.com/avulanov/scala-blas

I was able to use all 3 GPUs for NVBLAS but BIDMat used only one GPU.

John, could you suggest how to force BIDMat to use all GPUs? Also, could you suggest how to test Double matrices multiplication in BIDMat-cuda (in GPU and with copy from/to main memory)?

Best regards, Alexander


-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, April 01, 2015 12:11 PM
To: Xiangrui Meng; Sean Owen
Cc: Evan R. Sparks; Sam Halliday; [hidden email]; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

FYI, I've added instructions to Netlib-java wiki, Sam added the link to them from the project's readme.md https://github.com/fommil/netlib-java/wiki/NVBLAS

Best regards, Alexander
-----Original Message-----
From: Xiangrui Meng [mailto:[hidden email]]
Sent: Monday, March 30, 2015 2:43 PM
To: Sean Owen
Cc: Evan R. Sparks; Sam Halliday; [hidden email]; Ulanov, Alexander; jfcanny
Subject: Re: Using CUDA within Spark / boosting linear algebra

Hi Alex,

Since it is non-trivial to make nvblas work with netlib-java, it would be great if you can send the instructions to netlib-java as part of the README. Hopefully we don't need to modify netlib-java code to use nvblas.

Best,
Xiangrui

On Thu, Mar 26, 2015 at 9:54 AM, Sean Owen <[hidden email]> wrote:

> The license issue is with libgfortran, rather than OpenBLAS.
>
> (FWIW I am going through the motions to get OpenBLAS set up by default
> on CDH in the near future, and the hard part is just handling
> libgfortran.)
>
> On Thu, Mar 26, 2015 at 4:07 PM, Evan R. Sparks <[hidden email]> wrote:
>> Alright Sam - you are the expert here. If the GPL issues are
>> unavoidable, that's fine - what is the exact bit of code that is GPL?
>>
>> The suggestion to use OpenBLAS is not to say it's the best option,
>> but that it's a *free, reasonable default* for many users - keep in
>> mind the most common deployment for Spark/MLlib is on 64-bit linux on EC2[1].
>> Additionally, for many of the problems we're targeting, this
>> reasonable default can provide a 1-2 orders of magnitude improvement
>> in performance over the f2jblas implementation that netlib-java falls back on.
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: [hidden email] For
> additional commands, e-mail: [hidden email]
>
B KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCB  [  X  ܚX KK[XZ[
 ] ][  X  ܚX P \ ˘\X K ܙ B  ܈Y][ۘ[  [X[  K[XZ[
 ] Z[ \ ˘\X K ܙ B

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RE: Using CUDA within Spark / boosting linear algebra

Ulanov, Alexander-2
In reply to this post by fommil

Hi Everyone,

 

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

 

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

 

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Benchmark code:

https://github.com/avulanov/scala-blas

 

Best regards, Alexander

 

 

From: Sam Halliday [mailto:[hidden email]]
Sent: Thursday, March 26, 2015 9:27 AM
To: John Canny
Cc: Xiangrui Meng; [hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject: Re: Using CUDA within Spark / boosting linear algebra

 

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.

On 26 Mar 2015 16:20, "John Canny" <[hidden email]> wrote:

I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:

Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

 

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

 

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <[hidden email]> wrote:

As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday

Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21): http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in http://docs.nvidia.com/cuda/nvblas/#Usage without any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander; [hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?

https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <[hidden email]<mailto:[hidden email]>> writes:

> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>> https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>> https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>> https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>> [hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>> https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>> [hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>> [hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>> https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>> apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>> https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>> apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>> apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>> apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] - http://arxiv.org/abs/1409.5402 [2] -
>>>> http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc: [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>> apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>> https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>> https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>> https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail: [hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]
>>>> e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac> he.org<http://he.org>
>>>> <mailto:[hidden email]<mailto:[hidden email]
>>>> rk.apache.org>>> For additional commands, e-mail:
>>>> [hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>> [hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam

 

 

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RE: Using CUDA within Spark / boosting linear algebra

Kazuaki Ishizaki
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format

Our prototype http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki



From:        "Ulanov, Alexander" <[hidden email]>
To:        Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        2016/01/21 11:07
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Everyone,
 
I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.
 
This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.
 
Results are available at google docs (old experiments are in the other 2 sheets):
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:
https://github.com/avulanov/scala-blas
 
Best regards, Alexander
 
 
From: Sam Halliday [mailto:sam.halliday@...]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng; [hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

 

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <canny@...> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:

Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).
 
Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?
 
On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <alexander.ulanov@...> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday

Cc: dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
sam.halliday@...]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
sam.halliday@...<mailto:sam.halliday@...>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
dev@...<mailto:dev@...>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?

https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
mengxr@...<mailto:mengxr@...>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
joseph@...<mailto:joseph@...>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
evan.sparks@...<mailto:evan.sparks@...>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
evan.sparks@...<mailto:evan.sparks@...>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
joseph@...<mailto:joseph@...><mailto:
>>>>
joseph@...<mailto:joseph@...>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>><mailto:evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
dev@...<mailto:dev@...><mailto:dev@...<mailto:dev@...>><mailto:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam

 
 

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RE: Using CUDA within Spark / boosting linear algebra

Allen Zhang

Hi Kazuaki,

Jcuda is actually a wrapper of the **pure** CUDA, as your wiki page shows that 3.15x performance boost of logistic regression seems slower than BIDMat-cublas or pure CUDA.
Could you elaborate on why you chose Jcuda other then JNI to call CUDA directly?

Regards,
Allen Zhang






At 2016-01-21 19:34:14, "Kazuaki Ishizaki" <[hidden email]> wrote:
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format

Our prototype http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki



From:        "Ulanov, Alexander" <[hidden email]>
To:        Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        2016/01/21 11:07
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Everyone,
 
I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.
 
This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.
 
Results are available at google docs (old experiments are in the other 2 sheets):
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:
https://github.com/avulanov/scala-blas
 
Best regards, Alexander
 
 
From: Sam Halliday [[hidden email]]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng; [hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

 

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <[hidden email]> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:

Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).
 
Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?
 
On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <[hidden email]> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday

Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
[hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?

https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
[hidden email]<mailto:[hidden email]>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam

 
 



 

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RE: Using CUDA within Spark / boosting linear algebra

Ulanov, Alexander-2
In reply to this post by Kazuaki Ishizaki

Hi Kazuaki,

 

Indeed, moving data to/from GPU is costly and this benchmark summarizes the costs for moving different data sizes with regards to matrices multiplication. These costs are paid for the convenience of using the standard BLAS API that Nvidia NVBLAS provides. The thing is that there are no code changes required (in Spark), one just needs to reference BLAS implementation with the system variable. Naturally, hardware-specific implementation will always be faster than default. The benchmark results show that fact by comparing jCuda (by means of BIDMat) and NVBLAS. However, it also shows that it worth using NVBLAS for large matrices because it can take advantage of several GPUs and it will be faster despite the copying overhead. That is also a known thing advertised by Nvidia.

