[gmx-developers] pdb2gmx segmentation fault

Michel Cuendet michel.cuendet at isb-sib.ch
Wed Jun 24 21:48:33 CEST 2009

Dear David,

Thanks for your reply.

For the pdb2gmx problem: I tried several compilers on several  
machines. I always get the segfault for this system and others. Note  
that  the CVS version from 24.01.2009 works. The version from  
19.05.2009 does not work, as well as the latest CVS.

Linux machines say  (in gdb):

>> Program received signal SIGSEGV, Segmentation fault.
>> 0xb7e5b727 in set_histp ()
>>  from
>> /export/home/mcuendet/Gromacs/gromacs-4.0.cvs_12.6.2009// 
>> i686_gcc4.2.4//lib/libgmxpreprocess.so.0
>> Current language:  auto; currently asm

And my mac says :
Process:         pdb2gmx [24224]
Path:            /Users/mitch/src/gromacs-4.0.cvs_12.6.2009/ 
Identifier:      pdb2gmx
Version:         ??? (???)
Code Type:       X86 (Native)
Parent Process:  bash [14724]
[ ... ]
Exception Type:  EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000
Crashed Thread:  0

Thread 0 Crashed:
0   libgmxpreprocess.0.dylib      	0x000d6e57 set_histp + 4791

Thread 0 crashed with X86 Thread State (32-bit):
   eax: 0x00000000  ebx: 0x000d5bb6  ecx: 0x00722710  edx: 0x00813400
   edi: 0xffffffff  esi: 0x0000002a  ebp: 0x000005e8  esp: 0xbfff1550
    ss: 0x0000001f  efl: 0x00010216  eip: 0x000d6e57   cs: 0x00000017
    ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
   cr2: 0x00000000

Binary Images:
     0x1000 -     0xbff7 +pdb2gmx ??? (???)  
<04482c196e9bdfbb5f681b1a8393594f> /Users/mitch/src/ 
    0xb9000 -   0x13dfe3 +libgmxpreprocess.0.dylib ??? (???)  
<3e42ee6d1c95ec45d57a6d84fb91d307> /Users/mitch/src/ 
   0x1cd000 -   0x37efef +libmd.5.dylib ??? (???)  
<c041b169750e6c6a5e6942f790d21259> /Users/mitch/src/ 
   0x39a000 -   0x5c0fe3 +libgmx.5.dylib ??? (???)  
<ba7950f5768b117da2e2b8b6dc1d0602> /Users/mitch/src/ 
0x8fe00000 - 0x8fe2db43  dyld 97.1 (???)  
<45ae763de6d253ccfc0eded8d82876a6> /usr/lib/dyld
[ ... ]

Note that in both cases, set_histp seems to be the culprit...

Can you please try with the 2guo entry from the PDB database to see if  
you can reproduce the error?


Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne

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