[Dock-fans] SPHGEN segmentation fault

Philip Crawford p.crawford at unsw.edu.au
Wed Oct 12 18:34:00 PDT 2005


Terry,
Hi. I just recompiled sphgen.exe under cygwin after patching with bugfix 2
from the Dock bugfix site. It still gave a segmentation fault (core dumped)
when I executed sphgen in 2_site on the demo application.
Segmentation faults have many possible causes, one of which can be stack
size  allocation, which is compiled in on Windows applications. I'm a bit
rusty on this but I think that the default is 1 MB of stack space.
Here's the segmentation fault dumpfile contents:
-------
Exception: STATUS_ACCESS_VIOLATION at eip=00403DFD
eax=00000001 ebx=00000013 ecx=005F7490 edx=610063EE esi=00000003
edi=610063ED
ebp=0022EAF8 esp=0022E910 program=C:\cygwin\usr\local\bin\sphgen.exe, pid
3856, thread main
cs=001B ds=0023 es=0023 fs=003B gs=0000 ss=0023
Stack trace:
Frame     Function  Args
0022EAF8  00403DFD  (00503250, 0040F010, 0123FD10, 0151C3D0)
0022EFB8  0040166F  (00405240, 61814AD0, 61118080, 610063ED)
0022EFD0  004046F2  (00000001, 61814AD0, 0A0500A8, 0022F028)
0022F010  610068BC  (0022F028, 0022F850, 00000000, 7C912937)
0022FF90  61006AD0  (00000000, 00000000, 00000000, 00000000)
End of stack trace
-----------
I've experimented with modifying the reserved stack space of the executable,
sphgen.exe, in case that helped but it has had no effect. The only thing
that changes with successive stackdumps is the pid which is to be expected.

 
Cheers,
 
Phil
__________________________________________________
Philip Crawford, B. Comp. Sc., MIEEE
School of Medical Sciences
The University of NSW
Phone: +61-2-9385 2564
Mobile: +61-419-294 698
Fax: +61-2-9385 1059
Email: p.crawford at unsw.edu.au
__________________________________________________

-----Original Message-----
From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
On Behalf Of Terry Lang
Sent: Thursday, 13 October 2005 3:27 AM
To: Le Tien Dung
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] SPHGEN segmentation fault

Dear Le,

       Have you applied the bug fix for sphgen?  It can be found at 
http://dock.compbio.ucsf.edu/DOCK_5/DOCK_bugfixes.htm.

Sincerely,
Terry


Le Tien Dung wrote:

> Hello Dock-fans,
>  
> I have tried running the SPHGEN and all the time I got the 
> segmentation fault.
>  
> Can you suggest me how to solve this?
>  
> Thanks in advance
>  
> LE
>
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-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 


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