[gmx-users] very strange directory dependent segmentation faults please HELP!

[David van der Spoel]

On 26 Dec 2003, Claudio J. Margulis wrote:

>No, 
>Gromacs is in the original place where --prefix 
>was set at compilation.
>
>Other things i have found out are:
>
>1)if i use the full path to the executable it runs fine
>You might think that i am doing something stupid like not having mdrun
>in my executable path, but this is not the case
>
>check this out
>
>!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>node1-claudiom 31 % which mdrun
>/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun
>


have you done
source /usr/local/gromacs/serial/i686-pc-linux-gnu/bin/GMXRC
(or the . equivalent for bash users)

>
>
>node1-claudiom 32 % mdrun
>                         :-)  G  R  O  M  A  C  S  (-:
>                                                                                                                                                   
>Segmentation fault
>node1-claudiom 33 %
>!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>BUT NOW
>
>!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>node1-claudiom 33 %/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun
>                         :-)  G  R  O  M  A  C  S  (-:
>                                                                                                                                                   
>                   Good gRace! Old Maple Actually Chews Slate
>                                                                                                                                                   
>                            :-)  VERSION 3.1.4  (-:
>                                                                                                                                                   
>                                                                                                                                                   
>       Copyright (c) 1991-2002, University of Groningen, The Netherlands
>         This program is free software; you can redistribute it and/or
>          modify it under the terms of the GNU General Public License
>         as published by the Free Software Foundation; either version 2
>             of the License, or (at your option) any later version.
>                                                                                                                                                   
>        :-)  /usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun  (-:
>                                                                                                                                                   
>Option     Filename  Type          Description
>------------------------------------------------------------
>  -s      topol.tpr  Input         Generic run input: tpr tpb tpa
>  -o       traj.trr  Output        Full precision trajectory: trr trj
>  -x       traj.xtc  Output, Opt.  Compressed trajectory (portable xdr
>format)
>
>
>
>
>IT RUNS FINE ...
>
>
>WEIRD! I don't understand ...
>
>
>
>
>
>
>
>
>On Fri, 2003-12-26 at 13:21, David van der Spoel wrote:
>> On 26 Dec 2003, Claudio J. Margulis wrote:
>> 
>> >I renamed the directory as explained in my original message and rerun
>> \
>> 
>> Have you run a source of GMXRC?
>> 
>> Have you moved gromacs directories after installing gromacs? Directories 
>> are hardcoded at compile time.
>> 
>> 
>> >
>> >strace mdrun (now as i explained in my original posting mdrun runs fine)
>> >
>> >
>> >The next events ( that come instead of the SIGSEGV)  are
>> >
>> >
>> >open("bromacs.dat", O_RDONLY)           = -1 ENOENT (No such file or
>> >directory)
>> >open("/usr/local/gromacs/serial/share/top/bromacs.dat", O_RDONLY) = 3
>> >close(3)                                = 0
>> >open("/usr/local/gromacs/serial/share/top/bromacs.dat", O_RDONLY) = 3
>> >fstat64(3, {st_mode=S_IFREG|0644, st_size=1133, ...}) = 0
>> >old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
>> >-1, 0) = 0x40014000
>> >read(3, "26\n\270\220\220\233\337\230\255\236\234\232\336\337\260"...,
>> >4096) = 1133
>> >
>> >
>> >
>> >
>> >
>> >
>> >and so on.
>> >
>> >
>> >Clues?
>> >Thanks!!
>> >
>> >
>> >
>> >
>> >
>> >On Fri, 2003-12-26 at 02:35, Lieven Buts wrote:
>> >> On Wednesday 24 December 2003 19:00, Claudio J. Margulis wrote:
>> >> > Does anybody understand this behavior:
>> >> >
>> >> > node1-claudiom 63 % pwd
>> >> > /scratch/claudiom/111
>> >> > node1-claudiom 64 % ls
>> >> > topol.tpr
>> >> > node1-claudiom 65 % mdrun
>> >> >
>> >> >                          :-)  G  R  O  M  A  C  S  (-:
>> >> >
>> >> > Segmentation fault
>> >> 
>> >> You could try running mdrun through strace, if the latter is available on your 
>> >> system. (It should be present on most Linux systems.)
>> >> 
>> >> To do this, use "strace mdrun", which will print a list of the system calls 
>> >> mdrun uses up to the point of the segmentation fault. This might provide a 
>> >> clue as to what it is trying to do. Since it crashes pretty quickly, there 
>> >> shouldn't be too many calls to sort through.
>> >> 
>> >> 
>> >> Happy holidays to all,
>> >
>> >_______________________________________________
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>> >gmx-users at gromacs.org
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>> >
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
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://xray.bmc.uu.se/~spoel
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