Changes between Version 28 and Version 29 of doc/app/palmrun

Timestamp:

Jul 19, 2018 5:11:18 PM (6 years ago)

Author:

kanani

Comment:

--

doc/app/palmrun

@@ -2 +2 @@
 \\\\\\
 
-= 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 ([wiki:doc/palm_config here]).
+= Running PALM with {{{palmrun}}} =
+
+== Introduction == 
+PALM can be run in different modes: 
+* [#interactive interactive mode] | PALM executes (almost) immediately within your terminal session after entering the {{{palmrun}}} command.
+* [#batch batch mode] | PALM job is submitted by {{{palmrun}}} to a queuing/batch system (e.g. PBS, ...), where it is scheduled for execution.
+
+A batch system is a must-have on high-performance computers, and a nice-to-have for computers that are shared among a larger number of users.
+The handling of PALM differs between interactive and batch mode, and it slightly varies, depending if the PALM job is submitted to the
+* [#batchl local computer/host] | The computer that you are currently sitting at or are logged in via your terminal (ssh).
+* [#batchr remote computer/host] | Any computer with a batch system, that you have ssh access to, but are not logged in at the moment. The remote host becomes your local host as soon as you log in to the remote host via ssh.
+
+
+== [=#interactive Interactive mode] ==
+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}}}. 
 
 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
@@ -199 +211 @@
 If the run has finished successfully, results can be found in folders {{{JOBS/neutral/MONITORING}}} and {{{JOBS/neutral/OUTPUT}}}.
 
-== How to run PALM in batch mode
+== [#=batch Batch mode] ==
+{{{#!comment
+Running PALM in batch mode requires additional manual settings in the configuration file, which will be explained ([wiki:doc/palm_config here]).
+}}}
 
 Large simulation set-ups usually cannot be run interactively, since the large amount of required resources (memory as well as cpu-time) are only provided through batch environments. {{{palmrun}}} supports two different ways to run PALM in batch mode. In both cases it creates a batch job, i.e. a file containing directives for a queuing-system plus commands to run PALM, which is then either submitted to your local computer or to a remote computer. Running PALM in batch mode requires you to manually modify and extend your configuration file {{{.palm.config....}}}, and that a batch system (e.g. PBS or ...) is installed on the respective computer.
 
-=== Running PALM in batch on a local computer
+=== [#=batchl Running PALM in batch on a local computer] ===
 
 The local computer is the one where the commands that you enter in a terminal sessions are executed. This might be your local PC/workstation, or a login-node of a cluster-system / computer center where you are logged in via ssh. Regardless of the computer, it is assumed that PALM has been successfully installed on that machine, either using the automatic installer or via manual installation.
@@ -299 +314 @@
 
   
-=== Running PALM in batch on a remote computer
+=== [#=batchr Running PALM in batch on a remote computer] ===
 
 You can use the {{{palmrun}}} command on your local computer (e.g. your local PC or workstation) and let it submit a batch job to a remote computer at any place in the world. {{{palmrun}}} copies required input files from your local computer to the remote machine and transfers output files back to your local machine, depending on the settings in the {{{.palm.iofiles}}} file. The job protocol file will also be automatically copied back to your local computer.