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public:lle [2009-08-26 14:14] – Arno Schoenmakerspublic:lle [2020-11-04 15:49] (current) – Bernard Asabere
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 ====== The Lofar Login Environment (LLE) ====== ====== The Lofar Login Environment (LLE) ======
  
-This page describes the standard login environment for new users on the LOFAR cluster nodes. It can also be applied to accounts at the WRST site and on the Dwingeloo Linux systems. +This page describes the standard login environment for new users on the LOFAR cluster nodes like [[:cep3:start|CEP3]]. Existing accounts can be easily modified; see below for a manual to do this.
- +
-Existing accounts can be easily modified; see below for a manual to do this.+
  
 ===== General ===== ===== General =====
Line 12: Line 10:
  
 To be able to use the LLE environment you must either use a ''(t)csh'' or ''bash'' login shell. We do not support scripts for any other shells. To be able to use the LLE environment you must either use a ''(t)csh'' or ''bash'' login shell. We do not support scripts for any other shells.
- 
- 
 ===== What to do when you get an account ===== ===== What to do when you get an account =====
  
-==== (t)csh ==== +The CEP3 user creation system has been setup such that new accounts will have all needed files and links in ''$HOME'' in place already. So you do not have to chnage anything to work with the LLE. 
- +===== How to transform existing accounts? =====
-If you have chosen for the ''(t)csh'' shell, you do as follows: +
-  * Log in and go to your (empty) $HOME directory +
-  * ''> cp /opt/login/cshrc .cshrc'' +
-  * Log out and login again; you should see a welcome message. +
- +
-==== bash ==== +
- +
-If you have chosen for the ''bash'' shell, you do as follows: +
-  * Log in and go to your (empty) $HOME directory +
-  * ''> cp /opt/login/bashrc .bashrc'' +
-  * Log out and login again; you should see a welcome message. +
- +
  
 +To use the LLE in an existing account and ''$HOME'' dir, rename your existing ''.cshrc'', or ''.profile'' and ''.bashrc'', in your ''$HOME'' and follow the instructions given above.
 ===== The LLE scripts ===== ===== The LLE scripts =====
  
 Some of the details are presented here. Some of the details are presented here.
- 
-===== What is $APS_LOCAL ? ===== 
- 
-The root directory for the scripts is provided in environment variable ''$APS_LOCAL'', whose value is set in the cshrc or bashrc scripts. The actual value depends on your location: 
-  * CEP processing cluster: ''/opt'' 
-  * lioffen nodes: ''/app'' 
-  * WSRT: ''/wop25_1/aps_local'' 
-  * D'loo: ''/local'' 
  
 ==== Login scripts ==== ==== Login scripts ====
  
-In directory ''${APS_LOCAL}/login'' are a number of default login scripts. The scripts ending with ''.bash'' are for the ''bash'' shell, the others for the ''(t)csh'' shell: \\ +In directory ''/opt/cep/login'' are a number of default login scripts. The scripts ending with ''.bash'' are for the ''bash'' shell, the others for the ''(t)csh'' shell:
-  * ''cshrc'' -> sets APS_LOCAL and calls the other scripts +
-  * ''login'' -> Displays welcome message; no settings +
-  * ''setenv'' -> adds some items to $PATH, sets your prompt, etc. +
-  * ''alias'' -> some default aliases to make life easy +
-  * ''setpackages'' -> script to define packages to initialize at login-time +
-\\+
  
-Users should **NEVER** modify these default scripts at this location!+   * ''cshrc''  → login settings for (t)csh environments. 
 +  * ''bashrc''  → login settings for non-interactive logins. 
 +  * ''profile''  → login settings for interactive logins. 
 +  * ''login''  → Displays welcome message; no settings. 
 +  * ''setpackages''  → script to define packages to initialize at login-time.
  
 +Users should **NEVER**  modify these default scripts. In their ''$HOME''  these should be symlinks to the versions in ''/opt/cep/login''. Personalization of your login is possible through other scripts like ''.myalias''  and ''.mysetenv''  (see below).
  
-=== Transform existing accounts === +If you like to read more on the files that play a role in the bash login, [[https://stackoverflow.com/questions/415403/whats-the-difference-between-bashrc-bash-profile-and-environment|here is a nice link]].
- +
-To use the LLE in an existing account, copy the file ''${APS_LOCAL}/cshrc'' to ''$HOME/.cshrc'', or ''${APS_LOCAL}/bashrc'' to ''$HOME/.bashrc'' (mind the leading 'dot'!).  +
- +
-Do **not** modify this file in your ''$HOME''. Make sure that files such as ''$HOME/.login'', ''$HOME/.setenv'' and ''$HOME/.alias'' are renamed or removed if you want to use the LLE environment. +
  
 ==== Personal command aliasses: .myalias ==== ==== Personal command aliasses: .myalias ====
  
-Personal command aliases can be added to a file ''$HOME/.myalias''. When this file exists, the ''.cshrc'' or ''.bashrc'' script will read this file after reading the default ''${APS_LOCAL}/login/alias(.bash)''.+Personal command aliases can be added to a file ''$HOME/.myalias''. When this file exists, the ''.cshrc''  or ''.bashrc''  script will read this file.
  
