I'm getting plapack errors in "external library" with MatMatMult_MPIDense_MPIDense
with plapack? How is memory handled for a matrix of type MATMPIDENSE? Are all NxN entries allocated and ready for use at time of creation? or do I have to MatInsertValues then Assemble to be ready to use a matrix? [0]PETSC ERROR: --------------------- Error Message ---------------------------- -------- [0]PETSC ERROR: Error in external library! [1]PETSC ERROR: [0]PETSC ERROR: --------------------- Error Message ------------ ------------------------ [1]PETSC ERROR: Error in external library! Due to aparent bugs in PLAPACK,this is not currently supported! [1]PETSC ERROR: Due to aparent bugs in PLAPACK,this is not currently supported! [1]PETSC ERROR: ---------------------------------------------------------------- -------- [1]PETSC ERROR: Petsc Release Version 3.0.0, Patch 4, Fri Mar 6 14:46:08 CST 20 09 [1]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. On Thu, 12 Mar 2009, Hong Zhang wrote: > >>> >>> Is MatCreateMPIDense the recommended matrix type to interface w/ mumps ? >>> Does it use a sparse direct storage or allocate the full n x n matrix? >> >> >> No, MUMPS is "sparse direct" so it uses MPIAIJ. > > For mpi dense matrix, you can use plapack > > Hong >> >> >>> >>> df >>> >>> On Thu, 12 Mar 2009, Matthew Knepley wrote: >>> >>> You can try using a sparse direct solver like MUMPS instead of PETSc LU. >>>> >>>> Matt >>>> >>>> On Thu, Mar 12, 2009 at 9:17 AM, David Fuentes <fuentesdt at gmail.com> >>>> wrote: >>>> >>>> Thanks Hong, >>>>> >>>>> The complete error message is attached. I think I just had too big >>>>> of a matrix. The matrix i'm trying to factor is 327680 x 327680 >>>>> >>>>> >>>>> [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]PETSC ERROR: Memory allocated 2047323584 Memory used by process >>>>> 2074058752 >>>>> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. >>>>> [0]PETSC ERROR: Memory requested 1258466480! >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 2, Wed Jan 14 >>>>> 22:57:05 >>>>> CST 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: ./RealTimeImaging on a gcc-4.1.2 named DIPWS019 by >>>>> dfuentes >>>>> Wed Mar 11 20:30:37 2009 >>>>> [0]PETSC ERROR: Libraries linked from >>>>> /usr/local/petsc/petsc-3.0.0-p2/gcc-4.1.2-mpich2-1.0.7-dbg/lib >>>>> [0]PETSC ERROR: Configure run at Sat Jan 31 06:53:09 2009 >>>>> [0]PETSC ERROR: Configure options --download-f-blas-lapack=ifneeded >>>>> --with-mpi-dir=/usr/local --with-matlab=1 --with-matlab-engine=1 >>>>> --with-matlab-dir=/usr/local/matlab2007a --CFLAGS=-fPIC --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: PetscFreeSpaceGet() line 14 in src/mat/utils/freespace.c >>>>> [0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 381 in >>>>> src/mat/impls/aij/seq/aijfact.c >>>>> [0]PETSC ERROR: MatLUFactorSymbolic() line 2289 in >>>>> src/mat/interface/matrix.c >>>>> [0]PETSC ERROR: KalmanFilter::DirectStateUpdate() line 456 in >>>>> unknowndirectory/src/KalmanFilter.cxx >>>>> [0]PETSC ERROR: GeneratePRFTmap() line 182 in >>>>> unknowndirectory/src/MainDriver.cxx >>>>> [0]PETSC ERROR: main() line 90 in unknowndirectory/src/MainDriver.cxx >>>>> application called MPI_Abort(MPI_COMM_WORLD, 55) - process 0[unset]: >>>>> aborting job: >>>>> application called MPI_Abort(MPI_COMM_WORLD, 55) - process 0 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, 12 Mar 2009, Hong Zhang wrote: >>>>> >>>>> >>>>> David, >>>>>> >>>>>> I do not see any problem with the calling sequence. >>>>>> >>>>>> The memory is determined in MatLUFactorSymbolic(). >>>>>> Does your code crashes within MatLUFactorSymbolic()? >>>>>> Please send us complete error message. >>>>>> >>>>>> Hong >>>>>> >>>>>> On Wed, 11 Mar 2009, David Fuentes wrote: >>>>>> >>>>>> >>>>>> Hello, >>>>>>> >>>>>>> I have a sparse matrix, A, with which I want to solve multiple right >>>>>>> hand >>>>>>> sides >>>>>>> with a direct solver. Is this the correct call sequence ? >>>>>>> >>>>>>> >>>>>>> MatGetFactor(A,MAT_SOLVER_PETSC,MAT_FACTOR_LU,&Afact); >>>>>>> IS isrow,iscol; >>>>>>> MatGetOrdering(A,MATORDERING_ND,&isrow,&iscol); >>>>>>> MatLUFactorSymbolic(Afact,A,isrow,iscol,&info); >>>>>>> MatLUFactorNumeric(Afact,A,&info); >>>>>>> MatMatSolve(Afact,B,X); >>>>>>> >>>>>>> >>>>>>> my solve keeps running out of memory >>>>>>> >>>>>>> "[0]PETSC ERROR: Memory requested xxx!" >>>>>>> >>>>>>> >>>>>>> is this in bytes? I can't tell if the problem I'm trying to solve >>>>>>> is too large form my machine or if I just have bug in the call >>>>>>> sequence. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> thank you, >>>>>>> David Fuentes >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >>>> -- >>>> 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 >>>> >>>> >> >> >> -- >> 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 >> >
