[Users] Meeting Minutes for 2014-11-03

[Erik Schnetter]

If PETSc is not correctly configured on Stampede, then we should not
use it. I am now trying to build it ourselves instead.

-erik

On Tue, Nov 4, 2014 at 3:35 AM, Roland Haas
<roland.haas at physics.gatech.edu> wrote:
> Hello all,
>
> It's actually worse than that. TACC's petsc module is linked against
> their phdf5 library (but the module does not require it so module load
> petsc does not automatically pull it in or complain if a conflicting
> version is loaded), ie:
>
> rhaas at login4:~/work/ET_trunk/simfactory$ module list
> Currently Loaded Modules:
> 1) TACC-paths 3) cluster-paths 5) cluster 7) intel/13.1.1.163
> 9) petsc/3.5
> 2) Linux      4) xalt/0.4.6    6) TACC    8) mvapich2/1.9a2
> 10) papi/5.3.0 (m)
>
> rhaas at login4:~/work/ET_trunk/simfactory$ ldd
> $TACC_PETSC_LIB/libpetsc.so.3.5 | grep hdf5
>         libhdf5_fortran.so.7 =>
> /opt/apps/intel13/mvapich2_1_9/phdf5/1.8.9/lib/libhdf5_fortran.so.7
> (0x00002ae35eb38000)
>         libhdf5_hl.so.7 =>
> /opt/apps/intel13/mvapich2_1_9/phdf5/1.8.9/lib/libhdf5_hl.so.7
> (0x00002ae35ed7c000)
>         libhdf5.so.7 =>
> /opt/apps/intel13/mvapich2_1_9/phdf5/1.8.9/lib/libhdf5.so.7
> (0x00002ae35efaf000)
>         libsz.so.2 =>
> /opt/apps/intel13/mvapich2_1_9/phdf5/1.8.9/lib/libsz.so.2
> (0x00002ae364089000)
>
> so of
>> (a) disable petsc
>> (b) use the phdf5 module (this can be annoying since then every utility
>> that uses hdf5 uses ibrun and creates a unique ibrun/slurm control file
>> in $HOME/.slurm that is *not* ever deleted and can lead to quota
>> violations due to number of files in $HOME)
>> (c) check our own compiled HDF5 to make sure it builds the parallel
>> version if requested (no option to request this exists yet)
>> (d) (if this is possible) build our own petsc without parallel hdf5 support
> (c) is no longer viable since there'd be a comflict between the version
> petsc was compiled with and our hdf5 version (even if we can get the
> dynamic linker to use "our" version which we don't want to since we don
> not want to build dynamic libraries).
>
> Yours,
> Roland
>
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>
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-- 
Erik Schnetter <schnetter at cct.lsu.edu>
http://www.perimeterinstitute.ca/personal/eschnetter/