[petsc-users] SuperLU_dist issue in 3.7.4 failure of repeated calls to MatLoad() or MatMPIAIJSetPreallocation() with the same matrix
Barry Smith
bsmith at mcs.anl.gov
Mon Oct 24 09:13:25 CDT 2016
Hong wrote: (Note that it creates a new Mat each time so shouldn't be affected by the bug I fixed; it also "works" with MUMPs but not superlu_dist.)
It is not problem with Matload twice. The file has one matrix, but is loaded twice.
Replacing pc with ksp, the code runs fine.
The error occurs when PCSetUp_LU() is called with SAME_NONZERO_PATTERN.
I'll further look at it later.
Hong
________________________________________
From: Zhang, Hong
Sent: Friday, October 21, 2016 8:18 PM
To: Barry Smith; petsc-users
Subject: RE: [petsc-users] SuperLU_dist issue in 3.7.4
I am investigating it. The file has two matrices. The code takes following steps:
PCCreate(PETSC_COMM_WORLD, &pc);
MatCreate(PETSC_COMM_WORLD,&A);
MatLoad(A,fd);
PCSetOperators(pc,A,A);
PCSetUp(pc);
MatCreate(PETSC_COMM_WORLD,&A);
MatLoad(A,fd);
PCSetOperators(pc,A,A);
PCSetUp(pc); //crash here with np=2, superlu_dist, not with mumps/superlu or superlu_dist np=1
Hong
> On Oct 24, 2016, at 9:00 AM, Satish Balay <balay at mcs.anl.gov> wrote:
>
> Since the provided test code dosn't crash [and is valgrind clean] -
> with this fix - I'm not sure what bug Hong is chasing..
>
> Satish
>
> On Mon, 24 Oct 2016, Barry Smith wrote:
>
>>
>> Anton,
>>
>> Sorry for any confusion. This doesn't resolve the SuperLU_DIST issue which I think Hong is working on, this only resolves multiple loads of matrices into the same Mat.
>>
>> Barry
>>
>>> On Oct 24, 2016, at 5:07 AM, Anton Popov <popov at uni-mainz.de> wrote:
>>>
>>> Thank you Barry, Satish, Fande!
>>>
>>> Is there a chance to get this fix in the maintenance release 3.7.5 together with the latest SuperLU_DIST? Or next release is a more realistic option?
>>>
>>> Anton
>>>
>>> On 10/24/2016 01:58 AM, Satish Balay wrote:
>>>> The original testcode from Anton also works [i.e is valgrind clean] with this change..
>>>>
>>>> Satish
>>>>
>>>> On Sun, 23 Oct 2016, Barry Smith wrote:
>>>>
>>>>> Thanks Satish,
>>>>>
>>>>> I have fixed this in barry/fix-matmpixxxsetpreallocation-reentrant (in next for testing)
>>>>>
>>>>> Fande,
>>>>>
>>>>> This will also make MatMPIAIJSetPreallocation() work properly with multiple calls (you will not need a MatReset()).
>>>>>
>>>>> Barry
>>>>>
>>>>>
>>>>>> On Oct 21, 2016, at 6:48 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>>>>
>>>>>> On Fri, 21 Oct 2016, Barry Smith wrote:
>>>>>>
>>>>>>> valgrind first
>>>>>> balay at asterix /home/balay/download-pine/x/superlu_dist_test
>>>>>> $ mpiexec -n 2 $VG ./ex16 -f ~/datafiles/matrices/small
>>>>>> First MatLoad!
>>>>>> Mat Object: 2 MPI processes
>>>>>> type: mpiaij
>>>>>> row 0: (0, 4.) (1, -1.) (6, -1.)
>>>>>> row 1: (0, -1.) (1, 4.) (2, -1.) (7, -1.)
>>>>>> row 2: (1, -1.) (2, 4.) (3, -1.) (8, -1.)
>>>>>> row 3: (2, -1.) (3, 4.) (4, -1.) (9, -1.)
>>>>>> row 4: (3, -1.) (4, 4.) (5, -1.) (10, -1.)
>>>>>> row 5: (4, -1.) (5, 4.) (11, -1.)
>>>>>> row 6: (0, -1.) (6, 4.) (7, -1.) (12, -1.)
>>>>>> row 7: (1, -1.) (6, -1.) (7, 4.) (8, -1.) (13, -1.)
