Changes between Version 26 and Version 27 of doc/app/palmrun

Timestamp:

May 24, 2018 9:22:04 AM (6 years ago)

Author:

raasch

Comment:

--

doc/app/palmrun

@@ -4 +4 @@
 = Running PALM with {{{palmrun}}}
 
-PALM can be run in three different modes: interactive mode, batch mode, and batch mode on a remote computer. Here we explain how to run PALM in interactive mode, which means that PALM executes (almost) immediately within your terminal session after you entered the {{{palmrun}}} command. You can follow the progress of the simulation on the terminal where a lot of informative messages will be output. You can also stop the simulation at any time by typing {{{CTRL C}}}. Running PALM in batch mode requires additional manual settings in the configuration file, which will be explained here (add link).
-
-The following instructions assume, that the automatic installer has run without any problems. Please switch to your working directory and check if the default configuration and parameter files have been generated
+PALM can be run in three different modes: interactive mode, batch mode, and batch mode on a remote computer. Here we explain how to run PALM in interactive mode, which means that PALM executes (almost) immediately within your terminal session after you entered the {{{palmrun}}} command. You can follow the progress of the simulation on the terminal where a lot of informative messages will be output. You can also stop the simulation at any time by typing {{{CTRL C}}}. Running PALM in batch mode requires additional manual settings in the configuration file, which will be explained ([wiki:doc/palm_config here]).
+
+The following instructions assume, that the automatic installer has run without any problems. In case that the automatic installer has failed or cannot be used (e.g. on many supercomputer center systems), you need to adjust settings in the configuration file manually. If the automatic installer has run without problems, please switch to your working directory and check if the default configuration and parameter files have been generated
 {{{
    cd ~/palm/current_version
@@ -18 +18 @@
 {{{example_cbl}}} is the so-called ''run identifier'' and tells {{{palmrun}}} to use the NAMELIST file {{{example_cbl_p3d}}} from {{{JOBS/example_cbl/INPUT}}}. It also determines folders and names of output files generated by PALM using informations from the default file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}}. Chapter [wiki:doc/palm_iofiles INPUT/OUTPUT files] explains the format of this file and how you can modify or extend it. As a new user, you should not need to care about this file because the default settings should do the job for you.
 
-Option {{{-h}}} specifies the so-called host identifier. It tells {{{palmrun}}} which configuration file should be used. {{{-h default}}} means to use the configuration file {{{.palm.config.default}}}. The configuration file contains all the computer (host) specific settings, e.g. which compiler and compiler options should be used, the pathnames of libraries (e.g. NetCDF or MPI), or the name of the execution command (e.g. {{{mpirun}}} or {{{mpiexec}}}), as well as many other important settings. If the automatic installer worked correctly, it created this file for you with settings based on your responses during the installation process. You may create additional configuration files with different settings for other computers (hosts), or for the same computer, e.g. if you like to compile and run PALM with debug compiler options (see "creating configuration files manually").
+Option {{{-h}}} specifies the so-called host identifier. It tells {{{palmrun}}} which configuration file should be used. {{{-h default}}} means to use the configuration file {{{.palm.config.default}}}. The configuration file contains all the computer (host) specific settings, e.g. which compiler and compiler options should be used, the pathnames of libraries (e.g. NetCDF or MPI), or the name of the execution command (e.g. {{{mpirun}}} or {{{mpiexec}}}), as well as many other important settings. If the automatic installer worked correctly, it created this file for you with settings based on your responses during the installation process. You may create additional configuration files with different settings for other computers (hosts), or for the same computer, e.g. if you like to compile and run PALM with debug compiler options (see [wiki:doc/palm_config creating configuration files manually]).
 
 Option {{{-a}}} is used for steering the handling of input and output files that are required / generated by PALM. Its argument is called the file activation string(s). The file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}} contains a complete list of PALM's I/O files, one line per file. PALM expects its input files in a temporary working directory that is created by each call of {{{palmrun}}} and it outputs data to this temporary directory too. The file configuration file tells {{{palmrun}}} where to find your input files and where to copy the output files (because the temporary working directory is automatically deleted before {{{palmrun}}} has finished). The default setting is that all these files are in subdirectory {{{$HOME/palm/current_version/JOBS/<run_identifier>}}}, where {{{<run_identifier>}}} is the one given with option {{{-d}}}. The argument of option {{{-a}}} tells {{{palmrun}}} which of these files need to be copied. If the option is omitted, no I/O files will be copied at all. Argument {{{"d3#"}}} means that the parameter/NAMELIST file for steering PALM shall be provided as input file. This is the minimum setting for option {{{-a}}}, because PALM cannot run without this parameter file. Multiple activation strings can be given. See ... for handling PALM I/O files.