Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
User reported it's problem with input file. 2009/4/15 annalisa bordogna : > 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 >> >> >> 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 >>> 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 >> >
Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault
process crashes around 100 steps out of 1000 requested. On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul 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 > ___ gmx-users mailing listgmx-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
[gmx-users] mdrun_mpi error Signal: Segmentation fault
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 *** Thanks ___ gmx-users mailing listgmx-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
[gmx-users] gromac 4.0.4 g utilities freeze the OS with Out of Memory
I have experienced OS (RedHat Enterprise) for a hour or 3 hours whiling using gromacs 4.0.4 g-utilities such as g_vanhove. My log error messages are: Out of Memory g_vanhove_mpi Out of Memory g_anaeig_mpi Are g-utilites of Gromacs 4.0.4 buggy? Thanks -Nam ___ gmx-users mailing listgmx-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
