[petsc-users] SuperLU MPI-problem

Mahir.Ulker-Kaustell at tyrens.se Mahir.Ulker-Kaustell at tyrens.se
Mon Jul 20 10:44:01 CDT 2015

Ah, of course. Here it is:

Malloc fails for Lnzval_bc_ptr[*][] at line 626 in file zdistribute.c
Malloc fails for Lnzval_bc_ptr[*][] at line 626 in file zdistribute.c
col block 797 col block 1518 Malloc fails for Lnzval_bc_ptr[*][] at line 626 in file zdistribute.c
col block 6369 -------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X 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] SuperLU_DIST:pzgssvx_ABglobal line 405 /packages/petsc-3.6.0/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [0] MatLUFactorNumeric_SuperLU_DIST line 282 /packages/petsc-3.6.0/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c
[0]PETSC ERROR: [0] MatLUFactorNumeric line 2937 /packages/petsc-3.6.0/src/mat/interface/matrix.c
[0]PETSC ERROR: [0] PCSetUp_LU line 99 /packages/petsc-3.6.0/src/ksp/pc/impls/factor/lu/lu.c
[0]PETSC ERROR: [0] PCSetUp line 944 /packages/petsc-3.6.0/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: [0] KSPSetUp line 247 /packages/petsc-3.6.0/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: User provided function() line 0 in  unknown file (null)
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

 Process name: [[40547,1],3]
  Exit code:    255


Mahir Ülker-Kaustell, Kompetenssamordnare, Brokonstruktör, Tekn. Dr, Tyréns AB
010 452 30 82, Mahir.Ulker-Kaustell at tyrens.se

From: Matthew Knepley [mailto:knepley at gmail.com]
Sent: den 20 juli 2015 17:35
To: Ülker-Kaustell, Mahir
Cc: petsc-users
Subject: Re: [petsc-users] SuperLU MPI-problem

We cannot say anything without the full error message.


On Mon, Jul 20, 2015 at 9:38 AM, Mahir.Ulker-Kaustell at tyrens.se<mailto:Mahir.Ulker-Kaustell at tyrens.se> <Mahir.Ulker-Kaustell at tyrens.se<mailto:Mahir.Ulker-Kaustell at tyrens.se>> wrote:
Dear Petsc-Users,

I am trying to use PETSc to solve a set of linear equations arising from Naviers equation (elastodynamics) in the frequency domain.
The frequency dependency of the problem requires that the system

                             [-omega^2M + K]u = F

where M and K are constant, square, positive definite matrices (mass and stiffness respectively) is solved for each frequency omega of interest.
K is a complex matrix, including material damping.

I have written a PETSc program which solves this problem for a small (1000 degrees of freedom) test problem on one or several processors, but it keeps crashing when I try it on my full scale (in the order of 10^6 degrees of freedom) problem.

The program crashes at KSPSetUp() and from what I can see in the error messages, it appears as if it consumes too much memory.

I would guess that similar problems have occurred in this mail-list, so I am hoping that someone can push  me in the right direction…


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
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