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

[Roland Schulz]

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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