December 2023 - petsc-users - mailman3.cels.anl.gov

Re: [petsc-users] Domain decomposition in PETSc for Molecular Dynamics
by MIGUEL MOLINOS PEREZ 13 Dec '23

13 Dec '23

Thank you Mark! I will have a look to it. Best, Miguel On 4 Nov 2023, at 13:54, Matthew Knepley <knepley(a)gmail.com> wrote: On Sat, Nov 4, 2023 at 8:40 AM Mark Adams <mfadams(a)lbl.gov<mailto:[email protected]>> wrote: Hi MIGUEL, This might be a good place to start: https://petsc.org/main/manual/vec/ Feel free to ask more specific questions, but the docs are a good place to start. Thanks, Mark On Fri, Nov 3, 2023 at 5:19 AM MIGUEL MOLINOS PEREZ <mmolinos(a)us.es<mailto:[email protected]>> wrote: Dear all, I am currently working on the development of a in-house molecular dynamics code using PETSc and C++. So far the code works great, however it is a little bit slow since I am not exploiting MPI for PETSc vectors. I was wondering if there is a way to perform the domain decomposition efficiently using some PETSc functionality. Any feedback is highly appreciated. It sounds like you mean "is there a way to specify a communication construct that can send my particle information automatically". We use PetscSF for that. You can see how this works with the DMSwarm class, which represents a particle discretization. You can either use that, or if it does not work for you, do the same things with your class. Thanks, Matt Best regards, Miguel -- 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/>

