Kathleen wrote: > TIA: > > One thing to consider when using FPGAs for bioinformatics or any complex > computational life science application is whether or not the FPGA supports > cross coupled communication. ... which is needed in which algorithms? > I believe FPGAs do not, therefore, FPGAs will > be limited in scalability, performance and very expensive. FPGA performance on various algorithms is already 1 to 2 orders of magnitude (e.g. 10 to 100 times) faster than single CPUs. The price points of modern FPGA boards with modern algorithms is about 2-4x single node pricing. As FPGAs improve (and they are), expect to achieve significantly more performance. [...] > almost have HMMR and GROMACS parallelized and will be parallelizing AMBER or > some other MD code next. Hmmm.... HMMer was parallelized using PVM quite some time ago, and using MPI quite recently (with excellent results reported). GROMACS also has been parallel for a while. Gromacs: http://www.gromacs.org/benchmarks/scaling.php HMMer: http://hmmer.wustl.edu Amber and many other MD codes have been parallelized for a while now... > Kathleen Erickson > Senior Marcom Strategist , Massively Parallel Technologies, Inc. -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615