User reported it's problem with input file.
2009/4/15 annalisa bordogna <annalisa.bordo...@gmail.com>: > Hi, > I received a similar error during an equilibration by steepest descent in > which I had posed constraints on water, leaving the protein free to move. > I suggest to control your mdp file... maybe you did the same thing and the > system collapsed or exploded (you can see that reading the log file: if this > is the cause, you should see problems regarding water). > > Cheers, > Annalisa > > 2009/4/13 Justin A. Lemkul <jalem...@vt.edu> >> >> >> nam kim wrote: >>> >>> process crashes around 100 steps out of 1000 requested. >>> >> >> Fine, but you still haven't answered my question. Do you receive any >> other messages? >> >> Do other systems run on the specific hardware you're using? You may just >> have some instability in this particular system that is causing a crash. >> Examine the trajectory, see what's going wrong, and post any other >> relevant error messages, if you receive any. Often times there is some >> output before a seg fault. >> >> -Justin >> >>> On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul <jalem...@vt.edu> >>> wrote: >>>> >>>> nam kim wrote: >>>>> >>>>> I have segmentation fault error while running mdrun_mpi( gromacs >>>>> 4.0.4). >>>>> I have installed gromacs 4.0.4 two month ago and been working fine. >>>>> Today, I just got Segment errors. Rebooting does not much help. >>>>> >>>>> Here is log: >>>>> >>>>> [rd:06790] *** Process received signal *** >>>>> [d:06790] Signal: Segmentation fault (11) >>>>> [rd:06790] Signal code: (128) >>>>> [rd:06790] Failing at address: (nil) >>>>> [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] >>>>> [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] >>>>> [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] >>>>> [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] >>>>> [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] >>>>> [rd:06790] [ 5] >>>>> /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] >>>>> [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] >>>>> [rd:06790] *** End of error message *** >>>>> >>>> Are there any other messages from mdrun? Anything printed to the screen >>>> (LINCS warnings, etc)? >>>> >>>> -Justin >>>> >>>>> Thanks >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-us...@gromacs.org >>>>> http://www.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 >>>> Graduate Research Assistant >>>> 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-us...@gromacs.org >>>> http://www.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 >> Graduate Research Assistant >> 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-us...@gromacs.org >> http://www.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-us...@gromacs.org > http://www.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://www.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
