[gmx-users] segmentation fault in g_anaeig

[Inon Sharony]

Thanks, Tsjerk, you're absolutely right. I looked at the bugzilla  
reports about g_anaeig. Bug 30 was already fixed on my version of the  
source (pre-compilation) code. Bug 198 might be still relevant since  
it's status is listed as NEW and it hasn't been resolved yet. The  
bugzilla listing is as follows:

Bug 198:

(quote:)

I encountered a segmentation fault when running g_anaeig, and found
out that it occurred when reading the eigenvectors. Apparently,
someone reported a similar problem for GMX 3.3.1. However, I looked
for the differences between the versions in eigio.c, and found out
that the original 3.3.1 code worked fine for me (under the specified
platform at least).

The changes I introduced:diff eigio.c eigio.org.c

110,112c110,112

  <   /* eignr=NULL;  */
  <   /* eigval=NULL; */
  <   /*eigvec=NULL; */
---
>   eignr=NULL;   eigval=NULL;   eigvec=NULL;

Best,

Ran.

(end quote)


I'm not sure I understand how to implement this change: Currently, in  
the eigio.c file in my source code the three lines do appear. Should I  
turn them into comment lines and re-compile?

For general reference, I'm running GROMACS 3.3.3 on an AMD 64-bit  
quadrocore, running under Fedora 8 and using bash. Any further  
relevant details will be  given happily.


Thanks again,


Inon.

Quoting "Tsjerk Wassenaar" <tsjerkw at gmail.com>:

> Hi Inon,
>
> Please be as complete as you can when posting questions. You've
> omitted the (probably) most important piece of information: what
> version are you using? (You might also want to include platform,
OS,
> compiler, etc.). Note that just a few days ago it was already
reported
> on this list that g_anaeig of version 3.3.3 gave a segfault.
>
> Cheers,
>
> Tsjerk
>
> On Sun, Aug 3, 2008 at 2:57 PM, Inon Sharony
<InonShar at post.tau.ac.il> wrote:
>>  I am preforming a normal mode analysis (NMA) in Pentane, using
the
>> following command sequence (all functions ending in *_d are so
named because
>> they were compiled in double-precision into a directory where the
single
>> precision-functions already existed):
>>
>> editconf_d
>>
>> grompp_d em.mdp   ;energy minimization
>>
>> mdrun_d em.mdp
>>
>> grompp_d nm.mdp  ;write Hessian matrix
>>
>> mdrun_d nm.mdp
>>
>> g_nmeig_d
>>
>> g_anaeig_d
>>
>> when running this last command I got:
>>
>> trn version: GMX_trn_file (double precision)
>> Read mass weighted average/minimum structure with 5 atoms from
eigenvec.trr
>> Segmentation fault
>>
>> Why do I get a segmentation fault (segfault)?
>>
>> Could it be because the energy minimization only reached a maximal
force of
>> 1E-02 kJ / mole nm instead of the recommended 1E-05? Or is it some
more
>> serious problem?
>>
>> I looked at the eigenfreq.xvg and saw 2 zero frequencies, and 4
more which
>> are nearly zero.
>>
>> I've already issued "make distclean" before the re-compilation in
>> double-precision (see my
>>
http://www.gromacs.org/pipermail/gmx-users/2008-August/035535.html)
>>
>> Also, I viewed the eigenvec.tpr file and, indeed, the coordinates
are in
>> double-precision format (i.e., five significant digits to the
right of the
>> decimal point are non-zero).
>>
>> Any and all assistance would be greatly appreciated.
>> Enjoy your weekend,
>>
>> --
>> Inon   Sharony
>> ×™× ×•×Ÿ     ×©×¨×•× ×™
>> +972(3)6407634
>> atto.TAU.ac.IL/~inonshar
>> Please consider your environmental responsibility before printing
this
>> e-mail.
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>

-- 
Inon   Sharony
×™× ×•×Ÿ     ×©×¨×•× ×™
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing
this e-mail.