how do I pass environmental variables to namd on BlueGene/P?

From: Aaron Oakley (
Date: Thu Aug 02 2012 - 23:39:06 CDT

Hello all,

I am running NAMD2.9 on BlueGene/P.

I have a script which I submit which contains the following:

export NAMD_USER=10


# @ environment = COPY_ALL;

in the namd input file I have:

set oldname run${env(NAMD_USER)}
set newname run[expr ${env(NAMD_USER)} +1]

i.e, oldname is set to run10 and newname is set to run11

but when executed the program exits with error:

Reason: FATAL ERROR: can't read "env(NAMD_USER)": no such variable

The namd input script DOES however work on my mac, so the problem
appears to be in the passing of an environmental variable to namd2.9 on BlueGene/P.
Any clues on how to do this successfully would be appreciated!


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