 

By the way, I don’t think that the column/row friendly format is an issue, because one can use transposed matrices to fit the required format. I believe that is just a software preference.

 

My suggestion with regards to your prototype would be to make comparisons with Spark’s implementation of logistic regression (that does not take advantage of GPU) and also with BIDMach’s (that takes advantage of GPUs). It will give the users a better understanding of your’s implementation performance. Currently you compare it with Spark’s example logistic regression implementation that is supposed to be a reference for learning Spark rather than benchmarking its performance.

 

Best regards, Alexander

 

From: Kazuaki Ishizaki [mailto:[hidden email]]
Sent: Thursday, January 21, 2016 3:34 AM
To: [hidden email]; Ulanov, Alexander; Joseph Bradley
Cc: John Canny; Evan R. Sparks; Xiangrui Meng; Sam Halliday
Subject: RE: Using CUDA within Spark / boosting linear algebra

 

Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format

Our prototype http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki



From:        "Ulanov, Alexander" <[hidden email]>
To:        Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        2016/01/21 11:07
Subject:        RE: Using CUDA within Spark / boosting linear algebra





Hi Everyone,
 
I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.
 
This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.
 
Results are available at google docs (old experiments are in the other 2 sheets):
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:
https://github.com/avulanov/scala-blas
 
Best regards, Alexander
 
 
From: Sam Halliday [[hidden email]]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng; [hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

 

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <[hidden email]> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:

Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).
 
Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?
 
On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <[hidden email]> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday

Cc: [hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
[hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?

https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
[hidden email]<mailto:[hidden email]>> writes:

> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam

 
 

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RE: Using CUDA within Spark / boosting linear algebra

Kazuaki Ishizaki
In reply to this post by Allen Zhang
Hi Allen,
Thank you for your feedback.
An API to launch GPU kernels with JCuda is the our first step. A purpose to release our prototype is to get feedback. In the future, we may use other wrappers instead of JCuda.

We are very appreciate it if you would suggest or propose APIs to effectively exploit GPUs such as BIDMat in Spark.
If we would run BIDMat with our columnar strorage, the performance boost would be good as others reported.

Best Regards,
Kazuaki Ishizaki,



From:        "Allen Zhang" <[hidden email]>
To:        Kazuaki Ishizaki/Japan/IBM@IBMJP
Cc:        "[hidden email]" <[hidden email]>, "Ulanov, Alexander" <[hidden email]>, "Joseph Bradley" <[hidden email]>, "John Canny" <[hidden email]>, "Evan R. Sparks" <[hidden email]>, "Xiangrui Meng" <[hidden email]>, "Sam Halliday" <[hidden email]>
Date:        2016/01/21 21:05
Subject:        RE: Using CUDA within Spark / boosting linear algebra





Hi Kazuaki,

Jcuda is actually a wrapper of the **pure** CUDA, as your wiki page shows that 3.15x performance boost of logistic regression seems slower than BIDMat-cublas or pure CUDA.
Could you elaborate on why you chose Jcuda other then JNI to call CUDA directly?

Regards,
Allen Zhang






At 2016-01-21 19:34:14, "Kazuaki Ishizaki" <[hidden email]> wrote:

Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format


Our prototype
http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki




From:        
"Ulanov, Alexander" <alexander.ulanov@...>
To:        
Sam Halliday <sam.halliday@...>, John Canny <canny@...>
Cc:        
Xiangrui Meng <mengxr@...>, "dev@..." <dev@...>, Joseph Bradley <joseph@...>, "Evan R. Sparks" <evan.sparks@...>
Date:        
2016/01/21 11:07
Subject:        
RE: Using CUDA within Spark / boosting linear algebra




Hi Everyone,

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:

https://github.com/avulanov/scala-blas

Best regards, Alexander


From:
Sam Halliday [
mailto:sam.halliday@...]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng;
dev@...; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra


John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <
canny@...> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
alexander.ulanov@...> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
sam.halliday@...]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
sam.halliday@...<mailto:sam.halliday@...>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
dev@...<mailto:dev@...>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?


https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
mengxr@...<mailto:mengxr@...>> writes:

> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
joseph@...<mailto:joseph@...>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
evan.sparks@...<mailto:evan.sparks@...>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
evan.sparks@...<mailto:evan.sparks@...>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
joseph@...<mailto:joseph@...><mailto:
>>>>
joseph@...<mailto:joseph@...>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>><mailto:evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
dev@...<mailto:dev@...><mailto:dev@...<mailto:dev@...>><mailto:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam



 


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RE: Using CUDA within Spark / boosting linear algebra

Kazuaki Ishizaki
In reply to this post by Ulanov, Alexander-2
Hi Alexander,
The goal of our columnar to effectively drive GPUs in Spark. One of important items is to effectively and easily enable highly-tuned libraries for GPU such as BIDMach.

We will enable BIDMach with our columnar storage. On the other hand, it is not easy task to scaling BIDMach with current Spark. I expect that this talk would help us.
http://conferences.oreilly.com/strata/hadoop-big-data-ca/public/schedule/detail/47565

We appreciate your great feedback.

Best Regards,
Kazuaki Ishizaki, Ph.D., Senior research staff member, IBM Research - Tokyo



From:        "Ulanov, Alexander" <[hidden email]>
To:        Kazuaki Ishizaki/Japan/IBM@IBMJP, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>
Cc:        John Canny <[hidden email]>, "Evan R. Sparks" <[hidden email]>, Xiangrui Meng <[hidden email]>, Sam Halliday <[hidden email]>
Date:        2016/01/22 04:20
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Kazuaki,
 
Indeed, moving data to/from GPU is costly and this benchmark summarizes the costs for moving different data sizes with regards to matrices multiplication. These costs are paid for the convenience of using the standard BLAS API that Nvidia NVBLAS provides. The thing is that there are no code changes required (in Spark), one just needs to reference BLAS implementation with the system variable. Naturally, hardware-specific implementation will always be faster than default. The benchmark results show that fact by comparing jCuda (by means of BIDMat) and NVBLAS. However, it also shows that it worth using NVBLAS for large matrices because it can take advantage of several GPUs and it will be faster despite the copying overhead. That is also a known thing advertised by Nvidia.
 
By the way, I don’t think that the column/row friendly format is an issue, because one can use transposed matrices to fit the required format. I believe that is just a software preference.
 
My suggestion with regards to your prototype would be to make comparisons with Spark’s implementation of logistic regression (that does not take advantage of GPU) and also with BIDMach’s (that takes advantage of GPUs). It will give the users a better understanding of your’s implementation performance. Currently you compare it with Spark’s example logistic regression implementation that is supposed to be a reference for learning Spark rather than benchmarking its performance.
 
