RE: Loadleveler Script on Bluegene for NAMD

From: hannes.loeffler_at_stfc.ac.uk
Date: Sat Jul 03 2010 - 06:56:49 CDT

Does namd actually take the -i and -o options?

Just -args 3CAP_DOPC_DOPEminequi_july2.conf
should be fine. The output is then going to stdout which
you can capture with #@ output = filename.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Dan J Martingano
Sent: Sat 7/3/2010 4:48 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Loadleveler Script on Bluegene for NAMD
 
Hey all,

I just had a question about submitting the loadleveler script on Bluegene. I created and submitted the one I created and each time it says that it cannot find my configuration file (using NAMD) I am wondering if I am writing the "-args" section incorrectly.

What I am submitting is this:

# @ bg_size = 32

# @ initialdir = /gpfs/home3/d/dmartingano/experiment_001

# @ input = /dev/null
# @ output = $(jobid).out
# @ error = $(jobid).err
# @ executable = /bgl/BlueLight/ppcfloor/bglsys/bin/mpirun

# @ wall_clock_limit = 72:00:00

# @ notification = complete
# @ notify_user = dynamic00_at_msn.com

# @ arguments = -exe /bgl/apps/namd2.7b1/memory-optimized/NAMD_2.7b1_Source/BlueGeneL-MPI-xlC/namd2 -mode VN -cwd /gpfs/home3/d/dmartingano/experiment_001 -args "-i 3CAP_DOPC_DOPEminequi_july2.conf -o 3CAP_DOPC1_DOPC3WIminequ1_july2.log"

# @ queue

Maybe because I am using NAMD the problem is not so obvious, but I am certain the "-args" section must be wrong since it is saying that the program cannot find the configuration file and I triple checked to make sure it is in the correct directory and such (so its not the directory of problem accessing the NAMD program.)

If anyone can shed light on the subject it is greatly appreciated!

Thanks a lot!

-Dan M

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