From: Cade Markegard (cmarkega_at_uci.edu)
Date: Mon Jun 04 2012 - 16:57:06 CDT
Hi All,
I am currently trying to run the NAMD 2.9 replica exchange example. I am on
a Rocks Cluster (v. 5.4.3) with all the rolls installed, and the NAMD
binary I am using is from NAMD_2.9_Linux-x86_64. When I run the example
command located in fold_alanin.conf but without the hostfile option (since
I am trying to run this on a single node):
mpirun -np 8 $bindir/namd2 +replicas 8 job0.conf +stdout
output/%d/job0.%d.log
where $bindir is my NAMD 2.9 path, I am currently receiving the error:
*FATAL ERROR: Unknown command-line option +replicas*
Is this the wrong pre-compiled NAMD binary or is there something else that
I am missing here? Could someone please point me to the correct binary? I
rather not have to compile NAMD from the source... Also I really like the
idea of the new MPI based method implemented in 2.9 rather than the TCL
method in 2.8, so when it comes time it will be easier to run a simulation
across multiple nodes.
Any help regarding this subject would be greatly appreciated!
Many thanks,
Cade Markegard
UC Irvine Chemical Engineering Graduate Student
http://compnano.eng.uci.edu
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