Best regards, Alexander
 
From: Kazuaki Ishizaki [mailto:ISHIZAKI@...]
Sent:
Thursday, January 21, 2016 3:34 AM
To:
[hidden email]; Ulanov, Alexander; Joseph Bradley
Cc:
John Canny; Evan R. Sparks; Xiangrui Meng; Sam Halliday
Subject:
RE: Using CUDA within Spark / boosting linear algebra

 
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format


Our prototype
http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki




From:        
"Ulanov, Alexander" <alexander.ulanov@...>
To:        
Sam Halliday <sam.halliday@...>, John Canny <canny@...>
Cc:        
Xiangrui Meng <mengxr@...>, "dev@..." <dev@...>, Joseph Bradley <joseph@...>, "Evan R. Sparks" <evan.sparks@...>
Date:        
2016/01/21 11:07
Subject:        
RE: Using CUDA within Spark / boosting linear algebra





Hi Everyone,

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:

https://github.com/avulanov/scala-blas

Best regards, Alexander


From:
Sam Halliday [
mailto:sam.halliday@...]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng;
dev@...; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <
canny@...> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
alexander.ulanov@...> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
sam.halliday@...]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
dev@...; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
sam.halliday@...<mailto:sam.halliday@...>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
dev@...<mailto:dev@...>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?


https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
mengxr@...<mailto:mengxr@...>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
joseph@...<mailto:joseph@...>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
evan.sparks@...<mailto:evan.sparks@...>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
alexander.ulanov@...<mailto:alexander.ulanov@...>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
evan.sparks@...<mailto:evan.sparks@...>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
joseph@...<mailto:joseph@...><mailto:
>>>>
joseph@...<mailto:joseph@...>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>><mailto:evan.sparks@...<mailto:evan.sparks@...><mailto:
>>>>
evan.sparks@...<mailto:evan.sparks@...>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
dev@...<mailto:dev@...><mailto:dev@...<mailto:dev@...>><mailto:
>>>>
dev@...<mailto:dev@...><mailto:dev@spark.
>>>>
apache.org<mailto:dev@...>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>><mailto:
>>>>
alexander.ulanov@...<mailto:alexander.ulanov@...><mailto:alexander.ulanov@...<mailto:alexander.ulanov@...>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam


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Re: Using CUDA within Spark / boosting linear algebra

Max Grossman
Hi all,

I’m jumping on this thread to point out another Spark+GPU project for people to take a look at: https://github.com/agrippa/spark-swat

SWAT (Spark with Accelerated Tasks) is a third-party JAR sitting on top of Spark that uses runtime code generation to convert user-written transformations into OpenCL kernels. SWAT’s lightweight runtime supports multi-GPU systems, managing each device and its memory automatically. You write your own Spark programs, and the runtime takes care of offloading your transformations to the GPUs in your system:

val rdd = CLWrapper.cl(sc.objectFile(inputPath))
val next = rdd.map(i => 2 * i).collect

SWAT primarily distinguishes itself in programmability: an explicit goal of this project is to have as few user-visible API changes as possible from what people have come to know and love in Spark. There are a number of fixed-function GPU libraries out there now, so we wanted to look instead at something that could be used to build new but still well-performing Spark apps.

SWAT is currently more of a research project than a production-ready system, so there’s a chance it won’t work out-of-the-box on some systems. With that said, it does have fairly comprehensive functional and code generation testing. If you’re interested in trying it out and having trouble setting up, feel free to contact me directly. And of course, any questions or feedback from the community are always welcome.

Thanks,

Max

On Jan 22, 2016, at 3:42 AM, Kazuaki Ishizaki <[hidden email]> wrote:

Hi Alexander,
The goal of our columnar to effectively drive GPUs in Spark. One of important items is to effectively and easily enable highly-tuned libraries for GPU such as BIDMach.

We will enable BIDMach with our columnar storage. On the other hand, it is not easy task to scaling BIDMach with current Spark. I expect that this talk would help us.
http://conferences.oreilly.com/strata/hadoop-big-data-ca/public/schedule/detail/47565

We appreciate your great feedback.

Best Regards,
Kazuaki Ishizaki, Ph.D., Senior research staff member, IBM Research - Tokyo



From:        "Ulanov, Alexander" <[hidden email]>
To:        Kazuaki Ishizaki/Japan/IBM@IBMJP, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>
Cc:        John Canny <[hidden email]>, "Evan R. Sparks" <[hidden email]>, Xiangrui Meng <[hidden email]>, Sam Halliday <[hidden email]>
Date:        2016/01/22 04:20
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Kazuaki,
 
Indeed, moving data to/from GPU is costly and this benchmark summarizes the costs for moving different data sizes with regards to matrices multiplication. These costs are paid for the convenience of using the standard BLAS API that Nvidia NVBLAS provides. The thing is that there are no code changes required (in Spark), one just needs to reference BLAS implementation with the system variable. Naturally, hardware-specific implementation will always be faster than default. The benchmark results show that fact by comparing jCuda (by means of BIDMat) and NVBLAS. However, it also shows that it worth using NVBLAS for large matrices because it can take advantage of several GPUs and it will be faster despite the copying overhead. That is also a known thing advertised by Nvidia.
 
By the way, I don’t think that the column/row friendly format is an issue, because one can use transposed matrices to fit the required format. I believe that is just a software preference.
 
My suggestion with regards to your prototype would be to make comparisons with Spark’s implementation of logistic regression (that does not take advantage of GPU) and also with BIDMach’s (that takes advantage of GPUs). It will give the users a better understanding of your’s implementation performance. Currently you compare it with Spark’s example logistic regression implementation that is supposed to be a reference for learning Spark rather than benchmarking its performance.
 
Best regards, Alexander
 
From: Kazuaki Ishizaki [[hidden email]]
Sent:
Thursday, January 21, 2016 3:34 AM
To:
[hidden email]; Ulanov, Alexander; Joseph Bradley
Cc:
John Canny; Evan R. Sparks; Xiangrui Meng; Sam Halliday
Subject:
RE: Using CUDA within Spark / boosting linear algebra

 
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format


Our prototype
http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki




From:        
"Ulanov, Alexander" <[hidden email]>
To:        
Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        
Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        
2016/01/21 11:07
Subject:        
RE: Using CUDA within Spark / boosting linear algebra





Hi Everyone,

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:

https://github.com/avulanov/scala-blas

Best regards, Alexander


From:
Sam Halliday [
[hidden email]]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng;
[hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <
[hidden email]> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
[hidden email]> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
[hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?


https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
[hidden email]<mailto:[hidden email]>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam



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Re: Using CUDA within Spark / boosting linear algebra

Allen Zhang
Hi Max,

I will look at it tomorrow. but a quick question, does it support CUDA from Nvidia, not only OpenCL?

