June 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Petsc Parallel Matrix Vector Multiplication for Skew-Symmetric Matrix
by Matthew Knepley 02 Jun '21

02 Jun '21

On Wed, Jun 2, 2021 at 3:23 PM Yağmur Aksan <yagmuraksan(a)gmail.com> wrote: > Hello, > > I need a function that parallelly multiplies skew-symmetric matrix and > vector. Is there any function that Petsc provides? > To do so, I think of using matMult function in Petsc and changing it to > work with skew-symmetric matrices. But, I haven't found the implementation > of MatMult function. If there isn't any other better option that you can > recommend me, could you please tell me the link for the implementation of > MatMult function? > Do you want to save memory by using the special format? It will not save computing, and the speed improvement can be very small. Thanks, Matt > Thank you. > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

1 0

Petsc Parallel Matrix Vector Multiplication for Skew-Symmetric Matrix
by Yağmur Aksan 02 Jun '21

02 Jun '21

Hello, I need a function that parallelly multiplies skew-symmetric matrix and vector. Is there any function that Petsc provides? To do so, I think of using matMult function in Petsc and changing it to work with skew-symmetric matrices. But, I haven't found the implementation of MatMult function. If there isn't any other better option that you can recommend me, could you please tell me the link for the implementation of MatMult function? Thank you.

