Differences

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--- other:newppl:starting [2025/08/29 15:26] – [Dealing with disk space] Finished rewriting the section jypeter
+++ other:newppl:starting [2026/09/10 10:48] (current) – [Available servers] Updated intranet links jypeter
@@ Line 191: / Line 191: @@
 ==== Working directly on your desktop ====
-Always remember that **your local LSCE desktop/laptop can [[#accessing_remote_disks|access remote disks on the LSCE servers]]**.
+  * **your local LSCE desktop/laptop can [[#accessing_remote_disks|access (some) disks on the LSCE servers]]**, if it is connected to the LSCE wired network
-There are **lots** of things you can do directly on your **local** computer (displaying pdf, images, using a text editor, ...), rather than on the remote servers. For example, if a script running on the servers generates a pdf file, it is **more efficient** to open this pdf file using ''Acrobat''/''evince'' on your local computer, than by using ''evince'' on the server.
+  * You can do **many things** directly on your **local** computer (displaying pdf, images, using a text editor, ...), rather than on the obelix servers. For example, if a script running on the servers generates a pdf file, it is **more efficient** to open this pdf file using ''Acrobat''/''evince'' on your local computer, than by using ''evince'' on the server.
 ==== Available servers ====
@@ Line 210: / Line 210: @@
       * By **//inside LSCE//**, we mean that:
         * your computer is connected to the LSCE **wired** network
-        * or you are using the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php#vpnlsce|LSCE VPN]]
+        * or you are using the [[https://private.lsce.ipsl.fr/intranet/accueil-intranet-informatique/outils-pour-le-teletravail/vpn-forticlient/|LSCE VPN]]
         * or you have a //terminal// connected to the ''ssh1'' gateway
     * <wrap hi>Never forget that you are **sharing** these interactive servers with other users!</wrap>
-      * <wrap hi>Do not use too much CPU and/or memory for a long time</wrap>. Heavy computation should be done on the [[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|LSCE cluster]]
+      * <wrap hi>Do not use too much CPU and/or memory for a long time</wrap>. Heavy computation should be done on the [[https://private.lsce.ipsl.fr/intranet/calcul-stockage-informatique/batch/|LSCE cluster]]
       * Learn how to [[other:newppl:starting#determining_the_load_of_a_linux_server|use the top command]] to determine the current load of a server and the CPU/memory usage of your processes !
     * You can use one of the following commands if you want to know on which ''obelixNN'' you are
@@ Line 227: / Line 227: @@
 ('mylogin', 'obelix5')</code>
-  * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//)\\ Use this cluster for **//heavy duty// programs**, rather than killing the multi-users interactive servers
+  * **[[https://private.lsce.ipsl.fr/intranet/calcul-stockage-informatique/batch/|The LSCE cluster]]** (aka the //batch system//)\\ Use this cluster for **//heavy duty// programs**, rather than killing the multi-users interactive servers
     * //Heavy duty// programs are programs that will prevent other users from working on the same server because these programs use a lot of CPU and/or memory for more than a few minutes. Ask your advisor, if you are not sure
@@ Line 315: / Line 315: @@
 |  **P**  | Sort by CPU usage  (''%CPU'' columun) (Default) |
-==== Using the kill command to terminate processes ====
+==== Listing processes with 'ps' ====
+==== Terminating processes will 'kill' ====
 FIXME
@@ Line 558: / Line 561: @@
 ==== Linux/UNIX ====
+=== The 'man' command ===
+You can use the ''man'' command in any terminal to access the full ''man''ual of a command
+  * Examples:
+    * ''man man'' => ''man - an interface to the on-line reference manuals''
+    * ''man ls''
+      * <code>NAME
+       ls - list directory contents
+SYNOPSIS
+       ls [OPTION]... [FILE]...
+DESCRIPTION
+       List information about the FILEs (the current directory by default).  Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.
+       Mandatory arguments to long options are mandatory for short options too.
+       -a, --all
+              do not ignore entries starting with .
