RE: AMBER: sander: cannot execute binary file

From: Ross Walker <>
Date: Thu, 14 Dec 2006 15:15:46 -0800

Dear Kailee,
A few things to check. Firstly that the path
/home/usr/kailee/amber8/exe/sander points to the correct file location.
Secondly that the permissions of this file are correct. I.e. that it is
executable and that the user account that runs the job on the cluster
machine can see this file.
You should also check that the architecture of the node you compiled the
executable on and the node that is running your job are the same. Often one
sees these sort 'cannot execute' errors when the executable file was
compiled on a different architecture than the one that you are trying to run
on. I.e. you compile on a pentium Xeon X86_64 machine but then try to run it
on a Itanium.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: [] On Behalf Of
Sent: Thursday, December 14, 2006 07:54
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
/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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Received on Sun Dec 17 2006 - 06:07:06 PST
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