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? 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