[gmx-users] Question about gcc version

[Justin A. Lemkul]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> Justin A. Lemkul wrote:
> > Hi All,
> >
> > I recently installed Gromacs version 3.3.3 on a dual-core Intel MacBook
> running
> > OS X 10.5.2 (Leopard).  The default gcc from XCode was 4.0.1, and the
> Gromacs
> > installation went just fine (serial and parallel) when using this gcc.  I
> know
> > that the download site mentions that gcc  4.1.x is broken, and the problems
> > with such compilers have been well-documented across this list, but I was
> > wondering if anyone know if gcc 4.0.1 was problematic as well.  I had no
> > problems during any phase of the installation, but I just wasn't sure if
> I'd
> > develop some strange error using an analysis tool.
> >
> > I can also install gcc-3.3 in another location, and can easily make that
> the
> > default gcc, but I was just curious to see if 4.0.1 was alright to avoid
> the
> > effort, if possible :)
> >
> I think it is fine, but you can run the test set to be ( a bit more ) sure.

Thanks David.  I ran the test set, and got the following:

$ ./gmxtest.pl all
No topol.tpr file in morse. grompp failed
FAILED. Check files in morse
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
Error not all 45 pdb2gmx tests have been done successfully
Only 38 energies in the log file

For the "No topol.tpr file in morse" error, the grompp.out file shows:

Fatal error:
number of coordinates in coordinate file (conf.gro, 1490)
             does not match topology (topol.top, 0)

...although I'm not sure why.

The dec+water failure has been discussed before, although the discrepancy is
slightly different than that listed on the wiki:

There are 5 terms to compare in the energy files

LJ (SR)          step  34:      -0.21167,  step  34:    -0.171631

The pdb2gmx.log file shows that there is some discrepancy in the .mdp
parameters:

WARNING 1 [file ../../../../em.mdp, line unknown]:
  Unknown left-hand 'bd-temp' in parameter file

checking input for internal consistency...
processing coordinates...

-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: futil.c, line: 345

File input/output error:
b4em.gro
-------------------------------------------------------

I'm guessing this is just a reflection of changes that have been made between
versions 3.3.2 and 3.3.3?  But I don't know what to make of the "38 energies in
log file."  Is there some more relevant output I can post to help clarify the
situation?

Thanks,
Justin

>
> > Thanks for any insights.
> >
> > -Justin
> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================