charmrun not found

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Tue Jun 24 2008 - 21:59:24 CDT

Hi all,
I installed NAMD not so long ago and have been trying to run it. I am
working on a linux amd64 cluster with Rocks. I have been attempting to run a
small simulation folding alanine through the configuration file that comes
with NAMD. But when I try to use the command 'charmrun', it is not being
found even though the executable is present in the working directory.

I am able to run it in one processor using mpirun, but it keeps arriving at
a fatal error: Error in the configuration file. The error is copied after my
name, in case it may be of use.

Is this due to a failure in translation of charmrun options into mpirun
options?

Thank you for your attention,
Diego A. Vargas

Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-amd64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.6 Linux-amd64 1 Zlab-cluster.bme.utexas.edu Diego
Info: Running on 1 processors.
Info: 7476 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to lib/replica/example
Info: Configuration file is fold_alanin.conf
TCL: spawn_namd_ssh {cd
/home/Diego/Diego/NAMD_2.6_Linux-amd64/lib/replica/example;
/Projects/namd2/bin/current/Linux64/namd2 +netpoll} {beirut belfast}
TCL: Suspending until startup complete.
ERROR: 'exclude' is a required configuration option
ERROR: exclude defines: Electrostatic exclusion policy
ERROR: 'outputname' is a required configuration option
ERROR: outputname defines: prefix for the final PDB position and velocity
filenames
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Stack Traceback:
  [0] CmiAbort+0x4f [0x7eb405]
  [1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
  [2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73
[0x72343f]
  [3] _ZN9NamdState14configListInitEP10ConfigList+0x391 [0x6ae59b]
  [4] _ZN9ScriptTcl9initcheckEv+0x5e [0x6ff8ac]
  [5] _ZN9ScriptTcl3runEPc+0xb5 [0x6fba3f]
  [6] main+0x21b [0x4b69c3]
  [7] __libc_start_main+0xdb [0x3fbb11c3fb]
  [8] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

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