New Infiniband Policy for Biowulf Cluster (Biowulf)

This announcement is directed primarily to users of
the Infiniband network on the NIH Biowulf Cluster.

The IB network has been expanded to 132 (dual-processor)
nodes, and those nodes are now available for use. During
the past week, the systems staff has done extensive
benchmarking on the IB network using NAMD, which is by
far the most used program on IB.

NAMD on gigabit ethernet performs as well or better
than on IB for jobs up to 32 processors (16 nodes).
Therefore, the IB nodes will be reserved for larger
jobs that scale to 64 processors or more.

Effective immediately, jobs that require less than 32
nodes (64 processors) can no longer be submitted to the
IB nodes. The maximum possible IB allocation is for 64
nodes (128 processors).

These new allocation limits are designed to allow the
simulation of larger molecular systems than were possible
before. The systems staff has seen very good performance on
systems of up to 1 million atoms when running on 128
processors.

If you plan to run applications other than NAMD on the IB
nodes please contact the systems staff before doing so.

Please send questions and commment to staff@biowulf.nih.gov.