 ==== Personal environment settings: .mysetenv ==== ==== Personal environment settings: .mysetenv ====
  
-Personal extensions to ''$PATH'', personal environment variables, or overloaded existing environment variables can be added to a file ''$HOME/.mysetenv''. The cshrc-script will source this file after all other files if it is found.+Personal extensions to ''$PATH'', personal environment variables, personal prompt setting, or overloaded existing environment variables should be done in a file ''$HOME/.mysetenv''. If this file exists, the cshrc or bashrc script will read this file.
  
 +===== Package initialisation =====
  
-===== Package initialisation: .mypackages =====+Many packages are available from the distribution of the Operating System. Several packages are added lateron, see [[:cep3:usersoftware|this page for CEP3 packages]]. To activate these, environment variables like ''PATH'', ''LD_LIBRARY_PATH'', ''PYTHONPATH''  must be set correctly. To help you, we have installed the environment module software (see [[:cep3:usersoftware#using_packages_with_environment_modules|this section in the CEP3 user documentation]]).
  
-To initialize the use of installed packages on your system you must create a file ''$HOME/.mypackages''. It is used by the default script ''setpackages'' in ''$APS_LOCAL''.+==== .mypackages ====
  
-In the directory ''$APS_LOCAL/scripts'' you will find a list of available package initialization scripts ''do<package>'' (e.g., ''doAIPS'', ''doPython''). Whenever you add a package to the file ''$HOME/.mypackages'', the associated script in ''$APS_LOCAL/scripts'' will be ''source'''d.+To initialize the use of installed packages at login time you must create a file ''$HOME/.mypackages''. If this file exists, it is used by the LLE script ''setpackages''.
  
-The file ''$HOME/.mypackages'' can look like this:+The file ''$HOME/.mypackages''  can look like this example:
 <code> <code>
-AIPS++ + 
-doPyrap +casa 
-Tools Python doAIPS+lofim 
 </code> </code>
  
-The packages do not need to be on one line, nor does the file need to have only one package per line. Also note the use of ''<package>'' and ''do<package>''; both are accepted. If a initialization script cannot be found, it will be reported.+Provide only one package name per line. For packages that are build daily and that have a version available for all days of the week (LUS, LofIm), you can also specify a day of week in the ''.mypackages''  file: 
 + 
 +<code> 
 +lofim Tue
  
-To find out which packages should have been initialized, type <code> 
-packages 
 </code> </code>
-This is an alias for ''echo $packages'' and should give the list of packages as you defined in ''$HOME/.mypackages'', and from packages added manually later on. 
  
 ==== How to add a personal package ==== ==== How to add a personal package ====
  
-Apart from the systemwide ''do<package>'' files provided in directory ''$APS_LOCAL/scripts'', users can add their personal ''do<package>'' files in their ''$HOME'' and have these run at login time. If there is a ''do<package>'' file both in $HOME and in ''$APS_LOCAL/scripts'', the version in ''$HOME'' has preference and will be executed. This can be used to test a different version of a package, etc... To add a new, personal, package, act as follows:+Apart from the systemwide module initialization files provided in directory ''$APS_LOCAL/modulefiles'', users can add their personal modulefiles in their ''$HOME/modulefiles''  and have these run at login time. To add a new, personal, modulefile, act as follows: 
   * Install the package   * Install the package
-  * Create a ''$HOME/do<package>'' initialization script (e.g., adding the installation directory to your ''$PATH'')+  * Create a ''$HOME/modulefiles/<package>/<modulefile>''  environment module script (e.g., adding the installation directory to your ''$PATH''). See [[http://modules.sourceforge.net/man/modulefile.html|this manual for writing modulefiles yourself]].
   * Add <package> to the list of packages in file ''$HOME/.mypackages''   * Add <package> to the list of packages in file ''$HOME/.mypackages''
  
 +===== Starting X environment =====
  
 +To start up an X environment you have to make sure that
  
-==== Overview of packages and package initialization scripts ====+  * The files ''$HOME/.xinitrc''  and ''$HOME/.xsession''  are removed
  
-These are the files that you can find in ''$APS_LOCAL/scripts'' and their useage. Not all files may be present at all locations, as some only have use at a specific site (e.g., ''doTMS'' is only useful at the WSRT). +Determine the colordepth that you need (8, 16, 24 bit display) and type: 
 +<code>
  
-=== doAIPS [AIPS] ===+  startx -- :1 -depth <colordepth>
  
-Sources the classic AIPS initialization file (''/aips/LOGIN.CSH'') so classic AIPS can be run. This also requires that are member of the group ''aipsgrp'', otherwise you will not have access to AIPS-defined DATA disks. Contact Stefanie Muhle at JIVE for details about how to set up an AIPS session for the first time.+</code>
  
-=== doAIPS++ [AIPS++] ===+This should start your X environment at the proper colordepth. This will create an additional X Server next to the one you are already running. You can access this with Alt-F8 or Cntl-Alt-F8. The F7 variant will give you back your normal X.
  
