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On 2/03/2011 11:37 PM, Erik Marklund wrote:
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Selina Nawaz skrev 2011-03-02 11.54:
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<div style="font-family: Tahoma; font-size: 13px;">Hi, I am
a Phd student studying polymer membranes.</div>
<div style="font-family: Tahoma; font-size: 13px;"><br>
I have installed Gromacs version 4.5.2 on our department
cluster and attempted to run a simulations on a DPPC bilayer
membranes taken from the tielleman website.</div>
<div style="font-family: Tahoma; font-size: 13px;">I have set
the system up in an NPT ensemble using a semi-isotropic
pressure coupling. </div>
<div style="font-family: Tahoma; font-size: 13px;">The
simulation seems to run perfect in serial however I am
having problems to run the simulation in parallel.</div>
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<br>
You're going to have to be much more specific if you want useful
help.<br>
<br>
<blockquote cite="mid:4D6E3A05.7050007@xray.bmc.uu.se" type="cite">
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cite="mid:CF10920372D1574190BA8B5453695A0701A517@MBXP06.ds.man.ac.uk"
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<div style="font-family: Tahoma; font-size: 13px;">I
understand that this version of Gromacs uses threading to
parallelise the system. I wanted to know whether it is
possible to run this using openmpi and if not how do i use
this thread base parallelisation.</div>
<div style="font-family: Tahoma; font-size: 13px;"> </div>
<div style="font-family: Tahoma; font-size: 13px;">Many Thanks</div>
<div style="font-family: Tahoma; font-size: 13px;"> </div>
<div style="font-family: Tahoma; font-size: 13px;">Selina</div>
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Hi,<br>
<br>
It's slightly different than you think. Gromacs uses a thread
based MPI implementation for communications between cores on the
same machine. If you compile without threads it would use e.g.
OpenMPI instead of threads as far as I know. Note that it will
still use OpenMPI (or equivalent) for inter-node communication.<br>
</blockquote>
<br>
Not in 4.5.x. You can configure with MPI or threads (the default) or
neither. The two cannot co-exist. Threading is only useful if a
network is not involved. OpenMPI will do approximately the same via
shared-memory as you can get from threading in the cases where it is
useful.<br>
<br>
The OP should consult the GROMACS webpage for MPI installation
instructions.<br>
<br>
Mark<br>
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