[gmx-users] nature of gromacs / gcc-4.x problem

[Jones de Andrade]

Just addin my drop here:

Just did the same, both single and double precision, not parallel anyway.

What I get is the following:

*aurora down/gmxtest 41%* ./gmxtest.pl all
All 16 simple tests PASSED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
User:54.947s  Sys:13.548s  Elap:1:18.66  CPU util:87.0%  Memory:0k
*aurora down/gmxtest 42%* ./gmxtest.pl -double all
All 16 simple tests PASSED
All 14 complex tests PASSED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
User:62.427s  Sys:15.112s  Elap:1:25.65  CPU util:90.5%  Memory:0k
*aurora down/gmxtest 43%* gcc -v
Using built-in specs.
Target: x86_64-suse-linux*
.
.
.*
gcc version* 4.3.1 20080507* (prerelease) [gcc-4_3-branch revision 135036]
(SUSE Linux)
*.
.
.*
*aurora down/gmxtest 55%* more ./complex/dec+water/checkpot.out
                         :-)  G  R  O  M  A  C  S  (-:
*.
.
.*
There are 5 terms to compare in the energy files

LJ (SR)          step  34:      -0.21167,  step  34:    -0.230957

Files read succesfully

Again, it looks like the same "error" that appears in the wiki... except
that the wiki mentions two error lines in there instead of one. Also, the
wiki mentions the line differently:

LJ (SR)          step  34:     -0.176025,  step  34:     -0.21167

Which, on its turn, seems quite odd. I thought the first number was the
standard one, has it changed between 3.3.2 and 3.3.3 gmxtest' beds? And can
it be that the original problems with gcc4 has vanished with the newer
versions of it?

Thanks a lot, and hope it also helps.

Jones

On Thu, Aug 7, 2008 at 6:31 AM, David van der Spoel <spoel at xray.bmc.uu.se>wrote:

> chris.neale at utoronto.ca wrote:
>
>> Hello,
>>
>> I am trying to track down the exact nature of the gcc-4.1.x / gromacs bug.
>> I have a system on which we were forced to reinstall gromacs (3.3.1 and
>> 3.3.3) about 2 weeks ago and I didn't realize that the default gcc was
>> bumped to 4.1.2.
>>
>> I am interested because ideally we won't need to throw out the last two
>> weeks of simulation.
>>
>> The installation went fine and I have just run the tests in serial single
>> precision, which all passed (except dec+water, although that was as
>> indicated to be actually ok on the wiki... LJ (SR)          step  34:
>>  -0.21167,  step  34:    -0.147217)
>>
>>  That sounds good, but I'm not sure if it is enough.
>
>  I searched the archives, but a simple search for gcc is overwhelming and I
>> couldn't find anything specific. I did find some references to the bugzilla
>> (without links), but even when I search for gcc on bugzilla I get Zarro
>> Boogs found.
>>
> Did you select "Closed bugs" as well?
>
> It would indeed be great if we could do more exhaustive tests at compile
> time...
>
>>
>> Thanks,
>> Chris.
>>
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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