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You are here: ICE-HT > Facilities > Computer Center Facilities
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Informatics & Communications Centre

The ICEHT's Informatics & Communications Centre provides a wide range of IT facilities and services with a state-of-the-art networking environment to support all Institute staff for their research, learning and administration.




Mission


  • To facilitate the use of the latest information and communication technology in our Institute's research, learning and administration.
  • To provide an efficient and reliable network environment that facilitates the access and exchange of information.
  • To put innovation in our technology transfer to assist the Institute in its mission.
  • To enable our staff to use our computer and network resources effectively and efficiently.

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Simulation of CO2 diffusion and sorption on the surface of a nanoceramic gas sensor

High Performance Computing @ FORTH/ICEHT


The molecular design and computer simulation of materials and processes constitute one of the most active research areas at FORTH/ICE-HT. New strategies and efficient computer modeling techniques are developed and large-scale numerical calculations are performed to support and complement the experimental activities of the Institute. The modeling efforts are extended to all sectors of the Institute and provide critical understanding of the actual mechanisms and phenomena involved in the various processes FORTH/ICEHT has setup and supports a High Performance Computing Cluster to help researchers solve scientific and technical challenges. The ICEHT's Cluster is well suited for many research applications because it includes a large number of powerful multicore nodes, a significant amount of memory in each node, a high-bandwidth interconnect between the nodes, optimizing compilers and a growing set of application software.

ICEHT's Cluster is heavily used by many research teams as an indispensable tool for solving challenging and complex scientific and technological problems throughHPCC simulations in areas such as Weather, Climatology and Earth Science (i.e., air quality and climate change studies), Material Science and Chemistry (i.e., understanding complex materials, complex chemistry, nanoscience), Elementary particle physics (i.e., systems, structures which span a large range of different length and time scales) and Life Sciences (i.e., system biology, chromatin dynamics, protein association and aggregation, supramolecular systems).

The ICEHT's Cluster has 31 compute nodes. Each compute node has two Intel Xeon two-core, quad-core or six-core processors (5160, X5365/X5560 and E5645 respectively) and 2 GB RAM per core. That results in a total of 332 cores and 334GB of RAM available for jobs. Each compute node also provides at least 500GB of local scratch capacity on a directly attached hard disk. In addition, there are more than 20 TB of disk storage, providing both high performance and archival data storage to the ICEHT research community. Also, there are one login node and one control node for administrative purposes. The nodes are interconnected via a non-blocking Gigabit Ethernet switch providing high bandwidth and low latency for both computational communications and storage access.

For program development on ICEHT there are available Fortran, C and C++ compilers from Intel and GNU Compiler Collection. The supported MPI libraries are Open-MPI and MPICH2. Also, the following list of scientific software packages, libraries and other tools is installed and maintained on ICEHT's Cluster:


Package name Description From
GROMACS A versatile package to perform molecular dynamics Groningen University et. al.
LAMMPS A classical molecular dynamics code and can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. Sandia National Laboratories
NAMD A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems University of Illinois
VMD A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting University of Illinois
HMMER For searching sequence databases for homologs of protein sequences and for making protein sequence alignments. Washington University at St. Louis
NCBI BLAST Can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families National Center for Biotechnology Information
MpiBLAST A freely available, open-source, parallel implementation of NCBI BLAST Los Alamos National Laboratory
ClustalW A general purpose multiple sequence alignment program for DNA or proteins The European BioInformatics Institute
Emboss A software analysis package specially developed for the needs of the molecular biology user community. European Molecular Biology Institute
Fasta Find regions of local or global similarity between Protein or DNA sequences, either by searching databases or by identifying local duplications within a sequence. University of Virginia
WRF The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. National Center for Atmospheric Research (NCAR) et. al.

 

ICEHT's Cluster is intended for middle-size parallel jobs that scale reasonably well for large amount of processors and for serial jobs that need large amount of memory.

Network Connections


The ICEHT's Campus Network is made up of a high speed Gigabit Ethernet resilient network backbone with over 800 network connection points on Gigabit Ethernet/Fast Ethernet segments to the desktop,Computer Center WiFi hotspots to connect to the ICEHT network via radio transmission without using network cables from seminar room, library and open areas in the main campus, and Virtual Private Network (VPN) for access from the Internet.

ICEHT's  campus network is connected to the Internet via EDET (Greek Academic and Research Network), managed by the GRNET S.A., which provides high quality services of national and international interconnection and capacity in the Greek research, academic and educational community, covering their always increased requirements high level services and Internet applications. The GRNET international interconnection at the Pan European Network GEANT, was upgraded in 2006 to2x10Gbps.


 
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