Differences

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

--- other:newppl:starting [2016/02/11 10:45] – [Useful documentation for beginners] Improved the netcdf documentation jypeter
+++ other:newppl:starting [2022/11/18 11:46] – Added a specific Text editors section jypeter
@@ 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. 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 provides you with a variety of services and documentation to welcome international students and researchers under 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 =====
+==== Using existing information ====
+  * [[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
+  * [[https://intranet.lsce.ipsl.fr/PlanLabo/index.html|701 and 714 map]] (intranet)
+==== Updating the directory/map information ====
+<WRAP center round important 60%>
+It's very important that you update your phone/office information when you arrive at LSCE, so that other people can find you using the tools above!
+</WRAP>
+=== Finding your phone number ===
+Use the following sequence of keys on the //Mitel// phone in your office:
+  - Select **MENU** (use the downward arrow)
+  - Select **PARAMETRES** (use the downward arrow)
+  - Select **GENERAL** (use the downward arrow)
+  - Select **MON NUMERO**
+    * This will display your **2** + ''NNNN'' phone number
+    * You can be called from outside with ''01 69 08 NN NN''
+=== Updating your entry in the directory ===
+  - Find your name in the [[https://intranet.lsce.ipsl.fr/en/Phocea/Membres/Annuaire/index.php|phone directory]]
+  - Click on **Modifier mes coordonnées** (in blue on the right side)
+  - Click on **Informations dans l'annuaire** and update the different fields
+  - Click on **Envoyez votre demande**
+===== The LSCE mailing lists =====
+It is important to join the correct mailing lists, if you want to get all the information you need, on time.
+==== The 'all' list ====
+When your account is created, your email address should automatically be added to the the //all// list, that can be used to send mails to all the people working at LSCE. You will also get IPSL information through this list
+| [[all@lsce.ipsl.fr]] |  Everybody at LSCE  |
+| [[lsce-orme@lsce.ipsl.fr]] |  People working at Orme  |
+| [[lsce-gif@lsce.ipsl.fr]] |  People working in Gif  |
+Mails sent to these lists will reach lots of people. Think well **before** sending a mail to these lists!
+==== The teams mailing lists ====
+Ask your team leader to add you to your team's mailing list. Example below: the //CLIM// and //ESTIMR// lists
+^  List  ^  Team  ^  Archive  ^
+| [[clim@lists.lsce.ipsl.fr]] |  //clim//  | [[https://lists.lsce.ipsl.fr/sympa/arc/clim]] |
+| [[estimr@lists.lsce.ipsl.fr]] |  //estimr//  | [[https://lists.lsce.ipsl.fr/sympa/arc/estimr]] |
+==== Notes ====
+  * You have to be identified on the server to access most lists's details. Enter you login and email password in the //email address// and //pasword// fields at the top right of any mailing list web page
+  * You may want/need to join other mailing lists (project specific, sports, ...). Check the [[https://lists.lsce.ipsl.fr/sympa/lists|list of lists]] to find about all the existing lists
+  * It is possible to [[https://pmip2.lsce.ipsl.fr/lists.shtml|use mails to interact with the LSCE lists server]], rather than the web interface
 ===== 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 LSCE servers from the wifi network. If you need to do that, you will have to connect to a server outside LSCE first, and then back to LSCE...
+**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 21: / Line 103: @@
   * 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 =====
+===== Accessing the CEA Saclay intranet and other CEA web sites with vpnssl =====
-Web site: http://www-saclay.cea.fr/
+<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.
-You can only access it from the LSCE and CEA network! This intranet is the place where you can get information about:
+This is **not possible** anymore, now that LSCE is on the Paris-Saclay network (and not on the CEA network)
+</WRAP>
-  * [[http://www-saclay.cea.fr/Phocea/Page/index.php?id=374|CEA buses]]
+Use the following steps:
-  * [[http://www-saclay.cea.fr/fna/index.php|Security training registration]]
+  - Start Chrome (or try another browser)
+  - Open the following link: https://vpnssl.cea.fr/
+    * ignore the security 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**
+  - Select the CEA web site you want from the "Aventail WorkPlace" portal
+    * **Espace Sigma**: that's where you specify when you will be on holidays
+    * **Intranet Saclay**: where you can get information about the CEA buses, CEA directory, security training registration and information, practical information, etc...