Thanks,
Allen





At 2016-02-04 23:13:05, "Max Grossman" <[hidden email]> wrote:
Hi all,

I’m jumping on this thread to point out another Spark+GPU project for people to take a look at: https://github.com/agrippa/spark-swat

SWAT (Spark with Accelerated Tasks) is a third-party JAR sitting on top of Spark that uses runtime code generation to convert user-written transformations into OpenCL kernels. SWAT’s lightweight runtime supports multi-GPU systems, managing each device and its memory automatically. You write your own Spark programs, and the runtime takes care of offloading your transformations to the GPUs in your system:

val rdd = CLWrapper.cl(sc.objectFile(inputPath))
val next = rdd.map(i => 2 * i).collect

SWAT primarily distinguishes itself in programmability: an explicit goal of this project is to have as few user-visible API changes as possible from what people have come to know and love in Spark. There are a number of fixed-function GPU libraries out there now, so we wanted to look instead at something that could be used to build new but still well-performing Spark apps.

SWAT is currently more of a research project than a production-ready system, so there’s a chance it won’t work out-of-the-box on some systems. With that said, it does have fairly comprehensive functional and code generation testing. If you’re interested in trying it out and having trouble setting up, feel free to contact me directly. And of course, any questions or feedback from the community are always welcome.

Thanks,

Max

On Jan 22, 2016, at 3:42 AM, Kazuaki Ishizaki <[hidden email]> wrote:

Hi Alexander,
The goal of our columnar to effectively drive GPUs in Spark. One of important items is to effectively and easily enable highly-tuned libraries for GPU such as BIDMach.

We will enable BIDMach with our columnar storage. On the other hand, it is not easy task to scaling BIDMach with current Spark. I expect that this talk would help us.
http://conferences.oreilly.com/strata/hadoop-big-data-ca/public/schedule/detail/47565

We appreciate your great feedback.

Best Regards,
Kazuaki Ishizaki, Ph.D., Senior research staff member, IBM Research - Tokyo



From:        "Ulanov, Alexander" <[hidden email]>
To:        Kazuaki Ishizaki/Japan/IBM@IBMJP, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>
Cc:        John Canny <[hidden email]>, "Evan R. Sparks" <[hidden email]>, Xiangrui Meng <[hidden email]>, Sam Halliday <[hidden email]>
Date:        2016/01/22 04:20
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Kazuaki,
 
Indeed, moving data to/from GPU is costly and this benchmark summarizes the costs for moving different data sizes with regards to matrices multiplication. These costs are paid for the convenience of using the standard BLAS API that Nvidia NVBLAS provides. The thing is that there are no code changes required (in Spark), one just needs to reference BLAS implementation with the system variable. Naturally, hardware-specific implementation will always be faster than default. The benchmark results show that fact by comparing jCuda (by means of BIDMat) and NVBLAS. However, it also shows that it worth using NVBLAS for large matrices because it can take advantage of several GPUs and it will be faster despite the copying overhead. That is also a known thing advertised by Nvidia.
 
By the way, I don’t think that the column/row friendly format is an issue, because one can use transposed matrices to fit the required format. I believe that is just a software preference.
 
My suggestion with regards to your prototype would be to make comparisons with Spark’s implementation of logistic regression (that does not take advantage of GPU) and also with BIDMach’s (that takes advantage of GPUs). It will give the users a better understanding of your’s implementation performance. Currently you compare it with Spark’s example logistic regression implementation that is supposed to be a reference for learning Spark rather than benchmarking its performance.
 
Best regards, Alexander
 
From: Kazuaki Ishizaki [[hidden email]]
Sent:
Thursday, January 21, 2016 3:34 AM
To:
[hidden email]; Ulanov, Alexander; Joseph Bradley
Cc:
John Canny; Evan R. Sparks; Xiangrui Meng; Sam Halliday
Subject:
RE: Using CUDA within Spark / boosting linear algebra

 
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format


Our prototype
http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki




From:        
"Ulanov, Alexander" <[hidden email]>
To:        
Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        
Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        
2016/01/21 11:07
Subject:        
RE: Using CUDA within Spark / boosting linear algebra





Hi Everyone,

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:

https://github.com/avulanov/scala-blas

Best regards, Alexander


From:
Sam Halliday [
[hidden email]]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng;
[hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <
[hidden email]> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
[hidden email]> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
[hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?


https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
[hidden email]<mailto:[hidden email]>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]
>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>
>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam





 

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Re: Using CUDA within Spark / boosting linear algebra

Max Grossman
Allen,

Currently it only supports OpenCL because the code generator we’ve extended targeted OpenCL. There’s no technical reason that CUDA couldn’t be supported if people would be interested in that, but it would require a rewrite of some of the code generator as well as some ifdefs in the runtime to allow us to compile with either OpenCL or CUDA support. There are actually a few components that support both OpenCL and CUDA for when they’ve been reused for other projects that did use CUDA, just not all of them.

Thanks,

Max

On Feb 4, 2016, at 9:42 AM, Allen Zhang <[hidden email]> wrote:

Hi Max,

I will look at it tomorrow. but a quick question, does it support CUDA from Nvidia, not only OpenCL?

Thanks,
Allen





At 2016-02-04 23:13:05, "Max Grossman" <[hidden email]> wrote:
Hi all,

I’m jumping on this thread to point out another Spark+GPU project for people to take a look at: https://github.com/agrippa/spark-swat

SWAT (Spark with Accelerated Tasks) is a third-party JAR sitting on top of Spark that uses runtime code generation to convert user-written transformations into OpenCL kernels. SWAT’s lightweight runtime supports multi-GPU systems, managing each device and its memory automatically. You write your own Spark programs, and the runtime takes care of offloading your transformations to the GPUs in your system:

val rdd = CLWrapper.cl(sc.objectFile(inputPath))
val next = rdd.map(i => 2 * i).collect

SWAT primarily distinguishes itself in programmability: an explicit goal of this project is to have as few user-visible API changes as possible from what people have come to know and love in Spark. There are a number of fixed-function GPU libraries out there now, so we wanted to look instead at something that could be used to build new but still well-performing Spark apps.

SWAT is currently more of a research project than a production-ready system, so there’s a chance it won’t work out-of-the-box on some systems. With that said, it does have fairly comprehensive functional and code generation testing. If you’re interested in trying it out and having trouble setting up, feel free to contact me directly. And of course, any questions or feedback from the community are always welcome.

Thanks,

Max

On Jan 22, 2016, at 3:42 AM, Kazuaki Ishizaki <[hidden email]> wrote:

Hi Alexander,
The goal of our columnar to effectively drive GPUs in Spark. One of important items is to effectively and easily enable highly-tuned libraries for GPU such as BIDMach.

