Yes, 8396 fixes the tests from Openblas_matrix_issue for all our archs. Waiting for test results from a user that had problems with OpenBLAS/0.3.1 too.
On 5/28/19 5:14 PM, Pablo Escobar Lopez wrote: > thank you Carlos! You did a great job figuring out this fix :) > > I can confirm that after applying this patch in our cluster the issue > seems to be solved for us. Now we pass these tests with > "OpenBLAS/0.3.1-GCC-7.3.0-2.30": > https://github.com/eylenth/Openblas_matrix_issue > https://github.com/xianyi/BLAS-Tester > > I also got a confirmation from a colleague in our user support team that > a problem he was trying to debug with some R code is solved after this > fix was applied. > > I have sent a PR with the fix upstream: > https://github.com/easybuilders/easybuild-easyconfigs/pull/8396 > > In case anyone else test the workaround it would be nice if you report > in the mailing list or in the pull request in github if it's working > fine for you too. > > regards, > Pablo > > > On Tue, May 28, 2019 at 2:32 PM Carlos Fenoy <[email protected] > <mailto:[email protected]>> wrote: > > Hi, > > After fighting a long time with this, we managed to get a solution > that passes both the "Openblas_matrix_issue" and "BLAS_tester" test > suites. > > To solve the issue we had to apply a patch and add a new build > parameter (USE_SIMPLE_THREADED_LEVEL3=1) to OpenBLAS to make it work > with multiple openmp threads. > > This is how the buildopts line looks like for us: > > buildopts = ' USE_SIMPLE_THREADED_LEVEL3=1 BINARY=64 USE_THREAD=1 > USE_OPENMP=1 CC="$CC" FC="$F77" DYNAMIC_ARCH=1' > > And the patch, we got it from this commit on the OpenBLAS > repo: > https://github.com/xianyi/OpenBLAS/commit/b14f44d2adbe1ec8ede0cdf06fb8b09f3c4b6e43 > (you > can get the patch by adding .patch at the end of the URL) > > Regards, > Carlos > > On Mon, May 27, 2019 at 6:15 PM Pablo Escobar Lopez > <[email protected] <mailto:[email protected]>> > wrote: > > Hi, > > did anyone found a working patch or workaround for the matrix > issue when using OpenBLAS-0.3.1 ? > > After a lot of try&error I couldn't pass the tests > in https://github.com/eylenth/Openblas_matrix_issue when > using > https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb > . > No matter what patches, toolchainopts or buildopts I use (and I > have tried few different combinations) . Is anyone able to pass > the tests using openblas-0.3.1 ? > > I could pass the tests using openblas-0.3.5 but upgrading my > foss/2018b toolchain would be quite messy because I use RPATH. > The less intrusive solution for my users would be to be able to > patch openblas-0.3.1 somehow but I couldn't find a working > solution. Any suggestions? > > regards, > Pablo. > > p.s. in a related topic, IMHO unless there is a proper > workaround I would suggest to stop providing openblas-0.3.1 with > easybuild. Right now we are distributing a broken library > > > On Tue, May 7, 2019 at 6:34 PM Mikael Öhman <[email protected] > <mailto:[email protected]>> wrote: > > Hi Thomas, > > I can also confirm these issues. I tried rebuilding > OpenBLAS+R after the fix in #7180, but I still saw the same > problems. > Very large matrix-matrix multiplications randomly gave the > wrong result. Very large errors. The larger the matrix, the > more frequent the errors. > > In the end, I compiled an intel-version (but I had to remove > a few extensions that didn't build) and removed my Foss > version from our installations. > > Perhaps it's related to hardware; I saw this on happen > skylake servers. I haven't had time to check if this > https://github.com/easybuilders/easybuild-easyconfigs/issues/8197 > also affects 0.3.1 > > Best regards, Mikael > > > On Tue, May 7, 2019 at 6:12 PM Thomas Eylenbosch > <[email protected] > <mailto:[email protected]>> wrote: > > Hello____ > > __ __ > > Some of our end users reported a calculation issue with > matrices when they are working with a foss/2018b module____ > > __ __ > > I reproduced this error with Python and R that are > compiled with the foss/2018b toolchain, the output > returns unexcepted results. ____ > > Then I reproduced this error with Python and R that are > compiled with the foss/2016b toolchain , then it gives > me the expected behavior. ____ > > __ __ > > You can reproduce this error with the following github > repository: ____ > > https://github.com/eylenth/Openblas_matrix_issue____ > > __ __ > > I have also tried to recompile the > OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb easyconfig file with > “toolchainopts = {'vectorize': False}” ( cfr. > > https://github.com/easybuilders/easybuild-easyconfigs/issues/7180)____ > > But is still giving me unexpected behavior____ > > __ __ > > Can someone try to reproduce the error with the > R/Python(foss/2018b) modules. Or can someone give me > feedback on this?____ > > __ __ > > Thank you in advance. ____ > > __ __ > > Met vriendelijke groet / Kind regards / Beste Grüße*____* > > *Thomas Eylenbosch____* > > /Ext: Gluo N.V.//____/ > > __ __ > > BASF Agricultural Solutions Belgium NV____ > > Technologiepark 101____ > > B-9052 Ghent (Zwijnaarde)____ > > BELGIUM____ > > E-mail: *[email protected] > <mailto:[email protected]>*____ > > cid:[email protected]____ > > BASF Agricultural Solutions Belgium NV, Registered > Office: 9052 Gent, Belgium____ > > Registration: RPR Gent: 0685.756.742____ > > __ __ > > > > -- > Pablo Escobar López > Linux/HPC systems engineer > sciCORE, University of Basel > SIB Swiss Institute of Bioinformatics > > > > -- > Pablo Escobar López > Linux/HPC systems engineer > sciCORE, University of Basel > SIB Swiss Institute of Bioinformatics -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: [email protected] Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
