Vital-IT / High Performance Computing Center

Molecule
 

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(VF, 18.09.2009)


Resources

Access to the development farm is freely available to all developers of the partner institutions. Access to the production cluster is limited to accepted projects. Please follow the instructions to submit a project (pdf) to the Vital-IT technical comittee and fill in a project submission form.

Job Submission

To submit jobs to the Vital-IT environment most users will use the wsub.py script. This job submission information page contains a short tutorial as well as the possibility to download the script, as well as links to the cluster and job status pages.

Applications and Tools

Bioinformatics Applications

Check out our list of bioinformatics applications.

Compilers

We have gcc 3.4.6, and the Intel C, C++ and Fortran compilers version 9.0.

gcc can be invoked in the usual way while the Intel compilers reside in /mnt/local/bin and can be invoked as icc for C, C++ and ifort for Fortran. The Intel compiler provides about 20% better performance so please use it. Refer to the documentation below for information about compiler switches.

Debuggers

We have gdb for gcc and idb for the Intel compilers.

Profilers

  1. gprof
  2. Intel Vtune
  3. HP Caliper

Batch job scheduler

We currently use LSF as resource manager which allows advanced scheduling strategies. For information on how to submit jobs to this scheduler see the corresponding LSF howto page.

Technical Documentation

  1. LSF documentation
  2. Intel software tools documentation

Documents describing Intel tools

  1. Getting the most out of the Intel® Itanium® Architecture (pdf)
  2. Intel® Compilers for Itanium® Architecture (pdf)
  3. Quick-Reference Guide to Optimization with Intel® Compilers (pdf)
  4. Intel® Software Development Products Overview (pdf)
  5. Itanium® Architecture (pdf)
  6. Extracting the best performance from Itanium® Processor (pdf)
  7. Intel® Math Kernel Library (pdf)
  8. The Basics of VTune® Performance Analyzer (ppt)
  9. Intel® VTune® Performance Analyzer Linux Remote Agents (ppt)
  10. An Accelerated, Hands-on Introduction to the VTune® Performance Analyzer for Linux (ppt)

User Howtos

  1. Start a job using the LSF queueing system
  2. Do phylogenetic analyses on Vital-IT

Admin Howtos

  1. Install NCBI 2.2.12 and mpiBLAST 1.4.0
  2. Install SSAHA v31c
  3. Install NestedMICA 0.7.2
  4. Optimizing CHARMM (pdf)

Training and Education

Computing-specific talks given by Vital-IT team members:
  1. Software optimization, part 1 (pdf), Bruno Nyffeler, Dec 1, 2004
  2. Software optimization, part 2 (pdf), Jacques Rougemont, Dec 1 2004

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