AMBER Archive (2009)

Subject: RE: [AMBER] Error message in "make test.sander"

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 06 2009 - 01:28:01 CDT

Hi Catherine,

> I have the owership to the test directory, and I run the jobs in the
> test directory. I tried to open the mdout.dmp file and write some
> words and save the files. It seems to me that I have the right to
> write to this file too.
>

The issue is not whether you have write permission to the file on the login
node but that the user account that runs the parallel calculation on the
'compute' node has permission to write to this file. How this is setup and
specifically how this works is likely specific to your supercomputer setup.
Who setup the machine for you? Can you check with them to make sure you have
write permission on compute nodes to the $AMBERHOME/test directory?

Try running a calculation manually in your home directory - you can take one
of the DNA inputs from tutorial B1 on http://ambermd.org/tutorials/

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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