[petsc-users] Reading a complex vector from HDF5

[Sajid Ali]

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.
[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
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