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

[Åsmund Ervik]

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?

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 473 bytes
Desc: OpenPGP digital signature
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20140901/e7d18132/attachment.pgp>