AMBER Archive (2006)

Subject: RE: AMBER: sander: cannot execute binary file

From: Michael John Hanby (
Date: Thu Dec 14 2006 - 15:52:23 CST

Howdy, you might also want to add this to your script, although I don't
think it's going to help in this particular error.







From: [] On Behalf
Of Kailee
Sent: Thursday, December 14, 2006 9:54 AM
To: amber
Subject: AMBER: sander: cannot execute binary file


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 message:



/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.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to