[gmx-users] pbc_dx specific compilation or linking problem

Berk Hess gmx3 at hotmail.com
Fri Mar 23 09:42:47 CET 2007

>From: Chris Neale <chris.neale at utoronto.ca>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] pbc_dx specific compilation or linking problem
>Date: Thu, 22 Mar 2007 19:15:25 -0400
>I have installed gromacs successfully on many systems. Recently I found 
>that for two installations pbc_dx is not working properly. I initially 
>found that this is the case when using one of my own programs built on 
>template.c. I made that program more verbose and found that there are tens 
>of successful calls to pbc_dx but that eventually it hangs (for >10h). If I 
>repeat with a different trajectory the same thing happens, but at a 
>different number of successful calls. In order to get a cleaner test I use 
>g_rdf on a .gro file from this point on (g_rdf calls pbc_dx). On 
>compilations that I declare to work, g_rdf finishes in a couple of seconds. 
>I judge that there is some problem when tens of seconds have elapsed 
>without any result.
>i)One of these installations was installed by another (root) user via 
>apt-get. Since this didn't work, I have installed my own version using the 
>--prefix option to configure and that version works fine.
>ii)The other installation is the one that I made on my local computer. This 
>is the only installation that I have made as root (didn't use the --prefix 
>option to configure). It doesn't work. I then compiled a second time using 
>the --prefix option (with and without a newly compiled fftw using the 
>--prefix option) and this version has the same problem
>I then copied g_rdf from one of my working installations to my local 
>computer and executed it. It executes, but still hangs.
>I have assumed that there may be some problem with GMXRC. Therefore I have 
>sourced that file. g_rdf still hangs.
>It always hangs like this:
>Select a reference group and 1 group
>Group     0 (      System) has  5175 elements
>Group     1 (         DPC) has  5175 elements
>Select a group: 1
>Selected 1: 'DPC'
>Select a group: 1
>Selected 1: 'DPC'
>Reading frames from gro file 'Generated by trjconv', 5175 atoms.
>Reading frame       0 time    0.000
>My gromacs compilation is like this:
>export FFTW_LOCATION=/home/cneale/install/src/fftw-3.1.2/exec
>export GROMACS_LOCATION=/home/cneale/install/src/gromacs-3.3.1/exec
>./configure --prefix=$GROMACS_LOCATION
>make install
>make distclean
>After the configure stage, my config.log indicates CC=cc
>Many thanks if anybody has had this problem and can clear up for me what 
>mistake I have made.

Did I get this correct?
You have different installations compiled from exactly the same Gromacs 
Some of these run g_rdf and do not hang in pbc_dx, some run g_rdf and
do hang in pbc_dx.
The problems when running all happen on the same machine?

If this is the case, there can only be two explanations.
Or there is a memory managment error in Gromacs, which shows
up in pbc_dx.
Or there is a bug in a compiler.

With which compilers have the different installations been compiled?

Do you have a triclinic box?
There is a problem with triclinic boxes in 3.3.1, but that problem
will always show up with warnings, not silently.


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