AMBER Archive (2006)

Subject: AMBER: sander: cannot execute binary file

From: Kailee (
Date: Thu Dec 14 2006 - 09:53:50 CST

Hi all,

I am new to amber. I have just compiled amber8 on the cluster myself, i
think i compiled it successfully, and I did all the tests, both serial and
parallel. However, when I tried to run some of my own jobs, I had such error

/home/usr/kailee/mpich-1.2.7p1/bin/mpirun: line 1:
/home/usr/kailee/amber8/exe/sander: cannot execute binary file

And this is my run script (named as script_test):

export AMBERHOME=/home/usr/kailee/amber8

export MPICH_HOME=/home/usr/kailee/mpich-1.2.7p1

export DO_PARALLEL="$MPICH_HOME/bin/mpirun -np 4"

$DO_PARALLEL $AMBERHOME/exe/sander -O -i -o test.out -p model.prmtop-c
model.inpcrd -r test.rst -x test.mdcrd


And then I used "qsub script_test" to submit my job.

Have you encountered similar problem before? how to solve this? thank you
all for your help.


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