Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"
Hi, GROMACS works correctly if you have permissions to read and write and enough space to do so. But I expect that you can't try to run from $WORK using mdrun -cpi $HOME/old.cpt if $HOME is full. I suggest you consult the docs for the cluster, and consult your sysadmins for any help with your script. Mark On Sun, Feb 14, 2016 at 7:17 PM Ray Chaowrote: > Hi, Mark, > > Thank you for your response. I am not sure if this is the right way to > reply, because I cannot see the content of gmx maillist emails. > > I am running in my own space. Here is the story. Everybody has a $HOME and > $WORK directory on the cluster. The $HOME is for permanent storage with > 100GB disk space and $WORK is for temporary storage with 1TB storage. > Initially I was running my case on $HOME. Since the files begin to pile up, > the space is running out, I turned to the $WORK directory. At that time, I > began to receive such an error message. Even I then move my cases back to > $HOME, it did not work either. > > Best regards, > Lei Zhao > Ph.D Student in Mechanical Engineering, Virginia Tech > Mobile:+1-540-750-9042 > -- > 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.
Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"
Hi, Mark, Thank you for your response. I am not sure if this is the right way to reply, because I cannot see the content of gmx maillist emails. I am running in my own space. Here is the story. Everybody has a $HOME and $WORK directory on the cluster. The $HOME is for permanent storage with 100GB disk space and $WORK is for temporary storage with 1TB storage. Initially I was running my case on $HOME. Since the files begin to pile up, the space is running out, I turned to the $WORK directory. At that time, I began to receive such an error message. Even I then move my cases back to $HOME, it did not work either. Best regards, Lei Zhao Ph.D Student in Mechanical Engineering, Virginia Tech Mobile:+1-540-750-9042 -- 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.
Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"
Hi, You need write permission for the folder as well. Thus, run in your own file space. Mark On Sun, 14 Feb 2016 01:16 Ray Chaowrote: > Dear gmx users, > > Just a little revision for my last question. > > I am running my cases on the cluster. The simulation was always terminated > after running for a while. The error was always " > *cannot rename checkpoint file: maybe you are out of disk space*". However, > I have 1TB of disk > allocation, which is enough, and the disk is in good condition. Besides, I > created the .top .gro .mdp files on my own workstation and also changed the > permission from "read-only" to "read and write". The gromacs version is > 5.0.2 or 5.1.2 on the clusters. > > Is there any specific requirement about running gromacs on clusters? Your > response is very much appreciated. > > You all have a good Valentine's day. > -- > 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.