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
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
begin:vcard
fn:Nicolas SAPAY
n:SAPAY;Nicolas
org:University of Calgary;Biological Sciences
adr:;;2500 University drive NW;Calgary;AB;T2N 1N4;Canada
email;internet:[EMAIL PROTECTED]
title:PhD
tel;work:(403) 220-6869
tel;fax:(403) 289-9311
x-mozilla-html:TRUE
version:2.1
end:vcard
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