Matt, thanks for the confirmation. Yan
On Sat, Sep 19, 2009 at 3:24 PM, Matthew Knepley <knepley at gmail.com> wrote: > 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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