[petsc-users] DMForestTransferVec with -petscspace_order 0
Yann Jobic
yann.jobic at univ-amu.fr
Wed Apr 4 10:31:30 CDT 2018
Hi Isaac,
It's working !!
Many thanks !
Regards,
Yann
Le 04/04/2018 à 15:18, Tobin Isaac a écrit :
> 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 at 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 at 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 petsc-maint at mcs.anl.gov----------
>> --------------------------------------------------------------------------
>> 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 at 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 petsc-maint at mcs.anl.gov----------
>> --------------------------------------------------------------------------
>> 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)
--
___________________________
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
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