Re: unable to open binary file

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 04 2010 - 10:03:32 CDT

On Mon, Oct 4, 2010 at 10:00 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> Hi.
>
> I had my system run at a single workstation for 1ns and it completed
> successfully. Then I extend the simulation to 5ns using a 14 nodes cluster.
>
> And half way through the simulation, I got this error:
>
> WRITING COORDINATES TO DCD FILE AT STEP 1605500
> WRITING COORDINATES TO RESTART FILE AT STEP 1605500
> ERROR: Error on renaming file 2mrt_md_extend.restart.coor to
> 2mrt_md_extend.restart.coor.old: Invalid cross-device link
> FATAL ERROR: Unable to open binary file 2mrt_md_extend.restart.coor: File
> exists
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Unable to open binary file 2mrt_md_extend.restart.coor:
> File exists
>
> After reading the mailing list, I realised it might be caused by NAMD is
> computer architecture dependent. May I know is there a way to solve it? Or I
> would need to rerun the whole 5ns simulation on the cluster?

joyce,

no. this has nothing to do with it.

the problem is the call to rename(2) preceding the attempt to
open the file. for some reason, you cannot overwrite the old
backup file. do you have some kind of parallel filesystem on
that new cluster? you should carefully check the status, ownership
and permissions of the existing and old restart files.

cheers,
    axel.

>
> Thanks.
>
> Regards,
> Joyce
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:15 CST