Re: PBS & local (scratch) space
I think that the best way would you to ask to your system
administrator, since it is more a system-dependent issue than anything
related to NAMD in particular. Once you figure out how to do that, you
can use a similar pbs script for any program, not just NAMD. Anyway,
this is how I do it here, but as I said, things might be different in
#PBS -l nodes=1,ncpus=.....,mem=.....,walltime=.....
#PBS -m abe
# Define the directories
# Create a directory for me in /scratch on the compute node if it does
if [ ! -d /scratch/$USER]; then
cp -pr * $TARG_DIR
cp -pr $TARG_DIR WHERE_YOU_WANT_YOUR_FINISHED_JOBS_TO_BE_PUT
Anyway, I don't seem to recall any significant speedup in doing that on
the altix we have here, at least when you save your trajectory every
few hundreds steps. It's anyway safer to do that, so that if your home
crashes or there are problems in the nework, your job can still keep
Arturas Ziemys wrote:
Few months ago I posted a question about scratch space and NAMD on cluster without answers. I just wanna check if somebody MAYBE now have ana advice or clue ...
How to ensure that NAMD job using PBS will be submitetd to the local (scratch) space of nodes instead of using user disk space ?
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: Wed Feb 29 2012 - 15:44:01 CST