Differences

This shows you the differences between two versions of the page.

--- other:newppl:starting [2019/07/12 15:13]
jypeter [Project specific directories] Added warning
+++ other:newppl:starting [2024/04/03 11:33] (current)
jypeter [Available servers] Added getlogin and getenv Python example
@@ Line 1: / Line 1: @@
-====== Getting started in CLIM & ESTIMR ======
+====== Getting started at LSCE (by JYP) ======
-<note tip>Welcome to the CLIM & ESTIMR teams!\\ \\ You are probably reading this page because you are a new intern student, visitor, etc...\\ This page will help you survive your first steps at LSCE, at least survive the computers...\\ \\ Reading this page will save your life (and a lot of time)!</note>
+<note tip>Welcome to LSCE!\\ \\ You are probably reading this page because you are a new PhD or intern student, visitor, etc...\\ This page will help you survive your first steps at LSCE, at least survive using the computers (LSCE computers are your future best friends)...\\ \\ Reading this page will save your life (and a lot of time)!\\ \\ This page used to be for the newcomers in the //CLIM// and //ESTIMR// teams, but we can share information LOL</note>
 ===== Miscellaneous information =====
-A few useful links that have nothing to do with science and software resources!
+A few useful links. Some have nothing to do with science and LSCE hardware/software resources!
+  * [[#accessing_the_lsce_intranet|LSCE intranet]]
+  * [[other:newppl:pub_transport|LSCE-related public transport]]
   * [[other:newppl:riealgo|Adding money online to your restaurant account]]
   * [[https://intranet.lsce.ipsl.fr/Phocea/Page/index.php?id=97|Survival kit and other information for CDD and interns]] (LSCE intranet)
-  * [[http://internationaloffice.ceasaclay.com/?lang=en|CEA Saclay International Office]] //Our multilingual staff is readily available to assist you through immigration procedures and to help you settle in France//
+  * [[https://www.universite-paris-saclay.fr/en/campus-life/international-welcome-desk|International welcome desk]] //Université Paris-Saclay supports international students, PhD students and researchers as soon as they arrive in France to ensure their stay take place under the best conditions//
-  * [[https://www.universite-paris-saclay.fr/en/e-international-welcome-office|e-International Welcome Office]] //Paris-Saclay university help to prepare for your arrival in France and help you settle down in the best conditions//
   * [[https://logement.campus-paris-saclay.fr/| Trouver un logement dans une résidence universitaire]] (in French... //Finding a room in a student dorm//)
   * [[https://www.science-accueil.org/en/|Science Accueil]]
+    * [[https://www.science-accueil.org/en/request-services/|Service request page]]
+  * {{:other:newppl:uvsq-guide-du-personnel-nov2019.pdf|Guide du Personnel UVSQ}}
 ===== Phone directory, and map of the building =====
@@ Line 20: / Line 24: @@
   * [[https://intranet.lsce.ipsl.fr/en/Phocea/Membres/Annuaire/index.php|Phone directory]] (intranet)
-    * Dial **2** + ''NNNN'' (last 4 digits) to call somebody at LSCE (or CEA Saclay) from LSCE
+    * Dial **2** + ''NNNN'' (last 4 digits) to **call somebody at LSCE** (or CEA Saclay) from LSCE
+    * Dial **0** + ''NNNNNNNNNNNNNNNNNNNN''  to **call somebody outside LSCE** from LSCE
+    * <wrap hi>Dial **18** to call FLS (CEA security & firemen)</wrap>
+      * [[https://intranet.lsce.ipsl.fr/Phocea/Page/index.php?id=312|Other security related phone numbers]]
+        * <wrap hi>Recommended</wrap>: add the FLS full phone number to your cell phone
   * [[https://intranet.lsce.ipsl.fr/PlanLabo/index.html|701 and 714 map]] (intranet)
@@ Line 60: / Line 68: @@
 Mails sent to these lists will reach lots of people. Think well **before** sending a mail to these lists!
-==== The 'clim' and 'estimr' lists ====
+==== The teams mailing lists ====
-Ask your team leader or Jean-Yves to add you to your team's mailing list
+Ask your team leader to add you to your team's mailing list. Example below: the //CLIM// and //ESTIMR// lists
 ^  List  ^  Team  ^  Archive  ^
@@ Line 76: / Line 84: @@
 ===== Using your own computer at LSCE? =====
-No need to try to connect your laptop to the LSCE wire network, it will not work!
