[gmx-users] Problems with NFS

[Natalia Alveal F.]

we known that gromacs not find the directories. When mount the directories
in NFS, that we dont known is why gromacs makes that NFS falls down.

Any help!
Best regards.


2014-07-03 12:36 GMT-04:00 Victor Rosas Garcia <rosas.victor at gmail.com>:

> 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
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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