Re: [gmx-users] Replica exchange checkpoint error
Hello Mark It makes sense to me , I have already restarted my simulations, hopefully it will write up cpt as it supposed to do. Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Mark Abraham Date: 28/1/18 1:17 am (GMT+10:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange checkpoint error Hi, They got opened immediately. Fifteen minutes before the checkpoint file. Mark On Sat, Jan 27, 2018, 15:09 金 瑞涛 wrote: > Hello Mark > > Thanks for repling me, i am wondering if it is file system problem, why > the other files like trr, xtc and log file were still updated? > > Best regards > > Riotto > > > > Sent from my Samsung Galaxy smartphone. > > > Original message > From: Mark Abraham > Date: 28/1/18 12:47 am (GMT+10:00) > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Replica exchange checkpoint error > > Hi, > > That sounds most likely a file system has decided to go missing by the time > the first checkpoint file is written after fifteen minutes. As such, all > you can do is try again and complain to the cluster admins if it keeps > happening. > > Mark > > On Fri, Jan 26, 2018, 04:09 金 瑞涛 wrote: > > > Dear Gromacs users and developers > > > > > > I am currently facing a problem from one of my simulations. I am doing > > replica exchange simulation which has 48 subsystems, when I started the > > simulation, everything wss fine, but when I restarted them from > checkpoint > > file, they looked running, were keeping generating log file, trr file, > edr > > file, etc, but not checkpoint file were generated at all. > > > > > > The version I am using is gromacs/5.1.3, any idea what is going wrong > with > > simulations of grimaces? > > > > > > Best regards > > > > > > Riotto > > > > > > -- > > 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. > -- > 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. -- 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] Replica exchange checkpoint error
Yes On Sat, Jan 27, 2018, 15:10 金 瑞涛 wrote: > Hello Dhaniram > > Thanks for repling me! Is -append option a default option? > > Best regards > > Riotto > > > > Sent from my Samsung Galaxy smartphone. > > > Original message > From: Dhaniram Mahato > Date: 27/1/18 3:14 pm (GMT+10:00) > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Replica exchange checkpoint error > > you can try by adding this line in your mdrun_mpi command. > > mdrun_mpi -s topol.tpr -cpi state.cpt -append -multi 48 > -- > 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. > -- 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] Replica exchange checkpoint error
Hi, They got opened immediately. Fifteen minutes before the checkpoint file. Mark On Sat, Jan 27, 2018, 15:09 金 瑞涛 wrote: > Hello Mark > > Thanks for repling me, i am wondering if it is file system problem, why > the other files like trr, xtc and log file were still updated? > > Best regards > > Riotto > > > > Sent from my Samsung Galaxy smartphone. > > > Original message > From: Mark Abraham > Date: 28/1/18 12:47 am (GMT+10:00) > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Replica exchange checkpoint error > > Hi, > > That sounds most likely a file system has decided to go missing by the time > the first checkpoint file is written after fifteen minutes. As such, all > you can do is try again and complain to the cluster admins if it keeps > happening. > > Mark > > On Fri, Jan 26, 2018, 04:09 金 瑞涛 wrote: > > > Dear Gromacs users and developers > > > > > > I am currently facing a problem from one of my simulations. I am doing > > replica exchange simulation which has 48 subsystems, when I started the > > simulation, everything wss fine, but when I restarted them from > checkpoint > > file, they looked running, were keeping generating log file, trr file, > edr > > file, etc, but not checkpoint file were generated at all. > > > > > > The version I am using is gromacs/5.1.3, any idea what is going wrong > with > > simulations of grimaces? > > > > > > Best regards > > > > > > Riotto > > > > > > -- > > 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. > -- > 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] Replica exchange checkpoint error
Hello Dhaniram Thanks for repling me! Is -append option a default option? Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Dhaniram Mahato Date: 27/1/18 3:14 pm (GMT+10:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange checkpoint error you can try by adding this line in your mdrun_mpi command. mdrun_mpi -s topol.tpr -cpi state.cpt -append -multi 48 -- 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] Replica exchange checkpoint error
Hello Mark Thanks for repling me, i am wondering if it is file system problem, why the other files like trr, xtc and log file were still updated? Best regards Riotto Sent from my Samsung Galaxy smartphone. Original message From: Mark Abraham Date: 28/1/18 12:47 am (GMT+10:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange checkpoint error Hi, That sounds most likely a file system has decided to go missing by the time the first checkpoint file is written after fifteen minutes. As such, all you can do is try again and complain to the cluster admins if it keeps happening. Mark On Fri, Jan 26, 2018, 04:09 金 瑞涛 wrote: > Dear Gromacs users and developers > > > I am currently facing a problem from one of my simulations. I am doing > replica exchange simulation which has 48 subsystems, when I started the > simulation, everything wss fine, but when I restarted them from checkpoint > file, they looked running, were keeping generating log file, trr file, edr > file, etc, but not checkpoint file were generated at all. > > > The version I am using is gromacs/5.1.3, any idea what is going wrong with > simulations of grimaces? > > > Best regards > > > Riotto > > > -- > 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. -- 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] Replica exchange checkpoint error
Hi, That sounds most likely a file system has decided to go missing by the time the first checkpoint file is written after fifteen minutes. As such, all you can do is try again and complain to the cluster admins if it keeps happening. Mark On Fri, Jan 26, 2018, 04:09 金 瑞涛 wrote: > Dear Gromacs users and developers > > > I am currently facing a problem from one of my simulations. I am doing > replica exchange simulation which has 48 subsystems, when I started the > simulation, everything wss fine, but when I restarted them from checkpoint > file, they looked running, were keeping generating log file, trr file, edr > file, etc, but not checkpoint file were generated at all. > > > The version I am using is gromacs/5.1.3, any idea what is going wrong with > simulations of grimaces? > > > Best regards > > > Riotto > > > -- > 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] Replica exchange checkpoint error
you can try by adding this line in your mdrun_mpi command. mdrun_mpi -s topol.tpr -cpi state.cpt -append -multi 48 -- 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.
[gmx-users] Replica exchange checkpoint error
Dear Gromacs users and developers I am currently facing a problem from one of my simulations. I am doing replica exchange simulation which has 48 subsystems, when I started the simulation, everything wss fine, but when I restarted them from checkpoint file, they looked running, were keeping generating log file, trr file, edr file, etc, but not checkpoint file were generated at all. The version I am using is gromacs/5.1.3, any idea what is going wrong with simulations of grimaces? Best regards Riotto -- 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.
