AMBER Archive (2000)

Subject: MPI on SUN

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Thu Dec 14 2000 - 06:00:29 CST

Hello,
        I am Sanjeev, a PhD student. I compiled sander on a MPI based on
SUN architecture (PARAM10000). The following is the shell script called
md.sh (chmod 700). When I executed it as 'md.sh' it gives a problem of
unknown flag (also given below). When I tried instead 'mpirun -np 4 md.sh'
without the coressponding words in the shell scripit, it runs but only on
one processor! This is the fourth operating system I tried to compile
AMBER5 out of which only power challenge worked (which is too slow for my
task). Can anyone kindly let me know how to cirumvent the problem please?
Thanking you in advance,
-Sanjeev

-------------------------- md.sh -------------------------------------
mpirun -np 4 /tmp/amber5/exe/sander -O \
                -i md_0_1.in \
                -o md_0_1.out \
                -p parm.MEDN.w.top \
                -c sander.MEDN.w.res \
                -r md_0_1.out.res \
                -ref sander.MEDN.w.out.pdb \
                -x md_0_1.out.crd \
                -v md_0_1.out.vel \
                -e md_0_1.en \
                -inf md_0_1.info
----------------------------------------------------------------------

% mpirun -np 4 md.sh
----------------------------------------------------------------------
     unknown flag: -p4pg

     usage: sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo]
----------------------------------------------------------------------