Gordon User Guide: Technical Summary

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Gordon is a dedicated XSEDE cluster designed by Appro and SDSC consisting of 1024 compute nodes and 64 I/O nodes. Each compute node contains two 8-core 2.6 GHz Intel EM64T Xeon E5 (Sandy Bridge) processors and 64 GB of DDR3-1333 memory. The I/O nodes each contain two 6-core 2.67 GHz Intel X5650 (Westmere) processors, 48 GB of DDR3-1333 memory, and sixteen 300 GB Intel 710 solid state drives. The network topology is a 4x4x4 3D torus with adjacent switches connected by three 4x QDR InfiniBand links (120 Gbit/s). Compute nodes (16 per switch) and I/O nodes (1 per switch) are connected to the switches by 4x QDR (40 Gbit/s). The theoretical peak performance of Gordon is 341 TFlop/s.

Technical Summary

System Component Configuration
Intel EM64T Xeon E5 Compute Nodes
Sockets 2
Cores 16
Clock speed 2.6 GHz
Flop speed 333 Gflop/s
Memory capacity 64 GB
Memory bandwidth 85 GB/s
STREAM Triad bandwidth GB/s
I/O Nodes
Sockets 2
Cores 12
Clock speed 2.67 GHz
Memory capacity 48 GB
Memory bandwidth 64 GB/s
Flash memory 4.8 TB
Full System
Total compute nodes 1024
Total compute cores 16384
Peak performance 341 Tflop/s
Total memory 64 TB
Total memory bandwidth 87 TB/s
Total flash memory 300 TB
QDR InfiniBand Interconnect
Topology 3D Torus
Link bandwidth 8 GB/s (bidirectional)
Peak bisection bandwidth TB/s (bidirectional)
MPI latency 1.3 µs
DISK I/O Subsystem
File Systems NFS, Lustre
Storage capacity (usable) 1.5 PB
I/O bandwidth 100 GB/s

Gordon supports the XSEDE core software stack, which includes remote login, remote computation, data movement, science workflow support, and science gateway support toolkits.

Systems Software Environment

Software Function Description
Cluster Management Rocks
Operating System CentOS
File Systems NFS, Lustre
Scheduler and Resource Manager Catalina, TORQUE
User Environment Modules
Compilers Intel and PGI Fortran, C, C++
Message Passing Intel MPI, MVAPICH, Open MPI
Debugger DDT
Performance IPM, mpiP, PAPI, TAU

Recent Gordon News & Events

Gordon Ranks No. 88

May 28, 2015
Still One of World's Fastest HPC Systems Gordon, the unique data-intensive flash-based HPC resource at the San Diego Supercomputer Center (SDSC) at t... more news...

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