[gmx-users] Problems with g_energy

[Justin A. Lemkul]

Gavin Melaugh wrote:
> 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 ?
> 

Yep.

-Justin

> 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
>>>
> 
> 

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

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

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