We will enable BIDMach with our columnar storage. On the other hand, it is not easy task to scaling BIDMach with current Spark. I expect that this talk would help us.
http://conferences.oreilly.com/strata/hadoop-big-data-ca/public/schedule/detail/47565

We appreciate your great feedback.

Best Regards,
Kazuaki Ishizaki, Ph.D., Senior research staff member, IBM Research - Tokyo



From:        "Ulanov, Alexander" <[hidden email]>
To:        Kazuaki Ishizaki/Japan/IBM@IBMJP, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>
Cc:        John Canny <[hidden email]>, "Evan R. Sparks" <[hidden email]>, Xiangrui Meng <[hidden email]>, Sam Halliday <[hidden email]>
Date:        2016/01/22 04:20
Subject:        RE: Using CUDA within Spark / boosting linear algebra




Hi Kazuaki,
 
Indeed, moving data to/from GPU is costly and this benchmark summarizes the costs for moving different data sizes with regards to matrices multiplication. These costs are paid for the convenience of using the standard BLAS API that Nvidia NVBLAS provides. The thing is that there are no code changes required (in Spark), one just needs to reference BLAS implementation with the system variable. Naturally, hardware-specific implementation will always be faster than default. The benchmark results show that fact by comparing jCuda (by means of BIDMat) and NVBLAS. However, it also shows that it worth using NVBLAS for large matrices because it can take advantage of several GPUs and it will be faster despite the copying overhead. That is also a known thing advertised by Nvidia.
 
By the way, I don’t think that the column/row friendly format is an issue, because one can use transposed matrices to fit the required format. I believe that is just a software preference.
 
My suggestion with regards to your prototype would be to make comparisons with Spark’s implementation of logistic regression (that does not take advantage of GPU) and also with BIDMach’s (that takes advantage of GPUs). It will give the users a better understanding of your’s implementation performance. Currently you compare it with Spark’s example logistic regression implementation that is supposed to be a reference for learning Spark rather than benchmarking its performance.
 
Best regards, Alexander
 
From: Kazuaki Ishizaki [[hidden email]]
Sent:
Thursday, January 21, 2016 3:34 AM
To:
[hidden email]; Ulanov, Alexander; Joseph Bradley
Cc:
John Canny; Evan R. Sparks; Xiangrui Meng; Sam Halliday
Subject:
RE: Using CUDA within Spark / boosting linear algebra

 
Dear all,

>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph

As Joseph pointed out before, there are two potential issues to efficiently exploit GPUs in Spark.
(1) the cost of data movement between CPU and GPU
(2) the cost of encoding/decoding between current row-format and GPU-friendly column format


Our prototype
http://kiszk.github.io/spark-gpu/addresses these two issues by supporting data partition caching in GPU device memory and by providing binary column storage for data partition. We really appreciate it if you would give us comments, suggestions, or feedback.

Best Regards
Kazuaki Ishizaki




From:        
"Ulanov, Alexander" <[hidden email]>
To:        
Sam Halliday <[hidden email]>, John Canny <[hidden email]>
Cc:        
Xiangrui Meng <[hidden email]>, "[hidden email]" <[hidden email]>, Joseph Bradley <[hidden email]>, "Evan R. Sparks" <[hidden email]>
Date:        
2016/01/21 11:07
Subject:        
RE: Using CUDA within Spark / boosting linear algebra





Hi Everyone,

I’ve updated the benchmark and done experiments with new hardware with 2x Nvidia Tesla K80 (physically 4x Tesla K40) and 2x modern Haswell CPU Intel E5-2650 v3 @ 2.30GHz.

This time I computed average and median of 10 runs for each of experiment and approximated FLOPS.

Results are available at google docs (old experiments are in the other 2 sheets):

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing
Benchmark code:

https://github.com/avulanov/scala-blas

Best regards, Alexander


From:
Sam Halliday [
[hidden email]]
Sent:
Thursday, March 26, 2015 9:27 AM
To:
John Canny
Cc:
Xiangrui Meng;
[hidden email]; Joseph Bradley; Evan R. Sparks; Ulanov, Alexander
Subject:
Re: Using CUDA within Spark / boosting linear algebra

John, I have to disagree with you there. Dense matrices come up a lot in industry,  although your personal experience may be different.
On 26 Mar 2015 16:20, "John Canny" <
[hidden email]> wrote:
I mentioned this earlier in the thread, but I'll put it out again. Dense BLAS are not very important for most machine learning workloads: at least for non-image workloads in industry (and for image processing you would probably want a deep learning/SGD solution with convolution kernels). e.g. it was only relevant for 1/7 of our recent benchmarks, which should be a reasonable sample. What really matters is sparse BLAS performance. BIDMat is still an order of magnitude faster there. Those kernels are only in BIDMat, since NVIDIAs sparse BLAS dont perform well on power-law data.

Its also the case that the overall performance of an algorithm is determined by the slowest kernel, not the fastest. If the goal is to get closer to BIDMach's performance on typical problems, you need to make sure that every kernel goes at comparable speed. So the real question is how much faster MLLib routines do on a complete problem with/without GPU acceleration. For BIDMach, its close to a factor of 10. But that required running entirely on the GPU, and making sure every kernel is close to its limit.

-John

If you think nvblas would be helpful, you should try it in some end-to-end benchmarks.
On 3/25/15, 6:23 PM, Evan R. Sparks wrote:
Yeah, much more reasonable - nice to know that we can get full GPU performance from breeze/netlib-java - meaning there's no compelling performance reason to switch out our current linear algebra library (at least as far as this benchmark is concerned).

Instead, it looks like a user guide for configuring Spark/MLlib to use the right BLAS library will get us most of the way there. Or, would it make sense to finally ship openblas compiled for some common platforms (64-bit linux, windows, mac) directly with Spark - hopefully eliminating the jblas warnings once and for all for most users? (Licensing is BSD) Or am I missing something?

On Wed, Mar 25, 2015 at 6:03 PM, Ulanov, Alexander <
[hidden email]> wrote:
As everyone suggested, the results were too good to be true, so I double-checked them. It turns that nvblas did not do multiplication due to parameter NVBLAS_TILE_DIM from "nvblas.conf" and returned zero matrix. My previously posted results with nvblas are matrices copying only. The default NVBLAS_TILE_DIM==2048 is too big for my graphic card/matrix size. I handpicked other values that worked. As a result, netlib+nvblas is on par with BIDMat-cuda. As promised, I am going to post a how-to for nvblas configuration.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing



-----Original Message-----
From: Ulanov, Alexander
Sent: Wednesday, March 25, 2015 2:31 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks; jfcanny
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi again,

I finally managed to use nvblas within Spark+netlib-java. It has exceptional performance for big matrices with Double, faster than BIDMat-cuda with Float. But for smaller matrices, if you will copy them to/from GPU, OpenBlas or MKL might be a better choice. This correlates with original nvblas presentation on GPU conf 2013 (slide 21):
http://on-demand.gputechconf.com/supercomputing/2013/presentation/SC3108-New-Features-CUDA%206%20-GPU-Acceleration.pdf

My results:

https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Just in case, these tests are not for generalization of performance of different libraries. I just want to pick a library that does at best dense matrices multiplication for my task.