+<wrap em>You can't connect your personal laptop to the LSCE wired network</wrap> (aka //ethernet//), it will **not** work!
-The best you can do is use the [[https://intranet.lsce.ipsl.fr/informatique/wifi/index.php|eduroam or guest wifi]] network, if your office is close enough to one of the access points.
+The best you can do is use the [[https://intranet.lsce.ipsl.fr/informatique/en/wifi/index.php|Guest WiFi]] or [[https://intranet.lsce.ipsl.fr/informatique/en/wifi/eduroam.php|eduroam]] network, if your office is close enough to one of the access points.
-**Warning!** You can't connect directly to the //obelix// LSCE servers from the wifi network. You first have to connect to ''ssh1.lsce.ipsl.fr'', and then to ''obelix''
+**Warning!** You **can't** connect directly to the //obelix// LSCE servers from the wifi network. You first have to connect to the ''ssh1.lsce.ipsl.fr'' //gateway// server, and then to ''obelix''. More details in [[other:ssh#lsce_servers|LSCE servers]]
 ===== Accessing the LSCE intranet =====
-Web site: https://intranet.lsce.ipsl.fr/
+<WRAP center round tip 60%>
+If you try to access the intranet **from outside the LSCE** network (including //eduroam//), your browser will open a ''login''/''password'' popup window.
+Use your LSCE login (not your email address!) and password\\ e.g. use ''jdoe'' and not ''jane.doe@lsce.ipsl.fr''
+</WRAP>
+Intranet web site: https://intranet.lsce.ipsl.fr/
 There is a lot of information available on the LSCE intranet, but you can only access it from a computer connected to the LSCE network
@@ Line 91: / Line 106: @@
   * Reading the mails with the [[https://agenda.lsce.ipsl.fr/|webmail]] or [[https://intranet.lsce.ipsl.fr/informatique/en/mail/thunderbird.php|Thunderbird]]
-    * As soon as you have a LSCE e-mail address, make sure it is added to the //clim// or //estimr// **mailing list**
+    * As soon as you have a LSCE e-mail address, make sure it is added to [[#the_teams_mailing_lists|you team's list]]
   * [[https://intranet.lsce.ipsl.fr/informatique/en/orme/imprimantes.php|Printers]]
-===== Accessing the CEA Saclay intranet and other CEA web sites with vpnssl =====
+===== Accessing the CEA Saclay intranet and other CEA web sites from a browser =====
 <WRAP center round important 60%>
-It used to be possible to access the CEA Saclay intranet by just clicking on http://www-saclay.cea.fr/ from any computer on the LSCE network.
+LSCE is on the Paris-Saclay network (and **not on the CEA network**)
-This is **not possible** anymore, now that LSCE is on the Paris-Saclay network (and not on the CEA network)
+It is therefore **not possible** to access the //CEA Saclay// intranet by just clicking on http://www-saclay.cea.fr/ from a computer on the LSCE wired network (or //eduroam//, or any network outside CEA)
 </WRAP>
 Use the following steps:
   - Start Chrome (or try another browser)
-  - Open the following link: https://vpnssl.cea.fr/
+    * it is even better if you use a [[https://support.google.com/chrome/answer/95464?hl=en|Private/Incognito window]] to do this
-    * ignore the security errors
+  - Open the following link: https://vpn.cea.fr/
+    * ignore the possible security/certificate errors
     * this link will work from the Paris Saclay network, and ANY other location (e.g. home) OUTSIDE of CEA
   - Use your initials and badge number as the **login** (e.g. "//James Bond//" => "**jb007007**") and the number supplied by the //activIDentity// keyring, followed by your 4 digits personal code, as your **password**
@@ Line 114: / Line 130: @@
     * ...
   - Click on //logout// when you are done
+    * ... and close your browser //Incognito// window if you used one
 ===== Setting up your desktop computer =====
-Everybody working for CLIM & ESTIMR gets a computer that can be connected to the LSCE network. Please take the time to read the instructions below, that may help make your life easier
+You should receive a desktop/laptop connected to the LSCE network when you arrive. Please take the time to read the instructions below, that may help make your life easier
 ==== Windows computer ====
-Read the notes in [[other:index#windows_7_notes|Windows 7 notes]] or [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows XX// section
+Read the [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows 10// section
 === Getting administrator's rights ===
@@ Line 127: / Line 144: @@
 <note warning>\\ Make sure you know what you are doing and that you are not executing a virus asking you suspicious access rights!\\ </note>
-If an application requests administrator's rights to install something or make changes to the computer, **and you are sure it's not a virus**, use the ''.\adminuser'' account and the ''adminuser'' password you received when your computer was configured, or ask the [[.:starting?do=edit#getting_help_from_the_lsce_system_administrators|system administrators]].
