Changes between Version 4 and Version 5 of doc/app/palmrun

Timestamp:

Sep 22, 2017 9:44:57 AM (7 years ago)

Author:

raasch

Comment:

--

doc/app/palmrun

@@ -9 +9 @@
 * The new scripts will run on any kind of Linux / Unix system without requiring any adjustments. All settings are controlled via configuration files.
 
+* {{{mbuild}}} is replaced by {{{palmbuild}}}, and {{{mrun}}} is replaced by {{{palmrun}}}. The old script {{{subjob}}} is not used any more (submitting jobs is now part of {{{palmrun}}}).
+
 * 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.
+
+* Only one call of {{{palmbuild}}} is required to compile for both the utilities and the PALM source code (there is no option {{{-u}}} anymore). The compiled routines (object files and executables) are put into folder {{{MAKE_DEPOSITORY_<configuration_identifier>}}}, where {{{<configuration_identifier>}}} is replaced by the string given with {{{palmbuild}}}-option {{{-h}}}.
+
+* {{{palmrun}}} does not compile any more at the beginning of a batch job. The palm-executable for the batch-job (or for the interactive session) is created as part of the {{{palmrun}}}-call that you have manually entered at your terminal, and it is created before the batch-job is submitted. The executable is put into the folder {{{SOURCE_FOR_RUN_<run_identifier>}}}, where {{{<run_identifier>}}} is the string provided with {{{palmrun}}}-option {{{-d}}}. This folder is now put into the folder set with variable {{{fast_io_catalog}}} (see below for {{{fast_io_catalog}}}). If you do not use a user-interface, {{{palmrun}}} will not compile at all and will take the executable from folder {{{MAKE_DEPOSITORY_<configuration_identifier>}}} that has been generated with your last call of {{{palmbuild}}}. If {{{palmrun}}} cannot find the folder {{{MAKE_DEPOSITORY_<configuration_identifier>}}}, it will internally call {{{palmbuild}}} in order to generate it. If {{{palmrun}}} finds a folder {{{SOURCE_FOR_RUN_<run_identifier>}}} that has been generated by a previous call of {{{palmbuild}}}, it will ask you if executables from that folder shall be used. This way, you can avoid to re-compile your user-interface with each call of {{{palmrun}}}. Automatically generated restart runs will always use executables from  {{{SOURCE_FOR_RUN_<run_identifier>}}}. \\\\ You may have to remove folders {{{SOURCES_FOR_RUN_...}}} manually frm time to time, because they are not deleted automatically at the end of a job (or the last job of a restart job chain).
 
 * 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 ....)
@@ -37 +43 @@
  - {{{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.
- - The compiler- and linker-options now require to give ALL the include- and library-paths for the libraries that you intend to use (e.g. MPI, NetCDF, FFTW), if they are not automatically set by a module-software running on your system. Old variables like {{{netcdf_inc}}} or {{{netcdf_lib}}} have been removed from the configuration file.
- - {{{execute_coammand}}} is required to define the command to execute PALM. This will depend on the MPI-library that you are using.
+ - The compiler- and linker-options now require to give '''ALL''' include- and library-paths for the libraries that you intend to use (e.g. MPI, NetCDF, FFTW), if they are not automatically set by a module-environment (like e.g. on Cray-systems). Old variables like {{{netcdf_inc}}} or {{{netcdf_lib}}} have been removed from the configuration file.
+ - {{{execute_coammand}}} is required to define the command to execute PALM. It will depend on the MPI-library that you are using. The wildcard{{{ {{MPI_TASKS}} }}}will be replaced by the value provided with {{{palmrun}}}-option {{{-X}}}. A further wildcard that can be used is{{{ {{TASKS_PER_NODE}} }}}, which will be replaced by the value provided with {{{palmrun}}}-option {{{-T}}}.
+ - The variable {{{write_binary}}} (formerly used to switch on the output of restart data) has been removed from the configuration file. Output of restart data is now switched on with the activation string {{{"restart"}}}, i.e. {{{palmrun ..... -a "...  restart"}}}.
  
 \\\\