+    * **Intranet du voyageur**: if you need to make a plane/train reservation
+    * ...
+  - Click on //logout// when you are done
 ===== 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 7 computer ====
+==== Windows computer ====
-Read the notes (and follow the instructions) in [[other:index#windows_7_notes|Windows 7 notes]], especially the [[other:win7config|Basic Windows 7 Configuration]] section
+Read the [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows 10// section
 === Getting administrator's rights ===
@@ Line 45: / Line 139: @@
 <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 got 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 65: / Line 159: @@
 ==== 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-)
-===== Accessing the Linux servers from your LSCE deskop =====
+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]]
-==== Linux or mac desktop ====
+===== Accessing the Windows cluster from a Linux computer =====
-Just open a terminal and [[#which_linux_servers_should_you_use|use ssh to connect to the appropriate server]]
+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.
+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.
+===== Accessing the LSCE Linux servers =====
+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]]
+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**!
-==== Windows desktop ====
-There should be an //Asterix// shortcut on the left side of your desktop. Double-click on it in order to open a window environment on one of the asterix servers. Each terminal you will open in this environment will run on the same asterix server. Use ssh to [[#which_linux_servers_should_you_use|connect to an obelix server]] if you need to run something that will require more computing resources
 ===== Which Linux servers should you use? =====
-There are lots of things you can do directly on your local Win7 or Linux desktop (displaying pdf, images, using a text editor, ...), rather than directly on the 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]]**.
-  * asterixN (''ssh asterix'', or ''ssh asterix.lscelb''): use these servers for the usual day-to-day work (things that use less than 1 Gb, don't use 100% CPU for a long time)
+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.
-  * obelixN (''ssh obelix'', or ''ssh obelix.lscelb''): use these servers for interactive processes that will need //more// ram and/or CPU during a //longer// time
-  * [[https://intranet.lsce.ipsl.fr/informatique/orme/calcul/batch.php|the batch system]] for really heavy duty programs
+==== Available servers ====
+  * **The LSCE interactive servers**: ''obelix//NN//''\\ Use ''ssh obelix'' to access these servers, and the //load balancing// system will send you to the server that has currently the smallest load.
+    * <wrap hi>Never forget that you are sharing these 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 !
+    * <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 $HOST
+obelix5
+$ hostname
+obelix5</code>
+  * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//)\\ Use this cluster for really heavy duty programs, rather than killing the multi-users interactive servers
+  * **The [[http://mesocentre.ipsl.fr/|IPSL/ESPRI Mesocenter servers/clusters]]** (''ciclad'' / ''climserv'' / etc...)\\ You will need an 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 that is already available on IPSL servers and that you can process there!
+    * [[http://mesocentre.ipsl.fr/account-opening/|Requesting a new account]]
+    * [[https://documentations.ipsl.fr/MESO_User/|IPSL ESPRI Mesocenter documentation]] (//English//)
+    * [[https://mesocentre.ipsl.fr/quick-start/|Utilisation du Mésocentre IPSL]] (//French//, the //English// documentation link above has more information)
+  * **The ''asterix//NN//'' servers**\\ Some wise LSCE elders may mention these servers, but they don't exist any more!
+==== Which shell are you using? ====
+It is important to know which //shell// you are using if you need to configure and tune your Linux account. The shell is basically the program that waits for you to type commands in a terminal and passes them to the computer
+If you are not sure which shell is running in your terminals, you can use ''echo $SHELL'' to find out:
+<code>
+# Somewhere with tcsh
+ > echo $SHELL
+ /bin/tcsh
+# Somewhere else with bash
+ $ echo $SHELL
+ /bin/bash
+</code>
 ==== Determining the load of a Linux server ====
@@ Line 91: / Line 231: @@
 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 99: / Line 242: @@
   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
     [...]