+If an application requests administrator's rights to install something or make changes to the computer, **and you are sure it's not a virus**, use the ''.\admin'' local account and the ''admin'' password you received when your computer was configured, or ask the [[.:starting?do=edit#getting_help_from_the_lsce_system_administrators|system administrators]].
 ==== Linux computer ====
@@ Line 147: / Line 164: @@
 ==== Mac ====
-Sorry, you are on your own, but it's soooo easy to use, right?
+Sorry, you are (almost) on your own, but a Mac is soooo easy to use, right? 8-)
+Some useful mac links:
+  * [[other:ssh#a_recommended_terminal_for_mac|A recommended terminal for Mac]]
+  * [[other:x_conf#using_an_x_server_on_a_mac|Using an X server on a Mac]]
+  * [[other:ssh#mac_ssh_agent|Mac ssh agent]]
 ===== Accessing the Windows cluster from a Linux computer =====
-Follow the instructions in the [[https://intranet.lsce.ipsl.fr/informatique/en/winsrv.php|Windows servers]] page. If you need to use a program that is missing on this cluster, see the [[#getting_help_from_the_lsce_system_administrators|Help]] section
+If you have a Linux computer, but need to use a Windows application, follow the instructions in the [[https://intranet.lsce.ipsl.fr/informatique/en/winsrv.php|Windows servers]] page.
-===== Accessing the Linux servers from your LSCE deskop =====
+If you need to use a program that is missing on the Windows cluster, see the [[#getting_help_from_the_lsce_system_administrators|Help]] section.
-==== Linux or mac desktop ====
+===== Accessing the LSCE Linux servers =====
-Just open a terminal and [[#which_linux_servers_should_you_use|use ssh to connect to the appropriate server]]
+You have to [[other:ssh|use ssh]] to connect to the [[other:ssh#lsce_servers|LSCE Linux servers]], and [[other:ssh#copying_files_with_scp|use scp to copy files between servers]]
-==== Windows desktop ====
+If you are really in a hurry, go directly to the [[other:ssh#connecting_to_servers_commonly_used_by_lsce_users|Connecting to servers commonly used by LSCE users]] section, but it is important that you **read the full [[other:ssh|ssh documentation]] page at least once**!
-There should be an //Obelix// shortcut on the left side of your desktop. Double-click on it in order to open a window (e.g. with graphics) environment on one of the obelix servers. Each terminal you will open in this environment will run on the same obelix server. Use ssh to [[#which_linux_servers_should_you_use|connect another server]]
-If there is not yet an //Obelix// shortcut, use the [[other:win7apps#setup|VcXsrv XLaunch]] program to create it
-Note: you can also use [[other:win7apps#putty|Putty]] if you just need text windows, or [[other:win7apps#vcxsrv_windows_x_server|VcXsrv]] or [[other:win7apps#putty|Putty]]+[[other:win7apps#cygwin-x|Cygwin-X]] if you also need graphics
 ===== Which Linux servers should you use? =====
-There are lots of things you can do directly on your **local** Win7/Win10 or Linux desktop (displaying pdf, images, using a text editor, ...), rather than on the remote servers. Never forget that **your local desktop has access to the remote disks on the Linux servers**.
+==== Working directly on your desktop ====
-Otherwise, **use the appropriate Linux servers**. The //load balancing// system will send you to the server that has currently the smallest load
+Always remember that **your local LSCE desktop/laptop can [[#accessing_remote_disks|access remote disks on the LSCE servers]]**.
-  * **obelix**//NN// (type ''ssh obelix'' to get there): never forget that you are sharing these servers with other users! Do not use too much CPU and memory for a long time. Heavy computation should be done on the obelix cluster
+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.
