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other:newppl:starting [2015/07/08 12:01] – Started the idefix1 section jypeterother:newppl:starting [2020/03/18 15:24] – [Windows computer] Updated jypeter
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 ====== Getting started in CLIM & ESTIMR ====== ====== Getting started in CLIM & ESTIMR ======
  
-<note tip>Welcome to LSCE! 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...</note>+<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> 
 + 
 +===== Miscellaneous information ===== 
 + 
 +A few useful links that have nothing to do with science and software resources! 
 + 
 +  * [[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/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]] 
 +  * {{: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 'clim' and 'estimr' lists ==== 
 + 
 +Ask your team leader or Jean-Yves to add you to your team's mailing list 
 + 
 +^  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? ===== ===== Using your own computer at LSCE? =====
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 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/wifi/index.php|eduroam or guest wifi]] 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 ''ssh1.lsce.ipsl.fr'', and then to ''obelix''
  
 ===== Accessing the LSCE intranet ===== ===== Accessing the LSCE intranet =====
  
-There is a lot of information available on the intranet, but you can only access it from a computer connected to the LSCE network: 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 
 +</WRAP>
  
-Everything about the LSCE servers (and other software and hardware information): https://intranet.lsce.ipsl.fr/informatique/index.php 
  
-  * Reading the mails with the [[https://agenda.lsce.ipsl.fr/|webmail]] or [[https://intranet.lsce.ipsl.fr/informatique/mail/thunderbird.php|Thunderbird]] +Intranet web site: https://intranet.lsce.ipsl.fr/
-    * As soon as you have a LSCE e-mail address, make sure it is added to the clim or estimr mailing list +
-  * [[https://intranet.lsce.ipsl.fr/informatique/orme/imprimantes.php|Printers]]+
  
-===== Accessing the CEA saclay intranet =====+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
  
-Web site: http://www-saclay.cea.fr/index.php+Everything about the LSCE servers (and other software and hardware information): https://intranet.lsce.ipsl.fr/informatique/en/orme/index.php
  
-You can only access it from the CEA network! This intranet is the place where you can get information about:+  * 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** 
 +  * [[https://intranet.lsce.ipsl.fr/informatique/en/orme/imprimantes.php|Printers]]
  
-  * [[http://www-saclay.cea.fr/Phocea/Page/index.php?id=374|CEA buses]] +===== Accessing the CEA Saclay intranet and other CEA web sites with vpnssl ===== 
-  * [[http://www-saclay.cea.fr/fna/index.php|Security training registration]]+ 
 +<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. 
 + 
 +This is **not possible** anymore, now that LSCE is on the Paris-Saclay network (and not on the CEA network) 
 +</WRAP> 
 + 
 +Use the following steps: 
 +  - 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 ===== ===== Setting up your desktop computer =====
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 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 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
  
-==== Windows 7 computer ====+==== Windows computer ==== 
 + 
 +Read the [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows 10// section
  
-Read the notes in [[other:index#windows_7_notes|Windows 7 notes]], especially the [[other:win7config|Basic Windows 7 Configuration]] section+Note: there are also some [[other:index#windows_7_notes|Windows 7 notes]], but you are supposed to use Windows 10 since January 2020!
  
 === Getting administrator's rights === === Getting administrator's rights ===
  
-<note warning>\\ Make sure you know what you are doing and that you are not executing a virus asking you suspicious access rights!</note>+<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 sur 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 ==== ==== Linux computer ====
  
-FIXME <= Add some stuff here+There are different window managers available, each one with different settings: you should the //Cinnamon// window manager (//xfce// is a bit too basic, and //Gnome// is not very convenient for doing actual work, and uses too much CPU). You can select the window manager by clicking on the little cogwheel below the password field, on the login screen. 
 + 
 +This is Linux, you are using it for work, you should be efficient, so you should be able to do most of your work by typing commands in a terminal. The true power is in the correct use of the command-line interfaces, rather than having to spend time finding where to click in the windows. You will find some [[#useful_documentation_for_beginners|Linux documentation]] below.
  
 === Using the root acount === === Using the root acount ===
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   * run a single command with the root access rights\\ **sudo //command//**   * run a single command with the root access rights\\ **sudo //command//**
   * become root in a terminal\\ **sudo //su -//**   * become root in a terminal\\ **sudo //su -//**
-  * use the root password when a program asks for it. Be sure the programs has legitimate reasons to ask for the root password!+  * use the root password when a program asks for it. Be sure the programs have legitimate reasons to ask for the root password!
  
