[petsc-users] Reading a complex vector from HDF5

[Matthew Knepley]

On Fri, Feb 1, 2019 at 3:21 PM Sajid Ali via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Hi,
>
> I'm trying to load a complex vector from hdf5 and I get and I get the
> following error:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: File contains real numbers but PETSc is configured for
> complex. The conversion is not yet implemented. Configure with
> --with-scalar-type=real.
>

When we save complex data in HDF5, we give it an extra dimension for the
two reals. This must be missing to get this message.

  Matt


> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision:
> ba892ce6f06cbab637e31ab2bf33fd996c92d19d  GIT Date: 2019-01-29 05:55:16
> +0100
> [0]PETSC ERROR: ./ex_modify on a  named xrm by sajid Fri Feb  1 14:18:30
> 2019
> [0]PETSC ERROR: Configure options
> --prefix=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/petsc-develop-gh5lollh4dzklppm7kb7wpjtyh4gi4mi
> --with-ssl=0 --download-c2html=0 --download-sowing=0 --download-hwloc=0
> CFLAGS="-march=native -O2" FFLAGS="-march=native -O2"
> CXXFLAGS="-march=native -O2"
> --with-cc=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/mpich-3.3-x4tesuo4sxsomfxns5i26vco7ywojdmz/bin/mpicc
> --with-cxx=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/mpich-3.3-x4tesuo4sxsomfxns5i26vco7ywojdmz/bin/mpic++
> --with-fc=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/mpich-3.3-x4tesuo4sxsomfxns5i26vco7ywojdmz/bin/mpif90
> --with-precision=double --with-scalar-type=complex
> --with-shared-libraries=1 --with-debugging=0 --with-64-bit-indices=0
> COPTFLAGS= FOPTFLAGS= CXXOPTFLAGS=
> --with-blaslapack-lib=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/openblas-0.3.5-heqggft2eii2xktdbyp2zovez2yj6ugd/lib/libopenblas.so
> --with-x=1 --with-clanguage=C --with-scalapack=0 --with-metis=1
> --with-metis-dir=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/metis-5.1.0-mugo6fn7u2nlz72vo4ajlhbba5q7a5jn
> --with-hdf5=1
> --with-hdf5-dir=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/hdf5-1.10.4-pes54zx5fsbgdg2nr7reyopc4zfc43wo
> --with-hypre=0 --with-parmetis=1
> --with-parmetis-dir=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/parmetis-4.0.3-kizvrkoos4ddlfc7jsnatvh3mdk3lgvg
> --with-mumps=0 --with-trilinos=0 --with-cxx-dialect=C++11
> --with-superlu_dist-include=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/superlu-dist-develop-d6dqq3ribpkyoawnwuckbtydgddijj6j/include
> --with-superlu_dist-lib=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/superlu-dist-develop-d6dqq3ribpkyoawnwuckbtydgddijj6j/lib/libsuperlu_dist.a
> --with-superlu_dist=1 --with-suitesparse=0
> --with-zlib-include=/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/zlib-1.2.11-v4lhujkxdy6ukr5ymjxgxcfb2qoo6vf3/include
> --with-zlib-lib="-L/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-8.2.0/zlib-1.2.11-v4lhujkxdy6ukr5ymjxgxcfb2qoo6vf3/lib
> -lz" --with-zlib=1
> [0]PETSC ERROR: #1 PetscViewerHDF5Load() line 1348 in
> /tmp/sajid/spack-stage/spack-stage-hy86Yb/petsc/src/sys/classes/viewer/impls/hdf5/hdf5v.c
> [0]PETSC ERROR: #2 VecLoad_HDF5() line 170 in
> /tmp/sajid/spack-stage/spack-stage-hy86Yb/petsc/src/vec/vec/utils/vecio.c
> [0]PETSC ERROR: #3 VecLoad_Default() line 288 in
> /tmp/sajid/spack-stage/spack-stage-hy86Yb/petsc/src/vec/vec/utils/vecio.c
> [0]PETSC ERROR: #4 VecLoad() line 933 in
> /tmp/sajid/spack-stage/spack-stage-hy86Yb/petsc/src/vec/vec/interface/vector.c
> [0]PETSC ERROR: #5 main() line 132 in
> /raid/home/sajid/packages/xwp_petsc/2d/matter_repeat/ex_modify.c
> [0]PETSC ERROR: No PETSc Option Table entries
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> As per src/vec/vec/examples/tutorials/ex10.c , a complex 1D vector is
> saves as a 2D real valued vector of shape dim,2. I've done the same with my
> data and yet I get the above error. Is there any special precaution I
> should take when making the HDF5 file ?
>
> Thank You,
> Sajid Ali
> Applied Physics
> Northwestern University
>


-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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