[gmx-developers] Re: grompp and vsites

[Michel Cuendet]

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.

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/
==========================================================