I've been running a large number of (independent) QM/MM umbrella sampling
simulations using multisander. I haven't done exhaustive tests, but running
a small (12) or modestly large (108) number of jobs works just fine.
However, using a larger number of jobs (192) results in a few errors:
=== STDERR ===
out of dynamic memory in opal_show_help_yylex()
<MPI_ABORT message omitted for brevity>
[c314-113.ls4.tacc.utexas.edu:11115] 4 more processes have sent help
message help-mpi-api.txt / mpi-abort
[c314-113.ls4.tacc.utexas.edu:11115] Set MCA parameter
"orte_base_help_aggregate" to 0 to see all help / error messages
======
=== STDOUT ===
Error in group input::atommask.f::eval
stack allocation error
======
A typical groupfile entry looks like:
-O -i r0/HEEP_QMMM_US_3.inp -o r0/HEEP_QMMM_US_3.out -p ../input/HEEP.parm7
-c r0/HEEP_QMMM_US_2.rst7 -r r0/HEEP_QMMM_US_3.rst7 -x r0/HEEP_QMMM_US_3.nc
-ref ../equilibration/minimize0.rst7
The only thing here that seems not so smart is that ALL of the trajectories
use the same file for the reference coordinates. Does that sound like it
could be a problem? Does that make any sense in giving rise to the errors
here? Other ideas?
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 11 2013 - 08:00:03 PST
