[petsc-users] Configure/make with "--download-hdf5" or "--with-hdf5-dir=" crashes

[Matthew Knepley]

On Mon, Sep 1, 2014 at 6:18 AM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:

>
>
> On 01. sep. 2014 12:51, Matthew Knepley wrote:
> > On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <asmund.ervik at ntnu.no>
> wrote:
> >
> >>
> >> Subsequently I installed HDF5 v. 1.8.12 using my OS package manager and
> >> then tried to configure with "--with-hdf5
> >> --with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time both
> >> configure and make were successful, but "make test" fails with loads of
> >> undefined references to PETSc HDF5 stuff (see below). configure.log and
> >> make.log attached also for this case (error-with-hdf5.tar.gz)
> >>
> >
> > It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the
> log.
> > However, it
> > should have. We have been trying to understand why Make behaves in a bad
> way
> > after configuration failure. It should go away with make clean and
> another
> > make.
>
> Thanks Matt, make clean and then make did result in make test passing
> all tests.
>
> However, I am still unable to use HDF5 functionality. When I compile and
> run e.g. vec/vec/examples/tutorials/ex10.c it works fine with binary
> output, but with HDF5 I get the error message below.
>
> I'm guessing this is some incompatibility between the various MPI, HDF5
> and PETSc versions, i.e. that the HDF5 from my OS is not using the same
> MPI as PETSc. Is it simple to edit something in PETSc and have
> "./configure --download-hdf5" get the most recent HDF5 library which
> compiles on my machine?
>

Yes, I cannot reproduce, so it must be something like that. Can you
reconfigure
using the --download version?

  Thanks,

     Matt


> Error message:
> $ ./ex10 -hdf5
> Vec Object:Test_Vec 1 MPI processes
>   type: seq
> 0
> 1
> 2
> 3
> 4
> 5
> 6
> 7
> 8
> 9
> 10
> 11
> 12
> 13
> 14
> 15
> 16
> 17
> 18
> 19
> writing vector in hdf5 to vector.dat ...
> [0]PETSC ERROR: #1 PetscViewerFileSetName_HDF5() line 81 in
> /opt/petsc/optim_gfortran/src/sys/classes/viewer/impls/hdf5/hdf5v.c
> [0]PETSC ERROR: #2 PetscViewerFileSetName() line 624 in
> /opt/petsc/optim_gfortran/src/sys/classes/viewer/impls/ascii/filev.c
> [0]PETSC ERROR: #3 PetscViewerHDF5Open() line 163 in
> /opt/petsc/optim_gfortran/src/sys/classes/viewer/impls/hdf5/hdf5v.c
> [0]PETSC ERROR: #4 main() line 66 in
> /opt/petsc/optim_gfortran/src/vec/vec/examples/tutorials/ex10.c
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> HDF5: infinite loop closing library
>
>
> D,T,AC,FD,P,FD,P,FD,P,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD
>
> Regards,
> Åsmund
>
>


-- 
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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