[petsc-users] eps_target malloc issue

[jifeng zhao]

Hello everyone,

Are there more ideas why when using MatSetOption(mat,
MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE), the processor seems trying to
access elements that are out of local range?

Anybody can help? Thank you so much.

Best regards,
Jifeng Zhao


On Sun, Jul 27, 2014 at 3:37 PM, jifeng zhao <
jifengzhao2015 at u.northwestern.edu> wrote:

> 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
>



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