AMBER Archive (2006)

Subject: AMBER: Middlebury College Cluster and Amber 8

From: Lubans, Peter S (
Date: Fri Aug 11 2006 - 11:55:19 CDT

Dear Amber Support,

I am attempting to install and test Amber 8 on a ten-node dual-processor dual-core opteron cluster running MPICH2 1.0.4 compiled with the PGI compiler suite. I have tested this MPICH2 build and it passes all of its tests except for two that are related to our automounter.

When I run mpdboot and specify that mpd should use either two processors on the local machine or one processor on each of two nodes (and set DO_PARALLEL="/opt/mpich2/mpich2-pgi-64/bin/mpiexec -n 2"), the parallel testing passes. However, if I tell the mpd system to use more than two processors (four on the headnode, two processors on each of two nodes, four processors on each of two nodes, etc) and set DO_PARALLEL to use the same number of processors, then one of the sander tests quits by calling MPI_Abort and complains that there must be more residues than processors. I'm not a chemist; I work in the IT department. What does this error message mean?

I tried to alleviate the situation by setting DO_PARALLEL to run more processes than the number of processors specified when I run mpdboot. When I do this, Amber's tests appear to hang right at the beginning. Sometimes it gets through the first two, on other runs it hangs immediately.

Does anyone have any ideas or suggestions?


Peter Lubans
Department of Library and Information Services.
Middlebury College

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to