AMBER: Replica Exchange crashing

From: Hayden Eastwood <s0237717.sms.ed.ac.uk>
Date: Fri, 18 Mar 2005 12:39:48 -0000

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

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

 





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Received on Fri Mar 18 2005 - 12:53:00 PST
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