AMBER Archive (2006)

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

From: Michael John Hanby (mhanby_at_uab.edu)
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.

 

export PATH=$AMBERHOME/exe:$PATH

 

 

 

________________________________

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] 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):

************************************************************************
*************

#!/bin/bash
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 test.in <http://test.in/> -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.

Kailee

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