Hi Yann, On Tue, Apr 03, 2018 at 05:29:39PM +0200, Yann Jobic wrote: > Hi, > > Thanks for the fast answer ! And sorry for my late one... > As a test, i'm using ex2.c in test/forest directory. > > I'm using 2 git depot (master), one from this week end, and one of today. I > see some different behaviors. > > For the git from the week end : v3.8.4-1-g756c7f9 > In 2D, everything is ok (petscspace_order = 0,1,2) : mpiexec -n 1 ./ex2 > -petscspace_poly_tensor -petscspace_order 2 -dim 2 > In 3D, only -petscspace_order 2 works. For the other ones, i put the full > message in a log file.
This looks like a version of petsc/maint commit. I have not tried to fix this (a new maintenance release is imminent). > > For the git from today : v3.8.4-2420-g8f4cb0b > In 2D, petscspace_order is ok for 2 and 1, but do not work for 0. > In 3D, same as 2D, it's working for petscspace_order 2 and 1, but not for 0. > (see log file) > Many thanks for the help ! I have fixed this in the branch `tisaac/fix-height-ds` on the repo. It does not require any interface changes, so as soon as it is approved, it will be integrated into the master branch and to-be-released maintained version v3.8.9. Cheers, Toby > > Regards, > > Yann > > > Le 03/04/2018 à 03:33, Tobin Isaac a écrit : > > Hi Yann, > > > > Thanks for pointing this out to us. Matt and I are the two most > > actively developing in this area. We have been working on separate > > threads and this looks like an issue where we need to sync up. I > > think there is a simple fix, but it would be helpful to know which > > version petsc you're working from: I'm seeing different > > behavior. Could you please send along more complete output? > > > > Cheers, > > Toby > > > > On Mon, Apr 02, 2018 at 04:42:29PM +0200, yann JOBIC wrote: > > > Hi, > > > > > > I'm using DMForestTransferVec, as in > > > "dm/impls/forest/examples/tests/ex2.c". > > > > > > I would like to use it with a space approximation order at zero > > > (-petscspace_order 0). However, in this case, it's not working (valgrind > > > output of ex2.c from forest test) : > > > > > > ==8604== Conditional jump or move depends on uninitialised value(s) > > > ==8604== at 0x47D74F: DMPlexVecGetClosure (plex.c:4035) > > > ==8604== by 0x557612: DMPlexLocatePoint_General_3D_Internal > > > (plexgeometry.c:153) > > > ==8604== by 0x559B85: DMPlexLocatePoint_Internal (plexgeometry.c:383) > > > ==8604== by 0x611EED: DMPlexComputeInjectorReferenceTree > > > (plextree.c:3247) > > > ==8604== by 0x6148DB: DMPlexReferenceTreeGetInjector (plextree.c:3454) > > > ==8604== by 0x61EAD8: DMPlexTransferVecTree_Inject (plextree.c:4319) > > > ==8604== by 0x620CC1: DMPlexTransferVecTree (plextree.c:4527) > > > ==8604== by 0x7F23D8: DMForestTransferVec_p8est (pforest.c:4239) > > > ==8604== by 0x429B48: DMForestTransferVec (forest.c:985) > > > ==8604== by 0x40BB8A: main (transf_test.c:136) > > > > > > With the error message : > > > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > > probably memory access out of range > > > > > > It's working fine in 2D (p4est). The problem arise in 3D (p8est). > > > > > > Is it an expected behavior ? Am i doing something wrong ? > > > > > > Thanks in advance, > > > > > > Yann > > > > > -- > ___________________________ > > Yann JOBIC > HPC engineer > IUSTI-CNRS UMR 7343 - Polytech Marseille > Technopôle de Château Gombert > 5 rue Enrico Fermi > 13453 Marseille cedex 13 > Tel : (33) 4 91 10 69 43 > Fax : (33) 4 91 10 69 69 > > > > --- > L'absence de virus dans ce courrier électronique a été vérifiée par le > logiciel antivirus Avast. > https://www.avast.com/antivirus > yann@crabe:~/projet/AMR/moulinette$ mpiexec -n 1 ./ex2 > -petscspace_poly_tensor -petscspace_order 0 -dim 3 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to > find memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] DMPlexVecGetClosure line 4020 > /home/yann/src/petsc-git/src/dm/impls/plex/plex.c > [0]PETSC ERROR: [0] DMPlexLocatePoint_General_3D_Internal line 150 > /home/yann/src/petsc-git/src/dm/impls/plex/plexgeometry.c > [0]PETSC ERROR: [0] DMPlexLocatePoint_Internal line 361 > /home/yann/src/petsc-git/src/dm/impls/plex/plexgeometry.c > [0]PETSC ERROR: [0] DMPlexComputeInjectorReferenceTree line 3008 > /home/yann/src/petsc-git/src/dm/impls/plex/plextree.c > [0]PETSC ERROR: [0] DMPlexReferenceTreeGetInjector