-    * <code> $ ssh obelix
+==== Available servers ====
+  * **The LSCE //gateway//**: ''ssh1.lsce.ipsl.fr''
+    * Use ''ssh ssh1.lsce.ipsl.fr'' when you are **outside the LSCE wired network**, before accessing any other LSCE server:
+      * By **//outside LSCE//**, we mean that your computer is:
+        * connected to the LSCE WiFi network (instead of the wired network)
+        * or physically outside LSCE
+    * You can also use ''ssh1'' when you are **copying files to/from outside LSCE** with ''scp'' or ssh-based tools
+    * <wrap hi>The ''ssh1'' gateway can **only** be used for copying files or accessing the LSCE interactive servers</wrap>!
+      * **You have to** connect to an ''obelix//NN//'' interactive server before doing any real work
+  * **The LSCE interactive servers**: ''obelix//NN//'' (''obelix2'' to ''obelix5'')
+    * Use ''ssh obelix'' to access the LSCE servers from **inside LSCE**.\\ The //load balancing// system will send you to the ''obelix//NN//'' server that has currently the smallest load.
+      * 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 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]]
+      * 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
+      * <code>$ ssh obelix
 Last login: Mon Jun  3 08:49:53 2019 from somewhere
-# You can use one of the following commands if you want to know on which obelix you are
+$ echo $HOST
- >echo $HOST
 obelix5
- >hostname
+$ hostname
 obelix5</code>
-  * [[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|the batch system]] (aka //obelix **cluster**//) for really heavy duty programs
+    * In a python script, you can use the following to get some information
-  * in some cases, you may need an account to use the [[http://mesocentre.ipsl.fr/|IPSL/ESPRI clusters]] (aka //ciclad// and //climserv//), especially if you need to use data that is already available/mirrored there, rather than copying the data to LSCE
+      * <code>>>> import os
-  * //asterixN//: some people may mention these servers, but they don't exist any more!
+>>> os.getlogin(), os.getenv('HOST')
+('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
+    * //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
+  * **The [[https://documentations.ipsl.fr/spirit/|IPSL Computing and Data Center]]**, aka //Mésocentre ESPRI// (''Spirit'' / ''SpiritX'' / ''HAL'')
+    * Note: the ''Spirit''/''X'' clusters have replaced the ''ciclad''/''climserv'' cluster (in 2022)
+    * You will need a specific account (different from your //LSCE// account) to access these servers and use data files that are already available/mirrored there (e.g. **''CMIPn'' data**).\\ **Do not duplicate** at LSCE data  already available on IPSL servers and that you can process there!
+    * [[https://mesocentre.ipsl.fr/account-opening/|Requesting an IPSL account]]
+    * [[https://documentations.ipsl.fr/spirit/|IPSL ESPRI Mesocenter documentation]]
+      * [[https://documentations.ipsl.fr/spirit/spirit_clusters/head_nodes.html|spirit clusters]]
+    * [[https://documentations.ipsl.fr/spirit/getting_started/support.html|Getting help]]
+  * **The ''asterix//NN//'' servers**\\ Some wise LSCE elders may mention these servers, but they don't exist any more!
 ==== Which shell are you using? ====
@@ Line 205: / Line 258: @@
 If the Linux server you are working on seems slow, or if you want to get an idea of the resources **you** are using, you should use the ''top'' command
-<code>jypeter@obelix4 - ...jypeter - 46 >top
+<code>  >hostname
+obelix3
+ >top
 top - 17:48:51 up 8 days, 23:43, 29 users,  load average: 1.22, 1.38, 1.98
 Tasks: 324 total,   2 running, 320 sleeping,   2 stopped,   0 zombie
@@ Line 213: / Line 269: @@
   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
- mpeau     20   0  302m 4336 2272 R 100.0  0.0   7033:08 emacs
+ john      20   0  302m 4336 2272 R 100.0  0.0   7033:08 emacs
- mpeau     20   0  110m 2008 1228 S  0.7  0.0   0:00.13 tcsh
+ john      20   0  110m 2008 1228 S  0.7  0.0   0:00.13 tcsh
- dzhu      20   0 1635m  20m 3880 S  0.3  0.1   0:44.90 ipython
+ jane      20   0 1635m  20m 3880 S  0.3  0.1   0:44.90 ipython
 root      20   0 21448 1108  892 S  0.0  0.0   0:01.61 init
     [...]