2 5

(no subject)
by 1807580692 13 Dec '23

13 Dec '23

Hello, I have encountered some problems. Here are some of my configurations. OS Version and Type:  Linux daihuanhe-Aspire-A315-55G 5.15.0-89-generic #99~20.04.1-Ubuntu SMP Thu Nov 2 15:16:47 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux PETSc Version: #define PETSC_VERSION_RELEASE    1 #define PETSC_VERSION_MAJOR      3 #define PETSC_VERSION_MINOR      19 #define PETSC_VERSION_SUBMINOR   0 #define PETSC_RELEASE_DATE       "Mar 30, 2023" #define PETSC_VERSION_DATE       "unknown" MPI implementation: MPICH Compiler and version: Gnu C The problem is when I type “mpiexec -n 4 ./ex19_1 -lidvelocity 100 -prandtl 0.72 -grashof 10000 -da_grid_x 128 -da_grid_y 128 -snes_type newtonls -pc_type fieldsplit -pc_fieldsplit_type multiplicative -pc_fieldsplit_block_size 4 -pc_fieldsplit_0_fields 0,2 -pc_fieldsplit_1_fields 1,3 -fieldsplit_0_pc_type asm -fieldsplit_0_pc_asm_type restrict -fieldsplit_0_pc_asm_overlap 5 -fieldsplit_0_sub_pc_type lu -fieldsplit_1_pc_type asm -fieldsplit_1_pc_asm_type restrict -fieldsplit_1_pc_asm_overlap 5 -fieldsplit_1_sub_pc_type lu -snes_monitor -snes_converged_reason  -fieldsplit_ksp_type gmres -fieldsplit_0_ksp_atol 1e-10 -fieldsplit_0_ksp_rtol 1e-8 -fieldsplit_1_ksp_atol 1e-10 -fieldsplit_1_ksp_rtol 1e-8” in the command line, where my path is /petsc/src/snes/tutorials. It returns “lid velocity = 100., prandtl # = 0.72, grashof # = 10000.   0 SNES Function norm 1.125212317214e+03 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid argument [0]PETSC ERROR: Block size 2 is incompatible with the indices: non consecutive indices 0 2 [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [1]PETSC ERROR: Invalid argument [1]PETSC ERROR: Block size 2 is incompatible with the indices: non consecutive indices 16384 16386 [1]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [1]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_atol value: 1e-10 source: command line [2]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [2]PETSC ERROR: Invalid argument [2]PETSC ERROR: Block size 2 is incompatible with the indices: non consecutive indices 32768 32770 [2]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [2]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_atol value: 1e-10 source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_rtol value: 1e-8 source: command line [2]PETSC ERROR: [3]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [3]PETSC ERROR: Invalid argument [3]PETSC ERROR: Block size 2 is incompatible with the indices: non consecutive indices 49152 49154 [3]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [3]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_atol value: 1e-10 source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_rtol value: 1e-8 source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_atol value: 1e-10 source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_rtol value: 1e-8 source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_overlap value: 5 source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_type value: restrict source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_type value: asm source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_0_sub_pc_type value: lu source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_atol value: 1e-10 source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_rtol value: 1e-8 source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_overlap value: 5 source: command line [0]PETSC ERROR: [1]PETSC ERROR:   Option left: name:-fieldsplit_0_ksp_rtol value: 1e-8 source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_overlap value: 5 source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_type value: restrict source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_type value: asm source: command line   Option left: name:-fieldsplit_0_pc_asm_overlap value: 5 source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_type value: restrict source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_type value: asm source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_0_sub_pc_type value: lu source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_atol value: 1e-10 source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_overlap value: 5 source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_asm_type value: restrict source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_0_pc_type value: asm source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_0_sub_pc_type value: lu source: command line   Option left: name:-fieldsplit_1_pc_asm_type value: restrict