 ==== Mac ==== ==== Mac ====
  
 Sorry, you are on your own, but it's soooo easy to use, right? Sorry, you are on your own, but it's soooo easy to use, right?
 +
 +===== 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
 +
 +===== Accessing the Linux servers from your LSCE deskop =====
 +
 +==== Linux or mac desktop ====
 +
 +Just open a terminal and [[#which_linux_servers_should_you_use|use ssh to connect to the appropriate server]]
 +
 +==== 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? ===== ===== 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**.+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**.
  
-Otherwise, use the appropriate Linux servers. The load balancing system will send you to the server that has currently the smallest load+Otherwise, **use the appropriate Linux servers**. The //load balancing// system will send you to the server that has currently the smallest load
  
-  * 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) +  * **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 
-  * 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 +    * <code> $ ssh obelix 
-  * [[https://intranet.lsce.ipsl.fr/informatique/orme/calcul/batch.php|the batch system]] for really heavy duty programs+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 batch system]] (aka //obelix **cluster**//) for really heavy duty programs 
 +  * 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 
 +  * //asterixN//: some people 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 ==== ==== Determining the load of a Linux server ====
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 ===== Which disks should you use? ===== ===== Which disks should you use? =====
 +
 +<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/users/your_login]]. 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
 +
 +  * Example path on the LSCE Linux server: ''/home/scratch01/your_lsce_login''
 +  * Accessing the path above from a local desktop:
 +    * Linux desktop: ''/home/scratch01/your_lsce_login''
 +    * Windows desktop: ''\\dfshost\dfs\scratch01\your_lsce_login''\\ {{ :other:newppl:dfs_on_win.png?nolink |}}
  
 ==== The home directory ==== ==== The home directory ====
  
 +  * **Location**: the location depends on the machine you are connected to in the current terminal
 +    * 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 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
 +
 +  * **Backup of the home directory on the LSCE servers**: YES! Every night
 +    * More details on the [[https://intranet.lsce.ipsl.fr/informatique/en/nsr/index.php|LSCE backup system]] page
 +    * <wrap em>Put the most important sources/scripts/data/papers in this directory</wrap>
 +    * **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
 +
 +  * **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):
 +     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
 +prolix3:/users/   4658M   4883M   4981M           23503       0       0</code>
  
 ==== The scratch directory ==== ==== 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''
 +
 +  * **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/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
  
  
 ==== Project specific directories ==== ==== 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)
  
-===== Useful documentation =====+\\ 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>
  
-===== Getting help from the LSCE system administrators ===== 
  
-Send a mail to: [[help-lsce@lsce.ipsl.fr]]+  * **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 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>jypeter@obelix4 - ...jypeter - 46 >cd /home/scratch01/jypeter 
 +/home/scratch01/jypeter 
 + 
 +jypeter@obelix4 - ...jypeter - 47 >du -sh * | sort -rh 
 +58M     GLAC1DHiceF26.nc 
 +47M     dashboard 
 +44M     GLAC1DdrainagePointerF26ka.nc 
 +15M     octcdf 
 +12M     1901.nc 
 +3.2M    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: 
 +  1) 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 ===== 
 + 
 +==== Linux/UNIX ==== 
 + 
 +  * {{:other:newppl:unix_doc_jyp.pdf|UNIX_doc_JYP.pdf}}: some basic Linux documentation. Make sure you read it! 
 +    - A list of the most useful commands 
 +    - 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]] 
 +  * 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 
 + 
 +==== NetCDF and file formats ==== 
 + 
 +  * What are binary ({{:other:newppl:binaire_jyp.pdf}}) and NetCDF ({{:other:newppl:netcdf_jyp.pdf}}) files? 
 +    * [[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 
 +  * [[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]] 
 +  - [[other:python:jyp_steps|JYP's recommended steps for learning python]] 
 + 
 +===== 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/jypeter/.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/jypeter/.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 
 +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> 
 + 
 +==== Taking a screenshot ==== 
 + 
 +Sometimes, it may also help to send a picture of what is wrong! 
 + 
 +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}} 
 + 
 +On Windows, you can use the //Capture screen// option of [[other:win7apps#xnview|XnView]] 
 +{{ :other:newppl:xnview_capture.jpg?200 |Click to get a larger version}}
  
 ===== Accessing the LSCE servers from outside the LSCE ===== ===== Accessing the LSCE servers from outside the LSCE =====
  
-The only way to access LSCE the LSCE server 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)+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''
  
-  - Send a mail to [[help-lsce@lsce.ipsl.fr]] and request an access to the idefix1 server +  * Example: 
-  - Use ssh to connect to idefix1 +    * 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/'' 
-    - ssh +    * 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? ===== ===== What next? =====
other/newppl/starting.txt · Last modified: 2025/02/04 14:39 by jypeter
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