Hi I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like to try the GROMACS patch for better all-to-all, as well as the all-to-all test program referred to on the paper. I can't find it on the GROMACS site.
We've got a Cisco 6500 and when I run tcpdump during MPI runs I see a huge amount of TCP lost packets with retransmits, and tcptrace confirms there are a large number of restransmits. I am trying to get our network admins to test the flow control setting option on our 16-processor cluster. Dave
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