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 <rmbio...@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 <jalem...@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@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-requ...@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@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
