Amil, would it be possible for you to compile with a different compiler? Ideally gcc 4.7.3. Alternative could you send us the stack for when it crashes? For that you need to: - compile with debug -DCMAKE_BUILD_TYPE=Debug - run under gdb "gdb --arg /path/to/mdrun {your mdrun arguments}" - enter "bt" after it crashes
Roland On Fri, Jun 7, 2013 at 12:19 PM, Amil Anderson <aander...@wittenberg.edu> wrote: > Roland, > > I have now run the regression test on my installation and it all fails for > runmd (segmentation fault). Don't see that anything else is being tested. > > I've placed the output of the make check (Make_check.out) at > > https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP > > I'll copy the first part here to give you a taste of it: > > ------------------------------------------------------------------------------- > [softwaremgmt@warp2-login build]$ more make_check.out > [ 64%] Built target gmx > [ 64%] Built target gmxfftw > [ 76%] Built target md > [ 92%] Built target gmxana > [ 92%] Built target editconf > [ 97%] Built target gmxpreprocess > [ 97%] Built target grompp > [ 98%] Built target pdb2gmx > [ 98%] Built target gmxcheck > [100%] Built target mdrun > [100%] Built target gmxtests > Test project /shared/software/temp/gromacs-4.6.1/build > Start 1: regressiontests/simple > 1/5 Test #1: regressiontests/simple ...........***Failed 0.83 sec > sh: line 1: 11622 Segmentation fault mdrun -notunepme -table ../table > -tabl > ep ../tablep > mdrun.out 2>&1 > > Abnormal return value for ' mdrun -notunepme -table ../table -tablep > ../table > p >mdrun.out 2>&1' was 139 > No mdrun output files. > FAILED. Check mdrun.out, md.log files in angles1 > sh: line 1: 11628 Segmentation fault mdrun -notunepme -table ../table > -tabl > ep ../tablep > mdrun.out 2>&1 > > Abnormal return value for ' mdrun -notunepme -table ../table -tablep > ../table > p >mdrun.out 2>&1' was 139 > No mdrun output files. > FAILED. Check mdrun.out, md.log files in angles125 > sh: line 1: 11637 Segmentation fault mdrun -notunepme -table ../table > -tabl > ep ../tablep -pd > mdrun.out 2>&1 > > Abnormal return value for ' mdrun -notunepme -table ../table -tablep > ../table > p -pd >mdrun.out 2>&1' was 139 > No mdrun output files. > FAILED. Check mdrun.out, md.log files in bham > > ... > > 0% tests passed, 5 tests failed out of 5 > > Total Test time (real) = 29.58 sec > > The following tests FAILED: > 1 - regressiontests/simple (Failed) > 2 - regressiontests/complex (Failed) > 3 - regressiontests/kernel (Failed) > 4 - regressiontests/freeenergy (Failed) > 5 - regressiontests/pdb2gmx (Failed) > -------------------------------------------------------------------------------------------- > > Amil > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008902.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists