AMBER Archive (2003)

Subject: parallelisation

From: gold gunaseelan (gold_smith_at_rediffmail.com)
Date: Mon Jul 14 2003 - 10:48:56 CDT

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
file.is 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 md.in ....
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 promblem.my whole department is anxiously waiting for
this parellisation.thanking u -goldsmith

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