+[...]</code>
+  * Reading a //man// page (''man less'' for all the options)
+    * ''SPACE''  /  ''b'': next / previous page
+    * ''q'': quit
+    * ''/pattern'': search ''pattern'' in the //man// page
+      * ''n''  /  ''N'': when searching, look for next / previous occurrence of ''pattern''
+=== Documents ===
   * {{:other:newppl:unix_doc_jyp.pdf|UNIX_doc_JYP.pdf}}: some basic Linux documentation. Make sure you read it!
@@ Line 565: / Line 598: @@
   * Using [[other:ssh|ssh]] and [[other:ssh#copying_files_with_scp|scp]]
-  * See also the //old// [[http://www.idris.fr/formations/utilisation-unix/unix-u-cours.html|IDRIS (advanced) Linux training]] (French tutorial)
+  * See also [[http://www.idris.fr/docs/jean-zay/cheatsheet/|IDRIS cheatsheet]]  (French tutorial)
+=== Example commands ===
+Misc (re)discovered Linux commands. Use ''[[#the_man_command|man]]'' for all the details
+  * ''column'': columnate lists
+  * ''find'': search for files in a directory hierarchy
+    * [[https://meetcyber.net/the-linux-command-i-used-wrong-for-years-e2492de5cfdf|examples]]
+    * (try to) exclude directories using the [[https://www.theunixschool.com/2012/07/find-command-15-examples-to-exclude.html|-prune]] option. Good luck!
+  * ''timeout'': run a command with a time limit
+  * ''tree'': list contents of directories in a tree-like format
+    * ''tree -d -L 2 -a /home/scratch01/$USER'': list 2 (''-L 2'') levels of directories (''-d''), including hidden ones (''-a'')
+  * ''watch'': execute a program periodically, showing output fullscreen
+=== Other commands ===
+Commands **useless for beginners, and probably most users**, but we needed a place to list them...
+  * ''ss'': another utility to [[https://systemweakness.com/the-linux-command-that-quietly-became-my-favorite-debugging-tool-bf51221c3471|investigate sockets]], similar to netstat
 ==== Text editors ====
-<note important>A //jupyter notebook// is **not** a text editor!
+<note important>
+  * <wrap em>Pleeeeeease do not use high-impact vscode on the multi-users servers when you just need a text editor and/or a file explorer</wrap>
-**You need a correct text editor to efficiently work with scripts and programs**
+  * A //jupyter notebook// is **not** a text editor...
+    * ... but it can be useful when you are a beginner, or an intern staying only for one month
+  * **You need a correct text editor if you want to <wrap em>work efficiently</wrap> with scripts and programs**
 {{ :other:newppl:real_programmers.png?direct&600 |}} [[https://www.explainxkcd.com/wiki/index.php/378:_Real_Programmers|xkcd & Real Programmers]]</note>
-There are **lots of text editors available** on Linux computers/servers (''emacs'', ''nano'', ''vi'', ''vim'', ''gvim'', ''gedit'', ...). You can use them:
+  * A **text editor** allows you to easily and <wrap em>efficiently</wrap> create/edit/view a **text file**
+    * <wrap em>Efficiently</wrap>? A text editor appropriate for your server should need only one process, use almost no CPU power, and not much RAM
+      * **Other users of the same server should not be able to notice that you are there** :-)
+      * If your text file is very big, you probably need to read {{:other:newppl:houchesa4_updated.pdf|Useful Linux commands for working with (potentially big) text files}}
+    * By the way, a **text file** is a collection of readable [[other:python:misc_by_jyp#strings|strings]] followed by [[https://mojoauth.com/blog/end-of-line-characters|EOL (End Of Line) characters]] :-)
+    * Other files are called **binary files** (e.g. [[#netcdf_and_related_conventions|NetCDF]])
+      * Real <del>nerds</del>scientists should have at least some notions of [[other:python:misc_by_jyp#data_representation|Data representation]]
-  * In basic **text terminals**
+  * **Most** text editors will use the text file extension (''.txt'', ''.sh'', ''.py'', ''.f90'', ...) to recognize the file content and automatically use colored //<wrap em>syntax highlighting</wrap>// to make the text more readable.\\ **Some** editors will also help you with //<wrap em>code indentation</wrap>// (the ''emacs'' //python mode// is quite efficient)
-    * **If you only need to read a text file**, use a //pager// like [[http://www.greenwoodsoftware.com/less|less]] (or ''more''): ''less my_text_file.txt''
+    * Example //syntax highlighting//:
-      * ''SPACE'' goes down one page
+      * <code bash># This is a comment in an example shell script that would have a '.sh'/'.ksh' extension
-      * ''b'' (//back//) goes back one page
+all_files=`ls`
-      * ''/STRING'' looks for ''STRING'' in the text (then ''n''ext, ''p''revious, ''q''uit)
+echo $all_files</code>
-      * ''q'' exits
-    * **[[#gnu_nano|nano]] is probably the easiest editor in text mode** to use!
