On Thu, Feb 25, 2010, bbalta.itu.edu.tr wrote:
> Pmemd has been successfully compiled only in serial. Parallel
> compilation appears to be successful, but when we try to run in
> parallel, there is no speed up with respect to a single processor run.
> When I look at the job status in the queue, I see that it runs on
> multiple processors, but the speed is the same as a single processor
> run. Also, in the output file the number of processors used is not
> written (I guess, for parallel pmemd, it should be written somewhere
> near the beginning of the output file).
My best (wild) guess is that your mpirun is still pointing to the serial
version of pmemd. Unlike sander, which creates separate executables
for serial and parallel ("sander" and "sander.MPI"), the pmemd setup uses
the same executable name for both serial and parallel versions; the idea
is that the "nopar" version is hardly ever used in practice.
Your symptoms (several processors running, but not having the number of
processors in the output) suggests that you are still running the serial
version. Check your timestamps carefully. Another trick is to run
"mpirun -np 1 pmemd ....". The serial pmemd would be OK with this, but the
parallel version will complain that it cannot run on one processor. So this
can be used to make sure you are actually running the parallel version.
Of course, the error could be somewhere else completely, but the above is
worth checking.
...dac
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Received on Thu Feb 25 2010 - 08:30:07 PST
