Re: unable to open binary file

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Mon Oct 04 2010 - 22:55:00 CDT

Hi Axel.

Thanks for your reply. We had got the problem solved. It got to do with the
file's permission.

But I got another problem when I tried to extend the simulation of another
structure.

I got this message:
*FATAL ERROR: Bad global angle count!*
*
*
*FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html*
*------------- Processor 0 Exiting: Called CmiAbort ------------*
*Reason: FATAL ERROR: Bad global angle count!*
*
*
*FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html*

After reading the NAMD troubleshooting and some posts at the mailing list,
I'm sure that i use the correct .xsc file at the restart with the margin set
at 2.5 in the config file. And when i visualised my system using vmd, I do
not find any long bonds. I don't understand why such situation happen.

Then I tried to run the simulation from the beginning (not using any restart
file), it return the same error, too. Is there any problem with my cluster
as I had the same system run on a single workstation for 1ns and it
completed successfully?

Regards,
Joyce

On Mon, Oct 4, 2010 at 11:03 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>

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