[gmx-users] rb1 test failed after recompiling gromacs 3.3.2

[Justin A. Lemkul]

Nicolas Sapay wrote:
> Nicolas Sapay wrote:
>> Hello,
>>
>> I've run the gmxtest on Gromacs-3.3.2. One simple test failed:
>>
>>    Testing rb1 . . . *** glibc detected *** realloc(): invalid next
>>    size: 0x082c0180 ***
>>    sh: line 1: 27398 Aborted                 mdrun >mdrun.out 2>&1
>>    FAILED. Check files in rb1
>>
> I have more closely looked the compilation logs and the files used for 
> the test. There is nothing particular to say about the compilation (no 
> error, no warning). note that I'm using glibc 2.3.4 compiled on a Linux 
> 2.4.20 system. The error seems to be due to the -DMOL1 define in 
> grompp.mdp of the rb1 test. When I replace it by -DBONDS (as in the 
> rb125 test), the test is successful. What the -DMOL1 statement means? I 
> though you can only use -DFLEXIBLE or -DPOSRES as defines in a mdp file. 
> I had a look in the 3.3.2 manual, but found nothing about it.
> 

Anything can be defined in the topology.  Look for the #ifdef statements in 
topol.top.  I checked the test suite (for mine it's 3.3.3), and found several 
instances where there is a -DMOL1 flag, but no corresponding definition in the 
topology:

angles1
dih1
rb1

In other tests, where it is defined, it appears to mean that the system should 
contain one molecule of interest.  No idea why it's missing from these others, 
and why it doesn't seem to cause problems, at least in angles1 and dih1.

-Justin

>>
>> And two complex tests failed as well:
>>
>>    Testing acetonitrilRF . . . FAILED. Check files in acetonitrilRF
>>    Testing dec+water . . . FAILED. Check files in dec+water
>>
>>
>> In the case of the rb1 test, I checked all the .out .log files but 
>> found anything wrong. For acetonitrilRF, I obtain this:
>>
>>    -------------------------------------------------------
>>    Program mdrun, VERSION 3.3.2
>>    Source code file: network.c, line: 437
>>
>>    Routine should not have been called:
>>    gmx_sumi
>>    ------------------------------------------------------
>>
>>
>> According to the mailing list, there is something to fix in 
>> src/mdlib/rf_util.c. For dec+water, I've got the same error than on 
>> the wiki, so nothing to worry about apparently.Following the advices 
>> found on the wiki or the mailing list, I have re-compiled FFTW and 
>> Gromacs (with fixed rf_util.c) from the sources. For FFTW, I've used 
>> the following command:
>>
>>    ./configure --prefix /usr/export/fftw-3.1.2/ --enable-float
>>    --enable-threads CC=/usr/bin/gcc
>>
>>
>> And for Gromacs:
>>
>>    ./configure --prefix /usr/export/gromacs-3.3.2 --without-x
>>    CC=/usr/bin/gcc CPPFLAGS=-I/usr/export/fftw-3.1.2/include/
>>    LDFLAGS=-L/usr/export/fftw-3.1.2/lib/
>>
>>
>> I have rerun the test but I still obtain the same error with the rb1 
>> test (and the dec+water test). Can someone explain to me what the it 
>> means exactly and how to fix it? (I guess it's related to the 
>> Ryckaert-Bellemans potential?).
>>
>>    Thanks,
>>    Nicolas
>>
>>
>> ps: I'm using RHE 4.7 and gcc 3.4.6
>>
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> 
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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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