@@ Line 111: / Line 254: @@
 <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 129: / Line 271: @@
 ===== Which disks should you use? =====
-<note important>It is very important to use the correct directories and make it easy for your advisor to find things after you have left\\ \\ Do not forget to clean your directories before you leave (ask your advisor what should be kept or cleaned)</note>
+<note warning>
+  * 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 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
+  *  Do not forget to clean your directories before you leave (ask your advisor what should be kept or cleaned)
+</note>
 ==== 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 same path 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''
+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 ====
   * **Location**: the location depends on the machine you are connected to in the current terminal
-    * On the LSCE servers (asterixN, obelixN): ''/home/users/your_lsce_login''
+    * On the LSCE servers (obelixN): ''/home/users/your_lsce_login''
+      * Non LSCE servers:
+        * TGCC: ''/ccc/cont003/home/dsm/your_tgcc_login''\\ You can find out the location of all your directories with ''ccc_home -a'' (use ''ccc_home -h'' to find out all the available options)
+        * ciclad: ''/home/your_ciclad_login''
     * On a local Linux desktop (lsceNNNN): ''/homel/your_lsce_login''
-    * The configuration files of your Linux account are stored in this directory (use ''ls -a'' to see hidden files and directories). Ask your advisor if you should copy somebody else's configuration files
+    * The configuration files of your Linux account are stored in the //home// directory (use ''ls -a'' to see hidden files and directories). Ask your advisor if you should copy somebody else's configuration files
       * tcsh shell users: ''.cshrc'' and ''.login''
       * bash shell users: ''.profile'' and ''.bashrc''
       * 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''
+      * 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
-    * Put the most important sources/scripts/data/papers in this directory
+    * More details on the [[https://intranet.lsce.ipsl.fr/informatique/en/nsr/index.php|LSCE backup system]] page
-    * Do not put temporary files, or big data files that are available somewhere else in this directory!
+    * <wrap em>Put the most important sources/scripts/data/papers in this directory</wrap>
-    * Your home directory will also be archived when your account is closed
+    * **Do not** use the //home// directory to store:
+      * temporary files (use ''scratch01'')
+      * big (or many) data files (use ''scratch01'' or a project specific disk)
+    * Your home directory will be archived when your account is closed, so that you or your advisor can access it later, if required
-  * **Quota**: YES!\\ There is a limit to what you can store in your home directory. If you reach this limit, you may experience some seemingly random errors (can't connect to the servers, the new files have a 0 size, ...)\\ <code>
+  * **Backup of the TGCC home directory**: YES!
+    * Use the following command to access the backup: ''cd ~/.snapshot''
+  * **Quota**: YES!\\ There is a limit to what you can store in your home directory. If you reach this limit, you may experience some seemingly random errors (can't connect to the servers, the new files have a 0 size, ...)\\ The example below shows how to determine the //quota// on the LSCE disks: you can never go above the size displayed in the ''limit column'', and you cannot stay more than 7 days above the limit displayed in the ''quota'' column! The ''grace'' column will display either ''None'' (you cannot write on the disk anymore, unless you get below the ''quota'' limit) or ''N days'' (you can use the disk, but you have ''N days'' to go below the ''quota'' limit)\\ <code>
  > 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>
 ==== The scratch directory ====
+<note warning>Do not put anything in the scratch directory that you can't recreate with a program, or copy/download from somewhere else!</note>
   * **Location**: ''/home/scratch01/your_lsce_login''
@@ Line 168: / Line 336: @@
   * **Backup**: NO
     * Use this directory for temporary and big data files
-    * The files older than 6 months (and possibly older than 1 month) will be **automatically deleted** if there is not enough free space. See the [[https://intranet.lsce.ipsl.fr/informatique/en/orme/disques.php|Scratch area]] section for more details
+    * The files older than 6 months (and possibly older than 1 month) will be **automatically deleted** if there is not enough free space. See the [[https://intranet.lsce.ipsl.fr/informatique/en/disques.php|Scratch area]] section for more details on the retention policy
+      * In other words, the files are guaranteed to stay 1 month and possibly longer
   * **Quota**: NO
@@ Line 174: / Line 343: @@
 ==== Project specific directories ====
