[gmx-developers] Re: grompp and vsites

[David van der Spoel]

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.


> 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/
> ==========================================================
> 
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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