1 0

Re: [petsc-dev] [petsc-users] CUDA MatSetValues test
by Barry Smith 02 Jun '21

02 Jun '21

> On Jun 2, 2021, at 2:06 AM, Stefano Zampini <stefano.zampini(a)gmail.com> wrote: > > Barry > > If I remember correctly, the ctable business was a limitation of Mark's initial implementation, which I removed here https://gitlab.com/petsc/petsc/-/merge_requests/3411/diffs?commit_id=361737… <https://gitlab.com/petsc/petsc/-/merge_requests/3411/diffs?commit_id=361737…>. Here colmap was "int" already. We made a mistake letting this branch fall so behind main. I will add my observations in the MR Thanks, likely it was the merge brought in the incorrect colmap. Yes, it was my fault the branch go neglected, I become too emotional over the configure issue with CUDA, stating it needed a completely rewrite and then forgot about the branch. I have "fixed" the CUDA configure issue with an "ok" but hacky manner, after MPI is configured and changes the compilers, thus removing all the compiler flags, I force a rerun of parts of cuda.py to add back their contributions to the CUDA compiler flags. There is a circular dependency that this change resolves. Barry > > Il giorno mer 2 giu 2021 alle ore 09:20 Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> ha scritto: > > Switching the thread to petsc-dev since users don't need this. > > Had a nasty failure on one the CI, turned out the GPU colmap was declared as PetscInt* but it was copied down from the CPU into the GPU memory as int. The power of void* interface. Thus ex5cu.cu <http://ex5cu.cu/> which was never CI tested was crashing very strangely. By declaring it properly as int* I got the example to run with 64 bit indices. Submitted a new pipeline to see what else pops up. > > I am a bit worried about the csr2csc data structures and code, one line declaring csr2csc_i inside the struct disappeared in the rebase on main, I stuck it in but don't understand that code at all. I'll report further when the CI is done or crashes. I will also need to make sure it is compiled pre and post PETSC_PKG_CUDA_VERSION_GE(11,0,0) > > I will also investigate this CTABLE business, the GPU doesn't need to know or care if the CPU is using a CTABLE or not; it just needs the colmap array format that it gets from spreading out the garray anyway to be copied to the GPU so PETSc can likely be built with CTABLES as normal; this will improve the testing a lot. > > > > Barry > > >> On May 30, 2021, at 11:54 AM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >> >> >> I believe I have finally successfully rebased the branch barry/2020-11-11/cleanup-matsetvaluesdevice against main and cleaned up all the issues. Please read the commit message. >> >> I have submitted a CI pipeline with ctables turned off temporarily for testing of the MatSetValuesDevice(). If it works hopefully Mark can maybe run a few additional tests of his Landau code that are not in the usual testing to verify and we can finally get the branch into main. >> >> Mark, >> >> Since this change is involved, it is likely your Landau mass matrix branch may not rebase cleanly. Let me know if you would like me to do the rebase and testing of your Landau mass matrix branch. I can get it ready to work with the results of barry/2020-11-11/cleanup-matsetvaluesdevice and then hand it back to you for further development. >> >> Barry >> >> >>> On May 29, 2021, at 11:32 AM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>> >>> >>> I am working away on this branch, making some progress, also cleaning things up with some small simplifications. Hope I can succeed, a bunch of stuff got moved around and some structs had changes, the merge could not handle some of these so I have to do a good amount of code wrangling to fix it. >>> >>> I'll let you know as I progress. >>> >>> Barry >>> >>> >>>> On May 28, 2021, at 10:53 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>> >>>> >>>> I have rebased and tried to fix everything. I am now fixing the issues of --download-openmpi and cuda, once that is done I will test, rebase with main again if needed and restart the MR and get it into main. >>>> >>>> Barry >>>> >>>> I was stupid to let the MR lay fallow, I should have figured out a solution to the openmpi and cuda issue instead of punting and waiting for a dream fix. >>>> >>>> >>>> >>>>> On May 28, 2021, at 2:39 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>> >>>>> Thanks, >>>>> >>>>> I did not intend to make any (real) changes. >>>>> The only thing that I did not intend to use from Barry's branch, that conflicted, was the help and comment block at the top of ex5cu.cu <http://ex5cu.cu/> >>>>> >>>>> * I ended up with two declarations of PetscSplitCSRDataStructure >>>>> * I added some includes to fix errors like this: >>>>> /ccs/home/adams/petsc/include/../src/mat/impls/aij/seq/seqcusparse/cusparsematimpl.h(263): error: incomplete type is not allowed >>>>> * I end ended not having csr2csc_i in Mat_SeqAIJCUSPARSE so I get: >>>>> /autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu <http://aijcusparse.cu/>(1348): error: class "Mat_SeqAIJCUSPARSE" has no member "csr2csc_i" >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, May 28, 2021 at 3:13 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>> I can take a quick look at it tomorrow, what are the main changes you made since then? >>>>> >>>>>> On May 28, 2021, at 9:51 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>> >>>>>> I am getting messed up in trying to resolve conflicts in rebasing over main. >>>>>> Is there a better way of doing this? >>>>>> Can I just tell git to use Barry's version and then test it? >>>>>> Or should I just try it again? >>>>>> >>>>>> On Fri, May 28, 2021 