[gmx-developers] Re: grompp and vsites

[Berk Hess]

David van der Spoel wrote:
> Michel Cuendet wrote:
>>
>> Dear Berk and David,
>>
>> Sorry, the SegFault appears also with a newly downloaded tree from
>> the CVS. And the error appears on several machines with several
>> compilers.
>>
>> You can get the input files for reproducing the problem at :
>> ludwig-sun1.unil.ch/~mcuendet/grompp_error.tgz
>>
>> On linux systems, the version without shared library works.
>> Unfortunately, on my mac with gcc4.0.1, even this one fails. It gives
>> the messages below.
>>
> I tried
>
> ~/software-4.0/bin/grompp -c confout.gro -v -e ener.edr -t
> traj_last.trr (latest release)
> ~/software-4.1/bin/grompp -c confout.gro -v -e ener.edr -t
> traj_last.trr (latest git development)
>
> and I have reprodced a crash in enx_names on my mac.
>
> Since CVS is dead this will only be fixed in the git repository.
If the energy file reading is the problem, it is not a serious problem.
We should have already gotten rid of the energy file reading by grompp.
Since we now have proper checkpointing it is no longer required.

Berk
>
>
>> Cheers,
>> Michel
>>
>> ---------------------------------------------------------------------------------------------------------------
>>
>> [ ... normal output ... ]
>> Will read whole trajectory
>> trn version: GMX_trn_file (single precision)
>> Last frame          0 time 1200.000
>> Using frame at t = 1200 ps
>> Starting time for run is 0 ps
>> Note: enx file_version 1, software version 2
>> Opened ener.edr as single precision energy file
>> Note: enx file_version 1, software version 2
>> grompp(26248) malloc: *** error for object 0x72617453: Non-aligned
>> pointer being freed
>> *** set a breakpoint in malloc_error_break to debug
>> Bus error
>> ---------------------------------------------------------------------------------------------------------------
>>
>> Exception Type:  EXC_BAD_ACCESS (SIGBUS)
>> Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000369f2c
>> Crashed Thread:  0
>>
>> Thread 0 Crashed:
>> 0   grompp                            0x00158651 do_enxnms + 449
>>
>> Thread 0 crashed with X86 Thread State (32-bit):
>>   eax: 0x00436000  ebx: 0x00158499  ecx: 0xbfff971c  edx: 0x91276286
>>   edi: 0x00000000  esi: 0x00369f2c  ebp: 0x00504730  esp: 0xbfff99c0
>>    ss: 0x0000001f  efl: 0x00010286  eip: 0x00158651   cs: 0x00000017
>>    ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
>>   cr2: 0x00369f2c
>>
>> Binary Images:
>>     0x1000 -   0x3a1fef +grompp ??? (???)
>> <001af0a0cfbe0ae3bb293da6c9ac912a>
>> /Users/mitch/src/gromacs-4.0.cvs_12.6.2009/osx_gcc4.0.1/bin/grompp
>> 0x8fe00000 - 0x8fe2db43  dyld 97.1 (???)
>> <45ae763de6d253ccfc0eded8d82876a6> /usr/lib/dyld
>> 0x90009000 - 0x900eaff7  libxml2.2.dylib ??? (???)
>> <2f6b294896866822330a8888b7f53b75> /usr/lib/libxml2.2.dylib
>> 0x90242000 - 0x9026ffeb  libvDSP.dylib ??? (???)
>> <4daafed78a471133ec30b3ae634b6d3e>
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
>>
>> 0x91275000 - 0x913dcff3  libSystem.B.dylib ??? (???)
>> <b47c8e6e45aef620730710a732bf1930> /usr/lib/libSystem.B.dylib
>> 0x915cf000 - 0x91708ff7  libicucore.A.dylib ??? (???)
>> <cac059ebdac7d9a63ee0f7a648c9f6cf> /usr/lib/libicucore.A.dylib
>> 0x919b3000 - 0x919c1ffd  libz.1.dylib ??? (???)
>> <a98b3b221a72b54faf73ded3dd7000e5> /usr/lib/libz.1.dylib
>> 0x91d7a000 - 0x91d81fe9  libgcc_s.1.dylib ??? (???)
>> <e280ddf3f5fb3049e674edcb109f389a> /usr/lib/libgcc_s.1.dylib
>> 0x92d56000 - 0x93114fea  libLAPACK.dylib ??? (???)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
>>
>> 0x93118000 - 0x93118ffd  com.apple.Accelerate.vecLib 3.4.2 (vecLib
>> 3.4.2)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
>>
>> 0x942ae000 - 0x946befef  libBLAS.dylib ??? (???)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>>
>> 0x94928000 - 0x94928ffd  com.apple.Accelerate 1.4.2 (Accelerate
>> 1.4.2)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
>> 0x9515b000 - 0x951d8fef  libvMisc.dylib ??? (???)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
>>
>> 0x95677000 - 0x9573eff2  com.apple.vImage 3.0 (3.0)
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
>>
>> 0x95a1a000 - 0x95a1efff  libmathCommon.A.dylib ??? (???)
>> /usr/lib/system/libmathCommon.A.dylib
>> 0x95a1f000 - 0x95a7cffb  libstdc++.6.dylib ??? (???)
>> <f75e5133d72769de5ce6c06153fc65f6> /usr/lib/libstdc++.6.dylib
>> 0xffff0000 - 0xffff1780  libSystem.B.dylib ??? (???)
>> /usr/lib/libSystem.B.dylib
>>
>> ---------------------------------------------------------------------------------------------------------------
>>
>>
>>
>> On 26 juin 09, at 12:00, gmx-developers-request at gromacs.org wrote:
>>
>>> Are you really, really sure you don't have any compilations problems?
>>> Did you try to compile from a completely clean tree?
>>> Also the energy file format has changed. Reading a new energy file
>>> with a pre 4.0.4 version of g_energy might give a segv and not a fatal
>>> error.
>>>
>>> Berk
>>
>> ==========================================================
>> Michel Cuendet, Ph.D
>> Molecular Modeling Group
>> Swiss Institute of Bioinformatics
>> CH-1015 Lausanne
>> Switzerland
>> http://ludwig-sun1.unil.ch/~mcuendet/
>> ==========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use thewww
>> interface or send it to gmx-developers-request at gromacs.org.
>
>