Changes between Version 40 and Version 41 of doc/app/palmrun
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- Nov 20, 2018 10:15:27 AM (6 years ago)
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doc/app/palmrun
v40 v41 1 1 = The PALM run script= 2 2 3 The main script to execute PALM is called {{{palmrun}}}. This chapter describes the actions / operations carried out by {{{palmrun}}} and gives a complete list and description of its available options.3 The main script to execute PALM is called {{{palmrun}}}. This chapter describes the actions / operations carried out by {{{palmrun}}} and gives a [#options complete list and description of its available options]. 4 4 5 5 … … 10 10 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. 11 11 The handling of PALM differs between interactive and batch mode, and it slightly varies, depending if the PALM job is submitted to the 12 * [#batch l local computer/host] | The computer that you are currently sitting at or are logged in via your terminal (ssh).13 * [#batch rremote 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.12 * [#batch_local local computer/host] | The computer that you are currently sitting at or are logged in via your terminal (ssh). 13 * [#batch_remote 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. 14 14 15 15 == [=#interactive Interactive mode] == … … 215 215 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. 216 216 217 === [#=batch l Running PALM in batch on a local computer] ===217 === [#=batch_local Running PALM in batch on a local computer] === 218 218 219 219 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. … … 311 311 312 312 313 === [#=batch rRunning PALM in batch on a remote computer] ===313 === [#=batch_remote Running PALM in batch on a remote computer] === 314 314 315 315 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. … … 360 360 361 361 362 == palmrun options==362 == [#=options palmrun options] == 363 363 There are two groups of options, one are the '''user options''' that you can specify yourself when manually calling {{{palmrun}}} from the terminal, and another group of '''internal options''' that are used for automatically created internal calls of {{{palmrun}}}. Internal calls of {{{palmrun}}} are those that are part of the batch job, and those used for automatically starting restart jobs. Normally, you should never use the internal options. User options from a manual call are automatically added to the internal calls of {{{palmrun}}}. 364 364 365 365 The following gives complete lists of {{{palmrun}}} user and internal options. A {{{---}}} in the second column means that the respective option has no argument. 366 366 367 === palmrun user options 367 === palmrun user options === 368 368 369 369 ||='''option''' =||='''default value''' =||='''meaning''' =|| … … 397 397 398 398 399 === {{{palmrun}}} internal options399 === palmrun internal options === 400 400 401 401 ||='''option''' =||='''default value''' =||='''meaning''' =||
