November 2022 - petsc-users - mailman3.cels.anl.gov

PCMGSetResidual and fortran
by Steven Dargaville 04 Nov '22

04 Nov '22

Hi all I have a quick question regarding the use of PCMGSetResidual within fortran code. I'm calling PCMGSetResidual from within fortran: call PCMGSetResidual(pc_mg, petsc_level, mg_residual, coarse_matrix ierr) and just for testing purposes I've written a trivial residual evaluation routine: subroutine mg_residual(mat, b, x, r, ierr) !!< Compute the residual ! ~~~~~~ type(tMat) :: mat type(tVec) :: b, x, r PetscErrorCode :: ierr ! ~~~~~~ print *, "inside residual evaluation" call MatResidual(mat, b, x, r, ierr) end subroutine The problem I am having is that this segfaults when the residual routine is called. Valgrind shows that it is failing in the fortran interface in ftn-custom/zmgfuncf.c, with the message: ==24742== Invalid read of size 8 ==24742== at 0x5B7CBC0: ourresidualfunction (in /home/projects/dependencies/petsc_main/arch-linux-c-opt/lib/libpetsc.so.3.015.0) ==24742== by 0x5B6D804: PCMGMCycle_Private (in /home/projects/dependencies/petsc_main/arch-linux-c-opt/lib/libpetsc.so.3.015.0) ==24742== Process terminating with default action of signal 11 (SIGSEGV) ==24742== Access not within mapped region at address 0x0 ==24742== at 0x5B7CBC0: ourresidualfunction (in /home/sdargavi/projects/dependencies/petsc_main/arch-linux-c-opt/lib/libpetsc.so.3.015.0) ==24742== by 0x5B6D804: PCMGMCycle_Private (in /home/sdargavi/projects/dependencies/petsc_main/arch-linux-c-opt/lib/libpetsc.so.3.015.0) I'm guessing this is because the fortran_func_pointers isn't pointing to the mg_residual routine, but I am not sure why. I noticed that in the C code of PCMGSetResidual that it calls MatDestroy on the A matrix in mg_levels and replaces it with the mat passed in: if (mat) PetscObjectReference((PetscObject)mat); MatDestroy(&mglevels[l]->A); mglevels[l]->A = mat so I modified my code to call PCMGSetResidual either before the operators are set, or after but passing in an extra copy, but this doesn't seem to help. I'm guessing I'm doing something silly, but just wondering if anyone had any ideas? Thanks for your help Steven

2 1

Issues linking petsc header files and lib from FORTRAN codes
by Jianbo Long 03 Nov '22

03 Nov '22

Hello, I'm struggling to make my FORTRAN code work with petsc as I cannot link the required header files (e.g., petscksp.h) and compiled library files to my FORTRAN code. Compiling petsc was not a problem. However, even with the fortran examples (see those on https://petsc.org/main/docs/manual/fortran/) and the guide on using petsc in c++ and fortran codes (see Section "Writing C/C++ or Fortran Applications" at https://petsc.org/main/docs/manual/getting_started/) I still cannot make my FORTRAN code work. The Fortran test code is exactly the example code ex83f.F90 (see attached files). Aftering following the 2nd method in the Guide (see the picture below), I still get errors: petsc/finclude/petscksp.h: No such file or directory Even if I set up the path of the header file correctly in my own makefile without using environment variables, I still can only find the file "petscksp.h" for my code. Of course, the trouble is that all other headers files required by KSP are recursively included in this petscksp.h file, and I have no way to link them together for my Fortran code. So, here are my questions: 1) in the Guide, how exactly are we supposed to set up the environment variables PETSC_DIR and PETSC_ARCH ? More details and examples would be extremely helpful ! 2) Is there a way to get rid of the *preprocessor* statement #include <petsc/finclude/petscvec.h> when using c++/Fortran codes ? For example, when using MUMPS package in a Fortran code, we can simply use *compiler* 'include', rather than a preprocessor, to extract all required variables for the user's codes : INCLUDE 'zmumps_struc.h' where the header file zmumps_struc.h is already provided in the package. Similarly, I think it's much more portable and easier when using petsc in other codes if we can make it work to use petsc. (Note: similar issues were discussed before, see https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2019-January/037499.html. Unfortunately, I have no clue about the solution archived there ...) Any thoughts and solutions would be much appreciated ! Thanks, Jianbo Long [image: image.png]

