AMBER Archive (2009)

Subject: [AMBER] -np not 2^x a problem w/ sander??? update

From: Dean Cuebas (
Date: Fri Nov 06 2009 - 13:46:39 CST


Actually, the job was setting up, but then stopped with this job error:

0 - MPI_REDUCE_SCATTER : Invalid buffer pointer: Arguments must specify
different buffers (no aliasing)
[0] [] Aborting Program!

Any suggestions?



Dear amber people,

The place I'm running sander.MPI limits np to 48.

I'm seeing a big performance hit with np 48 compared to np 32.

I don't see this performance hit with pmemd. Is this normal?

I'm doing SGLD, so I'm using sander.MPI

Thanks very much!!!


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