We would need more information about "hanging". Do PETSc examples and tiny problems "hang" on multiple nodes? If you run with -info what are the last messages printed? Can you run with a debugger to see where it is "hanging"?
> On Aug 9, 2023, at 5:59 PM, Ng, Cho-Kuen <[email protected]> wrote: > > Barry and Matt, > > Thanks for your help. Now I can use petsc GPU backend on Perlmutter: 1 node, > 4 MPI tasks and 4 GPUs. However, I ran into problems with multiple nodes: 2 > nodes, 8 MPI tasks and 8 GPUs. The run hung on KSPSolve. How can I fix this? > > Best, > Cho > > From: Barry Smith <[email protected] <mailto:[email protected]>> > Sent: Monday, July 17, 2023 6:58 AM > To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> > Cc: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-users] Using PETSc GPU backend > > > The examples that use DM, in particular DMDA all trivially support using the > GPU with -dm_mat_type aijcusparse -dm_vec_type cuda > > > >> On Jul 17, 2023, at 1:45 AM, Ng, Cho-Kuen <[email protected] >> <mailto:[email protected]>> wrote: >> >> Barry, >> >> Thank you so much for the clarification. >> >> I see that ex104.c and ex300.c use MatXAIJSetPreallocation(). Are there >> other tutorials available? >> >> Cho >> From: Barry Smith <[email protected] <mailto:[email protected]>> >> Sent: Saturday, July 15, 2023 8:36 AM >> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >> Cc: [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> Subject: Re: [petsc-users] Using PETSc GPU backend >> >> >> >> Cho, >> >> We currently have a crappy API for turning on GPU support, and our >> documentation is misleading in places. >> >> People constantly say "to use GPU's with PETSc you only need to use >> -mat_type aijcusparse (for example)" This is incorrect. >> >> This does not work with code that uses the convenience Mat constructors >> such as MatCreateAIJ(), MatCreateAIJWithArrays etc. It only works if you use >> the constructor approach of MatCreate(), MatSetSizes(), MatSetFromOptions(), >> MatXXXSetPreallocation(). ... Similarly you need to use VecCreate(), >> VecSetSizes(), VecSetFromOptions() and -vec_type cuda >> >> If you use DM to create the matrices and vectors then you can use >> -dm_mat_type aijcusparse -dm_vec_type cuda >> >> Sorry for the confusion. >> >> Barry >> >> >> >> >>> On Jul 15, 2023, at 8:03 AM, Matthew Knepley <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> On Sat, Jul 15, 2023 at 1:44 AM Ng, Cho-Kuen <[email protected] >>> <mailto:[email protected]>> wrote: >>> Matt, >>> >>> After inserting 2 lines in the code: >>> >>> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); >>> >>> ierr = MatSetFromOptions(A);CHKERRQ(ierr); >>> ierr = MatCreateAIJ(PETSC_COMM_WORLD,mlocal,mlocal,m,n, >>> d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);;CHKERRQ(ierr); >>> >>> "There are no unused options." However, there is no improvement on the GPU >>> performance. >>> >>> 1. MatCreateAIJ() sets the type, and in fact it overwrites the Mat you >>> created in steps 1 and 2. This is detailed in the manual. >>> >>> 2. You should replace MatCreateAIJ(), with MatSetSizes() before >>> MatSetFromOptions(). >>> >>> THanks, >>> >>> Matt >>> >>> Thanks, >>> Cho >>> >>> From: Matthew Knepley <[email protected] <mailto:[email protected]>> >>> Sent: Friday, July 14, 2023 5:57 PM >>> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>> Cc: Barry Smith <[email protected] <mailto:[email protected]>>; Mark Adams >>> <[email protected] <mailto:[email protected]>>; [email protected] >>> <mailto:[email protected]> <[email protected] >>> <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> On Fri, Jul 14, 2023 at 7:57 PM Ng, Cho-Kuen <[email protected] >>> <mailto:[email protected]>> wrote: >>> I managed to pass the following options to PETSc using a GPU node on >>> Perlmutter. >>> >>> -mat_type aijcusparse -vec_type cuda -log_view -options_left >>> >>> Below is a summary of the test using 4 MPI tasks and 1 GPU per task. >>> >>> o #PETSc Option Table entries: >>> -log_view >>> -mat_type aijcusparse >>> -options_left >>> -vec_type cuda >>> #End of PETSc Option Table entries >>> WARNING! There are options you set that were not used! >>> WARNING! could be spelling mistake, etc! >>> There is one unused database option. It is: >>> Option left: name:-mat_type value: aijcusparse >>> >>> The -mat_type option has not been used. In the application code, we use >>> >>> ierr = MatCreateAIJ(PETSC_COMM_WORLD,mlocal,mlocal,m,n, >>> d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);;CHKERRQ(ierr); >>> >>> >>> If