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

Segmentation Violation error using SuperLU_DIST in ex 19.c
by maitri ksh 25 Nov '23

25 Nov '23

Hi, I ran into an error while using SuperLU_DIST in ex 19.c, I am not sure how to debug this, can anyone please help. The 'configure.log' file is attached for your reference. Thanks, Maitri

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Test
by tarot1991 22 Nov '23

22 Nov '23

Test Gesendet von Proton Mail für Mobilgeräte

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Logging object creation and destruction counts
by Wells, David 21 Nov '23

21 Nov '23

Hi everyone, I just upgraded to PETSc 3.20 and read up on the new logging infrastructure - its a very nice improvement over the old version. I have some code which checks that every construction has a corresponding destruction via PetscStageLog stageLog; ierr = PetscLogGetStageLog(&stageLog); for (int i = 0; i < stageLog->stageInfo->classLog->numClasses; ++i) { if (stageLog->stageInfo->classLog->classInfo[i].destructions != stageLog->stageInfo->classLog->classInfo[i].creations) { crash(); } } This no longer works and I can't figure out how to port it. In particular, it looks like I need to get a PetscLogEvent number for creation and another for destruction to retrieve the relevant PetscEventPerfInfo objects per-class - is there some straightforward way to do that for every registered PETSc class? Best, David Wells

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MUMPS valgrind error
by Alexander Lindsay 21 Nov '23

21 Nov '23

I recently ran into some parallel crashes and valgrind suggests the issue is with MUMPS. Has anyone else run into something similar recently? ==4022024== Invalid read of size 4 ==4022024== at 0xF961266: dmumps_dr_assemble_local (dsol_distrhs.F:301) ==4022024== by 0xF961266: dmumps_scatter_dist_rhs_ (dsol_distrhs.F:169) ==4022024== by 0xF952669: dmumps_solve_driver_ (dsol_driver.F:3677) ==4022024== by 0xF8CA64A: dmumps_ (dmumps_driver.F:2035) ==4022024== by 0xF85E12B: dmumps_f77_ (dmumps_f77.F:291) ==4022024== by 0xF85C30E: dmumps_c (mumps_c.c:485) ==4022024== by 0xEBA8E56: MatSolve_MUMPS (mumps.c:1493) ==4022024== by 0xEE85D97: MatSolve (matrix.c:3631) ==4022024== by 0xF31B060: PCApply_LU (lu.c:169) ==4022024== by 0xF50FD3B: PCApply (precon.c:486) ==4022024== by 0xF511204: PCApplyBAorAB (precon.c:756) ==4022024== by 0xF51C5F0: KSP_PCApplyBAorAB (kspimpl.h:443) ==4022024== by 0xF51C5F0: KSPGMRESCycle (gmres.c:146) ==4022024== by 0xF51C5F0: KSPSolve_GMRES (gmres.c:227) ==4022024== by 0xF5F339D: KSPSolve_Private (itfunc.c:910) ==4022024== Address 0x308b338c is 4 bytes before a block of size 1 alloc'd ==4022024== at 0x4C37135: malloc (vg_replace_malloc.c:381) ==4022024== by 0xF960E93: dmumps_scatter_dist_rhs_ (dsol_distrhs.F:139) ==4022024== by 0xF952669: dmumps_solve_driver_ (dsol_driver.F:3677) ==4022024== by 0xF8CA64A: dmumps_ (dmumps_driver.F:2035) ==4022024== by 0xF85E12B: dmumps_f77_ (dmumps_f77.F:291) ==4022024== by 0xF85C30E: dmumps_c (mumps_c.c:485) ==4022024== by 0xEBA8E56: MatSolve_MUMPS (mumps.c:1493) ==4022024== by 0xEE85D97: MatSolve (matrix.c:3631) ==4022024== by 0xF31B060: PCApply_LU (lu.c:169) ==4022024== by 0xF50FD3B: PCApply (precon.c:486) ==4022024== by 0xF511204: PCApplyBAorAB (precon.c:756) ==4022024== by 0xF51C5F0: KSP_PCApplyBAorAB (kspimpl.h:443) ==4022024== by 0xF51C5F0: KSPGMRESCycle (gmres.c:146) ==4022024== by 0xF51C5F0: KSPSolve_GMRES (gmres.c:227)

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Fwd: Inquiry about DMPlexCreateSection
by neil liu 20 Nov '23

20 Nov '23

Hello, Petsc team, Previously, following the function setupseciton in the following case https://petsc.org/main/src/dm/impls/plex/tutorials/ex7.c.html I successfully created a section layout and then imposed the Dirchlet boundary conditions. It seems DMPlexCreateSection is able to replace the above setupsection function and specify points that are located on the boundary. My question is, does DMPlexCreateSection impose boundary condition automatically, e.g., Dirichlet boundary condition (u=0). Or we should impose these boundary conditions manually, then what is the benefit of DMPlexCreateSection compared with the above setupsection function? Thanks, Xiaodong

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Difficulty installing PETSC-3.17.0 on new macOS Sonoma
by Jan Izak C. Vermaak 20 Nov '23

