DMMG with different
Hi, I'm trying to use DMMG to solve linear Stokes flow discretised with finite elements. Does anyone know how to specify different matrices for the matrix associated with the linear system and the matrix used to construct the preconditioner? Ie, like choosing a different Amat and Bmat with KSPSetOperators(). In looking at DMMGSetKSP(), I don't see how this is possible. DMMG seems to generate the operator B via DMGetMatrix(), and then sets J equal to B. A dirty hack around the problem seemed to be to used PCDMMG, but I think I should be able to define different A and B mat's with DMMG directly. I also noted that PCDMMG does not appear to be a registered PC implementation in petsc 3. Thanks in advance, Dave -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/d98fb9e0/attachment.htm
MatMatMult_MPIDense_MPIDense() works currently?
to. Regards -- F?bio Leite Soares Undergraduate Student of Computing Engineering Centro de Inform?tica - UFPE - BRAZIL -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/b1f5bfcb/attachment.html
Problem with MatMatMultTranspose
Hi, I am just wondering if anything has changed on the status of this feature. Would be great to be able to perform matrix vector multiplications on complex Hermitian matrices by only providing one half of the matrix. Regards, Niall. zhifeng sheng wrote: Hi, you mean the conjugate transpose for complex matrix is not supported? then how can you implement the iterative solvers for complex matrices? because, some iterative solvers need it. Thanks Best regards Hong Zhang wrote: Zhifeng, We do not have support for matrix operations on Hermitian matrix yet. Hong On Mon, 20 Oct 2008, zhifeng sheng wrote: Dear all I am using this MatMatMultTranspose function for complex matrices, but it seems to be doing something weird. for instance, if I have complex matrix A, and I compute A^T*A with this function, it does not generate a Hermitian http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatIsHermitian.html matrix. I am thinking that maybe the function take the transpose of A instead of the conjugate transpose Do you know how I can get an A^H*A instead of A^T*A for complex matrices? Thanks a lot Best regards Zhifeng http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatIsHermitian.html
Problem with MatMatMultTranspose
On Thu, Sep 17, 2009 at 12:44 PM, Niall Moran nmoran at thphys.nuim.ie wrote: Hi, I am just wondering if anything has changed on the status of this feature. Would be great to be able to perform matrix vector multiplications on complex Hermitian matrices by only providing one half of the matrix. It is not curently in the todo list since we have only had one request. It seems like it would just take being careful about the complex case for SBAIJ if you would like the try the implementation. We can answer questions. Thanks, Matt Regards, Niall. zhifeng sheng wrote: Hi, you mean the conjugate transpose for complex matrix is not supported? then how can you implement the iterative solvers for complex matrices? because, some iterative solvers need it. Thanks Best regards Hong Zhang wrote: Zhifeng, We do not have support for matrix operations on Hermitian matrix yet. Hong On Mon, 20 Oct 2008, zhifeng sheng wrote: Dear all I am using this MatMatMultTranspose function for complex matrices, but it seems to be doing something weird. for instance, if I have complex matrix A, and I compute A^T*A with this function, it does not generate a Hermitian http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatIsHermitian.html matrix. I am thinking that maybe the function take the transpose of A instead of the conjugate transpose Do you know how I can get an A^H*A instead of A^T*A for complex matrices? Thanks a lot Best regards Zhifeng http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Mat/MatIsHermitian.html -- 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... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/88bdce57/attachment.htm
MatMatMult_MPIDense_MPIDense() works currently?
