[gmx-users] pbc_dx specific compilation or linking problem

Chris Neale chris.neale at utoronto.ca
Fri Mar 23 00:15:25 CET 2007

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.


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