Hi, It should work, but apparently doesn't. Please open an issue at redmine.gromacs.org and include a tarball of your tpr files so we can see the problem happen and fix it.
Meanwhile, I suggest the approach of using gmx grompp to construct a run that will complete in the maximum time you can run, and to use gmx tpbconv to extend suitably for the next phase. Mark On Tue, 5 Apr 2016 16:51 Maud Jusot <maud.ju...@impmc.upmc.fr> wrote: > Hello again > > I still don’t manage to restart correctly REMD simulation (see my > previous message) but I can add some details. When it restarts, gromacs > doesn’t create new checkpoint files (no matter –cpt option is), and > doesn’t stop at maxh time. I tried with 3 different versions of gromacs > (4.6.5, 5.1.0 and 5.1.2) on two different clusters, so I am quite sure > the problem does not come from the installation nor from the version. > > It’s a big issue for me because I try to run 2.4 micro seconds > simulation and on the cluster I use I can’t do simulation for more than > 24h (which correspond to 300 ns approximately) without doing restart. So > without checkpoint file I am unable to re-launch my simulation. > > Is there something wrong in what I do ? > Does any body have an idea or do you think it's a bug and I should write > to the developers mailing list ? > > Thanks, > > Maud > > Le 29/03/2016 11:33, Maud Jusot a écrit : > > Dear Gromacs users, > > > > I tried to do a REMD simulation with gromacs 5.1 which is re-launched > > every hour (in a queuing system) with the -maxh option. > > The first time it was launched, it worked : the run stoped at the maxh > > time and it was re-launched with the checkpoint files and continued > > the simulation. But during this second run, when the maxh time was > > achieved (step 1981062), gromacs said that it was going to stop but it > > did not stop until the system kill the job (step 2545600) . > > > > I tried with different maxh times ( 1/0.95/0.20 hour) to be sure that > > the time between maxh and the cluster maxtime was sufficient, but in > > any case the second run continued until it reached the one hour and > > was killed by the system. > > > > I find this very strange that it works the first time and that the > > second time gromacs says that it has to stop but does not. > > Moreover, I tried the same work but with a classical simulation > > (without REMD) and this time there was no problem. > > Did I forget an option or something like that for maxh being > > compatible with the REMD ? > > I searched on the web and the mailing list but I did not find any > > recording problems between maxh and REMD. > > > > Do you have any idea of what the problem is ? > > > > Here is the command lines in my script myJob.slurm : > > --------------------- > > srun --mpi=pmi2 -K1 --resv-ports -n $SLURM_NTASKS mdrun_mpi -ntomp 1 > > -multi 8 -replex 500 -maxh 0.2 -deffnm mdA_ -cpi mdA_.cpt -cpo > > mdA_.cpt -v 2>> remdA.log > > # resubmit the same job at the end for a long run: > > sbatch myJob.slurm > > --------------------- > > > > Here is a part of my remdA.log file : > > --------------------- > > starting mdrun 'myPeptide' > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > starting mdrun 'myPeptide' > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > 120000000 steps, 240000.0 ps (continuing from step 655701, 1311.4 ps). > > > > Step 1981061: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > Step 1981062: Run time exceeded 0.198 hours, will terminate the run > > > > step 1981100, will finish Sat Mar 26 11:14:40 2016 > > step 1981200, will finish Sat Mar 26 11:14:40 2016 > > ... > > step 2545600, will finish Sat Mar 26 11:15:49 2016srun: Job step > > aborted: Waiting up to 32 seconds for job step to finish. > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > > > Received the TERM signal, stopping at the next NS step > > --------------------- > > > > Thanks a lot, > > > > Maud > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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