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On 4/27/2011 9:08 PM, Natalie Stephenson wrote:
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<div>Hi,</div>
<div> </div>
<div>I was wondering if anyone new a way to run mdrun commands
through a condor system. I've been told by the people that
run our system that unless I can split it into seperate
threads then I would not be able to run it as a job, because
it would just get stopped in the morning - which from what
I've seen would just end my simulation and I would have to
start again.
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<br>
Condor is not a suitable platform for running molecular dynamics in
parallel, unfortunately. Low-latency communication is required if
the processors do not share the same piece of silicon, and nobody
running Condor will have that. You can get some value from Condor if
you have several simulations to run, by making it easy to run each
one on a different machine.<br>
<br>
Starting and stopping simulations is not much of a problem, with
checkpointing in GROMACS 4.x.<br>
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cite="mid:037BC2AE05ACF5459BEC1ACBFC4D914203394A@MBXP06.ds.man.ac.uk"
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<div>Currently my simulations are taking around a month - which
as I'm nearing the end of this project is getting quite
frustrating as you can imagine. Any ideas on how I can speed
this without buying a new computer (which is an idea I've had
veeto'd from my supervisor many many times!) would be much
appreciated!!! </div>
</div>
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<br>
Sounds like you need to work with your supervisor to change
expectations, or look around for some free time you can ask for...
try big or new computing facilities, especially new ones with
recently-installed under-utilized hardware.<br>
<br>
Mark<br>
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