1 0

Periodic boundary condition
by Sepideh Kavousi 03 Nov '22

03 Nov '22

Hello, I want to solve my 5 PDEs based on finite difference method using periodic BC in x-direction and non-periodic in y-direction but I run into error (Segmentation Violation, probably memory access out of range). For this, I discretize my equation in FormFunction function. My PDE discretization in (i,j) node needs data on (i+1,j), (i+2,j), (i-1,j), (i-2,j), (i,j+1), (i,j+2), (i,j-1), (i,j-2) points. In my previous codes that the x-direction was non-periodic (no flux) boundary condition, I: i) implemented the no flux BC for i=0 and i=Nx-1, ii) set i+2= Nx-1 in discretizing (Nx-2,j) and i+2= 0 in discretizing (1,j) iii) discretized my equation for i=1..Nx-2. I am not sure how I should do the periodic BC. From the following discussions (https://lists.mcs.anl.gov/pipermail/petsc-users/2012-May/013476.html and https://lists.mcs.anl.gov/pipermail/petsc-users/2016-May/029273.html) I guess I should not do step (i) (stated above) for the x-boundaries and just do step (iii) for i=0..Nx-1. If I just focus on solving 2 of the PDEs which does need data on (i+2,j), (i-2,j), (i,j+2), (i,j-2) points for discretizing equation in (i,j) node, I still run into error: Running with Valgrind (just 1 processor) gave the following file. I did not find any information which gives me hint on the error source. Can you please help me to find the error? Best, Sepideh ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x4C29E39: malloc (vg_replace_malloc.c:309) ==236074== by 0x1B79E59B: MPID_Init (mpid_init.c:1649) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so) ==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so) ==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so) ==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Use of uninitialised value of size 8 ==236074== at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so) ==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Use of uninitialised value of size 8 ==236074== at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so) ==236074== by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so) ==236074== by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so) ==236074== by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so) ==236074== by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Use of uninitialised value of size 8 ==236074== at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Use of uninitialised value of size 8 ==236074== at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2) ==236074== by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0) ==236074== by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155) ==236074== by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377) ==236074== by 0x1B7B5C55: ??? (mpid_nem_init.c:231) ==236074== by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954) ==236074== by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x1B1DA260: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0) ==236074== by 0x1B8CFBA1: ??? (simple_pmi.c:2376) ==236074== by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883) ==236074== by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751) ==236074== by 0x1B7CCC1E: ??? (mpidi_pg.c:949) ==236074== by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736) ==236074== by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421) ==236074== by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x1B1DA383: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0) ==236074== by 0x1B8CFBA1: ??? (simple_pmi.c:2376) ==236074== by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883) ==236074== by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751) ==236074== by 0x1B7CCC1E: ??? (mpidi_pg.c:949) ==236074== by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736) ==236074== by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421) ==236074== by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146) ==236074== by 0x1B79F02D: MPID_Init (mpid_init.c:1857) ==236074== by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717) ==236074== by 0x1B73D795: PMPI_Init_thread (initthread.c:1061) ==236074== by 0x5264A94: PetscInitialize (pinit.c:907) ==236074== by 0x40219D: main (one.c:335) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x1E48032E: __intel_sse4_strcpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so) ==236074== by 0x51FD8BE: PetscStrcpy (str.c:354) ==236074== by 0x51FD7A3: PetscStrallocpy (str.c:188) ==236074== by 0x52A39CE: PetscEventRegLogRegister (eventlog.c:313) ==236074== by 0x527D89A: PetscLogEventRegister (plog.c:693) ==236074== by 0x6A56A20: PCBDDCInitializePackage (bddc.c:3115) ==236074== by 0x6E1A515: PCInitializePackage (dlregisksp.c:59) ==236074== by 0x6DB1A86: PCCreate (precon.c:382) ==236074== by 0x6E05167: KSPGetPC (itfunc.c:1837) ==236074== by 0x6E0FC5C: KSPSetDM (iterativ.c:1150) ==236074== by 0x6FDD27B: SNESSetDM (snes.c:5402) ==236074== by 