MBG Cluster view

What follows is a short description of the computing cluster installed at the Department of Molecular Biology and Genetics, Democritus University of Thrace.

Software

All machines are triple-boot. The basic (with respect to clustering) operating system is based on the the OpenMosix Linux kernel which implements the Single System Image (SSI) clustering capabilities. The OpenMosix kernel allows for cluster-wide load balancing via transparent process migration between the cluster's nodes. It also offers a cluster-wide filesystem in the form of oMFS (openMosix File-System) and DFSA (Direct File-System Access). In addition to OpenMosix, the cluster supports MPI program execution via two MPI implementations : MPICH 1.2.5.2 (both ssh-based and with the OpenMosix patch) and MP_Lite (via ssh). Overlayed on top of OpenMosix is the 'Sun Grid Engine (SGE)', an advanced batch queueing system [actually, a Distributed Resource Management (DRM) system]. Note that each node has a complete and autonomous copy of a full GNU/Linux distribution (with its compilers, GNU programs and utilities, etc, see below), so any one node is suitable both for program development and execution.

Software available on the cluster includes :

Programming languages : C, C++, FORTRAN (GNU and Intel compilers), Perl, Python, Tcl/Tk, awk, Java, MPI (C and fortran bindings), and (of course) assembly. Debugging and profiling tools are available for most of these.
Other software and libraries : CCP4, XtalView, NAMD, CNS, MOSFLM, FFTW, PGPLOT, Molscript, Raster3D, SnB, Xplor, VMD, Solve/Resolve, ClustalW, NJplot, Modeller, DSSP, Rasmol, Babel, ...

A very short list of cluster-related links follows :

Linux : http://www.tldp.org/
OpenMOSIX : http://openmosix.sourceforge.net/
MPI and MPICH: http://www-unix.mcs.anl.gov/mpi/
Sun GridEngine : http://gridengine.sunsource.net/

With this setup (and taking into account the type of hardware, see below), the cluster is classified as a Beowulf class I cluster (although purists would more properly call it a 'Cluster Of Workstations', see the Beowulf HOWTO for more details). Things related to the cluster [ but of evolving nature (like current projects, benchmarks, submitting jobs, compilers' flags, etc) ] will be posted in the MBG's cluster wiki.

Hardware

The cluster is heterogeneous and comprises 18 nodes connected via a 100Mbps full-duplex fast ethernet switch. Individual nodes range from one Pentium IV machine with 512 MBytes of main memory, to nine Pentium III machines (at 733 MHz) with 320 MBytes of main memory. All nodes are complete with video cards, monitors, keyboards, etc. In more detail :

Master node (x1) :

	model name      : Intel(R) Pentium(R) 4 CPU 2.60GHz
	stepping        : 9
	cpu MHz         : 2605.933
	cache size      : 512 KB
	fpu             : yes
	bogomips        : 5203.55
	MemTotal:       514204 kB
	SwapTotal:     1044216 kB
	Disks: 2 x 80GBytes ATA RAID 1  Hardware inventory

Newest nodes (x8) :

	model name      : Intel(R) Celeron(R) CPU 2.40GHz
	stepping        : 9
	cpu MHz         : 2405.522
	cache size      : 128 KB
	fpu             : yes
	bogomips        : 4797.23
	MemTotal:       255660 kB
	SwapTotal:      522072 kB
	Disks: 40 or 80 GBytes IDE      Hardware inventory

Older nodes (x9) :

	model name      : Pentium III (Coppermine)
	stepping        : 3
	cpu MHz         : 731.498
	cache size      : 256 KB
	fpu             : yes
	bogomips        : 1458.17
	MemTotal:       320296 kB
	SwapTotal:      521632 kB
	Disks: 20 GBytes IDE            Hardware inventory