source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_type value: asm source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_1_sub_pc_type value: lu source: command line [0]PETSC ERROR:   Option left: name:-fieldsplit_ksp_type value: gmres source: command line [0]PETSC ERROR:   Option left: name:-snes_converged_reason (no value) source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_0_sub_pc_type value: lu source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_atol value: 1e-10 source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_rtol value: 1e-8 source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_overlap value: 5 source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_type value: restrict source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_type value: asm source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_atol value: 1e-10 source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_1_ksp_rtol value: 1e-8 source: command line [3]PETSC ERROR: [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.20.2, unknown [0]PETSC ERROR: ./ex19_1 on a arch-linux-c-debug named daihuanhe-Aspire-A315-55G by daihuanhe Wed Dec 13 16:47:08 2023   Option left: name:-fieldsplit_1_ksp_rtol value: 1e-8 source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_overlap value: 5 source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_type value: restrict source: command line [1]PETSC ERROR: [2]PETSC ERROR:   Option left: name:-fieldsplit_1_sub_pc_type value: lu source: command line [2]PETSC ERROR:   Option left: name:-fieldsplit_ksp_type value: gmres source: command line [2]PETSC ERROR:   Option left: name:-snes_converged_reason (no value) source: command line   Option left: name:-fieldsplit_1_pc_asm_overlap value: 5 source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_asm_type value: restrict source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_1_pc_type value: asm source: command line [3]PETSC ERROR: [0]PETSC ERROR: Configure options   Option left: name:-fieldsplit_1_pc_type value: asm source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_1_sub_pc_type value: lu source: command line [1]PETSC ERROR:   Option left: name:-fieldsplit_ksp_type value: gmres source: command line [2]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [2]PETSC ERROR: Petsc Release Version 3.20.2, unknown [2]PETSC ERROR:   Option left: name:-fieldsplit_1_sub_pc_type value: lu source: command line [3]PETSC ERROR:   Option left: name:-fieldsplit_ksp_type value: gmres source: command line [3]PETSC ERROR:   Option left: name:-snes_converged_reason (no value) source: command line [0]PETSC ERROR: #1 ISSetBlockSize() at /home/daihuanhe/petsc-v3.20.2/src/vec/is/is/interface/index.c:1933 [0]PETSC ERROR: [1]PETSC ERROR:   Option left: name:-snes_converged_reason (no value) source: command line [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [1]PETSC ERROR: Petsc Release Version 3.20.2, unknown ./ex19_1 on a arch-linux-c-debug named daihuanhe-Aspire-A315-55G by daihuanhe Wed Dec 13 16:47:08 2023 [2]PETSC ERROR: Configure options [2]PETSC ERROR: [3]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [3]PETSC ERROR: Petsc Release Version 3.20.2, unknown [3]PETSC ERROR: ./ex19_1 on a arch-linux-c-debug named daihuanhe-Aspire-A315-55G by daihuanhe Wed Dec 13 16:47:08 2023 #2 PCSetUp_FieldSplit() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c:633 [0]PETSC ERROR: #3 PCSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/interface/precon.c:1080 [1]PETSC ERROR: ./ex19_1 on a arch-linux-c-debug named daihuanhe-Aspire-A315-55G by daihuanhe Wed Dec 13 16:47:08 2023 [1]PETSC ERROR: Configure options #1 ISSetBlockSize() at /home/daihuanhe/petsc-v3.20.2/src/vec/is/is/interface/index.c:1933 [2]PETSC ERROR: #2 PCSetUp_FieldSplit() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c:633 [2]PETSC ERROR: [3]PETSC ERROR: Configure options [3]PETSC ERROR: #1 ISSetBlockSize() at /home/daihuanhe/petsc-v3.20.2/src/vec/is/is/interface/index.c:1933 [0]PETSC ERROR: #4 KSPSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:415 [0]PETSC ERROR: #5 KSPSolve_Private() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:836 [1]PETSC ERROR: #1 ISSetBlockSize() at /home/daihuanhe/petsc-v3.20.2/src/vec/is/is/interface/index.c:1933 [1]PETSC ERROR: #2 PCSetUp_FieldSplit() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c:633 #3 PCSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/interface/precon.c:1080 [2]PETSC ERROR: #4 KSPSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:415 [2]PETSC ERROR: #5 KSPSolve_Private() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:836 [3]PETSC ERROR: #2 