CLaMS on JUROPATEST

CVS on JUROPATEST

Compile and execute CLaMS programs

Used Libraries

Debugging

Using Vampir

Using Scalasca

Netcdf4 Format

Access to Juropatest

• The Juropatest system is available by two Login nodes:

  ssh -X userid@juropatest1.fz-juelich.de
  ssh -X userid@juropatest2.fz-juelich.de

Software on Juropatest

• Access to installed software on JUROPATEST is organized through a hierarchy of modules.
• Show what modules are compatible available to load right now (given the toolchain modules you have already loaded):

  module avail

• Load a specific version of a module

  module load <modulename>/<moduleversion>

• List what modules are currently loaded

  module list

• Unload a module

  module unload <modulename>/<moduleversion>

• Unload all modules

  module purge

• Find the location of a module within the module hierarchy

  module spider <modulename>

• Show how to load NetCDF:

  module -r spider '.*netCDF.*'

CVS on JUROPATEST

• Mount CVS archive to ENIX:

  ssh enix.icg.kfa-juelich.de
  mkdir ~/cvsroot
  sshfs userid@hostid.icg.kfa-juelich.de:/usr/nfs/local/archive ~/cvsroot

  To use the CVS archive from ENIX, set the following environment variables:

  export CVSROOT=:ext:userid@enix.icg.kfa-juelich.de:/home/userid/cvsroot
  export CVS_RSH=ssh

Using NetCDF on Juropatest

• Loading NetCDF Module

  module load intel-para netCDF-Fortran/4.4.2
  or
  module load intel netCDF-Fortran/4.4.2

• Compilerversions loaded by intel-para (21.05.2015):
  • gcc-Version 4.9.2 (GCC)
  • icc version 15.0.2 (gcc version 4.9.0 compatibility)
  • ifort version 15.0.2
• If the netcdf module is loaded, "ncdump" and "ncgen" can be used and compilation of programs using netcdf is possible (without specifying any library or include path).
• Compile Fortran program with NetCDF:

  ifort -o progname progname.f90 -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz

Compile and Execute CLaMS programs on Juropatest

• Load following modules

  module load intel-para netCDF-Fortran/4.4.2

• Add current directory to PATH in .profile:

  PATH=.:$PATH
  export PATH

• The libraries used by CLaMS are installed in directory /homec/jicg11/jicg1108
• The CLaMS programs can be compiled with:

  make [useMPI=true] progname

• Create a batch script

  #SBATCH --nodes=1
  #SBATCH --ntasks=4
  #SBATCH --ntasks-per-node=4
  #SBATCH --output=mpi-out.%j
  #SBATCH --error=mpi-err.%j
  #SBATCH --time=00:05:00
  #SBATCH --partition=batch
  
  srun ./traj_mpi

• Submit job
  The job script is submitted using:

  • sbatch <jobscript>

  On success, sbatch writes the job ID to standard out.
• Other Slurm Commands

  • squeue
    Show status of all jobs.

  • scancel <jobid>
    Cancel a job.

  • scontrol show job <jobid>
    Show detailed information about a pending, running or recently completed job.

  • scontrol update job <jobid> set ...
    Update a pending job.

  • scontrol -h
    Show detailed information about scontrol.

  • sacct -j <jobid>
    Query information about old jobs.

  • sprio
    Show job priorities.

  • smap
    Show distribution of jobs. For a graphical interface users are referred to llview.

  • sinfo
    View information about nodes and partitions.

Used Libraries