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

[Justin A. Lemkul]

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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>> --
>>> ========================================
>>>
>>> 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
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www interface
>>> or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
> 

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

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

========================================