Differences

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

--- other:newppl:starting [2020/05/15 16:02] – [Which Linux servers should you use?] Improved jypeter
+++ other:newppl:starting [2020/10/01 09:38] – Renames "CLIM & ESTIMR" to "LSCE" 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 =====
@@ Line 78: / Line 78: @@
 ===== Using your own computer at LSCE? =====
-No need to try to connect your laptop to the LSCE wire network, it will not work!
+No need to try to connect your personal laptop to the LSCE wire network, 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 [[#accessing_the_lsce_servers_from_outside_the_lsce|Accessing the LSCE servers from outside the LSCE]]
 ===== Accessing the LSCE intranet =====
@@ Line 162: / Line 162: @@
 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
-===== Accessing the Linux servers from your LSCE deskop =====
+===== Accessing the LSCE Linux servers =====
-==== Linux or mac desktop ====
+You have to [[other:ssh|Use ssh to connect to the servers]]
-Just open a terminal and [[#which_linux_servers_should_you_use|use ssh to connect to the appropriate server]]
+If you are really in a hurry, go directly to the [[other:ssh#connecting_to_the_lsce_servers_ipsl_servers_tgcc|Connecting to the LSCE servers, IPSL servers, TGCC, ...]] section, but it is important that you **read the full //ssh documentation// page at least once**!
-==== Windows desktop ====
-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? =====
@@ Line 197: / Line 191: @@
   * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//). Use this for really heavy duty programs
   * **[[http://mesocentre.ipsl.fr/|The ciclad and climserv servers]]**. In some cases, you may need an account to use the [[http://mesocentre.ipsl.fr/|IPSL/ESPRI clusters]], especially if you need to use data files that are already available/mirrored there (e.g. **''CMIPn'' data**), rather than copying the data to LSCE
+    * [[http://mesocentre.ipsl.fr/account-opening/|Requesting a new account]]
   * **The ''asterix//N//'' servers**: some wise LSCE elders may mention these servers, but they don't exist any more!
@@ Line 219: / Line 214: @@
 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 227: / Line 225: @@
   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 239: / Line 237: @@
 <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 260: / Line 257: @@
   * 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 269: / Line 266: @@
 ==== 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 access directly all the disks on the LSCE servers from your //local// Linux or Windows computer\\ (//local// = a computer on the LSCE ethernet/wired network)
   * Example path on the LSCE Linux server: ''/home/scratch01/your_lsce_login''
-  * Accessing the path above from a local desktop:
+  * Accessing the path above from a //local// computer:
-    * Linux desktop: ''/home/scratch01/your_lsce_login''
+    * Linux computer: ''/home/scratch01/your_lsce_login''
-    * Windows desktop: ''\\dfshost\dfs\scratch01\your_lsce_login''\\ {{ :other:newppl:dfs_on_win.png?nolink |}}
+    * Windows computer: ''\\dfshost\dfs\scratch01\your_lsce_login''\\ {{ :other:newppl:dfs_on_win.png?nolink |}}
 ==== The home directory ====
@@ Line 288: / Line 285: @@
       * 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''
+    * 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 305: / Line 302: @@
  > 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 342: / Line 339: @@
 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 458: / Line 455: @@
 <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 464: / Line 461: @@
 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 473: / Line 470: @@
 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 489: / Line 484: @@
 {{ :other:newppl:xnview_capture.jpg?200 |Click to get a larger version}}
-===== Accessing the LSCE servers from outside the LSCE =====
-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 terminal on a Linux/Windows10/Mac computer: ''ssh -A -X your_lsce_login@ssh1.lsce.ipsl.fr''
-    * From a Windows computer:
-      * Text only: use [[other:win10apps#putty_pageant|Putty]]. Putty allows you to open text terminals on remote computers
-      * Text **and graphics**: you need to [[https://wiki.lsce.ipsl.fr/pmip3/doku.php/other:win10wsl#using_an_x_server|install an X server]] on your computer in order to display the graphics
-  - 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 //irene// 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 and Windows 10), or a graphical scp client such as [[other:win10apps#winscp|WinSCP]] (on Windows) between your computer and ''ssh1.lsce.ipsl.fr''
-  * Example:
-    * Sending **one file** from a Linux/Windows10/Mac computer to your //scratch// directory at LSCE:\\ ''scp -p file_on_your_computer_outside_lsce your_lsce_login@ssh1.lsce.ipsl.fr:/home/scratch01/your_lsce_login/''
-    * Sending recursively **a full directory**:\\ ''scp -pr directory_on_your_computer_outside_lsce your_lsce_login@ssh1.lsce.ipsl.fr:/home/scratch01/your_lsce_login/''
 ===== What next? =====