AMBER Archive (2006)

Subject: AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband

From: Fabian Boes (fabian.boes_at_itb.uni-stuttgart.de)
Date: Thu Jul 06 2006 - 03:29:35 CDT

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Hi,

just a quick notice that i was able to solve my problem with the PMEMD
jobs hanging and producing no output files.

The (maybe not so perfect) solution was to compile with
- -DSLOW_NONBLOCKING_MPI (see README file in src/pmemd). Now the jobs run
fine but at the cost of approx. 20% speed loss.

Unfortunately i can't provide details about the used Infiniband drivers
and MPI versions as we do not operate that cluster by ourselves.

Bye,

Fabian

- --

Fabian Bös

Institute of Technical Biochemistry
University of Stuttgart / Germany

Phone: +49-711-685-65156
Fax: +49-711-685-63196
Email: fabian.boes_at_itb.uni-stuttgart.de

http://www.itb.uni-stuttgart.de

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