[gmx-users] Problems with g_energy

[Gavin Melaugh]

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
>