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We're using the 64-bit beta version of ScienceMark for these tests, and several of its components are multithreaded. ScienceMark author Alexander Goodrich says this about the Molecular Dynamics simulation:
Molecular Dynamics is lightly multithreaded - one thread takes care of U/I aspects, and the other thread takes care of the computation. The computation itself is not multithreaded, though Tim and I were looking into ways of changing the algorithm to support multi-threading programming a couple years ago - it's a lot of effort, unfortunately. When MD [is] running there [is] a total of 2 threads for the process.
Here are the results:

The Primordia test "calculates the Quantum Mechanical Hartree-Fock Orbitals for each electron in any element of the periodic table." Alex says this about it:
Primordia is multithreaded. Two main tasks occur which allow this to happen. Essentially, we identified 2 parallel tasks that could be done. We could probably take this a step further and optimize it even more. There is an issue, however, with the Pentium Extreme Edition that we've identified. The second computation thread gets executed on the logical HT thread rather than the 2nd core, so performance isn't as good as it could be. This will be fixed in the next revision. This doesn't effect [sic] the regular Pentium D. A workaround could include disabling HT on Pentium EE. There are 3 threads for primordia - 2 threads for computation, 1 thread for U/I.

The next two tests are only single-threaded, and they don't make as good use of any of the CPUs here as they could if they were better optimized. The ScienceMark team has plans to incorporate linear algebra libraries from Intel and AMD in order to boost performance.