 </code>
-The top lines give you some summary information about the system, but you should monitor the memory usage (''VIRT'' and ''RES''), ''CPU'' and ''TIME'' columns. By default, ''top'' will will put the processes using the more CPU at the top (as shown above). You can see above that the ''emacs'' text editor has clearly crashed, because it should not use 100% CPU for such a long time
+The top lines give you some summary information about the system, but you should monitor the memory usage (''VIRT'' and ''RES''), ''CPU'' and ''TIME+'' columns. By default, ''top'' will will put the processes using the more CPU at the top (as shown above). You can see above that the ''emacs'' text editor has clearly crashed, because it should not use 100% CPU for such a long time
+  * The ''TIME+'' information is in //minutes// (e.g. ''5432:01'' means //5432 minutes and 1 second//, ''25:15.20'' means //25 minutes, 15 seconds and 20% of 1 second//)
+  * Memory usage:
+    * ''%MEM'' (Kb): percentage of the total available **physical memory** used by a process. This is based on ''RES'', the **non-swapped physical memory** used by a process
+    * ''VIRT'' (Kb): total  amount  of **virtual memory** (i.e. memory temporarily swapped/saved to disk) used by a process.  It includes all code, data and shared libraries plus pages that have been swapped out and pages that have been mapped but not used
+    * The ''free'' command can display the memory usage of a server at a given time. ''available'' is an estimation of how much memory is available for starting new applications, without swapping
+      * <code> % free -ht
+              total        used        free      shared  buff/cache   available
+Mem:            62G        1.5G         56G         11M        5.0G         60G
+Swap:           62G        1.7G         60G
+Total:         125G        3.3G        116G</code>
 If you type ''M'', the processes will be sorted my memory usage, as shown below
 <code>      PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
- jchang    20   0 8488m 8.1g 7912 R 99.6 25.9   1:41.38 idl
+ bob       20   0 8488m 8.1g 7912 R 99.6 25.9   1:41.38 idl
- pvait     20   0  232m  70m 2632 S  0.0  0.2   0:01.36 R
+ john      20   0  232m  70m 2632 S  0.0  0.2   0:01.36 R
- dzhu      20   0 1635m  20m 3880 S  0.0  0.1   0:44.87 ipython
+ jane      20   0 1635m  20m 3880 S  0.0  0.1   0:44.87 ipython
- astege    20   0  954m 9292 2664 S  0.0  0.0   0:40.67 gedit
+ bob       20   0  954m 9292 2664 S  0.0  0.0   0:40.67 gedit
 nslcd     20   0  442m 6056 2208 S  0.0  0.0   2:13.98 nslcd
-twang     20   0  128m 5068 2076 S  0.0  0.0   0:00.05 gconfd-2
+ john      20   0  302m 4336 2272 R 99.9  0.0   7024:13 emacs
- mpeau     20   0  302m 4336 2272 R 99.9  0.0   7024:13 emacs
     [...]</code>
@@ Line 237: / Line 304: @@
 |  **q**  | Quit |
-|  **c**  | Display the command line options of the running processes|
+|  **c**  | Display the command line options of the running processes |
 |  **u**  | List only the processes of a specific user |
+|  **M**  | Sort by memory usage  (''%MEM'' columun)  |
+|  **P**  | Sort by CPU usage  (''%CPU'' columun) (Default) |
+==== Using the kill command to terminate processes ====
+FIXME
+''kill proc_number''
+''kill -9 -1''
+''qdel''
 ===== Which disks should you use? =====
@@ Line 246: / Line 324: @@
   * It is very important to use the correct directories and make it easy for your advisor to find things after you have left
     * <wrap em>**Put the source codes, scripts and papers you are writing on a backed up disk**</wrap>
-      * The <wrap em>backed up disk at LSCE</wrap> is [[#the_home_directory|/home/users/your_login]]. You should have a few Gb available on //home// (use the ''quota -s'' command to find out the exact amount)
+      * The <wrap em>backed up disk at LSCE</wrap> is [[#the_home_directory|home directory]]\\ You should have a few Gb available on //home//\\ Use the ''quota -s'' command to find out the exact amount
     * Put **temporary files** on a scratch disk (''scratch01'' at LSCE)
     * Do **NOT** put (big) data files on a backed up disk
@@ Line 255: / Line 333: @@
 ==== Accessing remote disks ====