at 2:15 PM Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>> I am rebasing over main and its a bit of a mess. I must have missed something. I get this. I think the _n_SplitCSRMat must be wrong. >>>>>> >>>>>> >>>>>> In file included from /autofs/nccs-svm1_home1/adams/petsc/src/vec/is/sf/impls/basic/sfbasic.c:128:0: >>>>>> /ccs/home/adams/petsc/include/petscmat.h:1976:32: error: conflicting types for 'PetscSplitCSRDataStructure' >>>>>> typedef struct _n_SplitCSRMat *PetscSplitCSRDataStructure; >>>>>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>>> /ccs/home/adams/petsc/include/petscmat.h:1922:31: note: previous declaration of 'PetscSplitCSRDataStructure' was here >>>>>> typedef struct _p_SplitCSRMat PetscSplitCSRDataStructure; >>>>>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>>> CC arch-summit-opt-gnu-cuda/obj/vec/vec/impls/seq/dvec2.o >>>>>> >>>>>> On Fri, May 28, 2021 at 1:50 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>> OpenMPI.py depends on cuda.py in that, if cuda is present, configures using cuda. MPI.py or MPICH.py do not depend on cuda.py (MPICH, only weakly, it adds a print if cuda is present) >>>>>> Since eventually the MPI distro will only need a hint to be configured with CUDA, why not removing the dependency at all and add only a flag —download-openmpi-use-cuda? >>>>>> >>>>>>> On May 28, 2021, at 8:44 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>>>>> >>>>>>> >>>>>>> Stefano, who has a far better memory than me, wrote >>>>>>> >>>>>>> > Or probably remove —download-openmpi ? Or, just for the moment, why can’t we just tell configure that mpi is a weak dependence of cuda.py, so that it will be forced to be configured later? >>>>>>> >>>>>>> MPI.py depends on cuda.py so we cannot also have cuda.py depend on MPI.py using the generic dependencies of configure/packages >>>>>>> >>>>>>> but perhaps we can just hardwire the rerunning of cuda.py when the MPI compilers are reset. I will try that now and if I can get it to work we should be able to move those old fix branches along as MR. >>>>>>> >>>>>>> Barry >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On May 28, 2021, at 12:41 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>> >>>>>>>> OK, I will try to rebase and test Barry's branch. >>>>>>>> >>>>>>>> On Fri, May 28, 2021 at 1:26 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>> Yes, it is the branch I was using before force pushing to Barry’s barry/2020-11-11/cleanup-matsetvaluesdevice >>>>>>>> You can use both I guess >>>>>>>> >>>>>>>>> On May 28, 2021, at 8:25 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>> >>>>>>>>> Is this the correct branch? It conflicted with ex5cu so I assume it is. >>>>>>>>> >>>>>>>>> >>>>>>>>> stefanozampini/simplify-setvalues-device <https://gitlab.com/petsc/petsc/-/tree/stefanozampini/simplify-setvalues-dev…> >>>>>>>>> >>>>>>>>> On Fri, May 28, 2021 at 1:24 PM Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>> I am fixing rebasing this branch over main. >>>>>>>>> >>>>>>>>> On Fri, May 28, 2021 at 1:16 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>> Or probably remove —download-openmpi ? Or, just for the moment, why can’t we just tell configure that mpi is a weak dependence of cuda.py, so that it will be forced to be configured later? >>>>>>>>> >>>>>>>>>> On May 28, 2021, at 8:12 PM, Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>>> >>>>>>>>>> That branch provides a fix for MatSetValuesDevice but it never got merged because of the CI issues with the —download-openmpi. We can probably try to skip the test in that specific configuration? >>>>>>>>>> >>>>>>>>>>> On May 28, 2021, at 7:45 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ~/petsc/src/mat/tutorials (barry/2021-05-28/robustify-cuda-gencodearch-check=) arch-robustify-cuda-gencodearch-check >>>>>>>>>>> $ ./ex5cu >>>>>>>>>>> terminate called after throwing an instance of 'thrust::system::system_error' >>>>>>>>>>> what(): fill_n: failed to synchronize: cudaErrorIllegalAddress: an illegal memory access was encountered >>>>>>>>>>> Aborted (core dumped) >>>>>>>>>>> >>>>>>>>>>> requires: cuda !define(PETSC_USE_CTABLE) >>>>>>>>>>> >>>>>>>>>>> CI does not test with CUDA and no ctable. The code is still broken as it was six months ago in the discussion Stefano pointed to. It is clear why just no one has had the time to clean things up. >>>>>>>>>>> >>>>>>>>>>> Barry >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> On May 28, 2021, at 11:13 AM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Fri, May 28, 2021 at 11:57 AM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>>>>> If you are referring to your device set values, I guess it is not currently tested >>>>>>>>>>>> >>>>>>>>>>>> No. There is a test for that (ex5cu). >>>>>>>>>>>> I have a user that is getting a segv in MatSetValues with aijcusparse. I suspect there is memory corruption but I'm trying to cover all the bases. >>>>>>>>>>>> I have added a cuda test to ksp/ex56 that works. I can do an MR for it if such a test does not exist. >>>>>>>>>>>> >>>>>>>>>>>> See the discussions here https://gitlab.com/petsc/petsc/-/merge_requests/3411 <https://gitlab.com/petsc/petsc/-/merge_requests/3411> >>>>>>>>>>>> I started cleaning up the code to prepare for testing but we never finished it https://gitlab.com/petsc/petsc/-/commits/stefanozampini/simplify-setvalues-… <https://gitlab.com/petsc/petsc/-/commits/stefanozampini/simplify-setvalues-…> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> On May 28, 2021, at 6:53 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> Is there a test with MatSetValues and CUDA? >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > > > -- > Stefano