line 3449 > /home/yann/src/petsc-git/src/dm/impls/plex/plextree.c > [0]PETSC ERROR: [0] DMPlexTransferVecTree_Inject line 4309 > /home/yann/src/petsc-git/src/dm/impls/plex/plextree.c > [0]PETSC ERROR: [0] DMPlexTransferVecTree line 4486 > /home/yann/src/petsc-git/src/dm/impls/plex/plextree.c > [0]PETSC ERROR: [0] DMForestTransferVec_p8est line 4213 > /home/yann/src/petsc-git/src/dm/impls/forest/p4est/pforest.c > [0]PETSC ERROR: [0] DMForestTransferVec line 978 > /home/yann/src/petsc-git/src/dm/impls/forest/forest.c > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Signal received > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.8.4, unknown > [0]PETSC ERROR: ./ex2 on a depot-git named crabe by yann Tue Apr 3 17:18:02 > 2018 > [0]PETSC ERROR: Configure options > --prefix=/local/lib/petsc/depot-git/gcc/openmpi_gcc_all > --with-single-library=0 --with-debugging=1 --download-scalapack=1 > --download-metis=1 --download-parmetis=1 --download-ptscotch=1 > --download-mumps=1 --download-hypre=1 --download-superlu=1 > --download-superlu_dist=1 --download-fblaslapack=1 --download-metis=1 > --download-cmake=1 --download-ml=1 --download-p4est=1 --download-netcdf=1 > --download-pragmatic=1 --download-eigen=1 --download-parms=1 > --download-triangle=1 --download-hdf5=1 --with-zlib=1 --download-szlib=1 > --download-chaco=1 --download-spai=1 --download-suitesparse=1 > --with-shared-libraries=0 PETSC_ARCH=depot-git > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 59. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > ------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > ------------------------------------------------------- > -------------------------------------------------------------------------- > mpiexec detected that one or more processes exited with non-zero status, thus > causing > the job to be terminated. The first process to do so was: > > Process name: [[36533,1],0] > Exit code: 59 > -------------------------------------------------------------------------- > jobic@stargate:~/projet/AMR/moulinette$ mpirun -np 1 ./ex2 > -petscspace_poly_tensor -dim 3 -petscspace_order 0 > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Null argument, when expecting valid pointer > [0]PETSC ERROR: Null Object: Parameter # 2 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.8.4-2420-g8f4cb0b GIT > Date: 2018-04-02 16:00:52 -0500 > [0]PETSC ERROR: ./ex2 on a named stargate by jobic Tue Apr 3 17:22:04 2018 > [0]PETSC ERROR: Configure options --download-chaco=1 --download-cmake=1 > --download-eigen=1 --download-fblaslapack=1 --download-hdf5=1 > --download-hypre=1 --download-metis=1 --download-ml=1 --download-mumps=1 > --download-netcdf=1 --download-p4est=1 --download-parmetis=1 > --download-parms=1 --download-pragmatic=1 --download-ptscotch=1 > --download-scalapack=1 --download-spai=1 --download-suitesparse=1 > --download-superlu=1 --download-superlu_dist=1 --download-szlib=1 > --download-triangle=1 --prefix=/local/lib/petsc/git/gcc/openmpi_gcc_all > --with-debugging=1 --with-shared-libraries=0 --with-single-library=0 > --with-zlib=1 PETSC_ARCH=openmpi_gcc_all > [0]PETSC ERROR: #1 PetscFESetDualSpace() line 3615 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtfe.c > [0]PETSC ERROR: #2 PetscFEGetHeightSubspace() line 6630 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtfe.c > [0]PETSC ERROR: #3 PetscDSGetHeightSubspace() line 2880 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtds.c > [0]PETSC ERROR: #4 DMProjectLocal_Generic_Plex() line 325 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/plex/plexproject.c > [0]PETSC ERROR: #5 DMProjectFunctionLocal_Plex() line 428 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/plex/plexproject.c > [0]PETSC ERROR: #6 DMProjectFunctionLocal() line 6265 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #7 DMProjectFunctionLocal_p8est() line 4385 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/forest/p4est/pforest.c > [0]PETSC ERROR: #8 DMProjectFunctionLocal() line 6265 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #9 DMProjectFunction() line 6250 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #10 main() line 161 in /home/jobic/projet/AMR/moulinette/ex2.