[gmx-developers] gromacs 4 optimizations / cell support

Maik VP mnijhuis at virtualproteins.com
Tue Jul 1 15:45:11 CEST 2008

Dear developers,

I found a paper about gromacs 4 which describes: 'Algorithms for Highly
Efficient Load-Balanced, and Scalable Molecular Simulation' in the Journal
of Chemical Theory and Computation. The paper describes that gromacs 4
uses multithreading instead of MPI, and other interesting parallelization

However, when I try to enable multithreading in the latest-greatest
version from CVS, using ./configure --enable-threads --with-x
--with-gnu-ld, the linker fails because gmx_thread_mutex_lock and
gmx_thread_mutex_unlock are not defined. I have searched for these
functions in the code but I could indeed not find their implementations.

Since multithreading was described in the paper, I am wondering where I
can find a gromacs version in which multithreading and the other
optimizations from the paper are implemented.

Furthermore I am interested in running Gromacs on the Cell architecture,
since the folding at home project clearly shows that gromacs is able to
exploit the resources in this advanced processor. However, again, the
latest-greatest CVS version does not include Cell support, only generic
altivec support Does anybody know where I can find the Cell
implementation of gromacs, which uses the SPE accelators?

Maik Nijhuis
mnijhuis at virtualproteins.com || http://www.cs.vu.nl/~maik

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