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

[Claudio J. Margulis]

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



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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