-    * Useful if you are in a hurry, and/or working on a remote server with a bad network connection or have no local [[other:x_conf|X server]] running
-    * You should know the basic commands and shortcuts!
-  * With a **full Graphical User Interface** (aka //GUI//) allowing you to use the mouse+menus/buttons/etc...
+  * There are **lots of text editors available** on Linux computers/servers, that you can use directly in **text terminals**, or with a **graphical interface**
-    * you will need to have a //local// [[other:x_conf|X server]] running, if you want to use the text editor GUI on a //remote// server
+    * In basic **text terminals**:
+      * Editors => ''[[#gnu_nano|nano]]'', ''[[#vi_vim_gvim|vi]]'' or ''[[#vi_vim_gvim|vim]]'', ''[[other:emacs_doc|emacs]]''
+      * Note: if you only need to **read** a text file, use a //pager// like [[http://www.greenwoodsoftware.com/less|less]] (or ''more''):
+        * e.g. ''less my_text_file.txt''
+          * ''SPACE'' goes down one page
+          * ''b'' (//back//) goes back one page
+          * ''/STRING'' looks for ''STRING'' in the text (then ''n''ext, ''p''revious, ''q''uit)
+          * ''q'' exits
+      * ''[[#gnu_nano|nano]]'' is probably the easiest editor in text mode to use...\\ ...because the commands are displayed at the bottom of the windows
+      * Editors in text terminals are useful when you are in a hurry, and/or working on a remote server with a bad network connection or have no local [[other:x_conf|X server]] running
+      * You should know the basic commands and shortcuts of at least one editor you can use in a text terminal
+    * With a **full Graphical User Interface** (aka //GUI//) allowing you to use the mouse+menus/buttons/etc...
+      * Editors => ''gedit'', ''geany'', ''[[other:emacs_doc|emacs]]'', ''[[#vi_vim_gvim|gvim]]'', ...
+      * You will need to have a //local// [[other:x_conf|X server]] running, if you want to open the text editor GUI on a //remote// server
 === emacs ===
@@ Line 602: / Line 675: @@
 === vi (vim, gvim) ===
-  * [[https://www.atmos.albany.edu/daes/atmclasses/atm350/vi_cheat_sheet.pdf|vi cheat sheet]]
+You can use ''vi''/''vim'' in a basic text terminal. ''gvim'', the graphical version, is easier to use, but you need to have an [[other:x_conf|X server]] running in order to open the graphical window
-  * [[https://web.mit.edu/merolish/Public/vi-ref.pdf|vi reference card]]
+  * [[https://www.atmos.albany.edu/daes/atmclasses/atm350/vi_cheat_sheet.pdf|vi / vim cheat sheet]]
+  * [[https://web.mit.edu/merolish/Public/vi-ref.pdf|vi / vim reference card]]
 === Notepad++ ===
-[[other:win10apps#notepad|Notepad++]] is a nice and powerful text editor for **Windows**, but it is also very easy to [[other:emacs_doc#windows_installation|install emacs on Windows]]
+[[other:win10apps#notepad|Notepad++]] is a nice and powerful text editor for **Windows**
+Note: it is also very easy to [[other:emacs_doc#windows_installation|install emacs on Windows]] :-)
 ==== NetCDF and related Conventions ====