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Figure 1: C4130 Configuration Block Diagram
In this blog we evaluate improved NAMD performance with Tesla K80 GPUs. Two proteins F1ATPASE and STMV,
which consist of 327K and 1066K atoms respectively, have been selected due to their relatively large problem size.
The performance measure is in “days/ns”, which shows the number of days required to simulate 1 nanosecond of
real-time. Table 1 gives more information about the hardware configuration and application details used for the
tests.
Table 1: Hardware Configuration and Application Details
Server
C4130 Prototype System
Processor
1 or 2 x Intel Xeon CPU E5-2690 v3 @ 2.6 GHz (12 core)
Memory
64GB or 128GB @ 2,133MHz
GPU
2 or 4 x NVIDIA Tesla K80 (4,992 CUDA cores, base clock 562
MHz, boost clock 875MHz, power 300W)
Power supply
2 x 1,600W
Operating System
RHEL 6.5 – kernel 2.6.32-431.el6.x86_64
BIOS options
System Profile – Performance
Logical Processor – Disabled
Power Supply Redundancy Policy – Not Redundant
Power supply Hot Spare – Disabled
CUDA Version and driver
CUDA 6.5 (340.46)
BIOS firmware
1.1.0
iDRAC firmware
2.02.01.01
NAMD
2.9