VMD-L Mailing List

From: Benjamin Stauch (stauch_at_embl.de)
Date: Tue Sep 16 2008 - 07:47:16 CDT

dear community,

i'm running VMD in batch mode on a PBS cluster qsub'ing a job array script.
when i start VMD (on a single machin), it says "multithreading
available" and correctly prints out the number of processors i have. in
my job array script, i request a single node and 8 processors per job.
in the logfile produced by PBS on completion of the job, it puts that
the job is executed on all 8 processors. but when i log in to a
particular node (while running my job) and issue a 'top', i only get
100% CPU load (which should be ~800%). i also have slight doubts because
of the speed of my computation (i would expect it to be faster if all 8
processors were used).

is there a way to find out if all 8 processors per node are used? do i
have to specify a command line flag / environment variable? what i could
find out is that VMD needs to be configures with -P flag in order to
allow for parallel stuff. is the fact that it correctly indicates the 8
processors (and says, "multithreading available") already a sign for
that it was correctly configured for multiprocessor architecture?

thanks in advance,
all the best,
ben