[gmx-users] Problem in mdrun_mpi using MPICH

[David van der Spoel]

On Wed, 2005-10-19 at 18:55 +0530, Alok wrote:
> Greeting to All,
> 
> sorry for very silly question.I have very limited knowledge of parallel
> computing.
> 
> I am trying to install parallel version of gromacs 3.3 in SUN Cluster.I
> compiled  fftw,binutis & gromacs 3.3 without any error.
> 
> MPICH was already installed on the SUN Cluster.

But you compiled it with LAM.

That won't work. 

> 
> when i run grompp_mpi for 2 node it ran fine and generated the *.tpr file
> for two processors.
> 
> But i tried to  mdrun_mpi -h it gave following message.
> 
> -----------------------------------------------------------------------------
> It seems that there is no lamd running on this host, which indicates
> that the LAM/MPI runtime environment is not operating.  The LAM/MPI
> runtime environment is necessary for MPI programs to run (the MPI
> program tired to invoke the "MPI_Init" function).
> 
> Please run the "lamboot" command the start the LAM/MPI runtime
> environment.  See the LAM/MPI documentation for how to invoke
> "lamboot" across multiple machines.
> -----------------------------------------------------------------------------
> 
> 
> 
> Due to boundation of out computer center rules i could not use the
> "lamboot" command. I have to submit the job by using following script
> (provided by our system administrator)
> 
> 
> 
> 
> ---------------------------------------------------------------------------
> 
> #!/bin/csh -f
> #
> #
> # (c) 2004 Sun Microsystems, Inc. Use is subject to license terms.
> 
> # ---------------------------
> # our name
> #$ -N MPI_Job
> #
> # pe request
> #$ -pe mpich* 2-20
> #
> # MPIR_HOME from submitting environment
> #$ -v MPIR_HOME=/opt/mpichdefault-1.2.6
> # ---------------------------
> 
> #
> # needs in
> #   $NSLOTS
> #       the number of tasks to be used
> #   $TMPDIR/machines
> #       a valid machine file to be passed to mpirun
> 
> echo "Got $NSLOTS slots."
> 
> # enables $TMPDIR/rsh to catch rsh calls if available
> set path=($TMPDIR $path)
> 
> $MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines -nolocal *
> 
> ---------------------------------------------------------------------------
> 
> 
> and start the job by using following command.
> qsub -pe mpichpar <no of nodes> -q par.q <script_name>
> 
> where * is Path of the input file including parallel program name (in my
> case it is /users/alokjain/mdrun_mpi -s full.tpr -o full -x full -c
> after_full -e full -g full)
> 
> but it is not recognizing the mdrun_mpi command.(I already set the path)
> 
> can some one help me to overcome this problem?
> Is there some problem in installation or in the script?
> 
> Thanking you,
> Best regards,
> Alok Jain
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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