0x70B85F7: TSGetSNES (ts.c:2914) ==236074== by 0x70BE430: TSSetDM (ts.c:4949) ==236074== by 0x402496: main (one.c:378) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so) ==236074== by 0x51FFD24: PetscStrncpy (str.c:392) ==236074== by 0x51FEB03: PetscStrreplace (str.c:1142) ==236074== by 0x52C9958: PetscViewerFileSetName (filev.c:659) ==236074== by 0x52B743B: PetscViewerVTKOpen (vtkv.c:279) ==236074== by 0x70C76E6: TSMonitorSolutionVTK (ts.c:5580) ==236074== by 0x40313C: FormFunction (one.c:120) ==236074== by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82) ==236074== by 0x70BA5EF: TSComputeIFunction (ts.c:857) ==236074== by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368) ==236074== by 0x70C6E46: SNESTSFormFunction (ts.c:5014) ==236074== by 0x6FDC8A6: SNESComputeFunction (snes.c:2383) ==236074== by 0x7023556: SNESSolve_NEWTONTR (tr.c:297) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so) ==236074== by 0x51FFD24: PetscStrncpy (str.c:392) ==236074== by 0x51FEB03: PetscStrreplace (str.c:1142) ==236074== by 0x5224E4B: PetscFOpen (mpiuopen.c:52) ==236074== by 0x63A074B: DMDAVTKWriteAll_VTS.A (grvtk.c:72) ==236074== by 0x639A589: DMDAVTKWriteAll (grvtk.c:545) ==236074== by 0x52B66F3: PetscViewerFlush_VTK (vtkv.c:100) ==236074== by 0x52CFAAE: PetscViewerFlush (flush.c:26) ==236074== by 0x52CEA95: PetscViewerDestroy (view.c:113) ==236074== by 0x70C7717: TSMonitorSolutionVTK (ts.c:5582) ==236074== by 0x40313C: FormFunction (one.c:120) ==236074== by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82) ==236074== by 0x70BA5EF: TSComputeIFunction (ts.c:857) ==236074== by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368) ==236074== by 0x70C6E46: SNESTSFormFunction (ts.c:5014) ==236074== by 0x6FDC8A6: SNESComputeFunction (snes.c:2383) ==236074== by 0x7023556: SNESSolve_NEWTONTR (tr.c:297) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== ==236074== Conditional jump or move depends on uninitialised value(s) ==236074== at 0x5F10977: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:146) ==236074== by 0x5F10977: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284) ==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242) ==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79) ==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717) ==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== ==236074== Invalid write of size 4 ==236074== at 0x5F10983: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:150) ==236074== by 0x5F10983: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284) ==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242) ==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79) ==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717) ==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== Address 0x3a94fa80 is 0 bytes after a block of size 73,960,000 alloc'd ==236074== at 0x4C2C480: memalign (vg_replace_malloc.c:909) ==236074== by 0x522FFE2: PetscMallocAlign (mal.c:52) ==236074== by 0x52305F9: PetscMallocA (mal.c:418) ==236074== by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125) ==236074== by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284) ==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242) ==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79) ==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717) ==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== ==236074== Invalid write of size 8 ==236074== at 0x5F10991: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:151) ==236074== by 0x5F10991: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284) ==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242) ==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79) ==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717) ==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== Address 0x3a94fa88 is 8 bytes after a block of size 73,960,000 alloc'd ==236074== at 0x4C2C480: memalign (vg_replace_malloc.c:909) ==236074== by 0x522FFE2: PetscMallocAlign (mal.c:52) ==236074== by 0x52305F9: PetscMallocA (mal.c:418) ==236074== by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125) ==236074== by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284) ==236074== by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242) ==236074== by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79) ==236074== by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717) ==236074== by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324) ==236074== by 0x6FD160F: SNESSolve (snes.c:4569) ==236074== by 0x711917E: PetscMemcpy (bdf.c:223) ==236074== by 0x711917E: PetscCitationsRegister (petscsys.h:2689) ==236074== by 0x711917E: TSStep_BDF.A (bdf.c:265) ==236074== by 0x70C363A: TSStep (ts.c:3757) ==236074== by 0x70C1999: TSSolve (ts.c:4154) ==236074== by 0x402594: main (one.c:391) ==236074== Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Advice on coupling linear physics with Allen-Cahn
by Mike Welland 03 Nov '22

