[gmx-users] Problems with g_energy

[Gavin Melaugh]

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