[hdf-forum] Parallel hdf5 problem in 1.8.0 through 1.8.2

[Ricardo Fonseca]

Dear all

I'm having problems with parallel hdf5, specifically writing data by  
chunk using collective write. Simply compiling and running the example:

http://www.hdfgroup.org/HDF5/Tutor/examples/parallel/Hyperslab_by_chunk.c

fails with an MPI error:

Fatal error in MPI_Type_free: Invalid datatype, error stack:
MPI_Type_free(145): MPI_Type_free(datatype_p=0x520c20) failed
MPI_Type_free(96).: Cannot free permanent data type [cli_2]: aborting  
job:

I'm using mpich2-1.0.8 under OS X 10.5.5 on a single computer. (the  
same error occurs with openmpi-1.3)

A little investigation shows that the problem occurs in H5Dmpio.c in  
the MPi_Type_Free calls after line 976 in routine  
H5D_link_chunk_collective_io. The problem here is that HDF5 is  
attempting to free a permanent (not derived) datatype (specifically  
MPI_BYTE) which causes MPI to abort.

If I change the example to independent write then the code runs fine.  
Does anyone know if this is an OS X specific problem and/or if there  
are any workarounds?

All the best,
Ricardo

---
Prof. Ricardo Fonseca

GoLP - Grupo de Lasers e Plasmas
Instituto de Plasmas e Fusão Nuclear
Instituto Superior Técnico
Av. Rovisco Pais
1049-001 Lisboa
Portugal

tel: +351 21 8419202
fax: +351 21 8464455
web: http://cfp.ist.utl.pt/golp/

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