Darius is a 32-node cluster with InfiniBand QDR interconnections. It runs CentOS 5.4 (Linux kernel version 2.6), which is closely related to Red Hat Enterprise Linux. Its hostname is darius.mit.edu.
Installed software
software | location of source code |
|---|---|
NAMD 2.7b2 | /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI |
Charm++ 6.2 | /share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx |
VMD 1.8.7 | /share/apps/vmd-1.8.7/LINUXAMD64 |
AmberTools 1.4 | /share/apps/amber11 |
CHARMM c35b2 | not yet installed, source in /share/apps/c35b2 |
Performance
| Wiki Markup |
|---|
Using the 92 katom [ApoA1 benchmark|http://www.ks.uiuc.edu/Research/namd/performance.html] with NAMD 2.7, performance appears to compare very favorably with previously benchmarked clusters: its \[processor cores X time per step\] values (corresponding to the ordinate on the [figure|http://www.ks.uiuc.edu/Research/namd/apoa1_bench.png] on the linked page) vary from 1.8 sec (8 CPUs) to 2.1 sec (128 CPUs). !apoa_bench_scan.png|thumbnail! |
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