Ramadas Sunil Pophale wrote:
Ramadas Sunil Pophale wrote:
Dear gromacs users,
After configuring and installing gromacs, I tested it using 'make
tests'.
Got the following errors.
*** glibc detected *** realloc(): invalid next size: 0x08255310 ***
sh: line 1: 7535 Aborted (core dumped) mdrun >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
I checked the simple/rb1 directory for the .out files. I could not quite
see the problem described in those. Seems like it's related to 'allowing
a
memory location that has already been freed to be used again'.
Among the files I checked (checkptr.out, grompp.out, mdrun.out), the
closest thing to a warning seemed to be
gcq#288: "I Feel a Great Disturbance in the Force" (The Emperor Strikes
Back) in grompp.out :-)
is there anything in the script file (gmxtest.pl), I need to fix?
-----------------------------------------------------------------------------
FAILED. Check files in dec+water
FAILED. Check files in nacl
FAILED. Check files in tip4p
3 out of 14 complex tests FAILED
As for the errors with complex tests, I had 3 of those. I checked the
checkpot.out files. Only in one case (dec+water) were the LJ numbers
close
to zero (thus justifying the 'error due to numerical accuracy in adding
up
many interactions' on wiki). In other 2 cases, the deviations in LJ and
coloumb
energies were not small.
for example
LJ (SR) step 50: 14440.2, step 50: 13501.5
Coulomb (SR) step 50: -90740.2, step 50: -84154.3
Not sure if I can simply ignore these. Any suggestions?
-----------------------------------------------------------------------
How did you compile? What platform are you running on?
-----------------------------------------------------------------------
Hi David,
I used RedHat-linux 4.0 with intel mkl library for fftw.
The compilation went smoothly. Gromacs was installed in a non-standard
location as I am not the root.
It seems that nacl and tip4p are the two tests using PME, and hence the
mkl library could be the problem. Could you try it with FFTW?
Regards,
Ramdas.
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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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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