GUIDE TO THE LINUX CLUSTERS

This page is the main entry point to the support pages of the two IBM Linux clusters at Parallab. Answers to many frequently asked questions can be found here. We will do our best to keep these pages up-to-date. Please read and consult these support pages regularly, especially when you have just started using the machine(s).

The name of the IBM 1300 cluster is: fire.bccs.uib.no
The name of the IBM e1350 cluster is: fimm.bccs.uib.no

The systems are available to staff and students from the University of Bergen. Fire is also available for researchers that obtained quota through the NOTUR programme. In addition, the systems are available to partners through EU and other projects.

Both clusters target a variety of applications. In particular, applications from bio-informatics, climate sciences, computational physics, and computational chemistry will be promoted on the clusters and will in general be given higher priority.

User support. Questions and problems can be reported to hpc-support@hpc.uib.no or support-uib@notur.no and they will be handled as soon as possible. Working hours are roughly Monday-Friday 08:00-16:00.

Contents

• Basic information
  • A brief description of the installation
  • How to get an account on the machine
  • How to connect to the machine: Secure Shell

• Running jobs on the system
  • Job submission
  • CPU-hour accounting
  • File systems
  • Per node memory configuration

• Programming the computer
  • Compilers and Languages
  • Compiling and running MPI programs, choosing a communication library
  • MPICH
  • LAM
  • Open MPI
  • SCAMPI: the fast interconnect on fimm.
  • Debugging
    TotalView. See here.
  • Performance optimization
    See the page on file systems and the FAQ for I/O optimization.
  • Profiling - prof - gprof
    See on-line manual pages (e.g., 'man gprof').
  • FAQ for the cluster
  • General help for programming:
    Writing modern Fortran: tutorial by Paul Dubois (PDF 400kB)

• Mass storage
  • Retrieving files from backup
  • Automatic data migration is not available for fire and fimm

• Applications. Most application software is installed under directory /local.
  • AMBER (home page)
    - fire: directory sequential version /local/amber7
    - fire: directory MPI version /local/amber7mpi
    - fimm: directory /local/amber8
  • GAMESS
    - fire: directory /local/gamess
  • Gaussian 03 version C.02
    - fimm: directory /local/Gaussian
  • Magma version V2.8-10
    - fire: binary magma
  • MATLAB version 6.5.0 or 7.1.0 (home page)
    To avoid slow start-up, invoke matlab without graphics:

      % matlab -nosplash -nodesktop
      % matlab -nosplash -nojvm
    

  • MrBayes version 3.0
    - fire + fimm: binary mb
  • NAMD version 2.5
    - fire + fimm: directory /local/NAMD
  • mpiBLAST
    - fimm: directory /local/mpiblast

• Other software (see also directory /local)
  • NetCDF version 3.5.1 (documentation)
    - fire + fimm: directory /local/netcdf
  • ATLAS (documentation)
    - fire: /usr/local/ATLAS
    - fimm: /local/ATLAS
    - Example (fire): to use the BLAS and LAPACK libraries, use the GNU compiler and link with
      -L/usr/local/ATLAS/lib/Linux_PIIISSE1_2 -llapack -lf77blas -lcblas -latlas
  • FFTW (documentation)
    - fire: /home/parallab/plab/ragnhild/lib/fftw-3.0.1
    - fimm: /local/fftw/   (also ACML contains FFT routines)
  • Intel's Math Kernel Library MKL (documentation)
    - fire: installed but only available for "personal research and evaluation"
  • AMD Core Math Library ACML (documentation)
    - fimm: directory /local/acml/