AMBER Archive (2003)

Subject: AMBER: parallelisation

From: gold gunaseelan (gold_smith_at_rediffmail.com)
Date: Tue Aug 05 2003 - 08:55:31 CDT

espected sir
i am a new user to amber
we have two machines with Red Hat linux 7.3.
we installed mpich 1.2.5, and ran the sample programs
successfully.
we modified the MACHINE file for parallliztion

Iam able to run amber6 program sander_classic in parallel version
using mpich1.2.5 .but the program is using only 20 % of the cpu in
the master machine and 60 % in my slave machine.I am not able to
trace out the reason.Iam using 2 machines at present (2 nodes ;one
master and other slave).although no other jobs are running in the
machines.sir when i tried sander i get the following error

$ mpirun -np 2 sander -O -i dek.in -o dek.out -p hybrid.top -c
mdp1a.restart -r mdp.restart -ref mdp1a.restart
Segmentation fault
p0_2272: p4_error: Child process exited while making connection
to remote process on orange: 0
(/home/mpi/mpich-1.2.5/bin/mpirun: line 1: 2272 Broken pipe
/home/mpi/amber6/exe/sander "-O" "-i" "production.in" "-o" "s
.out" "-p" "test.top" "-c" "mdp1a.restart" "-r" "s.rest" "-ref"
"mdp1a.restart" -p4pg /home/mpi/amber6/exe/PI2188 -p4wd
/home/mpi/amb
er6/exe
$
note:orange is name of my node1(slave machine)
Iam able to run sander in one machine ,but when i try to run using
mpirun it says segmentation fault .can anyone kindly suggest
solution -smith

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