[gmx-users] Problems with NFS

[Victor Rosas Garcia]

So, if NFS is not functioning, there is little we can do on this list to
help.  My only guess about it is that maybe NFS is working but the home
directories have not been exported to the working nodes. Perhaps a failure
of NIS or LDAP configuration?

I do not have experience with NAMD, so I cannot comment on why the error
does not arise in that case.

Again, my recommendation is to talk to your system administrator about the
lack of the directory on a node where it is supposed to be.

Best regards

Victor


2014-07-03 11:22 GMT-05:00 Natalia Alveal F. <nalveal at bio.puc.cl>:

> This error is just for confirming that NFS falls, that is not functioning.
> But when run Gromacs, the connection with NFs is lost just few time of
> compute. This not happen when run NAMD 2.9 alone.
>
> And this is the command for the cluster:
> nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
>
> I hope can help me!!
> Best regards from Chile.
>
>
> 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia <rosas.victor at gmail.com>:
>
> > Hello Natalia,
> >
> > The error says that it is trying to change to a directory named
> > /home/fmontenegro, but that such a directory does not exist. This is not
> a
> > GROMACS error, but a problem related to how the cluster is setup.  Your
> > cluster administrator should be able to help with this problem.
> >
> > Best regards
> >
> > Victor
> >
> >
> > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. <nalveal at bio.puc.cl>:
> >
> > > Dear Gromacs users,
> > >
> > > I need your help, because when i run a dynamic in the cluster of my
> lab,
> > > the program makes the connection with NFS lost and my dynamics stop,
> > > together with the others of my coworkers.
> > > The version is GROMACS 4.5.4.
> > >
> > > This is the error:
> > >
> > > Could not chdir to home directory /home/fmontenegro: No such file or
> > > directory
> > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > >
> > > I hope can help me.
> > > Best regards!
> > >
> > > --
> > > Natalia Alveal Fuentealba
> > > Ingeniera en Bioinformática
> > > Laboratory of Membranes Proteins Structure and Signalling
> > > Departamento de Fisiología
> > > Pontificia Universidad Católica de Chile
> > > Alameda 340, Santiago, Chile
> > > Fono: 56-2-3542877
> > > --
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>
> --
> Natalia Alveal Fuentealba
> Ingeniera en Bioinformática
> Laboratory of Membranes Proteins Structure and Signalling
> Departamento de Fisiología
> Pontificia Universidad Católica de Chile
> Alameda 340, Santiago, Chile
> Fono: 56-2-3542877
> --
> Gromacs Users mailing list
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