P.S. My previous issue with nvblas was the following: it has Fortran blas functions, at the same time netlib-java uses C cblas functions. So, one needs cblas shared library to use nvblas through netlib-java. Fedora does not have cblas (but Debian and Ubuntu have), so I needed to compile it. I could not use cblas from Atlas or Openblas because they link to their implementation and not to Fortran blas.

Best regards, Alexander

-----Original Message-----
From: Ulanov, Alexander
Sent: Tuesday, March 24, 2015 6:57 PM
To: Sam Halliday
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra

Hi,

I am trying to use nvblas with netlib-java from Spark. nvblas functions should replace current blas functions calls after executing LD_PRELOAD as suggested in
http://docs.nvidia.com/cuda/nvblas/#Usagewithout any changes to netlib-java. It seems to work for simple Java example, but I cannot make it work with Spark. I run the following:
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64
env LD_PRELOAD=/usr/local/cuda-6.5/lib64/libnvblas.so ./spark-shell --driver-memory 4G In nvidia-smi I observe that Java is to use GPU:
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0      8873    C   bash                                            39MiB |
|    0      8910    C   /usr/lib/jvm/java-1.7.0/bin/java                39MiB |
+-----------------------------------------------------------------------------+

In Spark shell I do matrix multiplication and see the following:
15/03/25 06:48:01 INFO JniLoader: successfully loaded /tmp/jniloader8192964377009965483netlib-native_system-linux-x86_64.so
So I am sure that netlib-native is loaded and cblas supposedly used. However, matrix multiplication does executes on CPU since I see 16% of CPU used and 0% of GPU used. I also checked different matrix sizes, from 100x100 to 12000x12000

Could you suggest might the LD_PRELOAD not affect Spark shell?

Best regards, Alexander



From: Sam Halliday [mailto:
[hidden email]]
Sent: Monday, March 09, 2015 6:01 PM
To: Ulanov, Alexander
Cc:
[hidden email]; Xiangrui Meng; Joseph Bradley; Evan R. Sparks
Subject: RE: Using CUDA within Spark / boosting linear algebra


Thanks so much for following up on this!

Hmm, I wonder if we should have a concerted effort to chart performance on various pieces of hardware...
On 9 Mar 2015 21:08, "Ulanov, Alexander" <
[hidden email]<mailto:[hidden email]>> wrote:
Hi Everyone, I've updated the benchmark as Xiangrui suggested. Added the comment that BIDMat 0.9.7 uses Float matrices in GPU (although I see the support of Double in the current source code), did the test with BIDMat and CPU Double matrices. BIDMat MKL is indeed on par with netlib MKL.


https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx378T9J5r7kwKSPkY/edit?usp=sharing

Best regards, Alexander

-----Original Message-----
From: Sam Halliday [mailto:
[hidden email]<mailto:[hidden email]>]
Sent: Tuesday, March 03, 2015 1:54 PM
To: Xiangrui Meng; Joseph Bradley
Cc: Evan R. Sparks; Ulanov, Alexander;
[hidden email]<mailto:[hidden email]>
Subject: Re: Using CUDA within Spark / boosting linear algebra

BTW, is anybody on this list going to the London Meetup in a few weeks?


https://skillsmatter.com/meetups/6987-apache-spark-living-the-post-mapreduce-world#community

Would be nice to meet other people working on the guts of Spark! :-)


Xiangrui Meng <
[hidden email]<mailto:[hidden email]>> writes:


> Hey Alexander,
>
> I don't quite understand the part where netlib-cublas is about 20x
> slower than netlib-openblas. What is the overhead of using a GPU BLAS
> with netlib-java?
>
> CC'ed Sam, the author of netlib-java.
>
> Best,
> Xiangrui
>
> On Wed, Feb 25, 2015 at 3:36 PM, Joseph Bradley <
[hidden email]<mailto:[hidden email]>> wrote:
>> Better documentation for linking would be very helpful!  Here's a JIRA:
>>
https://issues.apache.org/jira/browse/SPARK-6019
>>
>>
>> On Wed, Feb 25, 2015 at 2:53 PM, Evan R. Sparks
>> <
[hidden email]<mailto:[hidden email]>>
>> wrote:
>>
>>> Thanks for compiling all the data and running these benchmarks,
>>> Alex. The big takeaways here can be seen with this chart:
>>>
>>>
https://docs.google.com/spreadsheets/d/1aRm2IADRfXQV7G2vrcVh4StF50uZ
>>> Hl6kmAJeaZZggr0/pubchart?oid=1899767119&format=interactive
>>>
>>> 1) A properly configured GPU matrix multiply implementation (e.g.
>>> BIDMat+GPU) can provide substantial (but less than an order of
>>> BIDMat+magnitude)
>>> benefit over a well-tuned CPU implementation (e.g. BIDMat+MKL or
>>> netlib-java+openblas-compiled).
>>> 2) A poorly tuned CPU implementation can be 1-2 orders of magnitude
>>> worse than a well-tuned CPU implementation, particularly for larger matrices.
>>> (netlib-f2jblas or netlib-ref) This is not to pick on netlib - this
>>> basically agrees with the authors own benchmarks (
>>>
https://github.com/fommil/netlib-java)
>>>
>>> I think that most of our users are in a situation where using GPUs
>>> may not be practical - although we could consider having a good GPU
>>> backend available as an option. However, *ALL* users of MLlib could
>>> benefit (potentially tremendously) from using a well-tuned CPU-based
>>> BLAS implementation. Perhaps we should consider updating the mllib
>>> guide with a more complete section for enabling high performance
>>> binaries on OSX and Linux? Or better, figure out a way for the
>>> system to fetch these automatically.
>>>
>>> - Evan
>>>
>>>
>>>
>>> On Thu, Feb 12, 2015 at 4:18 PM, Ulanov, Alexander <
>>>
[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>> Just to summarize this thread, I was finally able to make all
>>>> performance comparisons that we discussed. It turns out that:
>>>> BIDMat-cublas>>BIDMat
>>>> MKL==netlib-mkl==netlib-openblas-compiled>netlib-openblas-yum-repo=
>>>> =netlib-cublas>netlib-blas>f2jblas
>>>>
>>>> Below is the link to the spreadsheet with full results.
>>>>
>>>>
https://docs.google.com/spreadsheets/d/1lWdVSuSragOobb0A_oeouQgHUMx
>>>> 378T9J5r7kwKSPkY/edit?usp=sharing
>>>>
>>>> One thing still needs exploration: does BIDMat-cublas perform
>>>> copying to/from machine’s RAM?
>>>>
>>>> -----Original Message-----
>>>> From: Ulanov, Alexander
>>>> Sent: Tuesday, February 10, 2015 2:12 PM
>>>> To: Evan R. Sparks
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: RE: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Thanks, Evan! It seems that ticket was marked as duplicate though
>>>> the original one discusses slightly different topic. I was able to
>>>> link netlib with MKL from BIDMat binaries. Indeed, MKL is
>>>> statically linked inside a 60MB library.
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-MKL  from BIDMat|
>>>> Breeze+Netlib-OpenBlas(native system)| Breeze+Netlib-f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,000381 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,038316857 | 0,51803557
>>>> |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 32,94546697 |445,0935211 |
>>>> 1569,233228 |
>>>>
>>>> It turn out that pre-compiled MKL is faster than precompiled
>>>> OpenBlas on my machine. Probably, I’ll add two more columns with
>>>> locally compiled openblas and cuda.
>>>>
>>>> Alexander
>>>>
>>>> From: Evan R. Sparks
>>>> [mailto:
[hidden email]<mailto:[hidden email]>]
>>>> Sent: Monday, February 09, 2015 6:06 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Great - perhaps we can move this discussion off-list and onto a
>>>> JIRA ticket? (Here's one:
>>>>
https://issues.apache.org/jira/browse/SPARK-5705)
>>>>
>>>> It seems like this is going to be somewhat exploratory for a while
>>>> (and there's probably only a handful of us who really care about
>>>> fast linear
>>>> algebra!)
>>>>
>>>> - Evan
>>>>
>>>> On Mon, Feb 9, 2015 at 4:48 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for explanation and useful link. I am going to build
>>>> OpenBLAS, link it with Netlib-java and perform benchmark again.
>>>>
>>>> Do I understand correctly that BIDMat binaries contain statically
>>>> linked Intel MKL BLAS? It might be the reason why I am able to run
>>>> BIDMat not having MKL BLAS installed on my server. If it is true, I
>>>> wonder if it is OK because Intel sells this library. Nevertheless,
>>>> it seems that in my case precompiled MKL BLAS performs better than
>>>> precompiled OpenBLAS given that BIDMat and Netlib-java are supposed to be on par with JNI overheads.
>>>>
>>>> Though, it might be interesting to link Netlib-java with Intel MKL,
>>>> as you suggested. I wonder, are John Canny (BIDMat) and Sam
>>>> Halliday
>>>> (Netlib-java) interested to compare their libraries.
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:58 PM
>>>>
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I would build OpenBLAS yourself, since good BLAS performance comes
>>>> from getting cache sizes, etc. set up correctly for your particular
>>>> hardware - this is often a very tricky process (see, e.g. ATLAS),
>>>> but we found that on relatively modern Xeon chips, OpenBLAS builds
>>>> quickly and yields performance competitive with MKL.
>>>>
>>>> To make sure the right library is getting used, you have to make
>>>> sure it's first on the search path - export
>>>> LD_LIBRARY_PATH=/path/to/blas/library.so will do the trick here.
>>>>
>>>> For some examples of getting netlib-java setup on an ec2 node and
>>>> some example benchmarking code we ran a while back, see:
>>>>
https://github.com/shivaram/matrix-bench
>>>>
>>>> In particular - build-openblas-ec2.sh shows you how to build the
>>>> library and set up symlinks correctly, and scala/run-netlib.sh
>>>> shows you how to get the path setup and get that library picked up by netlib-java.
>>>>
>>>> In this way - you could probably get cuBLAS set up to be used by
>>>> netlib-java as well.
>>>>
>>>> - Evan
>>>>
>>>> On Fri, Feb 6, 2015 at 5:43 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Evan, could you elaborate on how to force BIDMat and netlib-java to
>>>> force loading the right blas? For netlib, I there are few JVM
>>>> flags, such as
>>>> -Dcom.github.fommil.netlib.BLAS=com.github.fommil.netlib.F2jBLAS,
>>>> so I can force it to use Java implementation. Not sure I understand how to force use a specific blas (not specific wrapper for blas).
>>>>
>>>> Btw. I have installed openblas (yum install openblas), so I suppose
>>>> that netlib is using it.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Friday, February 06, 2015 5:19 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Joseph Bradley;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Getting breeze to pick up the right blas library is critical for
>>>> performance. I recommend using OpenBLAS (or MKL, if you already have it).
>>>> It might make sense to force BIDMat to use the same underlying BLAS
>>>> library as well.
>>>>
>>>> On Fri, Feb 6, 2015 at 4:42 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Hi Evan, Joseph
>>>>
>>>> I did few matrix multiplication test and BIDMat seems to be ~10x
>>>> faster than netlib-java+breeze (sorry for weird table formatting):
>>>>
>>>> |A*B  size | BIDMat MKL | Breeze+Netlib-java
>>>> |native_system_linux_x86-64|
>>>> Breeze+Netlib-java f2jblas |
>>>> +-----------------------------------------------------------------------+
>>>> |100x100*100x100 | 0,00205596 | 0,03810324 | 0,002556 |
>>>> |1000x1000*1000x1000 | 0,018320947 | 0,51803557 |1,638475459 |
>>>> |10000x10000*10000x10000 | 23,78046632 | 445,0935211 | 1569,233228
>>>> ||
>>>>
>>>> Configuration: Intel(R) Xeon(R) CPU E31240 3.3 GHz, 6GB RAM, Fedora
>>>> 19 Linux, Scala 2.11.
>>>>
>>>> Later I will make tests with Cuda. I need to install new Cuda
