Changes between Version 27 and Version 28 of doc/app/palmrun

Timestamp:

Jul 16, 2018 12:43:50 PM (6 years ago)

Author:

raasch

Comment:

--

doc/app/palmrun

@@ -301 +301 @@
 === 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 on the world. {{{palmrun}}} copies required input files from your local computer to the remote machine and 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.
+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.
 
 If you like to use this {{{palmrun}}} feature, you need additional/special settings in the configuration file. Furthermore, you need to pre-compile the PALM-code for the remote machine using the {{{palmbuild}}} command. The automatic PALM installer can not be used to install PALM on that machine. You need to do most of the settings manually.
 
-Furthermore, passwordless ssh/scp access from the local computer to the remote computer, as well as from the remote to the local computer, is required. In remote mode, {{{palmrun}}} and {{{palmbuild}}} are heavily using ssh and scp commands, and if you have not established passwordless access, you would need to enter your password several times before the batch job is finally submitted. Moreover, the job protocol file and any output files cannot be transferred back to your local computer because there is no connection to the job which could be used to provide passwords for these transfers (and even if you could, your job may require your input during nighttime while you are sleeping). 
+Furthermore, passwordless ssh/scp access is required from the local computer to the remote computer, as well as from the remote to the local computer. In remote mode, {{{palmrun}}} and {{{palmbuild}}} are heavily using ssh and scp commands, and if you have not established passwordless access, you would need to enter your password several times before the batch job is finally submitted. Moreover, the job protocol file and any output files cannot be transferred back to your local computer because there is no connection to the job which could be used to provide passwords for these transfers (and even if you could, your job may require your input during nighttime while you are sleeping). 
 
 Now, let's start with the configuration file settings for remote batch jobs. For this it would be convenient to create a new configuration file based on the one you already used locally, e.g. by
@@ -338 +338 @@
 Keep in mind that the configuration file {{{.palm.config.<remote host identifier>}}} requires correct settings valid for your remote computer (compiler name, compiler options, include and library paths, etc.). If you forgot to call {{{palmbuild}}}, {{{palmrun}}} will ask you to do this for you.
 
-Now you can call {{{palmrun}}} with
+If {{{palmbuild}}} succeeded, you can enter the {{{palmrun}}} command, like
 {{{
    palmrun -d neutral -h <remote host identifier> ......
 }}}
-After confirming the {{{palmrun}}} settings by entering {{{y}}}, similar information as for local batch jobs will be output to the terminal. After the job has been finished, the job protocol will be transferred to your local computer and put into the folder defined by {{{local_jobcatalog}}}. If this file does not appear, because e.g. the transfer failed, you may find the protocol file on the remote host in the folder defined by {{{remote_jobcatalog}}}. Like in case of batch jobs running on local computers, check the contents of this file carefully. Beside some additional information, it mainly contains the output of the {{{palmrun}}} command as you get it during interactive execution, and especially you get information about where to find the output files on your local computer.
+After confirming the {{{palmrun}}} settings by entering {{{y}}}, similar information as for local batch jobs will be output to the terminal. {{{palmrun}}} finally terminates with messsage {{{--> palmrun finished}}}. The batch job is now queued on the remote system. After the job has been finished, the job protocol will be transferred back to your local computer and put into the folder defined by {{{local_jobcatalog}}}. If this file does not appear, because e.g. the transfer failed, you may find the protocol file on the remote host in the folder defined by {{{remote_jobcatalog}}}. Like in case of batch jobs running on local computers, check the contents of this file carefully. Beside some additional information, it mainly contains the output of the {{{palmrun}}} command as you get it during interactive execution, and especially you get information about where to find the output files on your local computer.
 
 The configuration file {{{.palm.iofiles}}} offers special controls for copying INPUT/OUTPUT files, since large PALM-setups (those using large number of grid points) can produce extremely large output files which would require long time for transferring them to your local system and which might have sizes that exceed the capacity of your local discs. See chapter [wiki:doc/palm_iofiles INPUT/OUTPUT files] which explains how to control copying of INPUT/OUTPUT files. 
 
-
-
 \\\\\\
+'''Attention: Following text is for experienced PALM-users who switch from the old {{{mrun / mbuild}}} scripts to the new scripts {{{palmrun / palmbuild}}}. It is not up-to-date and will be removed at a later time.
+'''
 
 = Configuring and running PALM with {{{palmbuild}}} and {{{palmrun}}}