-It is possible to access directly all the disks on the LSCE servers from your local Linux or Windows desktop
+It is possible to **directly** access some disks on the LSCE servers from:
-  * Example path on the LSCE Linux server: ''/home/scratch01/your_lsce_login''
+  * a Linux or Windows computer connected directly to the LSCE ethernet/wired network
-  * Accessing the path above from a local desktop:
+  * or a remote computer using the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php#vpnlsce|LSCE VPN]]
-    * Linux desktop: ''/home/scratch01/your_lsce_login''
-    * Windows desktop: ''\\dfshost\dfs\scratch01\your_lsce_login''\\ {{ :other:newppl:dfs_on_win.png?nolink |}}
+For security reasons, only backed up disks and ''scratch01'' can be accessed from Windows with //dfs//
+e.g. if you have a ''/home/scratch01/your_lsce_login'' path on a Linux server, you can access it the following way from your desktop/laptop:
+  * Linux computer: ''cd /home/scratch01/your_lsce_login''
+  * Windows computer explorer: ''\\dfshost\dfs\scratch01\your_lsce_login''\\ {{ :other:newppl:dfs_on_win.png?nolink |}}
 ==== The home directory ====
@@ Line 273: / Line 356: @@
       * tcsh shell users: ''.cshrc'' and ''.login''
       * bash shell users: ''.profile'' and ''.bashrc''
-      * emacs text editor: ''.emacs''
+      * [[other:emacs_doc|emacs text editor]]: ''.emacs''
-    * You can go to your home directory by typing ''cd'' (no arguments), and to the home directory of somebody else with ''cd ~login_name''
+    * You can go to your home directory by typing ''cd'' (no arguments),\\ and to the home directory of somebody else with ''cd ~login_name''
-    * At LSCE, you can't read the content of somebody else's //home// directory
+      * At LSCE, you can't read the content of somebody else's //home// directory by default
   * **Backup of the home directory on the LSCE servers**: YES! Every night
@@ Line 291: / Line 374: @@
  > quota -s
-Disk quotas for user jypeter (uid 6369):
+Disk quotas for user johndoe (uid 6369):
      Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
 prolix3:/users/   4658M   4883M   4981M           23503       0       0</code>
@@ Line 328: / Line 411: @@
 Your Linux environment may sometimes stop working correctly because you have exceeded the allowed quota on your disks (check your quotas with ''quota -s''). You can use the following command to get the size of all the directories and files in the current directory, sorted by size: ''du -sh * | sort -rh''
-<code>jypeter@obelix4 - ...jypeter - 46 >cd /home/scratch01/jypeter
+<code> >cd /home/scratch01/johndoe
-/home/scratch01/jypeter
+/home/scratch01/johndoe
-jypeter@obelix4 - ...jypeter - 47 >du -sh * | sort -rh
+ >du -sh * | sort -rh
 M     GLAC1DHiceF26.nc
 M     dashboard
@@ Line 340: / Line 423: @@
 ...</code>
+FIXME Add something about ''df''
 ===== Which programs should you use? =====
@@ Line 406: / Line 490: @@
     - A tutorial
   * Useful Linux commands for working with (potentially big) text files ({{:other:newppl:houchesa4_updated.pdf}})
-  * Using ssh on [[http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh-utilisateurs-unix.pdf|Linux]] and [[http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh_putty_v2_2011-1.pdf|Windows]]
+  * Using [[other:ssh|ssh]] and [[other:ssh#copying_files_with_scp|scp]]
-  * An annotated reference card of the emacs text editor ({{:other:newppl:emacs_jyp.pdf}})
-    * JYP's .emacs file: {{:other:emacs_linux_150806.tar|for Linux}} - {{:other:emacs_win_7_64_140408.zip|for Windows}}, with [[other:win7apps#gnu_emacs_gnuwin_diffutils|emacs for Windows]]
-You can also check the [[http://wiki.ipsl.jussieu.fr/FondamentauxpoleModelisationClimat|Les fondamentaux du pôle de modélisation du climat de l'IPSL]] wiki page
+==== Text editors ====
-==== NetCDF and file formats ====
+<note important>A //jupyter notebook// is **not** a text editor!
+**You need a correct text editor to efficiently work 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:
+  * In basic **text terminals**
+    * **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''
+      * ''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!
+    * 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...
