[gmx-users] Question about gcc version

[David van der Spoel]

Justin A. Lemkul wrote:
> 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.
Look further up in the grompp.out file


> 
> 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?
Again, here you may need to look more closely in the output file. If 
b4em.gro does not exist something went wrong before.



> 
> 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/
> 
> ========================================
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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