[gmx-users] Truncation of file traj.trr failed

ram bio rmbio861 at gmail.com
Tue Nov 10 15:03:22 CET 2009 

Dear justin,

The job was terminated as under:

vol 0.92  imb F  1% step 5860300, will finish Sun Nov 15 06:56:32 2009
=>> PBS: job killed: walltime 86438 exceeded limit 86400
mpiexec: killing job...

i think due to queueing system and maximum time being 24hrs.

i donot know how to know whether new cpt files are written all the
files i have are the same 2 cpt files state.cpt and state_prev.cpt.

when i did gmxcheck on both cpt files the output was
Checking file state.cpt

# Atoms  31609
Last frame         -1 time 2928.000


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1

for state_prev.cpt

# Atoms  31609
Last frame         -1 time 2896.000


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1

when the run is extended for the second time do gromacs generate a new
cpt file i mean with new name or same named files (state.cpt and
state_prev.cpt) with new check points written..

Please help

Thanks,

Ram




On Tue, Nov 10, 2009 at 7:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> As per the suggestions in the bug, i changed the line in
>> src/gmxlib/checkpoint.c file on the cluster:
>>
>> from
>> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t)
>> offset_low );
>>
>> to
>> outputfiles[i].offset = ( ((off_t) offset_high) << 32 )| ( (off_t)
>> offset_low & mask );
>>
>> and was able to use the -append option, my command was
>> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s
>> md20.tpr -cpi state.cpt -append
>>
>> and this run generated another 3ns production data (from the step
>> 2928600 - 5900000) and thus increasing the size of trr file to 4.8 GB
>> from 2.1 GB, because my simulation is for 20ns, i submitted one more
>> job with the same command after completing the 5.9 ns,
>>
>
> So the job crashed again, then?
>
>> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s
>> md20.tpr -cpi state.cpt -append
>>
>> now again the job is starting from same step 2928600, i also tried
>> using the command
>>
>> mpiexec -np 4 /usr/local/gromacs/bin/mdrun -v -g $myjob.log -s
>> md20.tpr -cpi state_prev.cpt
>>
>> -append
>>
>> here also the output is same that is starting from 2928600 step,
>>
>> i want to continue the run from 5900000 step, please let me know how
>> to proceed,  do i have to generate a new .tpr file (my mdp file is
>> defined for 20 ns and the output is md20.tpr) or can i use the same
>> tpr file (md20.tpr) or i require to change the command to continue..
>>
>
> Were new .cpt files actually written?  What does gmxcheck tell you about
> each of them?  It would seem that the simulation did not run long enough for
> new .cpt files to be generated, or there was otherwise some problem with
> writing the new file.  You should not need a new .tpr file if you have not
> yet completed the required 20 ns.  See here:
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> -Justin
>
>> Please help.
>>
>> Thanks,
>>
>> Ram
>>
>>
>>
>>
>> On Fri, Nov 6, 2009 at 10:15 PM, ram bio <rmbio861 at gmail.com> wrote:
>>>
>>> Dear Justin,
>>>
>>> Thanks for the information regarding the bug, will try the solutions
>>> in the site.
>>>
>>> Ram
>>>
>>> On Fri, Nov 6, 2009 at 8:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>> ram bio wrote:
>>>>>
>>>>> Dear Gromacs users,
>>>>>
>>>>> I am running a protein-lipid bilayer simulation for 20ns. I am using
>>>>> Gromacs version 4.0.5 and when i want to continue the mdrun using
>>>>> -append command , I am getting an error as follows:
>>>>>
>>>>> Getting Loaded...
>>>>> Reading file md20.tpr, VERSION 4.0.5 (single precision)
>>>>>
>>>>> Reading checkpoint file state.cpt generated: Fri Nov  6 15:22:25 2009
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> Program mdrun, VERSION 4.0.5
>>>>> Source code file: checkpoint.c, line: 1248
>>>>>
>>>>> Fatal error:
>>>>> Truncation of file traj.trr failed.
>>>>>
>>>>> Please suugest me how to overcome this error and continue the mdrun.
>>>>>
>>>> http://bugzilla.gromacs.org/show_bug.cgi?id=341
>>>>
>>>> I believe this bug has been fixed in the development version (available
>>>> through git).
>>>>
>>>> -Justin
>>>>
>>>>> Thanks,
>>>>>
>>>>> Ram
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> 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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>>>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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