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

[Claudio J. Margulis]

I renamed the directory as explained in my original message and rerun

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,