PCSetUp_FieldSplit() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c:633 [3]PETSC ERROR: [0]PETSC ERROR: #6 KSPSolve() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:1083 [0]PETSC ERROR: #7 SNESSolve_NEWTONLS() at /home/daihuanhe/petsc-v3.20.2/src/snes/impls/ls/ls.c:215 [0]PETSC ERROR: [1]PETSC ERROR: #3 PCSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/interface/precon.c:1080 [1]PETSC ERROR: #4 KSPSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:415 [1]PETSC ERROR: [2]PETSC ERROR: #6 KSPSolve() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:1083 [2]PETSC ERROR: #7 SNESSolve_NEWTONLS() at /home/daihuanhe/petsc-v3.20.2/src/snes/impls/ls/ls.c:215 [2]PETSC ERROR: #3 PCSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/pc/interface/precon.c:1080 [3]PETSC ERROR: #4 KSPSetUp() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:415 [3]PETSC ERROR: #5 KSPSolve_Private() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:836 [3]PETSC ERROR: #6 KSPSolve() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:1083 #8 SNESSolve() at /home/daihuanhe/petsc-v3.20.2/src/snes/interface/snes.c:4659 [0]PETSC ERROR: #9 main() at ex19_1.c:159 [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -da_grid_x 128 (source: command line) [0]PETSC ERROR: #5 KSPSolve_Private() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:836 [1]PETSC ERROR: #6 KSPSolve() at /home/daihuanhe/petsc-v3.20.2/src/ksp/ksp/interface/itfunc.c:1083 [1]PETSC ERROR: #7 SNESSolve_NEWTONLS() at /home/daihuanhe/petsc-v3.20.2/src/snes/impls/ls/ls.c:215 [1]PETSC ERROR: #8 SNESSolve() at /home/daihuanhe/petsc-v3.20.2/src/snes/interface/snes.c:4659 #8 SNESSolve() at /home/daihuanhe/petsc-v3.20.2/src/snes/interface/snes.c:4659 [2]PETSC ERROR: #9 main() at ex19_1.c:159 [2]PETSC ERROR: PETSc Option Table entries: [2]PETSC ERROR: -da_grid_x 128 (source: command line) [2]PETSC ERROR: -da_grid_y 128 (source: command line) [3]PETSC ERROR: #7 SNESSolve_NEWTONLS() at /home/daihuanhe/petsc-v3.20.2/src/snes/impls/ls/ls.c:215 [3]PETSC ERROR: #8 SNESSolve() at /home/daihuanhe/petsc-v3.20.2/src/snes/interface/snes.c:4659 [3]PETSC ERROR: -da_grid_y 128 (source: command line) [0]PETSC ERROR: -fieldsplit_0_ksp_atol 1e-10 (source: command line) [0]PETSC ERROR: -fieldsplit_0_ksp_rtol 1e-8 (source: command line) [0]PETSC ERROR: -fieldsplit_0_pc_asm_overlap 5 (source: command line) [1]PETSC ERROR: #9 main() at ex19_1.c:159 [1]PETSC ERROR: PETSc Option Table entries: [1]PETSC ERROR: -da_grid_x 128 (source: command line) [2]PETSC ERROR: -fieldsplit_0_ksp_atol 1e-10 (source: command line) [2]PETSC ERROR: -fieldsplit_0_ksp_rtol 1e-8 (source: command line) [2]PETSC ERROR: -fieldsplit_0_pc_asm_overlap 5 (source: command line) [2]PETSC ERROR: #9 main() at ex19_1.c:159 [3]PETSC ERROR: PETSc Option Table entries: [3]PETSC ERROR: -da_grid_x 128 (source: command line) [3]PETSC ERROR: [0]PETSC ERROR: -fieldsplit_0_pc_asm_type restrict (source: command line) [0]PETSC ERROR: -fieldsplit_0_pc_type asm (source: command line) [0]PETSC ERROR: -fieldsplit_0_sub_pc_type lu (source: command line) [0]PETSC ERROR: [1]PETSC ERROR: -da_grid_y 128 (source: command line) [1]PETSC ERROR: -fieldsplit_0_ksp_atol 1e-10 (source: command line) [1]PETSC ERROR: -fieldsplit_0_ksp_rtol 1e-8 (source: command line) -fieldsplit_0_pc_asm_type restrict (source: command line) [2]PETSC ERROR: -fieldsplit_0_pc_type asm (source: command line) [2]PETSC ERROR: -fieldsplit_0_sub_pc_type lu (source: command line) [2]PETSC ERROR: -fieldsplit_1_ksp_atol 1e-10 (source: command line) -da_grid_y 128 (source: command line) [3]PETSC ERROR: -fieldsplit_0_ksp_atol 1e-10 (source: command line) [3]PETSC ERROR: -fieldsplit_0_ksp_rtol 1e-8 (source: command line) [3]PETSC ERROR: -fieldsplit_1_ksp_atol 1e-10 (source: command line) [0]PETSC ERROR: -fieldsplit_1_ksp_rtol 1e-8 (source: command line) [0]PETSC ERROR: -fieldsplit_1_pc_asm_overlap 5 (source: command line) [0]PETSC ERROR: [1]PETSC ERROR: -fieldsplit_0_pc_asm_overlap 5 (source: command line) [1]PETSC ERROR: -fieldsplit_0_pc_asm_type restrict (source: command line) [1]PETSC ERROR: -fieldsplit_0_pc_type asm (source: command line) [2]PETSC ERROR: -fieldsplit_1_ksp_rtol 1e-8 (source: command line) [2]PETSC ERROR: -fieldsplit_1_pc_asm_overlap 5 (source: command line) [2]PETSC ERROR: -fieldsplit_1_pc_asm_type restrict (source: command line) [2]PETSC ERROR: -fieldsplit_0_pc_asm_overlap 5 (source: command line) [3]PETSC ERROR: -fieldsplit_0_pc_asm_type restrict (source: command line) [3]PETSC ERROR: -fieldsplit_0_pc_type asm (source: command line) [3]PETSC ERROR: -fieldsplit_1_pc_asm_type restrict (source: command line) [0]PETSC ERROR: -fieldsplit_1_pc_type asm (source: command