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

[Roland Schulz]

On Fri, Jun 7, 2013 at 2:06 PM, Mark Abraham <mark.j.abraham at 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 <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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>> >
>> >
>>
>>
>>
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