Technical Details
The Genetic Cluster Computer is part of the Dutch national compute cluster Lisa, hosted by SARA.
The LISA system configuration
715 compute nodes:
- 419 compute nodes, each equipped with:
- 2 Intel Xeon processors
- Speed: 3.4 GHz
- Extended Memory 64 Technology (EM64T)
- 800 MHz Front Side Bus
- Gigabit Ethernet adapter for maintenance
- 120, each equipped with:
- 2 Intel® quad-core Xeon” E5345 processors
- Speed: 2.33 GHz
- Extended Memory 64 Technology (EM64T)
- 1330 MHz Front Side Bus
- Gigabit Ethernet adapter for maintenance
- 32, each equipped with:
- 2 Intel® quad-core Xeon” L5420 processors
- Speed: 2.5 GHz
- Extended Memory 64 Technology (EM64T)
- 1330 MHz Front Side Bus
- Gigabit Ethernet adapter for maintenance
- 144, each equipped with:
- 2 Intel® quad-core Xeon” L5520 processors
- Speed: 2.26 GHz
- 8M cache 5.86 GT/s QPI, Turbo
- Gigabit Ethernet adapter for maintenance
- Topspin’s Infiniband network:
Bandwidth: 800 MB/sec
Latency: <6 millisec - Total peak performance: 16 TFlop/sec
- Disk space: 25 TB SUN Thor systems for the home file systems
- Operating system: Debian Linux 32bit and AMD64. We are in the process of migrating all nodes of lisa to the AMD64 architecture.
There are five types of compute nodes:
| Number | Processors | Memory | InfiniBand |
|---|---|---|---|
| 254 | 2*single-core | 4GByte | YES |
| 165 | 2*single-core | 4GByte | NO |
| 40 | 2*quad-core | 8GByte | YES |
| 80 | 2*quad-core | 8GByte | NO |
| 32 | 2*quad-core | 16GByte | YES |
| 144 | 2*quad-core | 24GByte | YES |
Managing the national compute cluster
In order to keep the national compute cluster manageable, use is made of the following software:
- Cfengine
- a configuration engine.
- SystemImager
- SARA has developed an add-on for SystemImager to manage the PXE boot process. It is available here. There is an excellent description available at the Technical University of Denmark.
- OpenPBS and TORQUE
- SARA has developed a Python interface for both batch systems.
So it is now possible to develop batch utilities in Python instead of C. The software package contains an example directory with an ASCII xpbsmon utility. - Ganglia
- For Ganglia SARA has developed an add-on to monitor OpenPBS and TORQUE queues. This creation is based on software included in the rocks toolkit.
- torque_2_deb
- SARA has developed software to make a debian package from the Torque source
- Dell
- OpenManage Server Administrator (OMSA): SARA has ported the OMSA tools to Debian