[petsc-users] hdf5 libraries

[George Pau]

Attached is the configure.log for the case where --download-hdf5 failed.

For the run time error, the IS has only 298.8M entries (from ISGetSize).
So, it shouldn't need a 64 bit integer.  In addition, I was able to get the
right output when petsc builds its own hdf5.  In addition, I don't have an
issue as well if I am using the Petsc Binary Viewer.   If this is really an
issue with NERSC's libraries, then I will work with NERSC to see if they
can help me figure out what is wrong.

Thanks
George


On Sun, Jul 3, 2016 at 3:13 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    Please send $PETSC_ARCH/lib/petsc/conf/configure.log for both cases to
> petsc-maint at mcs.anl.gov.
>
>    The fact that it kicks in for very large problems and reports a
> negative block length is indicative of a 64 bit integer not fitting into a
> 32 bit integer location.
>
>    Barry
>
>
> > On Jul 2, 2016, at 5:53 PM, George Pau <gpau at lbl.gov> wrote:
> >
> > 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/
>
>


-- 
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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