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

[Ricardo Fonseca]

Dear all

The problem is indeed apple specific, namely the config/apple file.  
Just adding :

hdf5_mpi_complex_derived_datatype_works='no'

at the end of this file fixes it.

The problem is that the mpi complex derived types that hdf5 tries to  
use are not supported by mpich (and openmpi). The linux config files  
know this and automatically set the above flag. The apple config file  
didn't, so hdf5 tries to call H5D_link_chunk_collective_io (which  
breaks) rather than H5D_multi_chunk_collective_io_no_opt (which works).

I hope this helps other people trying to use parallel hdf5 under OS X.

All the best,
Ricardo

P.S -> (rob) Thanks for the input, this work is actually in  
preparation for a BlueGene system. Could you tell me if that flag is  
set on your configuration? If you just look into $H5DIR/include/ 
H5pubconf.h around line 431 you can check the definition of the  
H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS macro.


web: http://cfp.ist.utl.pt/golp/

On Mar 5, 2009, at 21:13 , Robert Latham wrote:

> On Thu, Mar 05, 2009 at 06:13:24PM +0000, Ricardo Fonseca wrote:
>> 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)
>
> Hi Ricardo.  I ran this on BlueGene, which is roughly based on 1.0.8,
> compiled against HDF5-1.8.2 and did not get this error.   I hope other
> OS X users can report their experiences.
>
> ==rob
>
> -- 
> Rob Latham
> Mathematics and Computer Science Division    A215 0178 EA2D B059 8CDF
> Argonne National Lab, IL USA                 B29D F333 664A 4280 315B

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