line) [0]PETSC ERROR: -fieldsplit_1_sub_pc_type lu (source: command line) [0]PETSC ERROR: [1]PETSC ERROR: -fieldsplit_0_sub_pc_type lu (source: command line) [1]PETSC ERROR: -fieldsplit_1_ksp_atol 1e-10 (source: command line) [1]PETSC ERROR: -fieldsplit_1_ksp_rtol 1e-8 (source: command line) -fieldsplit_1_pc_type asm (source: command line) [2]PETSC ERROR: -fieldsplit_1_sub_pc_type lu (source: command line) [2]PETSC ERROR: -fieldsplit_ksp_type gmres (source: command line) [2]PETSC ERROR: -grashof 10000 (source: command line) -fieldsplit_0_sub_pc_type lu (source: command line) [3]PETSC ERROR: -fieldsplit_1_ksp_atol 1e-10 (source: command line) [3]PETSC ERROR: -fieldsplit_1_ksp_rtol 1e-8 (source: command line) [3]PETSC ERROR: -fieldsplit_ksp_type gmres (source: command line) [0]PETSC ERROR: -grashof 10000 (source: command line) [0]PETSC ERROR: -lidvelocity 100 (source: command line) [0]PETSC ERROR: -pc_fieldsplit_0_fields 0,2 (source: command line) [1]PETSC ERROR: -fieldsplit_1_pc_asm_overlap 5 (source: command line) [1]PETSC ERROR: -fieldsplit_1_pc_asm_type restrict (source: command line) [1]PETSC ERROR: -fieldsplit_1_pc_type asm (source: command line) [2]PETSC ERROR: -lidvelocity 100 (source: command line) [2]PETSC ERROR: -pc_fieldsplit_0_fields 0,2 (source: command line) [2]PETSC ERROR: -pc_fieldsplit_1_fields 1,3 (source: command line) [2]PETSC ERROR: -fieldsplit_1_pc_asm_overlap 5 (source: command line) [3]PETSC ERROR: -fieldsplit_1_pc_asm_type restrict (source: command line) [3]PETSC ERROR: -fieldsplit_1_pc_type asm (source: command line) [3]PETSC ERROR: [0]PETSC ERROR: -pc_fieldsplit_1_fields 1,3 (source: command line) [0]PETSC ERROR: -pc_fieldsplit_block_size 4 (source: command line) [0]PETSC ERROR: -pc_fieldsplit_type multiplicative (source: command line) [1]PETSC ERROR: -fieldsplit_1_sub_pc_type lu (source: command line) [1]PETSC ERROR: -fieldsplit_ksp_type gmres (source: command line) [1]PETSC ERROR: -grashof 10000 (source: command line) -pc_fieldsplit_block_size 4 (source: command line) [2]PETSC ERROR: -pc_fieldsplit_type multiplicative (source: command line) [2]PETSC ERROR: -pc_type fieldsplit (source: command line) [2]PETSC ERROR: -prandtl 0.72 (source: command line) -fieldsplit_1_sub_pc_type lu (source: command line) [3]PETSC ERROR: -fieldsplit_ksp_type gmres (source: command line) [3]PETSC ERROR: -grashof 10000 (source: command line) [3]PETSC ERROR: [0]PETSC ERROR: -pc_type fieldsplit (source: command line) [0]PETSC ERROR: -prandtl 0.72 (source: command line) [0]PETSC ERROR: -snes_converged_reason (source: command line) [1]PETSC ERROR: -lidvelocity 100 (source: command line) [1]PETSC ERROR: -pc_fieldsplit_0_fields 0,2 (source: command line) [1]PETSC ERROR: -pc_fieldsplit_1_fields 1,3 (source: command line) [2]PETSC ERROR: -snes_converged_reason (source: command line) [2]PETSC ERROR: -snes_monitor (source: command line) [2]PETSC ERROR: -snes_type newtonls (source: command line) -lidvelocity 100 (source: command line) [3]PETSC ERROR: -pc_fieldsplit_0_fields 0,2 (source: command line) [3]PETSC ERROR: -pc_fieldsplit_1_fields 1,3 (source: command line) [3]PETSC ERROR: [0]PETSC ERROR: -snes_monitor (source: command line) [0]PETSC ERROR: -snes_type newtonls (source: command line) [0]PETSC ERROR: [1]PETSC ERROR: -pc_fieldsplit_block_size 4 (source: command line) [1]PETSC ERROR: -pc_fieldsplit_type multiplicative (source: command line) [1]PETSC ERROR: -pc_type fieldsplit (source: command line) [2]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- Abort(62) on node 2 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0 -pc_fieldsplit_block_size 4 (source: command line) [3]PETSC ERROR: -pc_fieldsplit_type multiplicative (source: command line) [3]PETSC ERROR: -pc_type fieldsplit (source: command line) [3]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- Abort(62) on node 0 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0 [1]PETSC ERROR: -prandtl 0.72 (source: command line) [1]PETSC ERROR: -snes_converged_reason (source: command line) [1]PETSC ERROR: -snes_monitor (source: command line) -prandtl 0.72 (source: command line) [3]PETSC ERROR: -snes_converged_reason (source: command line) [3]PETSC ERROR: -snes_monitor (source: command line) [1]PETSC ERROR: -snes_type newtonls (source: command line) [1]PETSC ERROR: [3]PETSC ERROR: -snes_type newtonls (source: command line) [3]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- Abort(62) on node 1 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0 Abort(62) on node 3 (rank 0 in comm 16): application called MPI_Abort(MPI_COMM_SELF, 62) - process 0”. Please tell me what should I do?Thank you very much. 1807580692 1807580692(a)qq.com  

