sander with "-rem 1" will look for 4 sets of input files,
with .XXX appended to them with the numbering
according to the replica #. So, you need to have files
called initial.crd..000, initial.crd..001 etc. Since you
already appended a period, sander will add another.
also, your input will be mdin.rep1.000, mdin.rep1.001 etc.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Hayden Eastwood wrote:
> Dear Amber users
>
> I have recently installed the replica exchange suite on our
> parallelized computer cluster (Mandrake). The compilation happened
> without error and the test results were all fine.
>
> However, when I now run the replica exchange on the cluster it crashes
> out with the following error:
>
> 1. *forrtl: No such file or directory*
>
> *forrtl: severe (29): file not found, unit 9, file
> /home/mpiuser/haydentest/fort.9*
>
> *Image PC Routine Line Source *
>
> *sander 081EEE18 Unknown Unknown Unknown*
>
> *sander 081EE910 Unknown Unknown Unknown*
>
> *sander 081CDC5D Unknown Unknown Unknown*
>
> *sander 08197954 Unknown Unknown Unknown*
>
> *sander 08197DF7 Unknown Unknown Unknown*
>
> *sander 081ACF0F Unknown Unknown Unknown*
>
> *sander 080E867E Unknown Unknown Unknown*
>
> *sander 080E4AD8 Unknown Unknown Unknown*
>
> *sander 080E3A45 Unknown Unknown Unknown*
>
> *sander 080B19DA Unknown Unknown Unknown*
>
> *sander 0807C795 Unknown Unknown Unknown*
>
> *sander 0807BB1B Unknown Unknown Unknown*
>
> *sander 0804B678 Unknown Unknown Unknown*
>
> *Unknown 4022CC57 Unknown Unknown Unknown*
>
> *sander 0804B531 Unknown Unknown Unknown*
>
> I have looked for the file fort.9 and cannot find it. Presumably it
> needs this file to operate and can’t find it? However the tests ran
> without problem so presumably it doesn’t need this file.
>
> Any idea as to what’s going wrong?
>
> My input file looked like this:
>
> *#!/bin/csh -f*
>
> * *
>
> *set sander = "/home/mpiuser/amber8/exe/sander"*
>
> * *
>
> *set log = rem.log*
>
> *set output = mdout.rem*
>
> *touch dummy*
>
> */bin/rm -f $log*
>
> *mpirun -np 4 $sander -O \*
>
> * -rem 1 \*
>
> * -ng 4 \*
>
> * -i mdin.rep1 \*
>
> * -c initial.crd. \*
>
> * -o mdout.rep1 \*
>
> * -r restrt.rep1 \*
>
> * -x mdcrd.rep1 \*
>
> * < dummy*
>
> I have included as an attachment my bashrc and .bash_profile files in
> case the problem rests there.
>
> Many thanks
>
> Hayden Eastwood
>
> ______________________________________________
>
> Hayden Eastwood
>
> Perdita Barran Research Group
>
> Joseph Black Building
>
> Edinburgh University
>
> West Mains Road
>
> EH9 3JJ
>
> Tel: 0131 650 4773
>
> e-mail: s0237717.sms.ed.ac.uk <mailto:s0237717.sms.ed.ac.uk>
>
> Research page:http://homepages.ed.ac.uk/pbarran/PBRG/
>
> “You have to be an academic to believe some things, no
>
> ordinary person would be so stupid.” – George Orwell
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Mar 18 2005 - 13:53:01 PST
