[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

[Mark Abraham]

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.

Mark


On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz <roland at 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 <aanderson at 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 at 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.
> > --
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