[gmx-users] Problems with NFS

[Mark Abraham]

Hi,

GROMACS doesn't "make NFS go down," but it might expose the problem that
exists anyway - which happens frequently on clusters that aren't set up
appropriately. The GROMACS checkpoint process requires that the file system
be present, so that the checkpoint process can compute and record hash sums
of files that have been written to disk, so that GROMACS can guarantee the
integrity of your output with minimal loss, even if there's a power outage.
Your cluster admins are the people to whom to speak. Perhaps NAMD has
no/different checkpointing.

Mark
On Jul 3, 2014 6:47 PM, "Natalia Alveal F." <nalveal at bio.puc.cl> wrote:

> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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