Hi, all,
Thanks for your reply, as Ross has suggested, I have checked the location of
sander, it was correct, and also I can see this file using my account. As to
the architecture, the node I was trying to run was the one I compiled the
amber.
Are there any other reasons that may cause this cannot execute problem?
Thank you for any suggestions.
Best regards,
Kailee
On 12/14/06, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Kailee
> *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
> 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 -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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Received on Sun Dec 17 2006 - 06:07:19 PST
