[gmx-users] question about parallel runing of gromacs

[Justin A. Lemkul]

Xiang Mao wrote:
> I got something like this in log file
>  
> Host:XXX  pid:5504  nodeid :0  nnodes:1
>  
> and I think I compiled mdrun_mpi using --enable-mpi. I am wondeirng if I 
> should use lam_mpi instead of MPICH2?
>  

It is better to *know* than to *think.*  Did you try what was suggested to you 
with ldd?  If so, what did it show?  Based on the log file, you probably did not 
--enable-mpi.

MPICH2 is fine, no need to use LAM.

-Justin

> thanks.
> 
> On Mon, Mar 9, 2009 at 11:03 PM, Diego Enry Gomes <diego.enry at gmail.com 
> <mailto:diego.enry at gmail.com>> wrote:
> 
>     On Mar 9, 2009, at 5:12 PM, Mark Abraham wrote:
> 
>>     Xiang Mao wrote:
>>>     My PC has a intel core2 cpu. I compiled gromacs under cygwin, and
>>>     using MPICH2. After mpiboot, I use mpirun -n 2 mdrun_mpi .... to
>>>     run EM, MD.
>>
>>     OK that might be working right. Now you need to look in the log
>>     file for an indication of whether the run has two component
>>     processes or one - right at the top, usually.
>>
>>     Mark
> 
>     Hi Xiang, maybe the solution is simple and you just didn't use the
>     "--enable-mpi" flag in the ./configure step. 
>     That explains the duplicate steps.
> 
>     Try a quick "ldd" test to check if MPI compilation worked.
> 
>     % which mdrun_mpi     (find where mdrun was installed, mine is at
>     /usr/local/gmx4/bin/)
>     % ldd /usr/local/gmx4/bin/mdrun_mpi  
> 
>     You should see "libmpi.so.0" in the list of libraries, if not, go
>     back to the ./configure step.
> 
> 
>     Diego
> 
>     --
>     =========================================
>     Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
>     /tmp/home/@ Pacific Northwest National Laboratory
>     Richland, WA.  +1 (509) 372.6363 
>     diegoenry.gomes at pnl.gov <mailto:diegoenry.gomes at pnl.gov>
>     =========================================
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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