[petsc-users] eps_target malloc issue

[jifeng zhao]

Thank you all for the insights.

I tried to add MatSetOption(mat, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE).
It does solve the malloc error. However there appears to be another error:

In addition, 66324 appears to be the number of index that is assigned to
each processor.

Any more insights? Thanks a lot!

PETSC ERROR: Argument out of range!
PETSC ERROR: *Column too large: col 935748 max 66324!*
PETSC ERROR:
------------------------------------------------------------------------
PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014
PETSC ERROR: See docs/changes/index.html for recent updates.
PETSC ERROR: See docs/faq.html for hints about trouble shooting.
PETSC ERROR: See docs/index.html for manual pages.
PETSC ERROR:
------------------------------------------------------------------------
PETSC ERROR: eigen_solver20 on a arch-linux2-c-debug named qnode4091 by
jzh953 Sun Jul 27 15:17:28 2014
PETSC ERROR: Libraries linked from /software/petsc/3.4.4/lib
PETSC ERROR: Configure run at Tue Jul  8 14:20:27 2014
]PETSC ERROR: Configure options --prefix=/software/petsc/3.4.4
--with-blas-lib=/software/lapack/3.5.0/lib/libblas.so
--with-lapack-lib=/software/lapack/3.5.0/liblapack.so
--with-hdf5-dir=/software/hdf5/1.8.12 with-boost=1
--with-boost-dir=/software/hdf5/1.8.12 --with-fftw=1
--with-fftw-dir=/software/FFTW/3.3.3-gcc-threads
--with-valgrind-dir=/software/valgrind/3.8.1 --with-netcdf=1
--with-netcdf-dir=/software/netCDF/4.2 --with-hdf5=1 --with-debugging=1
--with-mpi-dir=/software/mpi/openmpi-1.6.3-gcc-4.6.3-trq4
--download-scalapack --download-mumps --download-hypre --download-parmetis
--download-metis

PETSC ERROR:
------------------------------------------------------------------------
PETSC ERROR: MatSetValues_SeqSBAIJ() line 986 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/impls/sbaij/seq/sbaij.c
PETSC ERROR: MatDisAssemble_MPISBAIJ() line 356 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/impls/sbaij/mpi/mmsbaij.c
PETSC ERROR: MatSetValues_MPISBAIJ() line 213 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/impls/sbaij/mpi/mpisbaij.c
PETSC ERROR: MatSetValues() line 1106 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/interface/matrix.c
PETSC ERROR: MatAXPY_Basic() line 78 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/utils/axpy.c
PETSC ERROR: MatAXPY_MPISBAIJ() line 1398 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/impls/sbaij/mpi/mpisbaij.c
PETSC ERROR: MatAXPY() line 39 in
/hpc/software/sources/builds/petsc-3.4.4/src/mat/utils/axpy.c
PETSC ERROR: STMatGAXPY_Private() line 375 in src/st/interface/stsolve.c
PETSC ERROR: STSetUp_Sinvert() line 138 in src/st/impls/sinvert/sinvert.c
PETSC ERROR: STSetUp() line 294 in src/st/interface/stsolve.c
PETSC ERROR: EPSSetUp() line 215 in src/eps/interface/setup.c
PETSC ERROR: EPSSolve() line 90 in src/eps/interface/solve.c
PETSC ERROR:
--------------------------------------------------------------------------


On Sat, Jul 26, 2014 at 12:35 PM, Jose E. Roman <jroman at dsic.upv.es> wrote:

> The problem is that your stiffness and mass matrices have different
> nonzero pattern.
>
> The -eps_target configuration computes a MatAXPY on the first matrix
> (stiffness), so MatSetOption(mat,
> MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) could be called on this matrix,
> as Barry suggests.
>
> Another workaround would be to force both of them having the same nonzero
> pattern, maybe using MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_FALSE).
>
> Also, this problem would not appear with target=0.0.
>
> See details on section 3.4.2 of SLEPc's users guide.
>
> Jose
>
>
>
> El 26/07/2014, a las 19:04, Barry Smith escribió:
>
> >
> >  We need the entire error message. A matrix is being formed that wasn’t
> fully preallocated for so you need to determine which matrix and make sure
> either 1) it gets fully preallocated or 2) MatSetOption(mat,
> MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE) is called on the matrix
> >
> >  Barry
> >
> > On Jul 26, 2014, at 10:34 AM, jifeng zhao <
> jifengzhao2015 at u.northwestern.edu> wrote:
> >
> >> Hello all,
> >>
> >> I am trying to use ex7 to solve series of generalized problem. The
> running commands are:
> >>
> >> ./ex7 -f1 petsc_stiff19.dat -f2 petsc_mass19.dat -mat_type sbaij
> -eps_gen_hermitian -eps_type krylovschur -eps_smallest_magnitude.
> -eps_monitor_conv -st_k    sp_type bcgs -st_pc_type bjacobi -st_sub_pc_type
> icc -st_ksp_rtol 1.e-4 -eps_tol 1.e-4 -eps_nev 40 -st_type sinvert
> >>
> >> It works fine, but when my problem contains zero eigenvalue, it fails
> to converge.
> >>
> >> Supposedly, I should use eps_target -0.1 instead of
> eps_smallest_magnitude. However if eps_target is used, I run into a memory
> issue:
> >>
> >> PETSC ERROR: --------------------- Error Message
> ------------------------------------
> >> PETSC ERROR: Argument out of range!
> >> PETSC ERROR: New nonzero at (0,6) caused a malloc!
> >> PETSC ERROR:
> ------------------------------------------------------------------------
> >>
> >> Does anybody know how to solve this? Thanks!
> >>
> >> Jifeng Zhao
> >> PhD candidate at Northwestern University, US
> >> Theoretical and Applied Mechanics Program
> >
>
>


-- 
Jifeng Zhao
PhD candidate at Northwestern University, US
Theoretical and Applied Mechanics Program
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