[gmx-users] FSync error

[Souparno Adhikary]

Hi Mark,

I understand it's prehistoric. But, I would be happier if somebody makes
understand the system admins at the CDAC-BRAF that their version is
prehistoric.

The problem has not been solved yet. I'm running the simulation in parts
reading from the checkpoint files. Will that be too risky for the results?

Regards,

Souparno.

On 24 Mar 2017 16:22, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Mdrun can't access that file properly, but there's no real way for it to
> understand why. A network file system could disappear and mdrun can't know
> that. By the way, 4.5.6 is prehistoric - please update for faster
> simulations, more chance of people being able to help you, and fewer bugs!
>
> Mark
>
> On Fri, 24 Mar 2017 09:34 Souparno Adhikary <souparnoa91 at gmail.com> wrote:
>
> > I'm getting the following error in a 500ps pull code simulation. I
> checked
> > out the forum for probable solve and it says it might be due to disk
> space
> > usage or permission. In my case, I have enough disk quota left and I have
> > permission to write in the directory. Can you please help?
> >
> > Usual MD simulations run fine. The error comes only when the pull code is
> > applied.
> >
> > Error:
> >
> > -------------------------------------------------------
> > Program mdrun_mpi, VERSION 4.5.6
> > Source code file: checkpoint.c, line: 1287
> >
> > File input/output error:
> > Cannot fsync 'tp_pull.xvg'; maybe you are out of disk space?
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > Attached is my mdp file for the pull code. Framed broadly on Justin
> > Lemkul's tutorial *.mdp file.
> >
> > Can you please help to indicate what might be the problem?
> >
> > Thanks,
> >
> > Souparno Adhikary,
> > University of Calcutta,
> > India
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