On Fri, Jun 7, 2013 at 2:06 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Running Amil's .tpr, the next output is from our CPU detection machinery. > While the Xeon 5500 is not exactly new, AFAIK there should be no reason for > the detection to fail. But the stack trace will tell. Good point. Amil, please post the cmake output and the CMakeFiles/CMakeError.log. Because the CPU detection probably also already failed there if this is the case.
Roland > > Mark > > > On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz <rol...@utk.edu> wrote: > >> 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 >> > -- > 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