Thanks Mark,
your information is always useful. In this case, the page that you
reference appears to be empty. All I see is "There is currently no
text in this page, you can search for this page title in other pages
or edit this page."
Thanks also for your consideration of the massive scaling issue.
Chris.
chris.neale at utoronto.ca wrote:
Hello,
I am currently testing a large system on a power6 cluster. I have
compiled gromacs 4.0.4 successfully, and it appears to be working
fine for <64 "cores" (sic, see later). First, I notice that it runs
at approximately 1/2 the speed that it obtains on some older
opterons, which is unfortunate but acceptable. Second, I run into
some strange issues when I have a greater number of cores. Since
there are 32 cores per node with simultaneous multithreading this
yields 64 tasks inside one box, and I realize that these problems
could be MPI related.
Some background:
This test system is stable for > 100ns on an opteron so I am quite
confident that I do not have a problem with my topology or starting
structure.
Compilation was successful with -O2 only when I modified the
./configure file as follows, otherwise I got a stray ')' and a
linking error:
[cneale at tcs-f11n05]$ diff configure.000 configure
5052a5053
ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib
-lxlf90 -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm
-lc"
Rather than modify configure, I suggest you use a customized command
line, such as the one described here
http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output
config.log will have a record of what you did, too.
Sorry I can't help with the massive scaling issue.
Mark
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