1 0

DMPlex "Could not find orientation for quadrilateral"
by onur.notonur 13 Dec '23

13 Dec '23

Hi, I hope this email finds you well. I am currently working on importing an OpenFOAM PolyMesh into DMPlex, and I've encountered an issue. The PolyMesh format includes face owner cells/neighbor cells and face-to-vertex connectivity. I was using the "DMPlexCreateFromCellListPetsc()" function, which required cell-to-vertex connectivity. However, when attempting to create the cell connectivity using an edge loop [p_0, p_1, ..., p_7] (p_n and p_(n+1) are valid edges in my mesh), I encountered an error stating, "Could not find orientation for quadrilateral." (Actually at first, I generated the connectivity list by simply creating a cell-to-face list and then using that to create a cell-to-vertex list. (just map over the list and remove duplicates) This created a DMPlex successfully, however, resulted in a mesh that was incorrect when looking with ParaView. I think that was because of I stated wrong edge loop to create cells) I understand that I may need to follow a different format for connectivity, but I'm not sure what that format is. My current mesh is hexahedral, consisting of 8 corner elements(if important). I would appreciate any guidance on a general approach to address this issue. Thank you for your time and assistance. Best, Onur Sent with Proton Mail secure email.

2 2

valgrind errors
by Randall Mackie 12 Dec '23

12 Dec '23

It now seems to me that petsc+mpich is no longer valgrind clean, or I am doing something wrong. A simple program: Program test #include "petsc/finclude/petscsys.h" use petscsys PetscInt :: ierr call PetscInitialize(PETSC_NULL_CHARACTER,ierr) call PetscFinalize(ierr) end program test PETSc compiled in debug mode, complex scalars, and download-mpich, when run with valgrind generates errors like these: ==3997== Syscall param writev(vector[...]) points to uninitialised byte(s) ==3997== at 0x8C31867: writev (writev.c:26) ==3997== by 0x9C20DE4: MPL_large_writev (mpl_sock.c:31) ==3997== by 0x9BF1050: MPIDI_CH3I_Sock_writev (sock.c:2689) ==3997== by 0x9BF9812: MPIDI_CH3_iStartMsgv (ch3_istartmsgv.c:92) ==3997== by 0x9BA7790: MPIDI_CH3_EagerContigSend (ch3u_eager.c:191) ==3997== by 0x9BCA7EC: MPID_Send (mpid_send.c:132) ==3997== by 0x9BCAC64: MPID_Send_coll (mpid_send.c:206) ==3997== by 0x9A2AC7C: MPIC_Send (helper_fns.c:126) ==3997== by 0x993A645: MPIR_Bcast_intra_binomial (bcast_intra_binomial.c:146) ==3997== by 0x99FF64A: MPIR_Bcast_allcomm_auto (mpir_coll.c:323) ==3997== by 0x99FFC06: MPIR_Bcast_impl (mpir_coll.c:420) ==3997== by 0x99FCF86: MPID_Bcast (mpid_coll.h:30) ==3997== by 0x99FFE13: MPIR_Bcast (mpir_coll.c:465) ==3997== by 0x974A513: internal_Bcast (bcast.c:93) ==3997== by 0x974A72B: PMPI_Bcast (bcast.c:143) ==3997== by 0x4B8D6DB: PETScParseFortranArgs_Private (zstart.c:182) ==3997== by 0x4B8DDFA: PetscInitFortran_Private (zstart.c:200) ==3997== by 0x4B34931: PetscInitialize_Common (pinit.c:974) ==3997== by 0x4B8E8C7: petscinitializef_ (zstart.c:284) ==3997== by 0x4959434: __petscsys_MOD_petscinitializenohelp (petscsysmod.F90:374) ==3997== Address 0x1ffeffcac0 is on thread 1's stack ==3997== in frame #4, created by MPIDI_CH3_EagerContigSend (ch3u_eager.c:160) ==3997== Uninitialised value was created by a stack allocation ==3997== at 0x9BA7601: MPIDI_CH3_EagerContigSend (ch3u_eager.c:160) ==3997== ==3997== Syscall param write(buf) points to uninitialised byte(s) ==3997== at 0x8C2B697: write (write.c:26) ==3997== by 0x9BF0F1D: MPIDI_CH3I_Sock_write (sock.c:2614) ==3997== by 0x9BF7AAE: MPIDI_CH3_iStartMsg (ch3_istartmsg.c:68) ==3997== by 0x9BA7A27: MPIDI_CH3_EagerContigShortSend (ch3u_eager.c:262) ==3997== by 0x9BCA766: MPID_Send (mpid_send.c:119) ==3997== by 0x9BCAC64: MPID_Send_coll (mpid_send.c:206) ==3997== by 0x9A2AC7C: MPIC_Send (helper_fns.c:126) ==3997== by 0x993A645: MPIR_Bcast_intra_binomial (bcast_intra_binomial.c:146) ==3997== by 0x99FF64A: MPIR_Bcast_allcomm_auto (mpir_coll.c:323) ==3997== by 0x99FFC06: MPIR_Bcast_impl (mpir_coll.c:420) ==3997== by 0x99FCF86: MPID_Bcast (mpid_coll.h:30) ==3997== by 0x99FFE13: MPIR_Bcast (mpir_coll.c:465) ==3997== by 0x974A513: internal_Bcast (bcast.c:93) ==3997== by 0x974A72B: PMPI_Bcast (bcast.c:143) ==3997== by 0x4DB95A2: PetscOptionsGetenv (pdisplay.c:61) ==3997== by 0x4E0D745: PetscStrreplace (str.c:572) ==3997== by 0x4AC8DEA: PetscOptionsFilename (options.c:416) ==3997== by 0x4ACF0B5: PetscOptionsInsertFile (options.c:632) ==3997== by 0x4AD3CB5: PetscOptionsInsert (options.c:861) ==3997== by 0x4B8E0EF: PetscInitFortran_Private (zstart.c:206) ==3997== Address 0x1ffeff7998 is on thread 1's stack ==3997== in frame #3, created by MPIDI_CH3_EagerContigShortSend (ch3u_eager.c:223) ==3997== Uninitialised value was created by a stack allocation ==3997== at 0x9BA788F: MPIDI_CH3_EagerContigShortSend (ch3u_eager.c:223) ==3997== Is this a known issue or am I doing something wrong? Thanks, Randy