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -dim 3 > [0]PETSC ERROR: -petscspace_order 0 > [0]PETSC ERROR: -petscspace_poly_tensor > [0]PETSC ERROR: ----------------End of Error Message -------send entire error > message to [email protected] > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 85. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > > > > > > With valgrind : > jobic@stargate:~/projet/AMR/moulinette$ valgrind mpirun -np 1 ./ex2 > -petscspace_poly_tensor -dim 3 -petscspace_order 0 > ==9730== Memcheck, a memory error detector > ==9730== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. > ==9730== Using Valgrind-3.12.0 and LibVEX; rerun with -h for copyright info > ==9730== Command: mpirun -np 1 ./ex2 -petscspace_poly_tensor -dim 3 > -petscspace_order 0 > ==9730== > ==10212== Warning: invalid file descriptor 1024 in syscall close() > ==10212== Warning: invalid file descriptor 1025 in syscall close() > ==10212== Warning: invalid file descriptor 1026 in syscall close() > ==10212== Warning: invalid file descriptor 1027 in syscall close() > ==10212== Use --log-fd=<number> to select an alternative log fd. > ==10212== Warning: invalid file descriptor 1028 in syscall close() > ==10212== Warning: invalid file descriptor 1029 in syscall close() > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Null argument, when expecting valid pointer > [0]PETSC ERROR: Null Object: Parameter # 2 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.8.4-2420-g8f4cb0b GIT > Date: 2018-04-02 16:00:52 -0500 > [0]PETSC ERROR: ./ex2 on a named stargate by jobic Tue Apr 3 17:27:58 2018 > [0]PETSC ERROR: Configure options --download-chaco=1 --download-cmake=1 > --download-eigen=1 --download-fblaslapack=1 --download-hdf5=1 > --download-hypre=1 --download-metis=1 --download-ml=1 --download-mumps=1 > --download-netcdf=1 --download-p4est=1 --download-parmetis=1 > --download-parms=1 --download-pragmatic=1 --download-ptscotch=1 > --download-scalapack=1 --download-spai=1 --download-suitesparse=1 > --download-superlu=1 --download-superlu_dist=1 --download-szlib=1 > --download-triangle=1 --prefix=/local/lib/petsc/git/gcc/openmpi_gcc_all > --with-debugging=1 --with-shared-libraries=0 --with-single-library=0 > --with-zlib=1 PETSC_ARCH=openmpi_gcc_all > [0]PETSC ERROR: #1 PetscFESetDualSpace() line 3615 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtfe.c > [0]PETSC ERROR: #2 PetscFEGetHeightSubspace() line 6630 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtfe.c > [0]PETSC ERROR: #3 PetscDSGetHeightSubspace() line 2880 in > /home/devel/src_linux/git.petsc/petsc/src/dm/dt/interface/dtds.c > [0]PETSC ERROR: #4 DMProjectLocal_Generic_Plex() line 325 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/plex/plexproject.c > [0]PETSC ERROR: #5 DMProjectFunctionLocal_Plex() line 428 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/plex/plexproject.c > [0]PETSC ERROR: #6 DMProjectFunctionLocal() line 6265 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #7 DMProjectFunctionLocal_p8est() line 4385 in > /home/devel/src_linux/git.petsc/petsc/src/dm/impls/forest/p4est/pforest.c > [0]PETSC ERROR: #8 DMProjectFunctionLocal() line 6265 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #9 DMProjectFunction() line 6250 in > /home/devel/src_linux/git.petsc/petsc/src/dm/interface/dm.c > [0]PETSC ERROR: #10 main() line 161 in /home/jobic/projet/AMR/moulinette/ex2.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -dim 3 > [0]PETSC ERROR: -petscspace_order 0 > [0]PETSC ERROR: -petscspace_poly_tensor > [0]PETSC ERROR: ----------------End of Error Message -------send entire error > message to [email protected] > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 85. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > ==9730== > ==9730== HEAP SUMMARY: > ==9730== in use at exit: 55,755 bytes in 116 blocks > ==9730== total heap usage: 19,779 allocs, 19,663 frees, 6,633,193 bytes > allocated > ==9730== > ==9730== LEAK SUMMARY: > ==9730== definitely lost: 2,675 bytes in 11 blocks > ==9730== indirectly lost: 48,765 bytes in 75 blocks > ==9730== possibly lost: 200 bytes in 1 blocks > ==9730== still reachable: 4,115 bytes in 29 blocks > ==9730== suppressed: 0 bytes in 0 blocks > ==9730== Rerun with --leak-check=full to see details of leaked memory > ==9730== > ==9730== For counts of detected and suppressed errors, rerun with: -v > ==9730== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