1 0

Re: [petsc-dev] I think main is broken
by Matthew Knepley 02 Jun '21

02 Jun '21

Thanks! Matt On Wed, Jun 2, 2021 at 11:14 AM Satish Balay <balay(a)mcs.anl.gov> wrote: > Fixes at https://gitlab.com/petsc/petsc/-/merge_requests/4059 > > Satish > > On Wed, 2 Jun 2021, Matthew Knepley wrote: > > > I just rebased on main and get this: > > > > config/BuildSystem/config/packages/kokkos-kernels.py:7: self.gitcommit = > > '54e4213ca028163a76639d23b1204b213203bc79' # origin/develop of 2021-04-28 > > 569 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L569 > >config/BuildSystem/config/packages/kokkos.py:7: > > self.gitcommit = 'd4ed86ffb1b156faaa0f936ce839cfd6d3282478' # > > origin/develop of 2021-04-28 > > 570 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L570 > >config/BuildSystem/config/packages/magma.py:17: > > self.gitcommit = 'origin/master' > > 571 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L571>Error: Do not > > use a branch name in a configure package file > > 572 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L572> > > > > > > Thanks, > > > > Matt > > > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

1 0

Re: [petsc-dev] I think main is broken
by Satish Balay 02 Jun '21

02 Jun '21

Fixes at https://gitlab.com/petsc/petsc/-/merge_requests/4059 Satish On Wed, 2 Jun 2021, Matthew Knepley wrote: > I just rebased on main and get this: > > config/BuildSystem/config/packages/kokkos-kernels.py:7: self.gitcommit = > '54e4213ca028163a76639d23b1204b213203bc79' # origin/develop of 2021-04-28 > 569 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L569>config/BuildSystem/config/packages/kokkos.py:7: > self.gitcommit = 'd4ed86ffb1b156faaa0f936ce839cfd6d3282478' # > origin/develop of 2021-04-28 > 570 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L570>config/BuildSystem/config/packages/magma.py:17: > self.gitcommit = 'origin/master' > 571 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L571>Error: Do not > use a branch name in a configure package file > 572 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L572> > > > Thanks, > > Matt > >

1 0

I think main is broken
by Matthew Knepley 02 Jun '21

02 Jun '21

I just rebased on main and get this: config/BuildSystem/config/packages/kokkos-kernels.py:7: self.gitcommit = '54e4213ca028163a76639d23b1204b213203bc79' # origin/develop of 2021-04-28 569 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L569>config/BuildSystem/config/packages/kokkos.py:7: self.gitcommit = 'd4ed86ffb1b156faaa0f936ce839cfd6d3282478' # origin/develop of 2021-04-28 570 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L570>config/BuildSystem/config/packages/magma.py:17: self.gitcommit = 'origin/master' 571 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L571>Error: Do not use a branch name in a configure package file 572 <https://gitlab.com/petsc/petsc/-/jobs/1312692810#L572> Thanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

1 0

Re: [petsc-dev] [petsc-users] CUDA MatSetValues test
by Stefano Zampini 02 Jun '21

