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Configuring and running PALM with palmbuild and palmrun

Changes compared to mrun/build

• The new scripts will run on any kind of Linux / Unix system without requiring any adjustments. All settings are controlled via configuration files.

• The old configuration file .mrun.config has been split into two files .palm.config.<configuration_identifier> and .palm.iofiles, where <configuration_identifier> is an arbitrary string that you can define. "Configuration" means a setting for a specific computer with a specific compiler, compiler options, libraries, etc. If you like to run palm with different configurations, e.g. one with debug options switched on, and one with high optimization, you need to create separate configuration files for each configuration, e.g. .palm.config.optimized and .palm.config.debug. This replaces the old block structure in .mrun.config. The configuration file to be used is defined by palmrun- or palmbuild-option -h., e.g. palmrun ... -h optimized will use .palm.config.optimized
  
  You will need only one file .palm.iofiles which contains the file connection statements to be used for all configurations.

• The .palm.config.<ci> file does not contain blocks any more. Several variable names have been changed (e.g. compiler_options instead of fopts) and new variables have been introduced (e.g. execute_command in order to give the command for starting the executable). Colons (:) for separating e.g. compiler options must not be used any more. Here is an example (with some lines truncated, as displayed by ....)

  #$Id$
  #column 1          column 2
  #name of variable  value of variable (~ must not be used, except for base_data)
  #------------------------------------------------------------------------------
  %base_data         ~/palm/current_version/JOBS
  %base_directory    $HOME/palm/current_version
  %source_path       $HOME/palm/current_version/trunk/SOURCE
  %user_source_path  $base_directory/JOBS/$fname/USER_CODE
  #
  %local_ip            111.11.111.111
  %local_username      your_linux_username
  %fast_io_catalog     /localdata/your_linux_username
  %compiler_name       mpif90
  %compiler_name_ser   ifort
  %cpp_options         -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__fftw -D__netcdf
  %make_options        -j 4
  %compiler_options    -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -ip -nbs -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/....
  %linker_options      -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -ip -nbs -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/....
  %hostfile            auto
  %execute_command     mpiexec  -machinefile hostfile  -n {{MPI_TASKS}}  palm
  

• Some further comments concerning specific variables:
  • fast_io_catalog replaces the old variables tmp_user_catalog and tmp_data_catalog. It should be a folder on a file system with fast discs, as typically provided on large computer systems for temporary I/O, e.g. something like /work/.... The temporary working catalog created by palmrun will be in this folder, and your restart data should be put in this folder too. The default .palm.iofiles is using fast_io_catalog for the restart files.
  • For cpp_options, you now have to give ALL switches required, especially -D__parallel to use the parallel version of PALM, which was implicitly set with mrun-option -K parallel before. The -K option has been removed.
  • nvnv

Package installation

The