[Users] Meeting Minutes for 2014-11-03

Roland Haas roland.haas at physics.gatech.edu
Mon Nov 3 16:32:35 CST 2014

Hello all,

> * GRHydro failing tests on stampede: Roland to check what is going on
> and to fix
It seems that this is not really a GRHydro issue. The code crashes in
HDF5's init routine (called once whenever any other HDF5 routine is
used). GRHydro may just trigger this because it relies on EOS_Omni which
uses HDF5.

I have not yet fully cornered the culprit but there are some iffy things
in the current stampede configuration files. We load the petsc module
and petsc normally requires parallel HDF5 (which rules out the C++
interface) but I am not sure if our own built hdf5 library enables this
or uses the correct MPI compiler. Also envsetup is rather sparse and
loads the intel 13 compiler and petsc but does not unload any other
potentially conflicting packages.

Switching the BUILD to /opt/apps/intel13/mvapich2_1_9/phdf5/1.8.9 and
loading the phdf5 module produces and executable that can run the tests.
It right now fails in the hdf5 utilities since they do not find MPI
anymore (which is odd since HDF5 should have and OPTIONAL MPI in
configure.ccl for exactly this reason).

So possible solutions may be:

(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

I will be offline for the next 6 hours, so if someone else wants to give
it a try, feel free to do so.


My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from http://keys.gnupg.net.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 181 bytes
Desc: OpenPGP digital signature
Url : http://lists.einsteintoolkit.org/pipermail/users/attachments/20141103/33561126/attachment.bin 

More information about the Users mailing list