02 Jun '21

Barry If I remember correctly, the ctable business was a limitation of Mark's initial implementation, which I removed here https://gitlab.com/petsc/petsc/-/merge_requests/3411/diffs?commit_id=361737…. Here colmap was "int" already. We made a mistake letting this branch fall so behind main. I will add my observations in the MR Il giorno mer 2 giu 2021 alle ore 09:20 Barry Smith <bsmith(a)petsc.dev> ha scritto: > > Switching the thread to petsc-dev since users don't need this. > > Had a nasty failure on one the CI, turned out the GPU colmap was > declared as PetscInt* but it was copied down from the CPU into the GPU > memory as int. The power of void* interface. Thus ex5cu.cu which was > never CI tested was crashing very strangely. By declaring it properly as > int* I got the example to run with 64 bit indices. Submitted a new pipeline > to see what else pops up. > > I am a bit worried about the csr2csc data structures and code, one line > declaring csr2csc_i inside the struct disappeared in the rebase on main, I > stuck it in but don't understand that code at all. I'll report further when > the CI is done or crashes. I will also need to make sure it is compiled pre > and post PETSC_PKG_CUDA_VERSION_GE(11,0,0) > > I will also investigate this CTABLE business, the GPU doesn't need to > know or care if the CPU is using a CTABLE or not; it just needs the colmap > array format that it gets from spreading out the garray anyway to be copied > to the GPU so PETSc can likely be built with CTABLES as normal; this will > improve the testing a lot. > > > > Barry > > > On May 30, 2021, at 11:54 AM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I believe I have finally successfully rebased the branch barry/2020-11-11/cleanup-matsetvaluesdevice > against main and cleaned up all the issues. Please read the commit message. > > I have submitted a CI pipeline with ctables turned off temporarily for > testing of the MatSetValuesDevice(). If it works hopefully Mark can maybe > run a few additional tests of his Landau code that are not in the usual > testing to verify and we can finally get the branch into main. > > Mark, > > Since this change is involved, it is likely your Landau mass matrix > branch may not rebase cleanly. Let me know if you would like me to do the > rebase and testing of your Landau mass matrix branch. I can get it ready to > work with the results of barry/2020-11-11/cleanup-matsetvaluesdevice and > then hand it back to you for further development. > > Barry > > > On May 29, 2021, at 11:32 AM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I am working away on this branch, making some progress, also cleaning > things up with some small simplifications. Hope I can succeed, a bunch of > stuff got moved around and some structs had changes, the merge could not > handle some of these so I have to do a good amount of code wrangling to fix > it. > > I'll let you know as I progress. > > Barry > > > On May 28, 2021, at 10:53 PM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I have rebased and tried to fix everything. I am now fixing the issues > of --download-openmpi and cuda, once that is done I will test, rebase with > main again if needed and restart the MR and get it into main. > > Barry > > I was stupid to let the MR lay fallow, I should have figured out a > solution to the openmpi and cuda issue instead of punting and waiting for a > dream fix. > > > > On May 28, 2021, at 2:39 PM, Mark Adams <mfadams(a)lbl.gov> wrote: > > Thanks, > > I did not intend to make any (real) changes. > The only thing that I did not intend to use from Barry's branch, that > conflicted, was the help and comment block at the top of ex5cu.cu > > * I ended up with two declarations of PetscSplitCSRDataStructure > * I added some includes to fix errors like this: > /ccs/home/adams/petsc/include/../src/mat/impls/aij/seq/seqcusparse/cusparsematimpl.h(263): > error: incomplete type is not allowed > * I end ended not having csr2csc_i in Mat_SeqAIJCUSPARSE so I get: > /autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/aij/seq/seqcusparse/ > aijcusparse.cu(1348): error: class "Mat_SeqAIJCUSPARSE" has no member > "csr2csc_i" > > > > > On Fri, May 28, 2021 at 3:13 PM Stefano Zampini <stefano.zampini(a)gmail.com> > wrote: > >> I can take a quick look at it tomorrow, what are the main changes you >> made since then? >> >> On May 28, 2021, at 9:51 PM, Mark Adams <mfadams(a)lbl.gov> wrote: >> >> I am getting messed up in trying to resolve conflicts in rebasing over >> main. >> Is there a better way of doing this? >> Can I just tell git to use Barry's version and then test it? >> Or should I just try it again? >> >> On Fri, May 28, 2021 at 2:15 PM Mark Adams <mfadams(a)lbl.gov> wrote: >> >>> I am rebasing over main and its a bit of a mess. I must have missed >>> something. I get this. I think the _n_SplitCSRMat must be wrong. >>> >>> >>> In file included from >>> /autofs/nccs-svm1_home1/adams/petsc/src/vec/is/sf/impls/basic/sfbasic.c:128:0: >>> /ccs/home/adams/petsc/include/petscmat.h:1976:32: error: conflicting >>> types for 'PetscSplitCSRDataStructure' >>> typedef struct _n_SplitCSRMat *PetscSplitCSRDataStructure; >>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>> /ccs/home/adams/petsc/include/petscmat.h:1922:31: note: previous >>> declaration of 'PetscSplitCSRDataStructure' was here >>> typedef struct _p_SplitCSRMat PetscSplitCSRDataStructure; >>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>> CC arch-summit-opt-gnu-cuda/obj/vec/vec/impls/seq/dvec2.o >>> >>> On Fri, May 28, 2021 at 1:50 PM Stefano Zampini < >>> stefano.zampini(a)gmail.com> wrote: >>> >>>> OpenMPI.py depends on cuda.py in that, if cuda is present, configures >>>> using cuda. MPI.py or MPICH.py do not depend on cuda.py (MPICH, only >>>> weakly, it adds a print if cuda is present) >>>> Since eventually the MPI distro will only need a hint to be configured >>>> with CUDA, why not removing the dependency at all and add only a flag >>>> —download-openmpi-use-cuda? >>>> >>>> On May 28, 2021, at 8:44 PM, Barry Smith <bsmith(a)petsc.dev> wrote: >>>> >>>> >>>> Stefano, who has a far better memory than me, wrote >>>> >>>> > Or probably remove —download-openmpi ? Or, just for the moment, why >>>> can’t we just tell configure that mpi is a weak dependence of cuda.py, so >>>> that it will be forced to be configured later? >>>> >>>> MPI.py depends on cuda.py so we cannot also have cuda.py depend on >>>> MPI.py using the generic dependencies of configure/packages >>>> >>>> but perhaps we can just hardwire the rerunning of cuda.py when the >>>> MPI compilers are reset. I will try that now and if I can get it to work we >>>> should be able to move those old fix branches along as MR. >>>> >>>> Barry >>>> >>>> >>>> >>>> On May 28, 2021, at 12:41 PM, Mark Adams <mfadams(a)lbl.gov> wrote: >>>> >>>> OK, I will try to rebase and test Barry's branch. >>>> >>>> On Fri, May 28, 2021 at 1:26 PM Stefano Zampini < >>>> stefano.zampini(a)gmail.com> wrote: >>>> >>>>> Yes, it is the branch I was using before force pushing to >>>>> Barry’s barry/2020-11-11/cleanup-matsetvaluesdevice >>>>> You can use both I guess >>>>> >>>>> On May 28, 2021, at 8:25 PM, Mark Adams <mfadams(a)lbl.gov> wrote: >>>>> >>>>> Is this the correct branch? It conflicted with ex5cu so I assume it is. >>>>> >>>>> >>>>> stefanozampini/simplify-setvalues-device >>>>> <https://gitlab.com/petsc/petsc/-/tree/stefanozampini/simplify-setvalues-dev…> >>>>> >>>>> On Fri, May 28, 2021 at 1:24 PM Mark Adams <mfadams(a)lbl.gov> wrote: >>>>> >>>>>> I am fixing rebasing this branch over main. >>>>>> >>>>>> On Fri, May 28, 2021 at 1:16 PM Stefano Zampini < >>>>>> stefano.zampini(a)gmail.com> wrote: >>>>>> >>>>>>> Or probably remove —download-openmpi ? Or, just for the moment, why >>>>>>> can’t we just tell configure that mpi is a weak dependence of cuda.py, so >>>>>>> that it will be forced to be configured later? >>>>>>> >>>>>>> On May 28, 2021, at 8:12 PM, Stefano Zampini < >>>>>>> stefano.zampini(a)gmail.com> wrote: >>>>>>> >>>>>>> That branch provides a fix for MatSetValuesDevice but it never got >>>>>>> merged because of the CI issues with the —download-openmpi. We can probably >>>>>>> try to skip the test in that specific configuration? >>>>>>> >>>>>>> On May 28, 2021, at 7:45 PM, Barry Smith <bsmith(a)petsc.dev> wrote: >>>>>>> >>>>>>> >>>>>>> ~/petsc/src/mat/tutorials* >>>>>>> (barry/2021-05-28/robustify-cuda-gencodearch-check=)* >>>>>>> arch-robustify-cuda-gencodearch-check >>>>>>> $ ./ex5cu >>>>>>> terminate called after throwing an instance of >>>>>>> 'thrust::system::system_error' >>>>>>> what(): fill_n: failed to synchronize: cudaErrorIllegalAddress: >>>>>>> an illegal memory access was encountered >>>>>>> Aborted (core dumped) >>>>>>> >>>>>>> requires: cuda !define(PETSC_USE_CTABLE) >>>>>>> >>>>>>> CI does not test with CUDA and no ctable. The code is still >>>>>>> broken as it was six months ago in the discussion Stefano pointed to. It is >>>>>>> clear why just no one has had the time to clean things up. >>>>>>> >>>>>>> Barry >>>>>>> >>>>>>> >>>>>>> On May 28, 2021, at 11:13 AM, Mark Adams <mfadams(a)lbl.gov> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Fri, May 28, 2021 at 11:57 AM Stefano Zampini < >>>>>>> stefano.zampini(a)gmail.com> wrote: >>>>>>> >>>>>>>> If you are referring to your device set values, I guess it is not >>>>>>>> currently tested >>>>>>>> >>>>>>> >>>>>>> No. There is a test for that (ex5cu). >>>>>>> I have a user that is getting a segv in MatSetValues with >>>>>>> aijcusparse. I suspect there is memory corruption but I'm trying to cover >>>>>>> all the bases. >>>>>>> I have added a cuda test to ksp/ex56 that works. I can do an MR for >>>>>>> it if such a test does not exist. >>>>>>> >>>>>>> >>>>>>>> See the discussions here >>>>>>>> https://gitlab.com/petsc/petsc/-/merge_requests/3411 >>>>>>>> I started cleaning up the code to prepare for testing but we never >>>>>>>> finished it >>>>>>>> https://gitlab.com/petsc/petsc/-/commits/stefanozampini/simplify-setvalues-… >>>>>>>> >>>>>>>> >>>>>>>> On May 28, 2021, at 6:53 PM, Mark Adams <mfadams(a)lbl.gov> wrote: >>>>>>>> >>>>>>>> Is there a test with MatSetValues and CUDA? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>>> >>>> >> > > > > -- Stefano

