[gmx-users] Problems with g_energy

[Gavin Melaugh]

Cheers Justin

Just to make sure then to run the simulation with -maxh to avoid the
24hr cut off I use the command:

mdrun -pd -s topol.tpr -maxh 23 (using 23 hrs to be overcautious)

then to restart:

mdrun -pd -cpi state.cpt
Do I have to use the  -append option in the above command to continue
writing to the existing files ?

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> 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.
>>
>
> That's not a bad idea, if you know there's a limit.  It looks like the
> file somehow got corrupted.  You might be able to parse out meaningful
> data from frames before the corruption using eneconv for the .edr file
> and trjconv for your trajectories.  Then, if you have a .cpt file from
> an earlier time point, you can restart.  If you've been continually
> over-writing the .cpt files, though, you won't be able to get an exact
> restart.
>
> -Justin
>
>> 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
>>
>>
>