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

[David van der Spoel]

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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-- 
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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