I sent the previous message before including comments: The Opteron 275 is 10-25% faster than the P4D for GROMACS. However the Opteron loses some of its edge when running dual threads. MPI/GAMMA outperforms both LAM and OpenMPI by a significant margin on DPPC and Villin benchmarks. With DPPC MPI/GAMMA scales as well as Infiniband but for Villin it is about 75% of the Infiniband performance. The reduced latency and more efficient flow control with the GAMMA protocol makes a significant difference to the scalability of Gigabit ethernet. In general the Intel NICS with GAMMA perform better than proprietary RDMA NICS from Ammasso and Level 5 networks.
I had to make a small change to Gromacs 3.3 to get MPI/GAMMA to run. In futil.c line 102 the code tries to close a NULL pointer which strictly speaking is illegal. This causes GAMMA to hang. It seems harmless to comment it out. More details can be found at http://ladd.che.ufl.edu/research/beoclus/beoclus.htm The GAMMA website is http://www.disi.unige.it/project/gamma/mpigamma Tony ------------------------------- Tony Ladd Chemical Engineering University of Florida PO Box 116005 Gainesville, FL 32611-6005 Tel: 352-392-6509 FAX: 352-392-9513 Email: [EMAIL PROTECTED] Web: http://ladd.che.ufl.edu _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
