What follows is a short description of the computing cluster installed at the Department of Molecular Biology and
Genetics, Democritus University of Thrace.
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 220.127.116.11 (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
Software available on the cluster includes :
A very short list of cluster-related links follows :
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.
- 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, ...
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