[gmx-users] Problems with g_energy

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================