[gmx-users] Problems with NFS

Thu Jul 3 22:42:19 CEST 2014

Thanks Mark and Victor. I will see the checkpoint files.
Best regards!!

2014-07-03 15:38 GMT-04:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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
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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