Daniel Adriano Silva M wrote:
Mark,
Thank you!!! It was non directly MPI, since I tried the fresh
installation with intel and gcc but none worked, then i realized that
my compilation of FFTW could be the problem (compiled with icc 11),
then I recompiled FFTW with gcc and linking to this new fftw3.2.2 I
recompiled gromacs booth with gcc and intel, booth compilations seems
to work. Do you think that it could be any problem at mix gcc-fftw and
intel mdrun??? I will continue the tests with the new gmx-tests and
other TPRs.
There have been known issues with linking and some versions of Intel
compilers under various conditions with stuff in general and GROMACS in
particular. I've never cared to understand why. Not mixing compilers is
usually a good idea if there are problems.
Mark
2009/10/30 Mark Abraham <mark.abra...@anu.edu.au>:
Daniel Adriano Silva M wrote:
Mark,
I will test, but please tell me: do you think MPI linking problem
could lead to problems with some dynamics and not with others as
happens to me? and also note that all my test where made with mvapich2
(even that with one core). Please justin, what do you think about?
For example, observing symptoms from buffer overruns can be sensitive to the
actual calculation being run because it can depend how the actual memory
gets laid out and used. So here, that might translate to the kind of system
being simulated, and the number of cores used. Such an overrun might be
present in the code all the time, or only exists after a linking mismatch,
or similar.
Mark
Thanks
Daniel
2009/10/30 Mark Abraham <mark.abra...@anu.edu.au>:
Daniel Adriano Silva M wrote:
Dear Gromacs users,
I am experimenting the next problem on an infiniband-cluster (8
intel-cores per node, GROMACS compiled with icc 11.1, all run through
mvapich2):
I have a molecule (protein 498aa, solvated or in vacuum I get the same
problem at any box shape), when I try to SD minimize it with
mvapich2-mdrun, it minimizes well with 1, 2 or 3 cores and reaches
convergence in around 1000steps, however any further combination (4,5,
...n cores) makes it to immediately stop (less than 20 steps) with:
"Steepest Descents converged to machine precision...".
Further if I take "the 1 core minimized structure" and try to make a
solvated-pr dynamics(2fs, MD, NTP, etc.) it also works with 1
processor, but with more cores it begins immediately to bring LINCS
warnings: and dies:
"Too many LINCS warnings" or "Water molecule starting at atom 16221
can not be settled"
For a "long time" I had made another md simulations on this cluster
with the same mdps and other proteic systems, and I only see this
behavior with this particular protein, of course before send this
mail I re-tested previuos-working tprs.
Finally, the most suspicious is that I have another very similar
8-core box (with the same processors) but with gromacs gcc compiled,
and it actually runs very well the same problematic molecule (even the
same tpr) with mpi and 8-cores.
What do you think??? Please, if you have some tpr to test something send
it.
I'd guess you're having some problem with (dynamic) linking of the MPI
library. Perhaps the version of some library has changed since recently,
etc. I'd suggest compiling two fresh copies of GROMACS with either icc
and
gcc on the troublesome machine and seeing what happens with them.
Mark
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