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. 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? Read http://www.gromacs.org/mailing_lists/users.php