+    * 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
+=== emacs ===
+<note important>Read the **dedicated [[other:emacs_doc|Using emacs]] page**, and become a power user!</note>
+=== Gnu nano ===
+<note tip>Gnu [[https://www.nano-editor.org/|nano]] is probably the easiest text editor in text mode to use!</note>
+You can easily view/edit a file by just typing ''nano my_text_file.txt'' in a terminal, and looking at the instructions displayed at the bottom of the screen (e.g. ''^X Exit'' means that you can exit the editor by typing ''CTRL-X'')
+=== vi (vim, gvim) ===
+  * [[https://www.atmos.albany.edu/daes/atmclasses/atm350/vi_cheat_sheet.pdf|vi cheat sheet]]
+  * [[https://web.mit.edu/merolish/Public/vi-ref.pdf|vi 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]]
+==== NetCDF and related Conventions ====
+=== Super-short introduction to NetCDF ===
   * What are binary ({{:other:newppl:binaire_jyp.pdf}}) and NetCDF ({{:other:newppl:netcdf_jyp.pdf}}) files?
@@ Line 419: / Line 542: @@
   * The NetCDF file format is **self-documented**, and the metadata of climate data files often follows the [[http://cfconventions.org/|CF (Climate and Forecast) Metadata Conventions]]
     * The files in the [[https://esgf-node.ipsl.upmc.fr/projects/esgf-ipsl/|CMIPn (n ≥ 5) database]] are written with the [[https://cmor.llnl.gov/|CMOR 3 library]] in order to make sure that they follow exactly the requested standards
-  * You can use [[other:win7apps#panoply|Panoply]] and [[http://meteora.ucsd.edu/~pierce/ncview_home_page.html|ncview]] for visualizing quickly the NetCDF files
-  * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] for manipulating NetCDF files (and some other formats)
-  * [[http://nco.sourceforge.net/#RTFM|netCDF Operator (NCO)]] for manipulating NetCDF files
-  * [[http://cfconventions.org/|NetCDF CF (Climate and Forecast) Metadata Conventions]]: this will help you understand the information you get when you do a ''ncdump -h some_climate_data_file.nc''
-  * Using Python to work with NetCDF data:
-    * Using the [[http://uv-cdat.llnl.gov/documentation/cdms/cdms.html|cdms2]] module if you work with the [[other:python:starting#uv-cdat|UV-CDAT distribution]]
-    * Using the [[http://unidata.github.io/netcdf4-python/|netCDF4]] module
-==== Using the Python language ====
-  - [[other:python:starting|Working with Python]]
+=== Some ways of working with NetCDF without programming ===
-  - [[other:python:jyp_steps|JYP's recommended steps for learning python]]
+  * Displaying the content of a NetCDF file in a text format\\ Check the ''ncdump'' [[https://docs.unidata.ucar.edu/nug/current/netcdf_utilities_guide.html#ncdump_guide|options]]. People usually want to quickly check the metadata, and use other programs to work with the actual data
+    * ''ncdump some_climate_data_file.nc'': dump the full content to text
+    * ''ncdump -h some_climate_data_file.nc'': only display the metadata
+  * You can use [[other:win7apps#panoply|Panoply]] and [[http://meteora.ucsd.edu/~pierce/ncview_home_page.html|ncview]] for quickly visualizing NetCDF files
+  * Manipulating NetCDF files:
+    * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] (''cdo'')
+    * [[http://nco.sourceforge.net/#RTFM|netCDF Operator]] (//NCO// operators)
+=== NetCDF related Conventions ===
+  * [[https://arxiv.org/abs/1911.08638|Gridspec: A standard for the description of grids used in Earth System models]]
+    * A nice document for discovering the different type of (ir)regular grids used in climate models!
+  * [[http://cfconventions.org/|NetCDF CF (Climate and Forecast) Metadata Conventions]]
+  * [[https://ugrid-conventions.github.io/ugrid-conventions/|UGRID Conventions]] for storing unstructured (or flexible mesh) model data
+  * [[http://sgrid.github.io/sgrid/|SGRID Conventions]] for storing staggered data on structured grids that are consistent with the UGRID conventions
+=== Using NetCDF with Python ===
+Check the [[other:python:jyp_steps#using_netcdf_files_with_python|dedicated section]] of the //Python// page
+==== Programming languages ====
+  * [[other:index#python_notes|JYP's Python notes]]
 ===== Getting help (from the LSCE system administrators) =====
@@ Line 444: / Line 585: @@
 <code> >ssh -v obelix
 OpenSSH_7.4p1, OpenSSL 1.0.2k-fips  26 Jan 2017
-debug1: Reading configuration data /home/users/jypeter/.ssh/config
+debug1: Reading configuration data /home/users/johndoe/.ssh/config
 debug1: Reading configuration data /etc/ssh/ssh_config
 debug1: /etc/ssh/ssh_config line 58: Applying options for *
@@ Line 450: / Line 591: @@
 debug1: Connection established.