-Calls doStableAIPS++ (see below) for the moment. Can be used (but only effective at WSRT, currently) to initialize a host-dependent version of AIPS++. Contact Arno Schoenmakers if you want to use AIPS++.+Due to the large latency and largte bandwidth required for X-traffic, it is advisable to connect to the CEP systems with the ''NX''-client on your system. See [[:public:freenx-windows-client|this page for more info]].
  
-=== doCuisine [Cuisine] ===+===== Help! =====
  
-Initialization script to use the Cuisine pipeline scripts. Maintained by Adriaan Renting. Contact him if you plan on using this.  +If you need help, or have questions, or want to give any other comments, contact Arno Schoenmakers or Jasmin Klipic.
- +
-=== doGIPSY [GIPSY] === +
- +
-Initialization script for the GIPSY package; for GIPSY we have a 32- and 64-bit version. The architecture of your machine deteremines which is activated. +
- +
-=== doIRAF [IRAF] === +
- +
-Initializes the IRAF data reduction package (optical/IR data). It will check if you are a first time user and run ''mkiraf'' if you are. +
- +
-=== doKarma [Karma] === +
- +
-Initialization script of Karma Miriad visualization tools. +
- +
-=== doMiriad4 [Miriad4] === +
- +
-Version 4 of the BIMA/CARMA Miriad version. +
- +
-=== doMiriad4p [Miriad4p] === +
- +
-Optimized version 4 provided by John Romein. Works only on the Adam cluster. Contact Adriaan Renting if you are interested in using this. +
- +
-=== doOosterloo [Oosterloo] === +
- +
-Script to create an environment that can execute most of Tom Oosterloo's personal doXXXX scripts most notably the doWsrtMiriad and related scripts.  +
- +
-=== doPipeline [Pipeline] === +
- +
-Initialization script to use the First-look WSRT data reduction pipeline. Uses Cuisine, Python, WsrtMiriad, WsrtAIPS++. Maintained by Adriaan Renting. Contact him if you plan on using this. +
- +
-=== doPython [Python] === +
- +
-Initialization script to use the Python Pipeline environment with iPython and PyLab.  +
-Maintained by Adriaan Renting. Contact him if you plan on using this. +
- +
-=== doROOT [ROOT] === +
- +
-Initialization script to use the ROOT package. +
- +
-=== doTMS [TMS] === +
- +
-Sets the environment for TMS developers/users (only effective at the WSRT site). Contact Arno Schoenmakers for more information. +
- +
-=== doWsrtAIPS++/doStableAIPS++ [WsrtAIPS++/StableAIPS++] === +
- +
-Initialization script for use of an old WSRT AIPS++ build (V19.1488). Works for Suse 8 and 9 32-bit systems, only. +
- +
-=== doWsrtMiriad [WsrtMiriad] === +
- +
-Version ATNF maintained by Tom Oosterloo. Calls doOosterloo and a scripts in Oosterloo's environment to initialize the wsrtMiriad version. Contact Tom Oosterloo or Rafaella Morganti if you plan to use Miriad. +
- +
- +
-===== How to modify existing accounts ===== +
- +
-There are a few basic steps to perform to use the LLE in existing accounts: +
-  * Make ''tcsh'' your default login shell; your system manager should be able to set this for you. Ask him to replace an existing ''$HOME/.cshrc'' with the default ''cshrc'' file of the Linux Login Environment. +
-  * Rename or remove possibly existing ''$HOME/.login'' file. +
- +
-This will give you the bare environment. To add package activation do the following: +
- +
-  * Copy ''$APS_LOCAL/login/setpackages'' to ''$HOME/.setpackages'', and then  +
-  * Edit this file to setup package activation (see [[#Package initialisation|above]]). +
-  * Try to login and see if the login goes well. +
- +
-===== Starting X environment ===== +
- +
-To start up your X environment you have to make sure that +
-  * The files ''$HOME/.xinitrc'' and ''$HOME/.xsession'' are removed +
- +
-Determine the colordepth that you need (8, 16, 24 bit display) and type:<code> +
-  startx -- :1 -depth <colordepth> +
-</code> +
-This should start your X environment at the proper colordepth. +
-This will create an additional X Server next to the one you are already running. You can access this with Alt-F8 or Cntl-Alt-F8. The F7 variant will give you back your normal X. +
- +
-===== Help! =====+
  
-If you need help, or have questions, or want to give any other comments, contact Arno Schoenmakers, Adriaan Renting or Henk Vosmeijer.+New module-files can be added at any time if you have a new package that should be available systemwide. Contact Arno Schoenmakers or Jasmin Klipic in this case.
  
-New ''do<xxxx>''-files can be added at any time if you have a new package that is available systemwide. Contact Arno Schoenmakers or Adriaan Renting in this case. 
  
  • Last modified: 2009-08-26 14:14
  • by Arno Schoenmakers