On Mon, Oct 29, 2007, Aaron Greenwood wrote:
>
> I tried to run amber 9 in parallel mode using mpich and submitting the
> job with qsub. I get a strange, at least to me, error.
>
> mdfil: Error unknown flag: -p4pg
Are you sure you are running sander.MPI and not plain sander? The former
should ignore the -p4pg flag (which is being added by the mpirun command, I
think), but the latter would give the error you see.
Unlike previous versions of amber, the parallel executable is now called
sander.MPI, and "sander" is strictly for serial runs.
If this isn't it, try running the job manually (without qsub), and let us know
the exact command line. Also, be sure that you did a "make clean" (in
amber9/src) before compiling the parallel code.
....regards...dac
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Received on Wed Oct 31 2007 - 06:07:43 PDT