: [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 rank 1 in job 1 hpcin08_34697 caused collective abort of all ranks exit status of rank 1: return code 59 rank 0 in job 1 hpcin08_34697 caused collective abort of all ranks exit status of rank 0: return code 59 I tried to execute the ex123.c example and I did not succeeded to. Regards -- F?bio Leite Soares Undergraduate Student of Computing Engineering Centro de Inform?tica - UFPE - BRAZIL -- 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... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/42e8ae3e/attachment-0001.htm
memory reporting question
Hi, I am wondering whether the -memory_info option and the PetscMemoryGetMaximumUsage() call report different things. The reason i am asking is because i call the PetscMemoryGetCurrentUsage fcn in my code and it shows: 5.25558e+08. At the end of the run the -memory_info option reports: max process malloc()'ed: 4.00524e+08 max petsc malloc()'ed: 1.15254e+08. So i am a little confused by those numbers unless the fcn call is the more complete picture (as said on the manual page) I guess then my question is whether the -memory_info corresponds to the PetscMalloc* fcns? thanks matt -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/d637ac28/attachment.htm
memory reporting question
I forgot to mention: Some of the memory allocated in the code is from non-petsc structures. Not sure if that is important. Another question: The number reported by -memory_info, is it in bytes? thanks matt On Thursday 17 September 2009, you wrote: Hi, I am wondering whether the -memory_info option and the PetscMemoryGetMaximumUsage() call report different things. The reason i am asking is because i call the PetscMemoryGetCurrentUsage fcn in my code and it shows: 5.25558e+08. At the end of the run the -memory_info option reports: max process malloc()'ed: 4.00524e+08 max petsc malloc()'ed: 1.15254e+08. So i am a little confused by those numbers unless the fcn call is the more complete picture (as said on the manual page) I guess then my question is whether the -memory_info corresponds to the PetscMalloc* fcns? thanks matt -- next part -- An HTML attachment was scrubbed... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/375be5a2/attachment.htm
memory reporting question
On Thu, Sep 17, 2009 at 6:04 PM, Matt Funk mafunk at nmsu.edu wrote: Hi, I am wondering whether the -memory_info option and the PetscMemoryGetMaximumUsagehttp://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/Sys/PetscMemoryGetMaximumUsage.html#PetscMemoryGetMaximumUsage() call report different things. The reason i am asking is because i call the PetscMemoryGetCurrentUsage fcn in my code and it shows: 5.25558e+08. This call get_rusage(), so it gives you the entire process size. At the end of the run the -memory_info option reports: max process malloc()'ed: 4.00524e+08 This is a sampling of rusage every time an object is destroyed. max petsc malloc()'ed: 1.15254e+08. This is all the memory malloced using PetscMalloc() summed. Matt So i am a little confused by those numbers unless the fcn call is the more complete picture (as said on the manual page) I guess then my question is whether the -memory_info corresponds to the PetscMalloc* fcns? thanks matt -- 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... URL: http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20090917/e13dc089/attachment.htm
MatMatMult_MPIDense_MPIDense() works currently?
Fabio, Did you install plapack with petsc? Hong On Thu, 17 Sep 2009, Matthew Knepley wrote: Give us the exact command line you use for ex123 and the error output. Send to petsc-maint. Matt On Thu, Sep 17, 2009 at 12:37 PM, Fabio Leite Soares fls2 at cin.ufpe.brwrote: Hi everyone, I have the same problem and I don't know how to fix it. I need to multiply two mpi dense matrices using the BLAS3 routines. I have tried the MatMatMult_MPIDense_MPIDense() function but the console shows this message: [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/petsc-as/documentation/troubleshooting.html#Signal[0]PETSChttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal%5B0%5DPETSCERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 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] MatMPIDenseCopyToPlapack line 1028 src/mat/impls/dense/mpi/mpidense.c [0]PETSC ERROR: [0] MatMatMultNumeric_MPIDense_MPIDense line 1078 src/mat/impls/dense/mpi/mpidense.c [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 8, Fri Aug 21 14:02:12 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: ./mult on a linux-gnu named hpcin08 by hpcin Thu Sep 17 14:28:28 2009 [0]PETSC ERROR: Libraries linked from /home/hpcin/soft/petsc-3.0.0-p8/linux-gnu-c-debug/lib [0]PETSC ERROR: Configure run at Wed Sep 16 17:06:08 2009 [0]PETSC ERROR: Configure options --download-f-blas-lapack=1 --download-plapack --with-mpi-dir=/usr/local/bin/mpich2-1.1.1p1 --with-scalar-type=real --with-precision=double --with-shared=0 [0]PETSC ERROR: --[1]PETSC ERROR: [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[1]PETSChttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal%5B1%5DPETSCERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [1]PETSC ERROR: likely location of problem given in stack below [1]PETSC ERROR: - Stack Frames [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [1]PETSC ERROR: INSTEAD the line number of the start of the function [1]PETSC ERROR: is given. [1]PETSC ERROR: [1] MatMPIDenseCopyToPlapack line 1028 src/mat/impls/dense/mpi/mpidense.c [1]PETSC ERROR: [1] MatMatMultNumeric_MPIDense_MPIDense line 1078 src/mat/impls/dense/mpi/mpidense.c [1]PETSC ERR-- [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 OR: - Error Message [1]PETSC ERROR: Signal received! [1]PETSC ERROR: [1]PETSC ERROR: Petsc Release Version 3.0.0, Patch 8, Fri Aug 21 14:02:12 CDT 2009 [1]PETSC ERROR: See docs/changes/index.html for recent updates. [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [1]PETSC ERROR: See docs/index.html for manual pages. [1]PETSC ERROR: [1]PETSC ERROR: ./mult on a linux-gnu named hpcin-desktop by hpcin Thu Sep 17 14:28:27 2009 [1]PETSC ERROR: Libraries linked from /home/hpcin/soft/petsc-3.0.0-p8/linux-gnu-c-debug/lib [1]PETSC ERROR: Configure run at Tue Sep 15 15:57:39 2009 [1]PETSC ERROR: Configure options --download-plapack=1 --download-f-blas-lapack=1 --with-mpi-dir=/usr/local/bin/mpich2-1.1.1p1 --with-scalar-type=real