+<note warning>The data on these disks is <wrap em>probably not backed up</wrap>... You are not protected against file deletion by mistake, or a disk crash (a major disk crash is not likely, but can happen)
+\\ You should <wrap em>store your source codes, scripts, notebooks, manuscripts, reports, figures, on a backed up directory</wrap>, and only store on the project disks data downloaded from outside, or that you can regenerate with the backed up scripts</note>
   * **Location**: ''/home/some_project_name/your_lsce_login''
     * Ask your advisor if you should use a specific project directory and the technical details about it
-    * Use this directory for storing the (big) data files that you can't store in the //home// directory, and should not store in the //scratch// directory
+    * Use this directory for storing the (big) data files that you can't store safely in the //scratch// directory, and should not store in the //home// directory
   * **Backup**: ask your advisor
   * **Quota**: ask your advisor
+==== Determining the space used by directories ====
+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> >cd /home/scratch01/johndoe
+/home/scratch01/johndoe
+ >du -sh * | sort -rh
+M     GLAC1DHiceF26.nc
+M     dashboard
+M     GLAC1DdrainagePointerF26ka.nc
+M     octcdf
+M     1901.nc
+.2M    cmake
+...</code>
+===== Which programs should you use? =====
+Your advisor will let you know which (version of which) programs you should use. Some programs are available by default, and you have to use the ''module'' command to access other programs.
+==== Which program am I using? ====
+At any time, you can use the ''which'' command to determine where a program is located. The option to get the //version// information of a program may vary (launch the program without arguments, with ''-v'' or ''%%--%%v'', ...).
+<code> > which ncdump
+/usr/bin/ncdump
+ > ncdump
+ncdump [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] file
+[...]
+netcdf library version 4.3.3.1 of Dec 10 2015 16:44:18 $
+ > which python
+/usr/bin/python
+ > python --version
+Python 2.7.5
+</code>
+==== Using module to access optional programs ====
+Main ''module'' options:
+  * ''module list'': list the currently loaded modules
+  * ''module avail'': list the available modules
+  * ''module load module_a ... module_n'': load modules (automatically including dependencies)
+    * ''module load module_a'': load default version of //module_a//
+    * ''module load module_a/vvv'': load ''vvv'' version of //module_a//
+  * ''module purge'': remove all modules
+Detailed example:
+<code> > which ncview
+ncview: Command not found.
+ > module list
+No Modulefiles Currently Loaded.
+ > module avail
+[...]
+batch_env          grib_api/1.14.0    netcdf/4           python/3.6
+[...]
+glost/0.3.1        ncview/2.1.7       python/2.7
+ > module load ncview netcdf/4
+ > module list
+Currently Loaded Modulefiles:
+) ncview/2.1.7   2) netcdf/4
+ > which ncview
+/usr/local/install/ncview-2.1.7/bin/ncview
+ > which ncdump
+/usr/local/install/netcdf-4.3.2/bin/ncdump</code>
 ===== Useful documentation for beginners =====
@@ Line 191: / Line 439: @@
     - 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}})
-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 ====
+<note important>A //jupyter notebook// is not a text editor! You need a correct text editor to efficiently work with scripts and programs</note>
+There are **lots** of text editors used on Linux computers/servers (vi, vim, gvim, emacs, nano, ...), that you can use:
+  * in basic text terminals (if you know the basic commands and shortcuts)
+  * or in graphic mode (you may need to have an [[other:x_conf|X server configured]])
+=== emacs ===
+    * 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]]
+=== 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]]
 ==== NetCDF and file formats ====
@@ Line 201: / Line 463: @@
     * [[http://www.unidata.ucar.edu/software/netcdf/|Network Common Data Form (NetCDF)]] official page
       * [[http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#How-many-netCDF-formats-are-there-and-what-are-the-differences-among-them|The different netCDF formats]] (and do not forget to use ''ncdump -k data.nc'' if you need to know the format)
+  * 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
@@ Line 207: / Line 472: @@
     * 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
-===== Getting help from the LSCE system administrators =====
-Send a mail to: [[help-lsce@lsce.ipsl.fr]]
+==== Programming languages ====
-===== Accessing the LSCE servers from outside the LSCE =====
+  * [[other:index#python_notes|JYP's Python notes]]
+===== Getting help (from the LSCE system administrators) =====
+Send a mail to //help-lsce//
+==== Describing your problem ====
+When you need help from the administrators or other people, it will save a lot of time if you describe your problem as accurately as possible (do **not** just report //XXXXX is not working as expected// !)
