[Pw_forum] newbie update
akohlmey at cmm.chem.upenn.edu
Thu Mar 5 01:03:27 CET 2009
On Wed, 4 Mar 2009, Lex Kemper wrote:
LK> Hey Axel,
LK> In my case, exporting OMP_NUM_THREADS from my .bashrc was sufficient.
LK> I guess that's not the case everywhere.
right. this happens mostly on batch systems when launching jobs through
libtorque (very convenient, but you don't get a login shell) and
some ssh setups also do not read .profile.
also one has to consider that debian based systems (incl ubuntu),
don't use /bin/bash as /bin/sh, but have a version of /bin/ash as
/bin/sh and that one only reads .profile (which many bash setups
in turn don't) but, of course, not .bashrc.
so it is actually a good idea to verify this, like JR did.
the case of a not exported environment is nasty, because it
will slow down the calculation (if you run 8 mpi tasks on a
2x quad-core node, mkl with spawn 8 threads for each of them),
without the telltale sign on the rank0 node of cpu time being
multiple times larger than the walltime.
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.
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