Lappeenranta University of Technology June 2015Igor Monastyrnyi HPC2N - High Performance Computing Center North System hardware and software overview INTRODUCTION TO PARALLEL COMPUTING Professor, TkT Jari Porras

Lappeenranta University of Technology June 2015Igor Monastyrnyi HPC2N - High Performance Computing Center North Umea University Sweden

Lappeenranta University of Technology June 2015Igor Monastyrnyi HPC2N Super Cluster 120 nodes, dual Athlon MP2000+ (1.66GHz) 1GB memory per node Wulfkit SCI high speed interconnect

Lappeenranta University of Technology June 2015Igor Monastyrnyi Facts Hardware –Rack chassis –2AMD Athlon MP2000+ runs at GHz –1 Tyan Tiger MPX Motherboard –1-4 GB Memory –1 Western Digital 20GB Hard disk –1 Fast Ethernet NIC –1 Wulfkit3 SCI Software –Linux 2.4.x –Debian 3.0 –ScaMPI –ATLAS –ScaLAPACK –PGI Compiler suite

Lappeenranta University of Technology June 2015Igor Monastyrnyi Technical characteristics 3 dimensional torus organized as a 4  5  6 grid Bandwidth 667 Mbytes/s Peak perfomance of 800 Gflops/s Floating poin perfomance 3334 Gflops/s Application level latency of 1.46  s

Lappeenranta University of Technology June 2015Igor Monastyrnyi Applications Molecular dynamics simulations Theoretical studies of the structure and function of metal proteins Virtual Radiography Real Time Visualization of Motion

Lappeenranta University of Technology June 2015Igor Monastyrnyi Links Dolphin Interconnect solutions – Scali A/S – Wulfkit – Debian –

Lappeenranta University of Technology June 2015Igor Monastyrnyi ScaMPI – High Perfomance MPI High optimised implementation Multi-Thread-Safe and Hot Fault Tolerance Automatic selection of physical transport mechnism MIMD Support Heterogeneous Clusters Exact Message Size Option

Lappeenranta University of Technology June 2015Igor Monastyrnyi SCI - Scalable Coherent Interface High-perfomance bus Extremely high speed Point-to-Point packet link protocol