Corina Stratan wrote:
Dear Gromacs users,
my name is Corina Stratan and I am a Ph.D. student in computer science.
We have a project in our group in which we try to analyze the behaviour
of a few typical scientific applications in a cluster environment, and
we would like to include Gromacs in our tests. We have a few general
questions about Gromacs, maybe somebody who has experience with it can
help us:
1) Which is the typical size of the input/output files for Gromacs
programs? The ones included in the tutorial are below 50K; are the files
larger in "real" situations? And if yes, is there any place we can find
some larger test files?
you can download the benchmark set, in particular the dppc benchmark.
2) Which would be the typical running time of an mdrun simulation? (or
put it another way, is the runtime usually significant - i.e., more than
a few minutes?)
between minutes and years. parallellization helps quite a bit, and with
modern code we scale to hundreds of nodes. however, sometimes on can do
a useful simulation in a couple of minutes and get meaningful (i.e.
publishable) results.
3) Are the jobs usually run in batch? And if yes, do the batches contain
a single program, run with different input files, or multiple programs?
most often in batch and usually as a single program. sometimes one uses
multiple programs with multiple inputs.
Thank you!
Corina
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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