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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--
========================================
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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