+You can copy-paste the error message(s). Finding the error //log file(s)// of the program/system (when available), or using the //verbose mode// of a program will make the problem resolution much easier and faster. The example below shows how to use the verbose mode of ''ssh''
+<code> >ssh -v obelix
+OpenSSH_7.4p1, OpenSSL 1.0.2k-fips  26 Jan 2017
+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 *
+debug1: Connecting to obelix [157.136.72.75] port 22.
+debug1: Connection established.
+debug1: key_load_public: No such file or directory
+debug1: identity file /home/users/johndoe/.ssh/id_rsa type -1
+[...]
+debug1: Entering interactive session.
+debug1: pledge: exec
+debug1: client_input_global_request: rtype hostkeys-00@openssh.com want_reply 0
+debug1: Requesting X11 forwarding with authentication spoofing.
+debug1: Sending environment.
+debug1: Sending env LANG = en_US
+Last login: Thu Mar  1 15:52:44 2018 from lsce4078.lsce.ipsl.fr
+ >
+</code>
-The only way to access the LSCE servers from outside LSCE is to connect first to the **idefix1.extra.cea.fr** gateway server. Unless you are on a machine that is outside LSCE, but still on the CEA network (e.g. one of the machines of the CEA computing center)
+==== Taking a screenshot ====
-  - Send a mail to [[help-lsce@lsce.ipsl.fr]], and request an access to the idefix1 server
+Sometimes, it may also help to send a picture of what is wrong!
-  - Use ssh to connect to idefix1
-    * From a Linux/mac desktop: ''ssh -A -X your_lsce_login@idefix1.extra.cea.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#putty|Putty]] **and** [[other:win7apps#cygwin-x|cygwin/X]]
-        * use [[other:index#virtualbox_notes|VirtualBox]]
-  - There is only a limited number of programs that you can run on idefix1, so you have to go from idefix1 to asterix, obelix or curie with on of the //ssh// commands below:
-    * ''ssh asterix.lscelb''
-    * ''ssh obelix.lscelb''
-    * ''ssh your_tgcc_login@curie-ccrt.ccc.cea.fr''
-  - It's possible to use only one line to to both ssh commands
-    * asterix: ''ssh -A -X your_lsce_login@idefix1.extra.cea.fr -t ssh -A asterix.lscelb''
-    * obelix: ''ssh -A -X your_lsce_login@idefix1.extra.cea.fr -t ssh -A obelix.lscelb''
-    * TGCC: ''ssh -A -X your_lsce_login@idefix1.extra.cea.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 iasterix 'ssh -A -X your_lsce_login@idefix1.extra.cea.fr -t ssh -A asterix.lscelb'''
-    * //bash// users: FIXME
-  - You should create and configure an //ssh key//, if you don't want to type your password each time you use ssh or scp: https://intranet.lsce.ipsl.fr/informatique/orme/ssh.php
-  - 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 ====
+On Linux, you should find a screenshot application in the tools available on the system. See the example below for people using the //xfce// windows manager
+{{ :other:newppl:screenshot_xfce.jpg?200 |Click to get a larger version}}
-If you are on a computer outside LSCE and you need to transfer a file to/from LSCE, you need to make the transfer between your current machine and idefix1!
+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}}
-  * Example from a Linux/mac desktop: ''scp -p file_outside_lsce your_lsce_login@idefix1.extra.cea.fr:/home/scratch01/your_lsce_login/''
+===== Getting help, when using the IPSL Mesocenter =====
-  * From a Windows desktop: use [[other:win7apps#winscp|winscp]]
+Check the [[https://mesocentre.ipsl.fr/contacts//|Contacts]] page
 ===== What next? =====