20 Nov '23

Hi all, I am in the process of upgrading our petsc version to 3.20.1 but I really need our current version to work with 3.17.0. I am having install issues. Attached is the config log. Command Line Tools 15.0 (CLT 15.0) used to be the source of my problems with the previous OS version for which the solution was to install the old CLT 14.3, however, CLT 14.3 is not compatible with macOS Sonoma (which INL is requiring us to have). Any help will be appreciated. Regards, Jan Jan Vermaak, Ph.D. Senior Nuclear Multiphysics Engineer | Reactor Physics Methods and Analysis Department (C110) Reactor Systems Design and Analysis Division | Nuclear Science & Technology Directorate JanIzak.Vermaak(a)inl.gov<mailto:[email protected]> | M 979-739-0789 Idaho National Laboratory | 1955 Fremont Ave. | Idaho Falls, ID | 83415 _______________________________ [signature_1025312815]

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Error in genmap
by Sandeep Haripuria 20 Nov '23

20 Nov '23

Dear Sir I am trying to run an oscillating airfoil case. For this purpose I am trying to make use of "neknek". I created two separate geometry files , one for the airfoil and other for the outside surrounding. I have created the geometry and mesh using GMSH. I have attached the .geo and .msh files for your perusal. Now, I am able to successfully create the "naca0012.map" but I am getting an error when I try to genmap the outside.rea file. The error is shown below: [ratnavk at vamana](https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users) :~/NEK/test_neknek$ ../trunk/bin/genmap Input (.rea) file name: outside Input mesh tolerance (default 0.2): NOTE: smaller is better, but generous is more forgiving for bad meshes. 0.01 reading .rea file data ... ERROR: error reading 1 1 406 aborting 510 in routine rdbdry. 1 quit Looking forward to your positive reply. Sandeep Haripuria [ThePlattery.Com](https://theplattery.com/)

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Error running make check with OneAPI C/C++ and Fortran compilers on Windows
by Maruthi NH 19 Nov '23

19 Nov '23

Hi all, I could successfully compile PETSc on Windows with Intel OneAPI C/C++ and Fortran compilers, however, when I tried to make a check after the successful installation, I got the following error message. I have also attached the configuration file. make PETSC_DIR=/home/ngh/petsc PETSC_ARCH=intel-petsc-tag-v3.20.1 check Running PETSc check examples to verify correct installation Using PETSC_DIR=/home/ngh/petsc and PETSC_ARCH=intel-petsc-tag-v3.20.1 Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See https://petsc.org/release/faq/ =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 13384 RUNNING AT BLRLAP1521 = EXIT STATUS: -1073741819 (c0000005) =================================================================================== Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See https://petsc.org/release/faq/ =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 20616 RUNNING AT BLRLAP1521 = EXIT STATUS: -1073741819 (c0000005) =================================================================================== =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 1 PID 16900 RUNNING AT BLRLAP1521 = EXIT STATUS: -1073741819 (c0000005) =================================================================================== Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See https://petsc.org/release/faq/ forrtl: severe (157): Program Exception - access violation Image PC Routine Line Source ex5f.exe 00007FF661DB569B Unknown Unknown Unknown ex5f.exe 00007FF661A760AF Unknown Unknown Unknown ex5f.exe 00007FF6619E6EBD Unknown Unknown Unknown ex5f.exe 00007FF6619C6294 Unknown Unknown Unknown ex5f.exe 00007FF6619C3152 Unknown Unknown Unknown ex5f.exe 00007FF6619C1051 Unknown Unknown Unknown ex5f.exe 00007FF662C3C16E Unknown Unknown Unknown ex5f.exe 00007FF662C3CA50 Unknown Unknown Unknown KERNEL32.DLL 00007FFB12187344 Unknown Unknown Unknown ntdll.dll 00007FFB140C26B1 Unknown Unknown Unknown Completed PETSc check examples Error while running make check make[1]: *** [makefile:132: check] Error 1 make: *** [GNUmakefile:17: check] Error 2 Regards, mnh

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VecNorm causes program to hang
by Sreeram R Venkat 17 Nov '23

17 Nov '23

I have a program which reads a vector from file into an array, and then uses that array to create a PETSc Vec object. The Vec is defined on the global communicator, but not all processes actually contain entries of it. For example, suppose we have 4 processors, and the vector is of size 10. Rank 0 will contain entries 0-4 and Rank 1 will contain entries 5-9. Ranks 2 and 3 will not have any entries of the Vec. This Vec is then used as an input to other parts of the code, and those work fine. However, if I try to take the norm of the Vec with VecNorm(), I get the error `MPI_Allreduce() called in different locations (code lines) on different processors` The stack trace shows that ranks 0 and 1 (from the above example) are still in the VecNorm() function while ranks 2 and 3 have moved on to a later part of the code. If I add a PetscBarrier() after the VecNorm(), I find that the program hangs. The funny thing is that part of the code duplicates the Vec with VecDuplicate() and assigns to the duplicated vector the result of some computations. The duplicated Vec has the same layout as the original Vec, but taking VecNorm() on the duplicated Vec works fine. If I use VecCopy(), however, the copied Vec also causes VecNorm() to hang. I've printed out the original Vec, and there are no corrupted/NaN entries. I have a temporary workaround where I perturb the original Vec slightly before copying it to another Vec. This causes the program to successfully terminate. Any advice on how to get VecNorm() working with the original Vec? Thanks, Sreeram

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Get DM used to create Vec
by Carl-Johan Thore 16 Nov '23

16 Nov '23

Hi, Given a Vec (or Mat) created at some point with DMCreate..., is it possible to retrieve from this Vec a pointer to the DM used to create it? (I could perhaps build my own Vec-type on top of PETSc's which carried with it such a pointer but that doesn't seem like a good idea) Kind regards, Carl-Johan

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