AMBER Archive (2003)

Subject: AMBER: sanderparallel

From: gold gunaseelan (gold_smith_at_rediffmail.com)
Date: Mon Aug 04 2003 - 02:32:48 CDT

respected sir
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).sir when i tried sander i get the
following error

$ mpirun -np 2 sander -O -i mdp.in -o s.out -p test.top -c
mdp1a.restart -r s.rest -ref mdp1a.restart
Segmentation fault
p0_2272: p4_error: Child process exited while making connection
to remote process on triplex: 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:triplex is name of my node1(slave machine)
I kindly request ,lookforward to answer from anyone whg knows a
solution to this.-smith

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