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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
 
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=== [=#package_installation]Package installation ===

The