Changes between Version 2 and Version 3 of doc/app/palmrun

Timestamp:

Sep 22, 2017 7:26:54 AM (8 years ago)

Author:

raasch

Comment:

--

doc/app/palmrun

@@ -1 @@
-A documentation of the palmrun and palmbuild scripts, as well as the palmrungui will follow soon.
+= '''This page is under construction! ''' =
+\\\\\\
+
+= 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]Package installation ===
+
+The