Thanks Mark and Victor. I will see the checkpoint files. Best regards!!
2014-07-03 15:38 GMT-04:00 Mark Abraham <mark.j.abra...@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." <nalv...@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.vic...@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. <nalv...@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.vic...@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. <nalv...@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 > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > > > > posting! > > > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > -- > > > > 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! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > 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! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
