[gmx-users] g_rdf on Mac OS X 10.3, 10.4

[David van der Spoel]

Jennifer Rendell wrote:
> Dear friends,
> 
> I have seen a couple of postings (January 2004, gmx-developers, David 
> Bostick, and November 2003, gmx-users, Kay Gottschalk) on segmentation 
> faults from g_rdf on Mac OS X systems.
> 
> I am using the "Getting Started" section of the  gromacs web pages, in 
> particular, the section on water, where the command g_rdf is called.
> 
> Below I show the results from two versions of gromacs, 3.2.1 on a Mac OS 
> X 10.4, and 3.1.5_pre2 on a Mac OS X 10.3. The results are similar in 
> that each results in a segmentation fault. g_rms and gmxcheck work as I 
> expect.
> 
> Any ideas on how to fix this? Jennifer
> 

Maybe you don't want to hear this, but please upgrade to 3.3.1 and try 
again. If the problem persists in the latest version please post a bugzilla.


> ******************************************************************************* 
> 
> 
> 1. gromacs 3.2.1 on Mac OS X 10.4 (Tiger). g_rdf gives the following
>    results:
> 
> % g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                Giving Russians Opium May Alter Current Situation
> 
>                             :-)  VERSION 3.2.1  (-:
> (deleted some lines)
>                                 :-)  g_rdf  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f      water.trr  Input        Generic trajectory: xtc trr trj gro 
> g96 pdb
>   -s      water.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro 
> g96 pdb
>                                    xml
>   -n     oxygen.ndx  Input, Opt!  Index file
>   -o        rdf.xvg  Output, Opt! xvgr/xmgr file
> (deleted all remaining option lines)
> 
> Reading file water.tpr, VERSION 3.2.1 (single precision)
> Reading file water.tpr, VERSION 3.2.1 (single precision)
> 
> How many groups do you want to calculate the RDF of?
> 1
> 
> Select a reference group and 1 group
> Group     0 (          OW) has   216 elements
> There is one group in the index
> There is one group in the index
> trn version: GMX_trn_file (single precision)
> Last frame         10 time   10.000
> 
> Segmentation fault
> 
> ******************************************************************************* 
> 
> 
> 2. gromacs 3.1.5_pre2 on Mac OS X 10.3 (Panther). g_rdf gives the
>    following results (which appear to be the same as the above):
> 
> $ g_rdf -f water.trr -n oxygen.ndx -o rdf.xvg -s water.tpr
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                Go Rough, Oppose Many Angry Chinese Serial killers
> 
>                           :-)  VERSION 3.1.5_pre2  (-:
> (deleted some lines)
>                                 :-)  g_rdf  (-:
> 
> Option     Filename  Type          Description
> ------------------------------------------------------------
>   -f      water.trr  Input         Generic trajectory: xtc trr trj gro 
> g96 pdb
>   -s      water.tpr  Input, Opt!   Structure+mass(db): tpr tpb tpa gro 
> g96 pdb
>   -n     oxygen.ndx  Input, Opt!   Index file
> (deleted all remaining option lines)
> 
> Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
> Reading file water.tpr, VERSION 3.1.5_pre2 (single precision)
> 
> How many groups do you want to calculate the RDF of?
> 1
> 
> Select a reference group and 1 group
> Group     0 (          OW) has   216 elements
> There is one group in the index
> There is one group in the index
> trn version: GMX_trn_file
> Last frame         10 time   10.000
> 
> Segmentation fault
> 
> ******************************************************************************* 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++