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Sandy Bridge nodes

The cluster was upgraded to contain 192 nodes with dual socket Intel Xeon E5-2670, 2.6 GHz "Sandy Bridge".

• 16 cores per node in 2 sockets, 32 threads, AVX support
• 32GB of DDR3 1600 Mhz memory
• 4 memory channels per CPU, total of >70GB/s memory bandwidth
• Mellanox QDR ConnectX-3 Infiniband HCA, connected with PCIe-gen3 bus, 2:1 overcommitted in the switch fabric

main user benefits through hardware compared to Nehalem nodes

• twice the core number per node
• twice the memory bandwidth per node
• higher IB bandwidth and throughput
• 2.66 times the memory per node, 30% more memory per core
• ~same CPU throughput per core with 2.6 GHz instead of 2.8 GHz.

new OS version offers

• AVX support (4 DP element vector instructions)
• transparent huge pages (less TLB misses for large memory blocks without any need to change code)

Remarks

• use -mAVX switches to generate best code with compilers, AVX is supported by Intel and GCC and ortland compilers, see details in manuals
• frontends are nehalem type CPUs, if compiler uses autodetection if no architecture switch is specified, you will get non-optimal code!
• redhat 6.2 based scientific linux 6.2 which is used on the new nodes shows performance degradation if SMT (hyperthreading) is enabled - which is the case - and MPI is used without using the additional threads. To get best performance, use CPU pinning.
  • for openmpi use mpirun -bind-to-core
  • for HP-MPI/Platform MPI use mpirun -cpu_bind=rank
  • for intel MPI pinning is on by default

An example for effect of pinning is IMB allreduce benchmark within 1 node, it gives for 4MB messages a time of ~13000us without pinning and 7500us with pinning, using 16 processes.