[gmx-users] mpi mdrun

jayant james jayant.james at gmail.com
Thu Jun 18 04:25:15 CEST 2009

Hi Mark!
Thanks for the tip I got it the mpi mdrun running on my quad core machine. I
just have one small clarification. In the output file md.log  I see this

"Started mdrun at node (0)"

I monitor my processor's load using gkrellm to see how many are running.
When I started the mdrun ( mpirun -np 4 mdrun ....) I specified 4 processors
and gkrellm displays the four processors running to full capacity but why
does the output in md.log give the above message.
I am wondering if I missed out some thing !!

On Tue, Jun 16, 2009 at 2:47 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> jayant james wrote:
>> Hi !!
>> I am attempting to install  mpi mdrun such that I can use all four
>> processors of my quad core system. But I keep running into this problem!! My
>> operating system is  Suse 10.1.
>> (cd .libs && rm -f libgmxpreprocess_mpi.la <
>> http://libgmxpreprocess_mpi.la> && ln -s ../libgmxpreprocess_mpi.la <
>> http://libgmxpreprocess_mpi.la> libgmxpreprocess_mpi.la <
>> http://libgmxpreprocess_mpi.la>)
>> make[1]: *** No rule to make target `../mdlib/libmd_mpi.la <
>> http://libmd_mpi.la>', needed by `mdrun'.  Stop.
>> make[1]: Leaving directory `/usr/local/gromacs-4.0.3/src/kernel'
>> I would appreciate help/suggestions in my installation.
> Don't install in root filespace. Unpack the distribution in your own home
> directory, configure, make, and then switch to root for "make install".
> Also, why bother installing a version that's months old?
> Mark
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Jayasundar Jayant James

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