From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Oct 12 2011 - 10:08:27 CDT
Neelanjana,
Two things stand out:
1) Is MPI installed?
2) mympiexec needs to be in the PATH that exists on your compute nodes.
It might be helpful for you to also contact your sysadmin for assistance
with the installation and insure all pre-NAMD requirements are
available.
Best,
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-0329 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 Neelanjana Sengupta <senguptan_at_gmail.com> writes: > Date: Wed, 12 Oct 2011 12:59:16 +0530 > From: Neelanjana Sengupta <senguptan_at_gmail.com> > To: Matteo Rotter <matteo.rotter_at_uniud.it> > Cc: NAMD <namd-l_at_ks.uiuc.edu> > Subject: Re: namd-l: rsh not working > > Hi Matteo and others, > > I have actually been trying out things from the notes. > > Since the ++mpiexec option had worked in a previous cluster (but it isn't > working here), here's one thing I tried: > > Create a mympiexec in home directory: > *#! /bin/bash > shift; shift; exec ibrun $** > > And: > *charmrun +p12 namd2 ++verbose ++mpiexec ++remote-shell > /home1/nsengupta/mympiexec min01.inp > min01.out* > > I now get: > *Charmrun> charmrun started... > Charmrun> mpiexec started > Charmrun> node programs all started > Charmrun> Couldn't find mpiexec program '/home1/nsengupta/mympiexec'! > Charmrun> error 0 attaching to node: > Timeout waiting for node-program to connect* > > The error message is similar if I do not give an mpiexec file; I get *Charmrun> > Couldn't find mpiexec program 'mpiexec'!* > > Can someone please help? > > Thanks, > Neelanjana > > On Wed, Oct 12, 2011 at 12:07 AM, Matteo Rotter <matteo.rotter_at_uniud.it>wrote: > > > read the notes > > > > Quoting Neelanjana Sengupta <senguptan_at_gmail.com>: > > > > Dear NAMD experts, > >> > >> We have installed NAMD2.8 in our cluster (Intel Xeon X5670 processors; > >> running RHEL5.0), which presently has rsh enabled on each node. I have a > >> .nodelist file of this type in my home directory: > >> *group main > >> > >> host cn001 > >> host cn002 > >> . > >> .* > >> > >> > >> My submit script contains the foll: > >> > >> *charmrun +p12 namd2 min01.inp > min01.out* > >> > >> > >> However, rsh is refusing the connection, and I get error messages of this > >> kind for each core: > >> > >> *trying normal rsh (/usr/bin/rsh) > >> > >> connect to address 10.1.128.12 port 544: Connection refused > >> .. > >> Permission denied. > >> Charmrun> Error 1 returned from rsh (cn001:0)* > >> *...* > >> > >> > >> Can someone throw some light on this? > >> > >> Thanks and regards, > >> Neelanjana > >> > >> > > > > > > ------------------------------**------------------------------**---------- > > SEMEL (SErvizio di Messaging ELettronico) - AINF, Universita' di Udine > > > > > >
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