From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sun May 07 2006 - 15:49:40 CDT
Dear list,
We have a cluster configured with clustermatic and we are using the NAMD
2.6b1 precompiled binaries for clustermatic.
I would like to start multiple simulations and for that I'm using the
flags "++startpe" and "++endpe" to specify the range of nodes to be used.
However, the master node is always included per default and to avoid that
I'm trying to use the flag "++skipmaster". Unfortunately, this gives me
the error "FATAL ERROR: chdir() failed!". By browsing the NAMD mailing
list archives I found the following message:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1841.html
stating that in order to skip the master node the filesystem needs to be
NFS mounted. How do you do that on a cluster running clustermatic? The
slave nodes have only a very basic operating system which is booted from a
CD. Each node has a harddrive but it is not used. How easy is it to export
the home directories to the slaves on such a system? Any hints how to do
that would be appreciated.
Thanks a lot,
Gianluca
-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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