>>>>>> row 8: (2, -1.) (7, -1.) (8, 4.) (9, -1.) (14, -1.)
>>>>>> row 9: (3, -1.) (8, -1.) (9, 4.) (10, -1.) (15, -1.)
>>>>>> row 10: (4, -1.) (9, -1.) (10, 4.) (11, -1.) (16, -1.)
>>>>>> row 11: (5, -1.) (10, -1.) (11, 4.) (17, -1.)
>>>>>> row 12: (6, -1.) (12, 4.) (13, -1.) (18, -1.)
>>>>>> row 13: (7, -1.) (12, -1.) (13, 4.) (14, -1.) (19, -1.)
>>>>>> row 14: (8, -1.) (13, -1.) (14, 4.) (15, -1.) (20, -1.)
>>>>>> row 15: (9, -1.) (14, -1.) (15, 4.) (16, -1.) (21, -1.)
>>>>>> row 16: (10, -1.) (15, -1.) (16, 4.) (17, -1.) (22, -1.)
>>>>>> row 17: (11, -1.) (16, -1.) (17, 4.) (23, -1.)
>>>>>> row 18: (12, -1.) (18, 4.) (19, -1.) (24, -1.)
>>>>>> row 19: (13, -1.) (18, -1.) (19, 4.) (20, -1.) (25, -1.)
>>>>>> row 20: (14, -1.) (19, -1.) (20, 4.) (21, -1.) (26, -1.)
>>>>>> row 21: (15, -1.) (20, -1.) (21, 4.) (22, -1.) (27, -1.)
>>>>>> row 22: (16, -1.) (21, -1.) (22, 4.) (23, -1.) (28, -1.)
>>>>>> row 23: (17, -1.) (22, -1.) (23, 4.) (29, -1.)
>>>>>> row 24: (18, -1.) (24, 4.) (25, -1.) (30, -1.)
>>>>>> row 25: (19, -1.) (24, -1.) (25, 4.) (26, -1.) (31, -1.)
>>>>>> row 26: (20, -1.) (25, -1.) (26, 4.) (27, -1.) (32, -1.)
>>>>>> row 27: (21, -1.) (26, -1.) (27, 4.) (28, -1.) (33, -1.)
>>>>>> row 28: (22, -1.) (27, -1.) (28, 4.) (29, -1.) (34, -1.)
>>>>>> row 29: (23, -1.) (28, -1.) (29, 4.) (35, -1.)
>>>>>> row 30: (24, -1.) (30, 4.) (31, -1.)
>>>>>> row 31: (25, -1.) (30, -1.) (31, 4.) (32, -1.)
>>>>>> row 32: (26, -1.) (31, -1.) (32, 4.) (33, -1.)
>>>>>> row 33: (27, -1.) (32, -1.) (33, 4.) (34, -1.)
>>>>>> row 34: (28, -1.) (33, -1.) (34, 4.) (35, -1.)
>>>>>> row 35: (29, -1.) (34, -1.) (35, 4.)
>>>>>> Second MatLoad!
>>>>>> Mat Object: 2 MPI processes
>>>>>> type: mpiaij
>>>>>> ==4592== Invalid read of size 4
>>>>>> ==4592== at 0x5814014: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1402)
>>>>>> ==4592== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>>>> ==4592== by 0x53373D7: MatView (matrix.c:989)
>>>>>> ==4592== by 0x40107E: main (ex16.c:30)
>>>>>> ==4592== Address 0xa47b460 is 20 bytes after a block of size 28 alloc'd
>>>>>> ==4592== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>>>> ==4592== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>>>> ==4592== by 0x5842C70: MatSetUpMultiply_MPIAIJ (mmaij.c:41)
>>>>>> ==4592== by 0x5809943: MatAssemblyEnd_MPIAIJ (mpiaij.c:747)
>>>>>> ==4592== by 0x536B299: MatAssemblyEnd (matrix.c:5298)
>>>>>> ==4592== by 0x5829C05: MatLoad_MPIAIJ (mpiaij.c:3032)
>>>>>> ==4592== by 0x5337FEA: MatLoad (matrix.c:1101)
>>>>>> ==4592== by 0x400D9F: main (ex16.c:22)
>>>>>> ==4592==
>>>>>> ==4591== Invalid read of size 4
>>>>>> ==4591== at 0x5814014: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1402)
>>>>>> ==4591== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>>>> ==4591== by 0x53373D7: MatView (matrix.c:989)
>>>>>> ==4591== by 0x40107E: main (ex16.c:30)
>>>>>> ==4591== Address 0xa482958 is 24 bytes before a block of size 7 alloc'd
>>>>>> ==4591== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>>>> ==4591== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>>>> ==4591== by 0x4F31FB5: PetscStrallocpy (str.c:197)
>>>>>> ==4591== by 0x4F0D3F5: PetscClassRegLogRegister (classlog.c:253)