1 0

Re: [petsc-dev] [petsc-users] CUDA MatSetValues test
by Barry Smith 02 Jun '21

02 Jun '21

Switching the thread to petsc-dev since users don't need this. Had a nasty failure on one the CI, turned out the GPU colmap was declared as PetscInt* but it was copied down from the CPU into the GPU memory as int. The power of void* interface. Thus ex5cu.cu which was never CI tested was crashing very strangely. By declaring it properly as int* I got the example to run with 64 bit indices. Submitted a new pipeline to see what else pops up. I am a bit worried about the csr2csc data structures and code, one line declaring csr2csc_i inside the struct disappeared in the rebase on main, I stuck it in but don't understand that code at all. I'll report further when the CI is done or crashes. I will also need to make sure it is compiled pre and post PETSC_PKG_CUDA_VERSION_GE(11,0,0) I will also investigate this CTABLE business, the GPU doesn't need to know or care if the CPU is using a CTABLE or not; it just needs the colmap array format that it gets from spreading out the garray anyway to be copied to the GPU so PETSc can likely be built with CTABLES as normal; this will improve the testing a lot. Barry > On May 30, 2021, at 11:54 AM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I believe I have finally successfully rebased the branch barry/2020-11-11/cleanup-matsetvaluesdevice against main and cleaned up all the issues. Please read the commit message. > > I have submitted a CI pipeline with ctables turned off temporarily for testing of the MatSetValuesDevice(). If it works hopefully Mark can maybe run a few additional tests of his Landau code that are not in the usual testing to verify and we can finally get the branch into main. > > Mark, > > Since this change is involved, it is likely your Landau mass matrix branch may not rebase cleanly. Let me know if you would like me to do the rebase and testing of your Landau mass matrix branch. I can get it ready to work with the results of barry/2020-11-11/cleanup-matsetvaluesdevice and then hand it back to you for further development. > > Barry > > >> On May 29, 2021, at 11:32 AM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >> >> >> I am working away on this branch, making some progress, also cleaning things up with some small simplifications. Hope I can succeed, a bunch of stuff got moved around and some structs had changes, the merge could not handle some of these so I have to do a good amount of code wrangling to fix it. >> >> I'll let you know as I progress. >> >> Barry >> >> >>> On May 28, 2021, at 10:53 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>> >>> >>> I have rebased and tried to fix everything. I am now fixing the issues of --download-openmpi and cuda, once that is done I will test, rebase with main again if needed and restart the MR and get it into main. >>> >>> Barry >>> >>> I was stupid to let the MR lay fallow, I should have figured out a solution to the openmpi and cuda issue instead of punting and waiting for a dream fix. >>> >>> >>> >>>> On May 28, 2021, at 2:39 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>> >>>> Thanks, >>>> >>>> I did not intend to make any (real) changes. >>>> The only thing that I did not intend to use from Barry's branch, that conflicted, was the help and comment block at the top of ex5cu.cu <http://ex5cu.cu/> >>>> >>>> * I ended up with two declarations of PetscSplitCSRDataStructure >>>> * I added some includes to fix errors like this: >>>> /ccs/home/adams/petsc/include/../src/mat/impls/aij/seq/seqcusparse/cusparsematimpl.h(263): error: incomplete type is not allowed >>>> * I end ended not having csr2csc_i in Mat_SeqAIJCUSPARSE so I get: >>>> /autofs/nccs-svm1_home1/adams/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu <http://aijcusparse.cu/>(1348): error: class "Mat_SeqAIJCUSPARSE" has no member "csr2csc_i" >>>> >>>> >>>> >>>> >>>> On Fri, May 28, 2021 at 3:13 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>> I can take a quick look at it tomorrow, what are the main changes you made since then? >>>> >>>>> On May 28, 2021, at 9:51 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>> >>>>> I am getting messed up in trying to resolve conflicts in rebasing over main. >>>>> Is there a better way of doing this? >>>>> Can I just tell git to use Barry's version and then test it? >>>>> Or should I just try it again? >>>>> >>>>> On Fri, May 28, 2021 at 2:15 PM Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>> I am rebasing over main and its a bit of a mess. I must have missed something. I get this. I think the _n_SplitCSRMat must be wrong. >>>>> >>>>> >>>>> In file included from /autofs/nccs-svm1_home1/adams/petsc/src/vec/is/sf/impls/basic/sfbasic.c:128:0: >>>>> /ccs/home/adams/petsc/include/petscmat.h:1976:32: error: conflicting types for 'PetscSplitCSRDataStructure' >>>>> typedef struct _n_SplitCSRMat *PetscSplitCSRDataStructure; >>>>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>> /ccs/home/adams/petsc/include/petscmat.h:1922:31: note: previous