On Sat, Sep 19, 2009 at 2:12 PM, Ryan Yan <vyan2000 at gmail.com> wrote:
> Hi All, > My application code is reading PETSc binary files to obtain the information > about a linear system and then solve it in parallel. > > The code works well for median size problem. Now, I am testing a largest > case requested by our custom on *one* processor. I got the following errors. > > It looks like that error happenned when PETSc is requesting an malloc of > size "[0]PETSC ERROR: Memory requested 44784088!", but I did see there are > PETSc routines the use even more memory than "44784088", > for instance, "[0] 46 5520000 ISGetIndices_Stride()". So can I guess error > is caused by the hardware memory limitation? > You are running out of memory. If you want to run bigger problems, you will have to use more nodes. Matt > The code was running on MPIS machine with 6 CPUs one each Node. > The code broke for 1 Node with 1 process > for 1 Node with 2 process > for 1 Node with 6 process > > But the code succeed for 2 Node with 2 process. > for 2 Node with 4 process. > The code also succeed when Node number is big than 2. > > Is this another indicator of the hardware limitation? > > Thanks a lot, > > Yan > > > $ srun -p sci-comp -N 1 -n 1 ./rpisolve_25_field -ksp_monitor_true_residual > -log_summary -malloc_dump -malloc_log >& out.rpisolve.N1.n1 > $ cat out.rpisolve.N1.n1 > > > > > > breakpoint 1 > breakpoint 2 > breakpoint 750000 > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Out of memory. This could be due to allocating > [0]PETSC ERROR: too large an object or bleeding by not properly > [0]PETSC ERROR: destroying unneeded objects. > [0] Maximum memory PetscMalloc()ed 3172769832 maximum size of entire > process 0 > [0] Memory usage sorted by function > [0] 2 3216 ClassPerfLogCreate() > [0] 2 1616 ClassRegLogCreate() > [0] 2 6416 EventPerfLogCreate() > [0] 1 12800 EventPerfLogEnsureSize() > [0] 2 1616 EventRegLogCreate() > [0] 1 3200 EventRegLogRegister() > [0] 92 11960 ISCreateBlock() > [0] 292 36792 ISCreateStride() > [0] 46 5520000 ISGetIndices_Stride() > [0] 78 21632 KSPCreate() > [0] 1 200 KSPCreate_FGMRES() > [0] 26 416 KSPDefaultConvergedCreate() > [0] 6 17600 KSPSetUp_FGMRES() > [0] 475 180880 MatCreate() > [0] 24 3648 MatCreate_MPIAIJ() > [0] 71 22152 MatCreate_SeqAIJ() > [0] 1 1504 MatGetRow_MPIAIJ() > [0] 23 368 MatGetSubMatrices_MPIAIJ() > [0] 690 140770488 MatGetSubMatrices_MPIAIJ_Local() > [0] 22 5280176 MatGetSubMatrix_MPIAIJ() > [0] 7 1497800024 MatLoad_MPIAIJ() > [0] 68 13920000 MatMarkDiagonal_SeqAIJ() > [0] 138 1236969200 MatSeqAIJSetPreallocation_SeqAIJ() > [0] 23 184 MatSetUpMultiply_MPIAIJ() > [0] 24 192 MatStashCreate_Private() > [0] 138 1288 MatStashScatterBegin_Private() > [0] 23 184 Mat_CheckCompressedRow() > [0] 45 8280360 Mat_CheckInode() > [0] 78 14768 PCCreate() > [0] 1 120 PCCreate_FieldSplit() > [0] 2 208 PCFieldSplitSetDefaults() > [0] 50 2400 PCFieldSplitSetFields_FieldSplit() > [0] 1 104 PCSetFromOptions_FieldSplit() > [0] 1 200 PCSetUp_FieldSplit() > [0] 3 24 PetscCommDuplicate() > [0] 1768 84864 PetscFListAdd() > [0] 46 368 PetscGatherNumberOfMessages() > [0] 237 1896 PetscMapSetUp() > [0] 4 32 PetscMaxSum() > [0] 22 5984 PetscOListAdd() > [0] 75 4800 PetscOptionsCreate_Private() > [0] 4 96 PetscOptionsGetEList() > [0] 6 384000 PetscOptionsInsertFile() > [0] 75 600 PetscOptionsInt() > [0] 92 736 PetscPostIrecvInt() > [0] 46 368 PetscPostIrecvScalar() > [0] 0 32 PetscPushSignalHandler() > [0] 4570 130832 PetscStrallocpy() > [0] 69 16924048 PetscTableCreate() > [0] 1 16 PetscViewerASCIIMonitorCreate() > [0] 1 16 PetscViewerASCIIOpen() > [0] 12 1952 PetscViewerCreate() > [0] 1 56 PetscViewerCreate_ASCII() > [0] 3 192 PetscViewerCreate_Binary() > [0] 2 528 StackCreate() > [0] 2 1008 StageLogCreate() > [0] 2 16 VecAssemblyBegin_MPI() > [0] 236 74104 VecCreate() > [0] 49 78003168 VecCreate_MPI_Private() > [0] 23 552 VecCreate_Seq_Private() > [0] 2 80 VecDuplicateVecs_Default() > [0] 92 11224 VecScatterCreate() > [0] 72 576 VecStashCreate_Private() > [0] 28 1056 VecStashScatterBegin_Private() > [0]PETSC ERROR: Memory requested 44784088! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 5, Mon Apr 13 09:15:37 > CDT 2009 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: > /tmp/lustre/home/yy2250/local/PETSc/petsc-3.0.0-p5/src/ksp/ksp/examples/tutorials/ttt_5fld/./rpisolve_25_field > on a O-hypre-n named sci-m0n0.scsystem by yy2250 Sat Sep 19 14:37:43 2009 > [0]PETSC ERROR: Libraries linked from > /home/yy2250/local/PETSc/petsc-test-3-p5/O-hypre-nodebug/lib > [0]PETSC ERROR: Configure run at Tue Jul 21 15:19:41 2009 > [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif77 > --with-mpiexec=srun --with-debugging=0 --with-fortran-kernels=generic > --with-shared=0 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c > [0]PETSC ERROR: PetscTrMallocDefault() line 194 in src/sys/memory/mtr.c > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2986 in > src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: MatSeqAIJSetPreallocation() line 2928 in > src/mat/impls/aij/seq/aij.c > [0]PETSC ERROR: MatGetSubMatrices_MPIAIJ_Local() line 1267 in > src/mat/impls/aij/mpi/mpiov.c > [0]PETSC ERROR: MatGetSubMatrices_MPIAIJ() line 787 in > src/mat/impls/aij/mpi/mpiov.c > [0]PETSC ERROR: MatGetSubMatrices() line 5524 in src/mat/interface/matrix.c > [0]PETSC ERROR: MatGetSubMatrix_MPIAIJ() line 3069 in > src/mat/impls/aij/mpi/mpiaij.c > [0]PETSC ERROR: MatGetSubMatrix() line 6212 in src/mat/interface/matrix.c > [0]PETSC ERROR: PCSetUp_FieldSplit() line 285 in > src/ksp/pc/impls/fieldsplit/fieldsplit.c > [0]PETSC ERROR: PCSetUp() line 794 in src/ksp/pc/interface/precon.c > [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: main() line 246 in > src/ksp/ksp/examples/tutorials/rpisolve_25_field.c > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process > 0) > srun: error: task 0: Exited with exit code 1 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... 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