2 2

difference in Face Sets in latest petsc release
by Sharan Roongta 12 Dec '23

12 Dec '23

Hello, I see discrepancy in the size/value of the 'Face Sets' printed in the current release v3.20.2 , and v3.18.6 Attached is the .msh file -dm_view with v3.18.6 DM Object: Generated Mesh 1 MPI process type: plex Generated Mesh in 3 dimensions: Number of 0-cells per rank: 14 Number of 1-cells per rank: 49 Number of 2-cells per rank: 60 Number of 3-cells per rank: 24 Labels: celltype: 4 strata with value/size (0 (14), 6 (24), 3 (60), 1 (49)) depth: 4 strata with value/size (0 (14), 1 (49), 2 (60), 3 (24)) Cell Sets: 1 strata with value/size (1 (24)) Face Sets: 5 strata with value/size (1 (4), 2 (4), 3 (4), 4 (4), 5 (4)) -dm_view with the current release (commit 4b9a870af96) DM Object: Generated Mesh 1 MPI process type: plex Generated Mesh in 3 dimensions: Number of 0-cells per rank: 14 Number of 1-cells per rank: 49 Number of 2-cells per rank: 60 Number of 3-cells per rank: 24 Labels: celltype: 4 strata with value/size (0 (14), 6 (24), 3 (60), 1 (49)) depth: 4 strata with value/size (0 (14), 1 (49), 2 (60), 3 (24)) Cell Sets: 1 strata with value/size (1 (24)) Face Sets: 12 strata with value/size (1 (5), 2 (5), 3 (5), 4 (5), 5 (5), 6 (1), 7 (1), 8 (1), 9 (1), 10 (1), 11 (1), 12 (1)) I believe the older version printed the correct thing? Has something changed in the interpretation of Face Sets? Thanks, Sharan Group - Theory & Simulation Department of Microstructure Physics & Alloy Design ------------------------------------------------- Stay up to date and follow us on LinkedIn, Twitter and YouTube. Max-Planck-Institut für Eisenforschung GmbH Max-Planck-Straße 1 D-40237 Düsseldorf Handelsregister B 2533 Amtsgericht Düsseldorf Geschäftsführung Prof. Dr. Gerhard Dehm Prof. Dr. Jörg Neugebauer Prof. Dr. Dierk Raabe Dr. Kai de Weldige Ust.-Id.-Nr.: DE 11 93 58 514 Steuernummer: 105 5891 1000 Please consider that invitations and e-mails of our institute are only valid if they end with …(a)mpie.de. If you are not sure of the validity please contact rco(a)mpie.de Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails aus unserem Haus nur mit der Endung …(a)mpie.de gültig sind. In Zweifelsfällen wenden Sie sich bitte an rco(a)mpie.de -------------------------------------------------

2 3

Applying Natural Boundary Conditions using PETSc FEM Technology
by Brandon Denton 12 Dec '23

12 Dec '23

Good Afternoon, I am currently working on an Inviscid Navier-Stokes problem and would like to apply DM_BC_NATURAL boundary conditions to my domain. Looking through the example files on petsc.org, I noticed that in almost all cases there are the following series of calls. PetscCall(DMAddBoundary(dm, DM_BC_NATURAL, "wall", label, 1, &id, 0, 0, NULL, NULL, NULL, user, &bd)); PetscCall(PetscDSGetBoundary(ds, bd, &wf, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL)); PetscCall(PetscWeakFormSetIndexBdResidual(wf, label, id, 0, 0, 0, f0_bd_u, 0, NULL)); Is this the standard way of applying Natural boundary conditions in PETSc for FEM? Also, I noticed in the signature for the f0_bd_u function, there is a const PetscReal n[] array. What is this array and what information does it hold. Is it the normal vector at the point? static void f0_bd_u(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], const PetscReal n[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) Thank you in advance for your time. Brandon

2 1

(no subject)
by 1807580692 11 Dec '23

11 Dec '23

Hello, I have encountered some problems. Here are some of my configurations. OS Version and Type:  Linux daihuanhe-Aspire-A315-55G 5.15.0-89-generic #99~20.04.1-Ubuntu SMP Thu Nov 2 15:16:47 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux PETSc Version: #define PETSC_VERSION_RELEASE    1 #define PETSC_VERSION_MAJOR      3 #define PETSC_VERSION_MINOR      19 #define PETSC_VERSION_SUBMINOR   0 #define PETSC_RELEASE_DATE       "Mar 30, 2023" #define PETSC_VERSION_DATE       "unknown" MPI implementation: MPICH Compiler and version: Gnu C The problem is when I type  “mpiexec -n 4 ./ex19 -lidvelocity 100 -prandtl 0.72 -grashof 10000 -da_grid_x 64 -da_grid_y 64 -snes_type newtonls -ksp_type gmres -pc_type fieldsplit -pc_fieldsplit_type symmetric_multiplicative -pc_fieldsplit_block_size 4 -pc_fieldsplit_0_fields 0,1,2,3 -pc_fieldsplit_1_fields 0,1,2,3 -fieldsplit_0_pc_type asm -fieldsplit_0_pc_asm_type restrict -fieldsplit_0_pc_asm_overlap 5 -fieldsplit_0_sub_pc_type lu -fieldsplit_1_pc_type asm -fieldsplit_1_pc_asm_type restrict -fieldsplit_1_pc_asm_overlap 5 -fieldsplit_1_sub_pc_type lu  -snes_monitor -snes_converged_reason -fieldsplit_0_ksp_atol 1e-10  -fieldsplit_1_ksp_atol 1e-10  -fieldsplit_0_ksp_rtol 1e-6  -fieldsplit_1_ksp_rtol 1e-6 -fieldsplit_0_snes_atol 1e-10  -fieldsplit_1_snes_atol 1e-10  -fieldsplit_0_snes_rtol 1e-6  -fieldsplit_1_snes_rtol 1e-6” in the command line, where my path is /petsc/src/snes/tutorials. It returns  “WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! There are 8 unused database options. They are: Option left: name:-fieldsplit_0_ksp_atol value: 1e-10 source: command line Option left: name:-fieldsplit_0_ksp_rtol value: 1e-6 source: command line Option left: name:-fieldsplit_0_snes_atol value: 1e-10 source: command line Option left: name:-fieldsplit_0_snes_rtol value: 1e-6 source: command line Option left: name:-fieldsplit_1_ksp_atol value: 1e-10 source: command line Option left: name:-fieldsplit_1_ksp_rtol value: 1e-6 source: command line Option left: name:-fieldsplit_1_snes_atol value: 1e-10 source: command line Option left: name:-fieldsplit_1_snes_rtol value: 1e-6 source: command line”. Please tell me what should I do?Thank you very much. 1807580692 1807580692(a)qq.com  