you create the Mat this way, then you need MatSetFromOptions() in order >>> to set the type from the command line. >>> >>> Thanks, >>> >>> Matt >>> >>> o The percent flops on the GPU for KSPSolve is 17%. >>> >>> In comparison with a CPU run using 16 MPI tasks, the GPU run is an order of >>> magnitude slower. How can I improve the GPU performance? >>> >>> Thanks, >>> Cho >>> From: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>> Sent: Friday, June 30, 2023 7:57 AM >>> To: Barry Smith <[email protected] <mailto:[email protected]>>; Mark Adams >>> <[email protected] <mailto:[email protected]>> >>> Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; >>> [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> Barry, Mark and Matt, >>> >>> Thank you all for the suggestions. I will modify the code so we can pass >>> runtime options. >>> >>> Cho >>> From: Barry Smith <[email protected] <mailto:[email protected]>> >>> Sent: Friday, June 30, 2023 7:01 AM >>> To: Mark Adams <[email protected] <mailto:[email protected]>> >>> Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; Ng, >>> Cho-Kuen <[email protected] <mailto:[email protected]>>; >>> [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> >>> Note that options like -mat_type aijcusparse -vec_type cuda only work if >>> the program is set up to allow runtime swapping of matrix and vector types. >>> If you have a call to MatCreateMPIAIJ() or other specific types then then >>> these options do nothing but because Mark had you use -options_left the >>> program will tell you at the end that it did not use the option so you will >>> know. >>> >>>> On Jun 30, 2023, at 9:30 AM, Mark Adams <[email protected] >>>> <mailto:[email protected]>> wrote: >>>> >>>> PetscCall(PetscInitialize(&argc, &argv, NULL, help)); gives us the args >>>> and you run: >>>> >>>> a.out -mat_type aijcusparse -vec_type cuda -log_view -options_left >>>> >>>> Mark >>>> >>>> On Fri, Jun 30, 2023 at 6:16 AM Matthew Knepley <[email protected] >>>> <mailto:[email protected]>> wrote: >>>> On Fri, Jun 30, 2023 at 1:13 AM Ng, Cho-Kuen via petsc-users >>>> <[email protected] <mailto:[email protected]>> wrote: >>>> Mark, >>>> >>>> The application code reads in parameters from an input file, where we can >>>> put the PETSc runtime options. Then we pass the options to >>>> PetscInitialize(...). Does that sounds right? >>>> >>>> PETSc will read command line argument automatically in PetscInitialize() >>>> unless you shut it off. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> Cho >>>> From: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>>> Sent: Thursday, June 29, 2023 8:32 PM >>>> To: Mark Adams <[email protected] <mailto:[email protected]>> >>>> Cc: [email protected] <mailto:[email protected]> >>>> <[email protected] <mailto:[email protected]>> >>>> Subject: Re: [petsc-users] Using PETSc GPU backend >>>> >>>> Mark, >>>> >>>> Thanks for the information. How do I put the runtime options for the >>>> executable, say, a.out, which does not have the provision to append >>>> arguments? Do I need to change the C++ main to read in the options? >>>> >>>> Cho >>>> From: Mark Adams <[email protected] <mailto:[email protected]>> >>>> Sent: Thursday, June 29, 2023 5:55 PM >>>> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>>> Cc: [email protected] <mailto:[email protected]> >>>> <[email protected] <mailto:[email protected]>> >>>> Subject: Re: [petsc-users] Using PETSc GPU backend >>>> >>>> Run with options: -mat_type aijcusparse -vec_type cuda -log_view >>>> -options_left >>>> >>>> The last column of the performance data (from -log_view) will be the >>>> percent flops on the GPU. Check that that is > 0. >>>> >>>> The end of the output will list the options that were used and options >>>> that were _not_ used (if any). Check that there are no options left. >>>> >>>> Mark >>>> >>>> On Thu, Jun 29, 2023 at 7:50 PM Ng, Cho-Kuen via petsc-users >>>> <[email protected] <mailto:[email protected]>> wrote: >>>> I installed PETSc on Perlmutter using "spack install petsc+cuda+zoltan" >>>> and used it by "spack load petsc/fwge6pf". Then I compiled the application >>>> code (purely CPU code) linking to the petsc package, hoping that I can get >>>> performance improvement using the petsc GPU backend. However, the timing >>>> was the same using the same number of MPI tasks with and without GPU >>>> accelerators. Have I missed something in the process, for example, setting >>>> up PETSc options at runtime to use the GPU backend? >>>> >>>> Thanks, >>>> Cho >>>> >>>> >>>> -- >>>> 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/> >>> >>> >>> >>> -- >>> 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/> >>> >>> >>> -- >>> 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/> > > From: Barry Smith <[email protected] <mailto:[email protected]>> > Sent: Monday, July 17, 2023 6:58 AM > To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> > Cc: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-users] Using PETSc GPU backend > > > The examples that use DM, in particular DMDA all trivially support using the > GPU with -dm_mat_type aijcusparse -dm_vec_type cuda > > > >> On Jul 17, 2023, at 1:45 AM, Ng, Cho-Kuen <[email protected] >> <mailto:[email protected]>> wrote: >> >> Barry, >> >> Thank you so much for the clarification. >> >> I see that ex104.c and ex300.c use MatXAIJSetPreallocation(). Are there >> other tutorials available? >> >> Cho >> From: Barry Smith <[email protected] <mailto:[email protected]>> >> Sent: Saturday, July 15, 2023 8:36 AM >> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >> Cc: [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> Subject: Re: [petsc-users] Using PETSc GPU backend >> >> >> >> Cho, >> >> We currently have a crappy API for turning on GPU support, and our >> documentation is misleading in places. >> >> People constantly say "to use GPU's with PETSc you only need to use >> -mat_type aijcusparse (for example)" This is incorrect. >> >> This does not work with code that uses the convenience Mat constructors >> such as MatCreateAIJ(), MatCreateAIJWithArrays etc. It only works if you use >> the constructor approach of MatCreate(), MatSetSizes(), MatSetFromOptions(), >> MatXXXSetPreallocation(). ... Similarly you need to use VecCreate(), >> VecSetSizes(), VecSetFromOptions() and -vec_type cuda >> >> If you use DM to create the matrices and vectors then you can use >> -dm_mat_type aijcusparse -dm_vec_type cuda >> >> Sorry for the confusion. >> >> Barry >> >> >> >> >>> On Jul 15, 2023, at 8:03 AM, Matthew Knepley <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>> On Sat, Jul 15, 2023 at 1:44 AM Ng, Cho-Kuen <[email protected] >>> <mailto:[email protected]>> wrote: >>> Matt, >>> >>> After inserting 2 lines in the code: >>> >>> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); >>> >>> ierr = MatSetFromOptions(A);CHKERRQ(ierr); >>> ierr = MatCreateAIJ(PETSC_COMM_WORLD,mlocal,mlocal,m,n, >>> d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);;CHKERRQ(ierr); >>> >>> "There are no unused options." However, there is no improvement on the GPU >>> performance. >>> >>> 1. MatCreateAIJ() sets the type, and in fact it overwrites the Mat you >>> created in steps 1 and 2. This is detailed in the manual. >>> >>> 2. You should replace MatCreateAIJ(), with MatSetSizes() before >>> MatSetFromOptions(). >>> >>> THanks, >>> >>> Matt >>> >>> Thanks, >>> Cho >>> >>> From: Matthew Knepley <[email protected] <mailto:[email protected]>> >>> Sent: Friday, July 14, 2023 5:57 PM >>> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>> Cc: Barry Smith <[email protected] <mailto:[email protected]>>; Mark Adams >>> <[email protected] <mailto:[email protected]>>; [email protected] >>> <mailto:[email protected]> <[email protected] >>> <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> On Fri, Jul 14, 2023 at 7:57 PM Ng, Cho-Kuen <[email protected] >>> <mailto:[email protected]>> wrote: >>> I managed to pass the following options to PETSc using a GPU node on >>> Perlmutter. >>> >>> -mat_type aijcusparse -vec_type cuda -log_view -options_left >>> >>> Below is a summary of the test using 4 MPI tasks and 1 GPU per task. >>> >>> o #PETSc Option Table entries: >>> -log_view >>> -mat_type aijcusparse >>> -options_left >>> -vec_type cuda >>> #End of PETSc Option Table entries >>> WARNING! There are options you set that were not used! >>> WARNING! could be spelling mistake, etc! >>> There is one unused database option. It is: >>> Option left: name:-mat_type value: aijcusparse >>> >>> The -mat_type option has not been used. In the application code, we use >>> >>> ierr = MatCreateAIJ(PETSC_COMM_WORLD,mlocal,mlocal,m,n, >>> d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);;CHKERRQ(ierr); >>> >>> >>> If you create the Mat this way, then you need MatSetFromOptions() in order >>> to set the type from the command line. >>> >>> Thanks, >>> >>> Matt >>> >>> o The percent flops on the GPU for KSPSolve is 17%. >>> >>> In comparison with a CPU run using 16 MPI tasks, the GPU run is an order