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 <bsm...@petsc.dev> Sent: Monday, July 17, 2023 6:58 AM To: Ng, Cho-Kuen <c...@slac.stanford.edu> Cc: petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> 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 <c...@slac.stanford.edu> 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 <bsm...@petsc.dev<mailto:bsm...@petsc.dev>> Sent: Saturday, July 15, 2023 8:36 AM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Sat, Jul 15, 2023 at 1:44 AM Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> Sent: Friday, July 14, 2023 5:57 PM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: Barry Smith <bsm...@petsc.dev<mailto:bsm...@petsc.dev>>; Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> Subject: Re: [petsc-users] Using PETSc GPU backend On Fri, Jul 14, 2023 at 7:57 PM Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> 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 <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Sent: Friday, June 30, 2023 7:57 AM To: Barry Smith <bsm...@petsc.dev<mailto:bsm...@petsc.dev>>; Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <bsm...@petsc.dev<mailto:bsm...@petsc.dev>> Sent: Friday, June 30, 2023 7:01 AM To: Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>>; Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Fri, Jun 30, 2023 at 1:13 AM Ng, Cho-Kuen via petsc-users <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Sent: Thursday, June 29, 2023 8:32 PM To: Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Sent: Thursday, June 29, 2023 5:55 PM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <bsm...@petsc.dev> Sent: Monday, July 17, 2023 6:58 AM To: Ng, Cho-Kuen <c...@slac.stanford.edu> Cc: petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> 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 <c...@slac.stanford.edu> 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 <bsm...@petsc.dev<mailto:bsm...@petsc.dev>> Sent: Saturday, July 15, 2023 8:36 AM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Sat, Jul 15, 2023 at 1:44 AM Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> Sent: Friday, July 14, 2023 5:57 PM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: Barry Smith <bsm...@petsc.dev<mailto:bsm...@petsc.dev>>; Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> Subject: Re: [petsc-users] Using PETSc GPU backend On Fri, Jul 14, 2023 at 7:57 PM Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> 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 <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Sent: Friday, June 30, 2023 7:57 AM To: Barry Smith <bsm...@petsc.dev<mailto:bsm...@petsc.dev>>; Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <bsm...@petsc.dev<mailto:bsm...@petsc.dev>> Sent: Friday, June 30, 2023 7:01 AM To: Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>>; Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>>; petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> 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 <knep...@gmail.com<mailto:knep...@gmail.com>> wrote: On Fri, Jun 30, 2023 at 1:13 AM Ng, Cho-Kuen via petsc-users <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Sent: Thursday, June 29, 2023 8:32 PM To: Mark Adams <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <mfad...@lbl.gov<mailto:mfad...@lbl.gov>> Sent: Thursday, June 29, 2023 5:55 PM To: Ng, Cho-Kuen <c...@slac.stanford.edu<mailto:c...@slac.stanford.edu>> Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov> <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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 <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> 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/>
