[gmx-users] trjconv, g_mindist and others in parallel

David spoel at xray.bmc.uu.se
Thu Apr 24 22:18:01 CEST 2003

On Thu, 2003-04-24 at 19:31, Mike Tallhammer wrote:
> I was wondering if one could run trjconv, g_mindist and other GROMACS
> utilities in parallel if you have the parallel version compiled on a dual
> processor machine. I'm trying to run some analysis on a trajectory of
> approx. 70 GB and running in parallel would be of great gain to me. Any help
> would be greatly appreciated.
Great stuff. The answer is no, but... As a workaround you can read the
trajectory in two bits, e.g.:
g_mindist -b 0
g_mindist -b 10000

However, you may find that your hard disk is the bottleneck here. In
that case it would be better to copy the second half of your trajectory
to another disk (using trjconv)
Then you can really profit from the above example.

The simplest solution is (ofcourse) to write a script to do what you
want from the existing trajectory, and go for a hike while you wait for
the computer to finish...

> Thanks 
> Michael Tallhamer
> Asst. Researcher
> Cleveland State University
> Cleveland, OH 44115
> E-Mail: m.tallhamer at csuohio.edu
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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