>>>>>> ==4591== by 0x4EF96E2: PetscClassIdRegister (plog.c:2053)
>>>>>> ==4591== by 0x51FA018: VecInitializePackage (dlregisvec.c:165)
>>>>>> ==4591== by 0x51F6DE9: VecCreate (veccreate.c:35)
>>>>>> ==4591== by 0x51C49F0: VecCreateSeq (vseqcr.c:37)
>>>>>> ==4591== by 0x5843191: MatSetUpMultiply_MPIAIJ (mmaij.c:104)
>>>>>> ==4591== by 0x5809943: MatAssemblyEnd_MPIAIJ (mpiaij.c:747)
>>>>>> ==4591== by 0x536B299: MatAssemblyEnd (matrix.c:5298)
>>>>>> ==4591== by 0x5829C05: MatLoad_MPIAIJ (mpiaij.c:3032)
>>>>>> ==4591== by 0x5337FEA: MatLoad (matrix.c:1101)
>>>>>> ==4591== by 0x400D9F: main (ex16.c:22)
>>>>>> ==4591==
>>>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Argument out of range
>>>>>> [0]PETSC ERROR: Column too large: col 96 max 35
>>>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.4-1729-g4c4de23 GIT Date: 2016-10-20 22:22:58 +0000
>>>>>> [0]PETSC ERROR: ./ex16 on a arch-idx64-slu named asterix by balay Fri Oct 21 18:47:51 2016
>>>>>> [0]PETSC ERROR: Configure options --download-metis --download-parmetis --download-superlu_dist PETSC_ARCH=arch-idx64-slu
>>>>>> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 585 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>>> [0]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 724 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>>> [0]PETSC ERROR: #3 MatAssemblyEnd() line 5298 in /home/balay/petsc/src/mat/interface/matrix.c
>>>>>> [0]PETSC ERROR: #4 MatView_MPIAIJ_ASCIIorDraworSocket() line 1410 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>>> [0]PETSC ERROR: #5 MatView_MPIAIJ() line 1440 in /home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>>>> [0]PETSC ERROR: #6 MatView() line 989 in /home/balay/petsc/src/mat/interface/matrix.c
>>>>>> [0]PETSC ERROR: #7 main() line 30 in /home/balay/download-pine/x/superlu_dist_test/ex16.c
>>>>>> [0]PETSC ERROR: PETSc Option Table entries:
>>>>>> [0]PETSC ERROR: -display :0.0
>>>>>> [0]PETSC ERROR: -f /home/balay/datafiles/matrices/small
>>>>>> [0]PETSC ERROR: -malloc_dump
>>>>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>>>> [cli_0]: aborting job:
>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>>>> ==4591== 16,965 (2,744 direct, 14,221 indirect) bytes in 1 blocks are definitely lost in loss record 1,014 of 1,016
>>>>>> ==4591== at 0x4C2FF83: memalign (vg_replace_malloc.c:858)
>>>>>> ==4591== by 0x4FD121A: PetscMallocAlign (mal.c:28)
>>>>>> ==4591== by 0x52F3B14: MatCreate (gcreate.c:84)
>>>>>> ==4591== by 0x581390A: MatView_MPIAIJ_ASCIIorDraworSocket (mpiaij.c:1371)
>>>>>> ==4591== by 0x5814A75: MatView_MPIAIJ (mpiaij.c:1440)
>>>>>> ==4591== by 0x53373D7: MatView (matrix.c:989)
>>>>>> ==4591== by 0x40107E: main (ex16.c:30)
>>>>>> ==4591==
>>>>>>
>>>>>> ===================================================================================
>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> = PID 4591 RUNNING AT asterix
>>>>>> = EXIT CODE: 63
>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>> ===================================================================================
>>>>>> balay at asterix /home/balay/download-pine/x/superlu_dist_test
>>>>>> $
>>>>>
>>>
>>
>>
>
More information about the petsc-users
mailing list