declaration of 'PetscSplitCSRDataStructure' was here >>>>> typedef struct _p_SplitCSRMat PetscSplitCSRDataStructure; >>>>> ^~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>> CC arch-summit-opt-gnu-cuda/obj/vec/vec/impls/seq/dvec2.o >>>>> >>>>> On Fri, May 28, 2021 at 1:50 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>> OpenMPI.py depends on cuda.py in that, if cuda is present, configures using cuda. MPI.py or MPICH.py do not depend on cuda.py (MPICH, only weakly, it adds a print if cuda is present) >>>>> Since eventually the MPI distro will only need a hint to be configured with CUDA, why not removing the dependency at all and add only a flag —download-openmpi-use-cuda? >>>>> >>>>>> On May 28, 2021, at 8:44 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>>>> >>>>>> >>>>>> Stefano, who has a far better memory than me, wrote >>>>>> >>>>>> > Or probably remove —download-openmpi ? Or, just for the moment, why can’t we just tell configure that mpi is a weak dependence of cuda.py, so that it will be forced to be configured later? >>>>>> >>>>>> MPI.py depends on cuda.py so we cannot also have cuda.py depend on MPI.py using the generic dependencies of configure/packages >>>>>> >>>>>> but perhaps we can just hardwire the rerunning of cuda.py when the MPI compilers are reset. I will try that now and if I can get it to work we should be able to move those old fix branches along as MR. >>>>>> >>>>>> Barry >>>>>> >>>>>> >>>>>> >>>>>>> On May 28, 2021, at 12:41 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>> >>>>>>> OK, I will try to rebase and test Barry's branch. >>>>>>> >>>>>>> On Fri, May 28, 2021 at 1:26 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>> Yes, it is the branch I was using before force pushing to Barry’s barry/2020-11-11/cleanup-matsetvaluesdevice >>>>>>> You can use both I guess >>>>>>> >>>>>>>> On May 28, 2021, at 8:25 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>> >>>>>>>> Is this the correct branch? It conflicted with ex5cu so I assume it is. >>>>>>>> >>>>>>>> >>>>>>>> stefanozampini/simplify-setvalues-device <https://gitlab.com/petsc/petsc/-/tree/stefanozampini/simplify-setvalues-dev…> >>>>>>>> >>>>>>>> On Fri, May 28, 2021 at 1:24 PM Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>> I am fixing rebasing this branch over main. >>>>>>>> >>>>>>>> On Fri, May 28, 2021 at 1:16 PM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>> Or probably remove —download-openmpi ? Or, just for the moment, why can’t we just tell configure that mpi is a weak dependence of cuda.py, so that it will be forced to be configured later? >>>>>>>> >>>>>>>>> On May 28, 2021, at 8:12 PM, Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>> >>>>>>>>> That branch provides a fix for MatSetValuesDevice but it never got merged because of the CI issues with the —download-openmpi. We can probably try to skip the test in that specific configuration? >>>>>>>>> >>>>>>>>>> On May 28, 2021, at 7:45 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ~/petsc/src/mat/tutorials (barry/2021-05-28/robustify-cuda-gencodearch-check=) arch-robustify-cuda-gencodearch-check >>>>>>>>>> $ ./ex5cu >>>>>>>>>> terminate called after throwing an instance of 'thrust::system::system_error' >>>>>>>>>> what(): fill_n: failed to synchronize: cudaErrorIllegalAddress: an illegal memory access was encountered >>>>>>>>>> Aborted (core dumped) >>>>>>>>>> >>>>>>>>>> requires: cuda !define(PETSC_USE_CTABLE) >>>>>>>>>> >>>>>>>>>> CI does not test with CUDA and no ctable. The code is still broken as it was six months ago in the discussion Stefano pointed to. It is clear why just no one has had the time to clean things up. >>>>>>>>>> >>>>>>>>>> Barry >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> On May 28, 2021, at 11:13 AM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, May 28, 2021 at 11:57 AM Stefano Zampini <stefano.zampini(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>>>> If you are referring to your device set values, I guess it is not currently tested >>>>>>>>>>> >>>>>>>>>>> No. There is a test for that (ex5cu). >>>>>>>>>>> I have a user that is getting a segv in MatSetValues with aijcusparse. I suspect there is memory corruption but I'm trying to cover all the bases. >>>>>>>>>>> I have added a cuda test to ksp/ex56 that works. I can do an MR for it if such a test does not exist. >>>>>>>>>>> >>>>>>>>>>> See the discussions here https://gitlab.com/petsc/petsc/-/merge_requests/3411 <https://gitlab.com/petsc/petsc/-/merge_requests/3411> >>>>>>>>>>> I started cleaning up the code to prepare for testing but we never finished it https://gitlab.com/petsc/petsc/-/commits/stefanozampini/simplify-setvalues-… <https://gitlab.com/petsc/petsc/-/commits/stefanozampini/simplify-setvalues-…> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> On May 28, 2021, at 6:53 PM, Mark Adams <mfadams(a)lbl.gov <mailto:[email protected]>> wrote: >>>>>>>>>>>> >>>>>>>>>>>> Is there a test with MatSetValues and CUDA? >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

1 0