2 1

Question on output vector in vtk file
by Gong Yujie 11 Dec '23

11 Dec '23

Dear PETSc developers, I have a DMPlex DM with 1 field 1dof. I'd like to output a vector with block size equals to 3. It seems that there is no response using command line option or using some code about PetscViewer. The DM is generated with (note that I'm not using PetscFE for discretization, just for allocate dof.) PetscCall(DMPlexCreateExodusFromFile(PETSC_COMM_WORLD,"tube.exo",interpolate,&dm)); PetscCall(PetscFECreateLagrange(PETSC_COMM_SELF,dim,1,PETSC_TRUE,1,PETSC_DETERMINE,&fe)); PetscCall(PetscObjectSetName((PetscObject)fe,"potential_field")); PetscCall(DMSetField(dm,0,NULL,(PetscObject)fe)); PetscCall(DMPlexDistribute(dm,0,&sf,&dmParallel)); The Vector is created using PetscCall(DMCreateGlobalVector(dm,&phi_1)); PetscCall(VecSetLocalToGlobalMapping(phi_1,Itog)); PetscCall(VecGetLocalSize(phi_1,&vec_local_size_test)); PetscCall(VecCreateMPI(PETSC_COMM_WORLD, vec_local_size_test*3, PETSC_DETERMINE, &u_grad_psi)); PetscCall(VecSetBlockSize(u_grad_psi, 3)); PetscCall(VecSetLocalToGlobalMapping(u_grad_psi,Itog)); The output command line option is just --vec_view vtk:test.vtk. The PETSc version I'm using is 3.19.5. Could you please give me some advice? Best Regards, Yujie

2 1

Bug report VecNorm
by Stephan Köhler 11 Dec '23

11 Dec '23

Dear PETSc/Tao team, there is a bug in the voector interface: In the function VecNorm, see, eg. https://petsc.org/release/src/vec/vec/interface/rvector.c.html#VecNorm line 197 the check for consistency in line 214 is done on the wrong communicator. The communicator should be PETSC_COMM_SELF. Otherwise the program may hang when PetscCheck is executed. Please find a minimal example attached. Kind regards, Stephan Köhler -- Stephan Köhler TU Bergakademie Freiberg Institut für numerische Mathematik und Optimierung Akademiestraße 6 09599 Freiberg Gebäudeteil Mittelbau, Zimmer 2.07 Telefon: +49 (0)3731 39-3188 (Büro)

5 7

Bug Report TaoALMM class
by Stephan Köhler 10 Dec '23

10 Dec '23

Dear PETSc/Tao team, I think there might be a bug in the Tao ALMM class: In the function TaoALMMComputeAugLagAndGradient_Private(), see, eg. https://petsc.org/release/src/tao/constrained/impls/almm/almm.c.html#TAOALMM line 648 the gradient seems to be wrong. The given function and gradient computation is Lc = F + Ye^TCe + Yi^T(Ci - S) + 0.5*mu*[Ce^TCe + (Ci - S)^T(Ci - S)], dLc/dX = dF/dX + Ye^TAe + Yi^TAi + 0.5*mu*[Ce^TAe + (Ci - S)^TAi], but I think the gradient should be (without 0.5) dLc/dX = dF/dX + Ye^TAe + Yi^TAi + mu*[Ce^TAe + (Ci - S)^TAi]. Kind regards, Stephan Köhler -- Stephan Köhler TU Bergakademie Freiberg Institut für numerische Mathematik und Optimierung Akademiestraße 6 09599 Freiberg Gebäudeteil Mittelbau, Zimmer 2.07 Telefon: +49 (0)3731 39-3173 (Büro)

2 2