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CIP HPC

CIP HPC. http://hpc.cip.cgiar.org. CIP - HPC. HPC = High Performance Computer It’s not a regular computer, it’s bigger, faster, more powerful, and more expensive. We would like it to be a Super computer but it is rather small so, High Performance Computer. http://hpc.cip.cgiar.org.

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CIP HPC

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  1. CIP HPC http://hpc.cip.cgiar.org

  2. CIP - HPC • HPC = High Performance Computer • It’s not a regular computer, it’s bigger, faster, more powerful, and more expensive. • We would like it to be a Super computer but it is rather small so, High Performance Computer http://hpc.cip.cgiar.org

  3. A Computer Cluster You regular PC A computer cluster Front-end node 1 CPU 1 or 2 Hard disks Some memory 512MB,.. 1GB,.. Compute-0-0 Compute-0-1 Compute-0-2 http://hpc.cip.cgiar.org

  4. CIP’s HPC: A High Performance Computer • CIP’s HPC is a computer cluster: A group of connected computers that work together as a unit. • Some computer clusters are called “Super Computers” specially when they have 50, 100, thousands of nodes, or more http://hpc.cip.cgiar.org

  5. CIP’s HPC: A High Performance Computer • From: http://www.top500.org/ we can notice that many of the TOP 500 Supercomputers are Linux Clusters. • “MareNostrum” from the Barcelona Supercomputer Center (The forth fastest computer in the world (Nov. 2004) with 3564 CPUs) 8th by May 2006

  6. CIP’s HPC: Hardware review… • 4 Nodes (1u cases) • 2 AMD Opteron 64 bits1.8 Ghz Cpu’s in each Node • 4 GB Ram on each Node • 750 GB Hard Disk in the front-end • 80 GB Hard disk on each compute-node http://hpc.cip.cgiar.org

  7. http://hpc.cip.cgiar.org

  8. CIP HPC The Software http://hpc.cip.cgiar.org

  9. CIP’s HPC: Software Review • Linux Operating System (Rocks Clusters), intended for command line use. • MPI and LSF for parallel processing • Java • Tomcat / PHP / Mysql / Perl • Paracel Blast • Structure, R, any software capable of running in Linux http://hpc.cip.cgiar.org

  10. CIP HPC Speed

  11. Structure Performance http://hpc.cip.cgiar.org

  12. http://hpc.cip.cgiar.org

  13. Using CIP HPC

  14. Providing Easy Access to users Web Pages Private Network Interface Front-end node Happy User Client Program Command line Compute-0-0 Compute-0-2 Compute-0-1 http://hpc.cip.cgiar.org

  15. CIP HPC Web http://hpc.cip.cgiar.org

  16. BLAST at CIP HPC http://hpc.cip.cgiar.org

  17. BLAST: Basic Local Alignment Search Tool • finds regions of local similarity between sequences • Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches • Can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://hpc.cip.cgiar.org

  18. Advantages of performing Blast at CIP HPC • Dedicated server, faster results • Searches against specific databases (potato, tobacco, sweet potato), more accurate results. • We can add sequence databases to the HPC as requested by users. http://hpc.cip.cgiar.org

  19. http://hpc.cip.cgiar.org/bwb

  20. http://hpc.cip.cgiar.org/bwb

  21. http://hpc.cip.cgiar.org/bwb

  22. http://hpc.cip.cgiar.org/bwb

  23. http://hpc.cip.cgiar.org/bwb

  24. The End

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