THE-ELEMENTS is a Beowulf-Type computer for supporting the project in Classical and Quantum Mechanical Molecular Dynamics of TCCC. This distributed parallel system is an effort to create large computational power by accumulating low cost CPUs, memory and hard discs for data storage, and using open software as far as possible. The current composition of The-Elements is eight dual Pentium II systems with CPUs at 350 and 450 MHz, total memory 5GBytes, total hard discs 76 GBytes and all these connected with a fast ethernet switch of 100 Mbits/s.

TECHNICAL CHARACTERISTICS

Dual Nodes: /Fire / Water / Air / Earth/

• CPUs: Eight Pentium II CPUs at 350 MHz - Cash Memory 512 KBytes
• Motherboards: QDI Brilliant V, Chipset INTEL 440 BX 100MHz
• Memory: 2.048 GBytes (4x512) (100 MHz SDRAM)
• Discs: 21 GBytes (5x4.2) (WESTERN DIGITAL ULTRA WIDE SCSI)
• Network: Bay 350T, 100 Mbits Switched, Backbone 1Gbits, 16 ports

Dual Nodes: /Hydrogen / Helium / Nitrogen[*] / Oxygen[*]/

• CPUs: Eight Pentium II CPUs at 450 MHz - Cash Memory 512 KBytes
• Motherboards: P2B-D, ASUS, Chipset INTEL 440 BX 100MHz
• Memory: 3.072 GBytes (2x512+2x1024[*]) (100 MHz SDRAM)
• Discs: 54.6 GBytes (6x9.1) (IBM, ULTRA WIDE2 SCSI)

• CPUs:        Sixteen Pentium II
• Memory: 5  GBytes
• Discs:    76 GBytes

SOFTWARE

• Operational System: Linux, Distributor Red Hat 6.1 (Cartman) (Kernel 2.2.13) (O)
• Communication Programs: Message Passing Interface (MPI) Argonne MPI (O)
• Batch Queuing Program: Generic NQS (Network Queuing System 3.50.6) - Sterling Software Incorporated (O)
• Compilers: /High Performance Fortran (HPF) / Fortran 90 / Fortran 77 / C / C++ / PortlandGroup 3.1 (C)
• Libraries: Numerical Recipes (C) - PETSc (O) - Lapack (O) - Lapack95 (O)
• More Documentation can be found in "doc" Directory (O)
• O = Open software
• C = Commercial software
• L = Local software

COMMUNICATION MODE

The eight dual PCs connected by the fast Ethernet consist an isolated local area network (ILAN). The mode of accessing The-Elements from the outside world is what is called the Guarded Beowulf. In this scheme only one of the nodes has an IP address recognizable from machines outside The-Elements. The worldly-node is Fire which has been upgraded to a 450 MHz dual Pentium II. Fire is protected by a firewall software. Each node has a local hard disc but a raid of 17 GBytes is supported my the server (Fire).

PROJECTS

• Molecular Potential Energy Surfaces and Clusters
  AUTO_DERIV (L)
• Non-Linear Classical Mechanical Analysis of Molecular Systems: Periodic Orbit Multiple Shooting Algorithms
  POMULT (L)
• Molecular Quantum Dynamics: Periodic Orbit-Assisted Grid Solutions of Time Dependent Schroedinger Equation
  POA-TDSE (L)
• Molecular Electronic Structure Calculations (Quantum Chemistry) Packages:
  GAUSSIAN94 (C)
  GAUSSIAN98 (C)
  MOLPRO2000 (C)
  NWCHEM4.0 (O)

FUNDING

The project was financed by the Ministry of Education within the program EPEAEK for postgraduate studies in Applied Molecular Spectroscopy.

The cost of The-Elements was :

Phase 1: ~7,000,000 Greek Drachmas (~$25000)

Phase 2: ~5,000,000 Greek Drachmas (~$17000)

BENCHMARKS

• Comparisons with Local Systems
• Speed of network
• Comparison of Compilers
• Comparison for GAUSSIAN94
• Comparison with SUN
• Comparison with DIGITAL/Alpha

HOW_TO_RUN

• Printers
• Submit a Batch
• Compilation
• Tcl-Tk
• Mpich
• Run Gaussian
• Run Molpro
• Run NWchem

ARTICLES

• Chemical & Engineering News Jan 10, 2000
• SIMU NEWS LETTERS

URL ADDRESSES

• ENACTS
• PRIMEUR
• Los Alamos Archives
• Chemistry Preprint Server (CPS)
• NR book in Fortran 77
• NR book in Fortran 90
• NR book in C
• Beowulf Project
• The Beowulf Underground
• Computer Clusters for Chemists
• Large list of cluster computing resources
• IEEE Task force on cluster computing
• The Journal of Networks, Software Tools & Applications
• High Performance Cluster Computing Resources
• Beowulf Project in Greece
• Linux-HA Project Web Site

USERS

• USERS

Back to TC3 Home page