[petsc-users] hdf5 libraries

[George Pau]

Hi,

I am trying to debug an error I am getting when using the HDF5 viewer.  I
am working on NERSC systems, and they have a precompiled hdf5 (module
cray-hdf5-parallel).  When I linked petsc libraries to their hdf5
libraries, it gives the following error at run time when I tried to do a
ISView:

Rank 0 [Sat Jul  2 15:34:48 2016] [c0-0c0s15n0] Fatal error in
MPI_Type_create_hindexed: Invalid argument, error stack:
MPI_Type_create_hindexed(150): MPI_Type_create_hindexed(count=1,
array_of_blocklengths=0x478b1e0, array_of_displacements=0x478b200,
MPI_BYTE, newtype=0x7fffffff3598) failed
MPI_Type_create_hindexed(98).: Invalid value for blocklength, must be
non-negative but is -1927660792

The hdf5 version on NERSC is 1.8.16 but the version that PETSc downloaded
when using --download-hdf5 is 1.8.12. So, could the error be due to this
difference? I also see the above error only when the length of the IS is
big (tested for about 200M total entries, using 1024 cores).

I don't have these errors when I used --download-hdf5=1 during configure
step.  However, while I was able to use --download-hdf5=1 on Edison, PETSc
was not able to compile hdf5 libraries properly on Cori.  The OS of Cori
was recently updated.  My primary interest in trying to use the version
provided by NERSC is to see if there is any improvement in the IO
performance.

Thanks,
George


-- 
George Pau
Earth Sciences Division
Lawrence Berkeley National Laboratory
One Cyclotron, MS 74R316C
Berkeley, CA 94720

(510) 486-7196
gpau at lbl.gov
http://esd.lbl.gov/profiles/george-shu-heng-pau/
<http://esd.lbl.gov/about/staff/georgepau/>
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