AMBER Archive (2005)

Subject: AMBER: PMEMD with big systems

From: Florian Barth (bio_hazard_at_gmx.de)
Date: Fri Mar 18 2005 - 17:25:41 CST

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Hi,

I have some trouble running PMEMD (amber8) with big sytems like hb or
factor_ix. For parallel runs a certain minimum number of cpus are needed
to run those systems otherwise PMEMD will segfault. For example, PMEMD
with factor_ix needs a minimun of 14 cpus to run (about 6500 atoms/cpus).
PMEMD is running on a linux cluster (gentoo linux kernel 2.4.28), with
dual athlon-mp nodes and myrinet interconnect. I used the intel ifort
8.1.024 compiler with the new_configure utility for compilation. Myrinet
software is gm version 1.6.5 (compiled with gcc) and mpich-gm 1.2.6..14a
(gcc/ifort).
Serial PMEMD and serial/parallel sander is running without problems with
factor_ix. Stack size is unlimited and shmem is set to 1 GB on all nodes.
I was able to run factor_ix on 2 cpus with PMEMD during the installation
phase of one of the nodes. But after some reboots the above limitation
came up; unfortunately I have no idea what could have changed.

Any hint would be greatly appreciated.

Florian Barth

____________________________________

Florian Barth
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart
Germany
tel.:+49-711-6853811
fax.:+49-711-6853196
email:bio_hazard_at_gmx.de
http://www.itb.uni-stuttgart.de
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