VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Feb 05 2008 - 12:54:36 CST

On Tue, 5 Feb 2008, Corenflos, Steven Charles wrote:

SCC> Is this an appropriate forum to ask for help with namd? I've tried
SCC> contacting the e-mail address listed for namd but haven't gotten
SCC> any response after a week or so.

no! there is a mailing list for NAMD.
also there is the NAMD-wiki. just look for
them on the NAMD home page.

SCC> Basically we have a dual-processor, quad-core Xeon system running
SCC> Ubuntu 64-bit linux. While we can get namd to run on a single
SCC> processor we're running into difficulties getting it to run on all
SCC> 8 cores. Perhaps it is the package I'm using--I downloaded the
SCC> Linux-AMD64-TCP package in case we later tried to make it run jobs
SCC> not only on the local server but also spread the workload onto
SCC> other machines.

SCC> I've tried various combinations of commands I've found suggested in
SCC> different places:
SCC> > charmrun +p8 namd2 sim.conf
SCC> > namd2 +p8 sim.conf
SCC> > charmrun namd2 ++local +p8 sim.conf
SCC>
SCC> None of these have worked.
SCC>
SCC> Any help on how to get this working would be greatly appreciated.

please read the error messages, they tell you exactly what
happened and what you have to do.

SCC> Here is some sample output when trying to run the program:
SCC> user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ namd2 +p8 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log
SCC> To use multiple processors, you must run this program as:
SCC> > charmrun +p8 namd2 <args>
SCC> or build the net-linux-amd64-tcp-iccstatic-smp version of Charm++.

=> the version you downloaded only supports a single processor
   without using charmrun.

[...]

SCC> user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ charmrun +p8 namd2 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log

SCC> user_at_localhost's password: user_at_localhost's password:
SCC> user_at_localhost's password: user_at_localhost's password:
SCC> user_at_localhost's password: user_at_localhost's password:
SCC> user_at_localhost's password: user_at_localhost's password:

to be able to use charmrun, you have to be able to log into
your machine without using a password. see the documentation
one what to do. if your machine is directly connected to the
internet, it is strongly recommended to use ssh instead of
rsh. how to changes this, is also in the NAMD/charm++ documetation.

SCC> Charmrun rsh(localhost.1)> Cannot locate this node-program: /home/user/namd/namd-1cwp/1cwp-NT0-vmd-H/namd2
SCC> Charmrun rsh(localhost.1)> Exiting with error code 1

SCC> user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$
SCC>
SCC> user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ charmrun namd2 ++local +p8 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log
SCC> execve failed to start process "namd2" with status: -1

looks like in this case charmrun was not able to find your
executable in your path. please provide a full path or put
namd2 where it can be found.

cheers,
   axel. 

-- 
=======================================================================
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.