I tested with only 48 CPUs and it worked!
Thank you so much.
Bongkeun Kim
Quoting case <case.biomaps.rutgers.edu>:
> On Thu, Feb 17, 2011, Bongkeun Kim wrote:
>
>> And I attached all prmtop, inpcrd, rst and input mdin files with zip.
>> You can execute it by the following command.
>>
>> sander.MPI -ng 12 -groupfile equilibrate.groupfile
>
> Works for me, if I precede the above command with "mpirun -np 12" or with
> "mpirun -np 24". So, you might check what the "ibrun" command in your
> "remd.job" script is really doing: how many threads is it actually using?
> Note that the number of threads must be a multiple of the number of groups
> (in this case, 12).
>
> Sander has an additional requirement that the number of residues must be
> greater than the number of threads used for member of the group. If you
> are indeed using 192 nodes, you would have 16 threads per group member
> (192/12) and an error would occur (since you have only 16 residues). This
> is supposed to be checked, but the check may be in error, or the error
> message could be getting lost in the multisander run. A quick check is to
> see if the job works on 96 threads (or, indeed, any multiple of 12 smaller
> than 16.)
>
> ....dac
>
>
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Received on Fri Feb 18 2011 - 10:30:06 PST
