Re: parallelisation

From: Carlos P. Sosa <>
Date: Mon, 14 Jul 2003 11:19:00 -0500


You might want to consult the installation guide for IBM Linux systems

This is for AMBER7.

gold gunaseelan wrote:

> respected sir,
> iam using 5 IBMp4 netvista machines with linux7.3 for
> parellisation purpose.i installed amber6 and mpich in all 5
> machines.i also put a copy of my input file and topology file in
> all five machines.if i don't do that i get error cannot open
> it necessary to have these things in all machines?.these
> are the changes i made before start
> In my .cshrc file i have set the path as
> setenv AMBERHOME /home/programs/amber6
> setenv DO_PARALLEL '/home/programs/mpich-1.2.5/bin/mpirun -np 4'
> set path = (. $path $AMBERHOME/exe)
> alias mpirun '/home/programs/mpich-1.2.5/bin/mpirun'
> alias mpif77 '/home/programs/mpich-1.2.5/bin/mpif77'
> In my machine file amber6/src/machine
> i introduced a statement as
> # setenv MPICH_HOME /usr/local/src/mpich/build/LINUX/ch_p4
> setenv MPICH_HOME /home/programs/mpich-1.2.5
> In mpich1.2.5/util/machines/machinesLINUX file i have given the
> names my five machines-this is in one pc only
> Sir i tried to run the sander program by typing
> mpirun -np 5 sander -O -i ....
> the message appears
> all processors started
> all processors started
> all processors started
> all processors started
> all processors started
> the job goes on in all machines.but outputs are created in all
> machines.the job gets killed at various steps in the various
> machines except from the machine from where i issue the command to
> run.It takes the same time no matter,the no. of processors i use
> whether it is one two or five.I think so the job is trying to run
> individually in each machine is that so.when i run the program in
> 4 processors i expected 1/4 th decrease in time .but that does not
> happen so.I think iam doing a terrible mistake in parellelising
> the amber program.sir very sorry to trouble u again and again.I
> will be extremely gratefull to u if u kindly help me out in
> solving this whole department is anxiously waiting for
> this parellisation.thanking u -goldsmith
> ___________________________________________________
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Carlos P. Sosa, Ph.D.
IBM & University of Minnesota
Supercomputing Institute for
Digital Simulation and Advanced Computation
599 Walter Library
117 Pleasant St. SE
Minneapolis, MN 55455                             email:
Received on Mon Jul 14 2003 - 17:53:00 PDT
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