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Home > Computer Science > Scientific computing

Scientific computing

by Pierre Solbes - published on , updated on

EDB-Calc

 

Configuration

1 Master server :

  • Dual Processor Intel Xeon E5-2640 (2,50GHz, 6Core, Cache 15Mo, 7,2GT/s QPI, 95W, Turbo)
  • 4x4GB RDIMM, 1333 MHz, Low Volt, Dual Rank
  • 6x Hard Drive 2To Near-Line SAS 6Gbit/s 7200tr/min 3,5" en RAID6 (7To utiles)

6 Computing nodes :

  • Bi-Processeur Intel Xeon E5-2450 (2,10GHz, 8Core, Cache 20Mo, 8GT/s QPI, 95W)
    • 96GB RDIMM, 1333 MHz, Low Volt (Node 1)
    • 32GB RDIMM, 1333 MHz, Low Volt (Node 2 à 5)
  • Bi-Processeur Intel Xeon E5-2670 v3 (2,3GHz, 12Core, Cache 30Mo, 9,6GT/s QPI, 120W)
    • 96GB RDIMM, 2133 Mhz (Node 6)

OS installed : Rocks 6.2 (Linux distribution basd on CentOS)
Scheduler : SGE (sun grid engine)
Cluster ressources Monitoring : Ganglia


Many softwares are installed for researchers :

  • Bio-Informatic tools : ABySS, MrBayes, FASTA, NCBI BLAST, OBITools, SUMATRA, Phyml, Biopython, Bioperl, ...
  • Phylogeny tools : BEAST1 & 2, RAxML, ...
  • Compilers : gcc, fortran, java, c++, mpi, mpicc, mpiCC, mpic++, mpiblast, ...
  • Libraries : GNU Scientific Linux, libRmath...
  • R and many packages : MCMCglmm, randomForest, vegan, lattice, plotrix, ENmisc, igraph, fields, sp, maptools, gstat, ade4, ape, permute, seqinr, gmt, phytools, picante, R2OpenBUGS, snow, snowfall, ...


For help on how to use the cluster, and the complete list of installed software, go to intranet website.