[gmx-users] "Lam" is not required for running parallel job

[sunita at chem.iitb.ac.in]

Thank you Mark.


Sorry, I forgot to mention that I already installed MPI library. I used
following .rpm files to install MPI.

openmpi-1.2.3-4.fc8.i386.rpm
openmpi-devel-1.2.3-4.fc8.i386.rpm
openmpi-libs-1.2.3-4.fc8.i386.rpm

The details of the installation:

Step 1: FFTW (fftw-3.0.1.tar.gz)
Step 2. MPI   (all the above openmpi rpms)
Step 3. GROMACS (gromacs-3.3.1.tar.gz)

The output of "which mpirun" is
====================================
[sanjay at proline ~]$ which mpirun
/usr/bin/mpirun
[sanjay at proline ~]$
====================================

I was thinking MPI and LAM are to be installed separately.
That's what confused me. But, now it is clear.
Thank you again.

Regards,
sunita

> ----- Original Message -----
> From: sunita at chem.iitb.ac.in
> Date: Wednesday, February 13, 2008 10:20 pm
> Subject: Re: [gmx-users] "Lam" is not required for running parallel job
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>> >
>> >
>> > ----- Original Message -----
>> > From: sunita at chem.iitb.ac.in
>> > Date: Wednesday, February 13, 2008 5:40 pm
>> > Subject: [gmx-users] "Lam" is not required for running
>> parallel job
>> > To: gmx-users at gromacs.org
>> >
>> >> Dear Users,
>> >>
>> >> Lam doesn't seem to be essential for running parallel job.
>> >
>> > An MPI library is essential.
>> >
>> >> Because in one of our Xeon machine with quardcore 1.6 Ghz
>> >> processor and
>> >> with 6 nodes we installed parallel version of gromacs (version
>> >> 3.3.1) and
>> >> its running without any problem. Lam is not installed in this
>> machine>> still it is running the parallel job.
>> >
>> > How are you running grompp and mdrun, and what makes you think the
>> > calculation is running in parallel?
>> >
>> I used the following command to run parallel job and tested it by
>> generating .tpr file for 2 nodes, 4 nodes and 6 nodes. With 6
>> nodes it
>> took least time to finish the mdjob.
>>
>> grompp -np 6 -f ......
>> mpirun -np 6 mdrun_mpi -v -s .....
>>
>> It seems correct to me.
>> What do you say?
>
> You have an MPI library installed, else mpirun would not exist. Said
> library doesn't have to be called LAM, however. It also existed when
> someone compiled mdrun_mpi, unless they actually did it single-processor
> and your above snippets don't reflect what you're actually doing.
>
> It's a good idea when seeking feedback to give full information, e.g.
> copying and pasting your actual commands. If the contents of your head
> were always right, you would probably already have solved your own
> problem. Accordingly, we'd much prefer know what you actually did, rather
> than something that's been filtered through your head. :-)
>
> Mark
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