 debug1: key_load_public: No such file or directory
-debug1: identity file /home/users/jypeter/.ssh/id_rsa type -1
+debug1: identity file /home/users/johndoe/.ssh/id_rsa type -1
 [...]
 debug1: Entering interactive session.
@@ Line 459: / Line 600: @@
 debug1: Sending env LANG = en_US
 Last login: Thu Mar  1 15:52:44 2018 from lsce4078.lsce.ipsl.fr
-Disk quotas for user jypeter (uid 6369):
-     Filesystem   space   quota   limit   grace   files   quota   limit   grace
+ >
- prolix3:/users   4558M   9766M  10743M           23741       0       0
-jypeter@obelix3 - ...jypeter - 41 >
 </code>
@@ Line 472: / Line 611: @@
 {{ :other:newppl:screenshot_xfce.jpg?200 |Click to get a larger version}}
-On Windows, you can use the //Capture screen// option of [[other:win7apps#xnview|XnView]]
+On Windows, you can use [[other:win10apps#snip_sketch|Snip & Sketch]], or the //Capture screen// option of [[other:win10apps#xnview_classic|XnView]]
 {{ :other:newppl:xnview_capture.jpg?200 |Click to get a larger version}}
-===== Accessing the LSCE servers from outside the LSCE =====
+===== Getting help, when using the IPSL Mesocenter =====
-The only way to access the LSCE servers from outside LSCE is to connect first to the **ssh1.lsce.ipsl.fr** gateway server.
-==== Interactive access ====
-  - Send a mail to //help-lsce//, and request an access to the //ssh1// server
-  - Use ''ssh'' to **connect** to //ssh1//
-    * From a Linux/mac desktop: ''ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr''
-    * From a Windows desktop:
-      * Text only: use [[other:win7apps#putty|Putty]]
-      * Text & graphics. This is more complex to set up, and you need to use one of the options below:
-        * use [[other:win7apps#vcxsrv_windows_x_server|VcXsrv]]
-        * use [[other:win7apps#cygwin-x|cygwin/X]]
-        * use [[other:index#virtualbox_notes|VirtualBox]]
-  - You can access all LSCE disks from //ssh1//, but there is only a limited number of programs that you can run, so you have to go from //ssh1// to //obelix// or //curie// with one of the ''ssh'' commands below:
-    * ''ssh obelix''
-    * ''ssh your_tgcc_login@curie-ccrt.ccc.cea.fr''
-  - It's possible to use only one line to to both ssh commands
-    * obelix: ''ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr -t ssh -A obelix''
-    * TGCC: ''ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr -t ssh -A your_tgcc_login@curie-ccrt.ccc.cea.fr''
-  - You can define an alias in order to connect more easily to the machines:
-    * //tcsh// users: add the following line to your ''~/.cshrc'' configuration file\\ ''alias sobelix 'ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr -t ssh -A obelix'''
-    * //bash// users: add the following line to your ''~/.bashrc'' configuration file\\ ''alias sobelix='ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr -t ssh -A obelix'''
-  - You should create and configure an //ssh key//, if you don't want to type your password each time you use ssh or scp
-  - If you want more information about ''ssh''
-    * Linux users: http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh-utilisateurs-unix.pdf
-    * Windows users: http://ciclad-web.ipsl.jussieu.fr/data/documents/ssh_putty_v2_2011-1.pdf
-==== Copying files to/from LSCE ====
-If you need to **transfer** files to/from LSCE, use ''scp'' (on Linux), or an scp client such as [[other:win7apps#winscp|WinSCP]] (on Windows) between your computer and ''ssh1.lsce.ipsl.fr''
-  * Example from a Linux/mac desktop: ''scp -p file_outside_lsce your_lsce_login@ssh1.lsce.ipsl.fr:/home/scratch01/your_lsce_login/''
+Check the [[https://mesocentre.ipsl.fr/contacts//|Contacts]] page
 ===== What next? =====

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