Cheers Justin Just to make sure then to run the simulation with -maxh to avoid the 24hr cut off I use the command:
mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious) then to restart: mdrun -pd -cpi state.cpt Do I have to use the -append option in the above command to continue writing to the existing files ? Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi justin >> >> Basically the gmxdump produces the same as below as does gmxcheck. >> gmxcheck also produces the following: >> >> Checking energy file ener.edr >> >> Opened ener.edr as single precision energy file >> frame: 0 (index 0), t: 0.000 Reading energy >> frame 4000 time 40000.000 WARNING: there may be something >> wrong with energy file ener.edr >> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >> to skip frame expect a crash though >> Timesteps at t=43010 don't match (10, -43010) >> >> WARNING: there may be something wrong with energy file ener.edr >> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >> to skip frame expect a crash though >> Timesteps at t=0 don't match (-43010, 0) >> >> WARNING: there may be something wrong with energy file ener.edr >> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >> Trying to skip frame expect a crash though >> >> >> It is at the point 43010 ps where the simulation had more than likely >> exceeeded the queue limit. >> Do you think it would be safer to use the -maxh option of mdrun ? as my >> jobs several days in duration. >> > > That's not a bad idea, if you know there's a limit. It looks like the > file somehow got corrupted. You might be able to parse out meaningful > data from frames before the corruption using eneconv for the .edr file > and trjconv for your trajectories. Then, if you have a .cpt file from > an earlier time point, you can restart. If you've been continually > over-writing the .cpt files, though, you won't be able to get an exact > restart. > > -Justin > >> Cheers >> >> Gavin >> >> >> >> Justin A. Lemkul wrote: >>> >>> Gavin Melaugh wrote: >>>> Hi folks >>>> >>>> I have recently encountered some problems with g_energy which I >>>> have not >>>> encountered before. I am running simulations for 32 molecular cages on >>>> 16 cpus in our local cluster. The maximum time for any one job is 24 >>>> hrs. Therfore after 24 hrs the jobs are killed so I countinue the job >>>> using the following script: >>>> >>>> #!/bin/bash >>>> #PBS -N mdsubhexcge >>>> #PBS -q long_eth >>>> #PBS -l nodes=2:ppn=8 >>>> #PBS -e test.e >>>> #PBS -o test.o >>>> #PBS -l walltime=23:59:59 >>>> >>>> . /etc/profile.d/modules.sh >>>> . ~/.bashrc >>>> >>>> cd /home/gmelaugh/phd/subhexyl/long600to200 >>>> cat $PBS_NODEFILE > machinefile >>>> >>>> module load maui torque >>>> >>>> mpirun -machinefile machinefile -np 16 >>>> /home/gmelaugh/gromacs-4.0.7-parallel/bin/mdrun -pd -s topol.tpr -cpi >>>> state.cpt -append >>>> >>>> >>>> The bottom command as I gather continues to write the relevant >>>> information to the relevant files starting from the last checkpoint. >>>> This seems to be the case as the new data is written to both the traj >>>> and log files. I am however encountering the following errors when >>>> trying to run g_energy: >>>> >>>> Reading energy frame 4000 time 40000.000 WARNING: >>>> there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >>>> to skip frame expect a crash though WARNING: >>>> there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >>>> to skip frame expect a crash though WARNING: >>>> there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >>>> to skip frame expect a crash though WARNING: >>>> there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. Trying >>>> to skip frame expect a crash though WARNING: >>>> there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=0, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> WARNING: there may be something wrong with energy file ener.edr >>>> Found: step=0, nre=0, ndisre=0, nblock=-1125995535, time=0. >>>> Trying to skip frame expect a crash though >>>> >>>> ------------------------------------------------------- >>>> Program g_energy, VERSION 4.0.7 >>>> Source code file: smalloc.c, line: 179 >>>> >>>> Fatal error: >>>> Not enough memory. Failed to realloc 846361600 bytes for fr->ener, >>>> fr->ener=0x7b0b40 >>>> (called from file enxio.c, line 354) >>>> ------------------------------------------------------- >>>> >>>> "I'd Like Monday Mornings Better If They Started Later" (Garfield) >>>> : Cannot allocate memory >>>> >>>> There is ample memory space on my machine so I can't see where the >>>> problem lies. Is there a way of viewing the energy file in nonbinary >>>> format? or has anybody ever come across this problem before? >>>> >>> You can run both gmxcheck and gmxdump on the .edr file. What does >>> that show? >>> >>> -Justin >>> >>>> Cheers >>>> >>>> Gavin >> >> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? 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