of >>> magnitude slower. How can I improve the GPU performance? >>> >>> Thanks, >>> Cho >>> From: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>> Sent: Friday, June 30, 2023 7:57 AM >>> To: Barry Smith <[email protected] <mailto:[email protected]>>; Mark Adams >>> <[email protected] <mailto:[email protected]>> >>> Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; >>> [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> Barry, Mark and Matt, >>> >>> Thank you all for the suggestions. I will modify the code so we can pass >>> runtime options. >>> >>> Cho >>> From: Barry Smith <[email protected] <mailto:[email protected]>> >>> Sent: Friday, June 30, 2023 7:01 AM >>> To: Mark Adams <[email protected] <mailto:[email protected]>> >>> Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; Ng, >>> Cho-Kuen <[email protected] <mailto:[email protected]>>; >>> [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> Subject: Re: [petsc-users] Using PETSc GPU backend >>> >>> >>> Note that options like -mat_type aijcusparse -vec_type cuda only work if >>> the program is set up to allow runtime swapping of matrix and vector types. >>> If you have a call to MatCreateMPIAIJ() or other specific types then then >>> these options do nothing but because Mark had you use -options_left the >>> program will tell you at the end that it did not use the option so you will >>> know. >>> >>>> On Jun 30, 2023, at 9:30 AM, Mark Adams <[email protected] >>>> <mailto:[email protected]>> wrote: >>>> >>>> PetscCall(PetscInitialize(&argc, &argv, NULL, help)); gives us the args >>>> and you run: >>>> >>>> a.out -mat_type aijcusparse -vec_type cuda -log_view -options_left >>>> >>>> Mark >>>> >>>> On Fri, Jun 30, 2023 at 6:16 AM Matthew Knepley <[email protected] >>>> <mailto:[email protected]>> wrote: >>>> On Fri, Jun 30, 2023 at 1:13 AM Ng, Cho-Kuen via petsc-users >>>> <[email protected] <mailto:[email protected]>> wrote: >>>> Mark, >>>> >>>> The application code reads in parameters from an input file, where we can >>>> put the PETSc runtime options. Then we pass the options to >>>> PetscInitialize(...). Does that sounds right? >>>> >>>> PETSc will read command line argument automatically in PetscInitialize() >>>> unless you shut it off. >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> Cho >>>> From: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>>> Sent: Thursday, June 29, 2023 8:32 PM >>>> To: Mark Adams <[email protected] <mailto:[email protected]>> >>>> Cc: [email protected] <mailto:[email protected]> >>>> <[email protected] <mailto:[email protected]>> >>>> Subject: Re: [petsc-users] Using PETSc GPU backend >>>> >>>> Mark, >>>> >>>> Thanks for the information. How do I put the runtime options for the >>>> executable, say, a.out, which does not have the provision to append >>>> arguments? Do I need to change the C++ main to read in the options? >>>> >>>> Cho >>>> From: Mark Adams <[email protected] <mailto:[email protected]>> >>>> Sent: Thursday, June 29, 2023 5:55 PM >>>> To: Ng, Cho-Kuen <[email protected] <mailto:[email protected]>> >>>> Cc: [email protected] <mailto:[email protected]> >>>> <[email protected] <mailto:[email protected]>> >>>> Subject: Re: [petsc-users] Using PETSc GPU backend >>>> >>>> Run with options: -mat_type aijcusparse -vec_type cuda -log_view >>>> -options_left >>>> >>>> The last column of the performance data (from -log_view) will be the >>>> percent flops on the GPU. Check that that is > 0. >>>> >>>> The end of the output will list the options that were used and options >>>> that were _not_ used (if any). Check that there are no options left. >>>> >>>> Mark >>>> >>>> On Thu, Jun 29, 2023 at 7:50 PM Ng, Cho-Kuen via petsc-users >>>> <[email protected] <mailto:[email protected]>> wrote: >>>> I installed PETSc on Perlmutter using "spack install petsc+cuda+zoltan" >>>> and used it by "spack load petsc/fwge6pf". Then I compiled the application >>>> code (purely CPU code) linking to the petsc package, hoping that I can get >>>> performance improvement using the petsc GPU backend. However, the timing >>>> was the same using the same number of MPI tasks with and without GPU >>>> accelerators. Have I missed something in the process, for example, setting >>>> up PETSc options at runtime to use the GPU backend? >>>> >>>> Thanks, >>>> Cho >>>> >>>> >>>> -- >>>> 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/> >>> >>> >>> >>> -- >>> 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/> >>> >>> >>> -- >>> 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/>