03 Nov '22

I am coupling a linear diffusion equation with Allen-Cahn in a time dependent problem. I'd like to take advantage of the linear block to speed things up. I'm trying two approaches: 1. Allen-Cahn with double well potential: phi^2*(1-phi^2), which makes it nonlinear. The best performance I have is with geometric multigrid on the full system. I tried using a schur complement with the linear diffusion block on A00 (both inside mg levels, and just mg on S) but didn't get good performance. 2. Allen-Cahn with the 'obstacle' potential: phi*(1-phi) which is linear but needs the vi solver to keep 0<=phi<=1. My whole system becomes linear (great!) but needs the nonlinear steps for the vi solver, and I'm not sure if it is reusing the factorization since the DOFs are being changed with the active step. Any suggestion / guidance would be appreciated! Thanks!

2 1

Doubt about PCILU
by Ahmed Mansur 03 Nov '22

03 Nov '22

Hi, I'm trying to use ILU as GMRES preconditioner (using PCILU), my question is how use ILU as 'ilutp' type like MATLAB ( ILU factorization with threshold and pivoting. ) Thanks. Regards

2 2

Redefining MPI functions as macros can break C++ code
by Erik Schnetter 03 Nov '22

03 Nov '22

PETSc redefines MPI functions as macros when logging is enabled. This breaks some C++ code; see e.g. < https://github.com/AMReX-Codes/amrex/pull/3005> for an example. The reason is that macros get confused about commas in template arguments. It would be convenient if PETSc used a different way to log MPI function calls, but I can't think of a good way. Alternatively, logging could be disabled by default, or MPI logging could be disabled by default, or there could be a simple way to opt out (e.g. use `#define PETSC_LOG_MPI` after `#include <petsc.h>` to enable it for a source file). -erik -- Erik Schnetter <eschnetter(a)perimeterinstitute.ca> http://www.perimeterinstitute.ca/personal/eschnetter/

2 2

Bug report LMVM matrix class
by Stephan Köhler 02 Nov '22

02 Nov '22

Dear PETSc/Tao team, it seems to be that there is a bug in the LMVM matrix class: In the function MatCreateVecs_LMVM, see, e.g., https://petsc.org/release/src/ksp/ksp/utils/lmvm/lmvmimpl.c.html at line 214. it is not checked if the vectors *L, or *R are NULL. This is, in particular, a problem if this matrix class is combined with the Schur complement matrix class, since MatMult_SchurComplement calls this function with NULL as *R, see, e.g. https://petsc.org/release/src/ksp/ksp/utils/schurm/schurm.c.html at line 66. I attach a minimal example. You need to modify the paths to the PETSc installation in the makefile. Best 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 1

Can I use PETSc DMPlex to output the surface mesh?
by Gong Yujie 02 Nov '22

02 Nov '22

Dear development team, Now I'm doing a project about visualization. In the process of visualization, the surface mesh is preferred. I have two questions about the DMPlex mesh. 1. Can I output the 3D volume mesh in DMPlex as a .obj or .fbx file? Both these two meshes are just surface mesh. 2. If not, can I output part of the mesh out? Since I have some labels for this part of mesh, can I output this part of mesh (boundary surface mesh) separately? Best Regards, Jerry

2 1

Field split degree of freedom ordering
by Alexander Lindsay 02 Nov '22

02 Nov '22

In the block matrices documentation, it's stated: "Note that for interlaced storage the number of rows/columns of each block must be the same size" Is interlacing defined in a global sense, or a process-local sense? So explicitly, if I don't want the same size restriction, do I need to ensure that globally all of my block 1 dofs are numbered after my block 0 dofs? Or do I need to follow that on a process-local level? Essentially in libMesh we always follow rank-major ordering. I'm asking whether for unequal row sizes, in order to split, would we need to strictly follow variable-major ordering (splitting here meaning splitting by variable)? Alex

2 3

PETSc Windows Installation
by Mohammad Ali Yaqteen 01 Nov '22

01 Nov '22

Dear Sir, During the Installation of PETSc in windows, I installed Cygwin and the required libraries as mentioned on your website: [cid:[email protected]] However, when I install PETSc using the configure commands present on the petsc website: ./configure --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich it gives me the following error: [cid:[email protected]] I already installed OpenMPI using Cygwin installer but it still asks me to. When I configure without "-download-mpich" and run "make check" command, it gives me the following errors: [cid:[email protected]] Could you kindly look into this and help me with this? Your prompt response will highly be appreciated. Thank you! Mohammad Ali Researcher, Sejong University

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