>>>> version for this purpose.
>>>>
>>>> Do you have any ideas why breeze-netlib with native blas is so much
>>>> slower than BIDMat MKL?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Joseph Bradley [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 5:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc: Evan R. Sparks;
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> Hi Alexander,
>>>>
>>>> Using GPUs with Spark would be very exciting.  Small comment:
>>>> Concerning your question earlier about keeping data stored on the
>>>> GPU rather than having to move it between main memory and GPU
>>>> memory on each iteration, I would guess this would be critical to
>>>> getting good performance.  If you could do multiple local
>>>> iterations before aggregating results, then the cost of data
>>>> movement to the GPU could be amortized (and I believe that is done
>>>> in practice).  Having Spark be aware of the GPU and using it as another part of memory sounds like a much bigger undertaking.
>>>>
>>>> Joseph
>>>>
>>>> On Thu, Feb 5, 2015 at 4:59 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote:
>>>> Thank you for explanation! I’ve watched the BIDMach presentation by
>>>> John Canny and I am really inspired by his talk and comparisons with Spark MLlib.
>>>>
>>>> I am very interested to find out what will be better within Spark:
>>>> BIDMat or netlib-java with CPU or GPU natives. Could you suggest a
>>>> fair way to benchmark them? Currently I do benchmarks on artificial
>>>> neural networks in batch mode. While it is not a “pure” test of
>>>> linear algebra, it involves some other things that are essential to machine learning.
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>]
>>>> Sent: Thursday, February 05, 2015 1:29 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd be surprised of BIDMat+OpenBLAS was significantly faster than
>>>> netlib-java+OpenBLAS, but if it is much faster it's probably due to
>>>> netlib-java+data
>>>> layout and fewer levels of indirection - it's definitely a
>>>> worthwhile experiment to run. The main speedups I've seen from
>>>> using it come from highly optimized GPU code for linear algebra. I
>>>> know that in the past Canny has gone as far as to write custom GPU
>>>> kernels for performance-critical regions of code.[1]
>>>>
>>>> BIDMach is highly optimized for single node performance or
>>>> performance on small clusters.[2] Once data doesn't fit easily in
>>>> GPU memory (or can be batched in that way) the performance tends to
>>>> fall off. Canny argues for hardware/software codesign and as such
>>>> prefers machine configurations that are quite different than what
>>>> we find in most commodity cluster nodes - e.g. 10 disk cahnnels and 4 GPUs.
>>>>
>>>> In contrast, MLlib was designed for horizontal scalability on
>>>> commodity clusters and works best on very big datasets - order of terabytes.
>>>>
>>>> For the most part, these projects developed concurrently to address
>>>> slightly different use cases. That said, there may be bits of
>>>> BIDMach we could repurpose for MLlib - keep in mind we need to be
>>>> careful about maintaining cross-language compatibility for our Java
>>>> and Python-users, though.
>>>>
>>>> - Evan
>>>>
>>>> [1] -
http://arxiv.org/abs/1409.5402[2] -
>>>>
http://eecs.berkeley.edu/~hzhao/papers/BD.pdf
>>>>
>>>> On Thu, Feb 5, 2015 at 1:00 PM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Hi Evan,
>>>>
>>>> Thank you for suggestion! BIDMat seems to have terrific speed. Do
>>>> you know what makes them faster than netlib-java?
>>>>
>>>> The same group has BIDMach library that implements machine
>>>> learning. For some examples they use Caffe convolutional neural
>>>> network library owned by another group in Berkeley. Could you
>>>> elaborate on how these all might be connected with Spark Mllib? If
>>>> you take BIDMat for linear algebra why don’t you take BIDMach for optimization and learning?
>>>>
>>>> Best regards, Alexander
>>>>
>>>> From: Evan R. Sparks [mailto:
[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]><mailto:
>>>>
[hidden email]<mailto:[hidden email]>>>]
>>>> Sent: Thursday, February 05, 2015 12:09 PM
>>>> To: Ulanov, Alexander
>>>> Cc:
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email].
>>>>
apache.org<mailto:[hidden email]>>>
>>>> Subject: Re: Using CUDA within Spark / boosting linear algebra
>>>>
>>>> I'd expect that we can make GPU-accelerated BLAS faster than CPU
>>>> blas in many cases.
>>>>
>>>> You might consider taking a look at the codepaths that BIDMat (
>>>>
https://github.com/BIDData/BIDMat) takes and comparing them to
>>>> netlib-java/breeze. John Canny et. al. have done a bunch of work
>>>> optimizing to make this work really fast from Scala. I've run it on
>>>> my laptop and compared to MKL and in certain cases it's 10x faster at matrix multiply.
>>>> There are a lot of layers of indirection here and you really want
>>>> to avoid data copying as much as possible.
>>>>
>>>> We could also consider swapping out BIDMat for Breeze, but that
>>>> would be a big project and if we can figure out how to get
>>>> breeze+cublas to comparable performance that would be a big win.
>>>>
>>>> On Thu, Feb 5, 2015 at 11:55 AM, Ulanov, Alexander <
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:
>>>>
[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>>> wrote:
>>>> Dear Spark developers,
>>>>
>>>> I am exploring how to make linear algebra operations faster within Spark.
>>>> One way of doing this is to use Scala Breeze library that is
>>>> bundled with Spark. For matrix operations, it employs Netlib-java
>>>> that has a Java wrapper for BLAS (basic linear algebra subprograms)
>>>> and LAPACK native binaries if they are available on the worker
>>>> node. It also has its own optimized Java implementation of BLAS. It
>>>> is worth mentioning, that native binaries provide better performance only for BLAS level 3, i.e.
>>>> matrix-matrix operations or general matrix multiplication (GEMM).
>>>> This is confirmed by GEMM test on Netlib-java page
>>>>
https://github.com/fommil/netlib-java. I also confirmed it with my
>>>> experiments with training of artificial neural network
>>>>
https://github.com/apache/spark/pull/1290#issuecomment-70313952.
>>>> However, I would like to boost performance more.
>>>>
>>>> GPU is supposed to work fast with linear algebra and there is
>>>> Nvidia CUDA implementation of BLAS, called cublas. I have one Linux
>>>> server with Nvidia GPU and I was able to do the following. I linked
>>>> cublas (instead of cpu-based blas) with Netlib-java wrapper and put
>>>> it into Spark, so Breeze/Netlib is using it. Then I did some
>>>> performance measurements with regards to artificial neural network
>>>> batch learning in Spark MLlib that involves matrix-matrix
>>>> multiplications. It turns out that for matrices of size less than
>>>> ~1000x780 GPU cublas has the same speed as CPU blas. Cublas becomes
>>>> slower for bigger matrices. It worth mentioning that it is was not a test for ONLY multiplication since there are other operations involved.
>>>> One of the reasons for slowdown might be the overhead of copying
>>>> the matrices from computer memory to graphic card memory and back.
>>>>
>>>> So, few questions:
>>>> 1) Do these results with CUDA make sense?
>>>> 2) If the problem is with copy overhead, are there any libraries
>>>> that allow to force intermediate results to stay in graphic card
>>>> memory thus removing the overhead?
>>>> 3) Any other options to speed-up linear algebra in Spark?
>>>>
>>>> Thank you, Alexander
>>>>
>>>> -------------------------------------------------------------------
>>>> -- To unsubscribe, e-mail:
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>>>>
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>>>>
e.org>><mailto:[hidden email]<mailto:[hidden email]
>>>> ark.apac>
he.org<http://he.org>
>>>> <mailto:
[hidden email]<mailto:[hidden email]
>>>>
rk.apache.org>>> For additional commands, e-mail:
>>>>
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>>>>
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>>>>
>>>>
>>>>
>>>>
>>>

--
Best regards,
Sam





 

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