[gmx-users] Test suit failures

[Justin A. Lemkul]

Bert wrote:
> Dear gmx-users,
> 
> I have done a test using test suit 4.0.4, and I got some failures as follows.
> 
> All 16 simple tests PASSED
> FAILED. Check files in aminoacids
> FAILED. Check files in field
> FAILED. Check files in tip4p
> FAILED. Check files in water
> 4 out of 14 complex tests FAILED

Check the files in these directories to see if the differences are acceptable, 
as explained on the wiki:

http://wiki.gromacs.org/index.php/Test-Set

<snip>

> 16 out of 63 kernel tests FAILED

These failures are a known issue and a bugzilla has been filed.  They affect 
Buckingham interactions.

> All 45 pdb2gmx tests PASSED
> 
> My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the
> same failures on my Xeon 8 core based linux. For example, in
> /kernel/kernel020
> 

As warned on the Gromacs site: "WARNING: do not use the gcc 4.1.x set of 
compilers. They are broken. These compilers come with recent Linux distrubutions 
like Fedora 5/6 etc."

Users have reported non-functional or improperly-functioning executables 
produced by the 4.1.x series.

-Justin

> checkpot.out gives:
> --------------------------------------------------------------------------
> comparing energy file reference_s.edr and ener.edr
> 
> There are 39 terms in the energy files
> 
> There are 12 terms to compare in the energy files
> 
> LJ-14            step   0:      -63.1209,  step   0:      6.50742
> Potential        step   0:      -321.601,  step   0:     -251.972
> 
> Files read succesfully
> --------------------------------------------------------------------------
> checkvir.out gives:
> --------------------------------------------------------------------------
> comparing energy file reference_s.edr and ener.edr
> 
> There are 39 terms in the energy files
> 
> There are 25 terms to compare in the energy files
> 
> LJ-14            step   0:      -63.1209,  step   0:      6.50742
> Potential        step   0:      -321.601,  step   0:     -251.972
> Kinetic En.      step   0:       15.0135,  step   0:      29.0739
> Total Energy     step   0:      -306.588,  step   0:     -222.898
> Temperature      step   0:       1.93226,  step   0:      3.74185
> Pressure (bar)   step   0:      -3095.37,  step   0:     -2497.79
> Vir-XX           step   0:       1127.45,  step   0:      1075.85
> Vir-XY           step   0:        63.524,  step   0:      21.7761
> Vir-XZ           step   0:      -264.813,  step   0:     -260.354
> Vir-YX           step   0:       63.5241,  step   0:       21.777
> Vir-YY           step   0:       803.252,  step   0:      581.702
> Vir-ZX           step   0:      -264.813,  step   0:     -260.354
> Vir-ZZ           step   0:       321.207,  step   0:      176.573
> 
> Files read succesfully
> ----------------------------------------------------------------------------
> The deviations are obvious. Any suggestion would be appreciate. Thank you.
> 
> Best Regards,
> Bert
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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