[Dock-fans] need HELP (segmentation error)

Praveen Madala p.madala at imb.uq.edu.au
Sun Sep 29 18:47:24 PDT 2002


Hi Scott Brozell,

Thank you for your advice, but still after making 
unlimited, the program is exiting with segmentation error.

What are the other possible reasons for this problem.

Here I am explain my problem again.

My database: DB1

My Targets: ABC, XYZ.

First trial:

Run the dock 5.1.1 (batch job) of DB1 database on ABC, the 
job was completed successfully.

NO PROBLEM WITH PROTEIN FILES

NO PROBLEM WITH DATABASE (DB1)

NO PROBLEM WITH THE METHOD

Second trial:

Run the dock 5.1.1 (batch job) of DB1 database on XYZ, the 
job exited, because of segmentation error.

MIGHT HAVE PROBLEM WITH PROTEIN FILES (XYZ)

Third trial:

Run dock 5.1.1 (batch job) of single molecule (from DB1 
databse). The docking was completed successfully.

IT SHOWS NO PROBLEM WITH PROTEIN FILES (XYZ)


I hope I have explained my problem, can someone... please 
give me a clue, why it is giving segmentation error.

regards,
Praveen



On Sat, 21 May 2005 12:00:33 -0700
  dock-fans-request at docking.org wrote:
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> Today's Topics:
> 
>   1. Re: Mac OS X, demo problem (Scott Brozell)
>   2. Re: need HELP (segmentation error) (Scott Brozell)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 20 May 2005 13:29:00 -0700
>From: Scott Brozell <sbrozell at scripps.edu>
> Subject: Re: [Dock-fans] Mac OS X, demo problem
> To: Kyle Allison <kralliso at umich.edu>
> Cc: dock-fans at docking.org
> Message-ID: 
><Pine.SGI.4.51.0505201308530.373470 at pusar.scripps.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> Hi Kyle,
> 
> On Thu, 19 May 2005, Kyle Allison wrote:
> 
>> I'm getting the following message when running the demo 
>>script:
>>
>> dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib
>>    Referenced from: 
>>/Users/kyleallison/Desktop/docking/dock.5.2_mac/
>> demo/2_site/../../bin/sphgen
>>    Reason: image not found
>>
>> Has anyone else had trouble running the demo?
> 
> Google is a useful tool for those not regularly reading 
>the list.
> Google on libg2c.0.dylib shows that others have had 
>trouble.
> In addition to Terry's suggestions below, you can try
> 
> g77 --print-file-name=libg2c.0.dylib
> 
> which will indicate whether you have g77 installed and 
>if so the full
> path of libg2c.0.dylib on your machine.  If a 
>libg2c.0.dylib does exist
> with a different path then you could short circut the 
>two install options
> mentioned by Terry via creating a symbolic link from 
>your libg2c.0.dylib
> to the required location, ie,
> 
> cd /usr/local/lib
> ln -s `g77 --print-file-name=libg2c.0.dylib`
> 
> Good luck,
> Scott Brozell
> 
>>Date: Mon, 18 Apr 2005 17:54:22 -0700
>>From: Terry Lang <terry at cgl.ucsf.edu>
>>Subject: Re: [Dock-fans] sphgen problem on OS X
>>
>>Dear Sebastien,
>>
>>    The sphgen code was compiled on the Mac OS X using a 
>>g77 compiler, which
>>it looks like you do not have.  You have two options:  1) 
>> you can
>>recompile sphgen (and probably all of the other 
>>executables) using the
>>compiler you have installed on your computer or 2) you 
>>can install the gcc
>>and g77 compilers on your system (for more information, 
>>go to
>>http://www.gnu.org/home.html).
>>
>>Sincerely,
>>Terry
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 20 May 2005 13:55:46 -0700
>From: Scott Brozell <sbrozell at scripps.edu>
> Subject: Re: [Dock-fans] need HELP (segmentation error)
> To: Praveen Madala <p.madala at imb.uq.edu.au>
> Cc: dock-fans at docking.org
> Message-ID: 
><Pine.SGI.4.51.0505201339170.373470 at pusar.scripps.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> Hi,
> 
> It is difficult to follow the thread of this question 
>because of the
> extraneous topics included with the posting.
> 
>> > When replying, please edit your Subject line so it is 
>>more specific
>> > than "Re: Contents of Dock-fans digest..."
> 
> In addition please delete the unrelated topics.
> I have trimmed some bloat.
> 
> 
> What are the limits of the system resources in your 
>shell ?
> See the man pages for the commands limit, ulimit, 
>unlimit.
> In particular, the stacksize is occasionally too small 
>for
> scientific applications.
> To increase the stacksize, the syntax is shell 
>dependent:
> csh like: limit stacksize unlimited
> ksh like: ulimit -s unlimited
> 
> Good luck,
> Scott Brozell
> 
> On Fri, 20 May 2005, Praveen Madala wrote:
> 
>> There is no chance of error in the smaller database,
>> because this database run perfectly well on anther
>> protein.
>>
>> Still I couldnt solve this problem.
>>
>> why DOCK will give error's like segemntation error and
>> SWAP memory etc....... (I icreased the SWAP memory, 
>>still
>> the same problem)
>>
>> > Date: Thu, 19 May 2005 15:04:31 +0530
>> >From: Prince Xavier <cochinprince at gmail.com>
>> > Subject: Re: [Dock-fans] need HELP
>> >
>> > Praveen,
>> > I think when you made the smaller database from the 
>>NCI
>> >database, some error
>> > would have crept into it. Please open your smaller
>> >database in a
>> > spread-sheet and veriy that there is no error. If 
>>there
>> >is error, try
>> > preparing a fresh database.
>> >
>> > Prince
>> >
>> > On 5/19/05, Praveen Madala <p.madala at imb.uq.edu.au>
>> >wrote:
>> >>
>> >> Hi DOCK users,
>> >>
>> >> I am Praveen, I am planing to do virtual screening of
>> >>NCI
>> >> database using DOCK 5.1.1 program.
>> >>
>> >> Before I jump in to big database I thought to run a 
>>test
>> >> run with small database. when I started running the 
>>DOCK
>> >> program on one target (ABC), It has successfully run 
>>the
>> >> program, with good predictions
>> >>
>> >> when I tried second test run with a anther protein
>> >>(DEF),
>> >> it has given a segmentation error, I tried again by
>> >> improving the RAM of the system. still It has given 
>>the
>> >> same problem. Then I got doubts on my protein files,
>> >> itself.
>> >>
>> >> Then I ran a thrird test run with single molecule
>> >>(instead
>> >> of databse) on protein DEF, this run was completed 
>>with
>> >> successful results. It means my protein files for DEF
>> >>are
>> >> not wrong.
>> >>
>> >> I didnt understand what is going wrong when I am 
>>running
>> >> small database with DEF protein,
>> >>
>> >> The difficult thing I found is, DOCK is not givign 
>>any
>> >>log
>> >> files to understand what is going wrong.
> 
> 
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