You are exactly right. The error was due to calling the wrong version
of sander.
Best regards,
Aaron
David A. Case wrote:
> 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 - 06:07:57 PDT
