[gmx-users] RE: pbc_dx specific compilation or linking problem

[Chris Neale]

Synopsis:
1. some versions of gcc are problematic for pbc_dx
2. apt-get edgy/universe gromacs 3.3.1-1 may have a broken pbc_dx
3. Detail that you requested (probably can be ignored)
###

1. Based on your reply I have downgraded my version of gcc and this has 
solved the problem.
The compiler that didn't work was:
cc (GCC) 4.1.2 20060928 (prerelease) (Ubuntu 4.1.1-13ubuntu5)
The compiler that did work was:
cc (GCC) 3.3.6 (Ubuntu 1:3.3.6-13ubuntu2)

2. For your notes, the apt-get command that retreives this:
Get:1 http://ca.archive.ubuntu.com edgy/main fftw3 3.1.1-2 [990kB]
Get:2 http://ca.archive.ubuntu.com edgy/universe gromacs 3.3.1-1 [3377kB]
Has the same problem with g_rdf (although tools that don't use pbc_dx 
work fine)

3. Here is the detail that you asked for, but it is probably irrelevant 
now that I have verified that it was a compiler issue. Thanks to your 
assistance I can now do my analysis on my local computer and avoid huge 
data transfers.

 >Did I get this correct? You have different installations compiled from
 >exactly the same Gromacs source. Some of these run g_rdf and do not hang
 >in pbc_dx, some run g_rdf and do hang in pbc_dx.

This is correct

 >The problems when running all happen on the same machine?
No. (See below for more details)
 >With which compilers have the different installations been compiled?

 > Do you have a triclinic box?
No, cubic

Computer 1:
Opteron Cluster
[configure/make]
cc (GCC) 3.3.3 (SuSE Linux)
g_rdf ok

Computer 2:
Pentium4 Cluster
[configure/make]
cc (GCC) 3.2 20020903 (Red Hat Linux 8.0 3.2-7)
g_rdf ok

Computer 3:
Pentium4
[apt-get]
g_rdf hangs

Computer 3 (same as above):
[configure/make]
cc (GCC) 3.2 20020903 (Red Hat Linux 8.0 3.2-7)
g_rdf ok

Computer 4:
Pentium4
[configure/make]
cc (GCC) 4.1.2 20060928 (prerelease) (Ubuntu 4.1.1-13ubuntu5)
g_rdf hangs

Computer 4 (same as above):
[configure/make]
cc (GCC) 3.3.6 (Ubuntu 1:3.3.6-13ubuntu2)
g_rdf ok