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

[ram bio]

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,

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..

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
>>> _______________________________________________
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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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>