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other:newppl:starting [2017/03/09 13:38] jypeter Added how to determine the shell |
other:newppl:starting [2023/03/08 16:33] jypeter [Available servers] Updated ciclad=>spirit |
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- | ====== 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 ===== | ===== The LSCE mailing lists ===== | ||
- | It is important to register to the correct mailing lists, if you want to get all the information you need, on time. | + | It is important to join the correct mailing lists, if you want to get all the information you need, on time. |
==== The 'all' list ==== | ==== The 'all' list ==== | ||
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Mails sent to these lists will reach lots of people. Think well **before** sending a mail to these lists! | 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 ^ | ^ List ^ Team ^ Archive ^ | ||
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===== Using your own computer at LSCE? ===== | ===== 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 ===== | ===== 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 | 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 | ||
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* Reading the mails with the [[https://agenda.lsce.ipsl.fr/|webmail]] or [[https://intranet.lsce.ipsl.fr/informatique/en/mail/thunderbird.php|Thunderbird]] | * 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]] | * [[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=502|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 ===== | ===== 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 === | === Getting administrator's rights === | ||
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<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 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 ==== | ==== Linux computer ==== | ||
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==== Mac ==== | ==== 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. |
- | ==== Windows desktop ==== | + | 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**! | ||
- | There should be an //Asterix// shortcut on the left side of your desktop. Double-click on it in order to open a window (e.g. with graohics) 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 | ||
- | Note: you can also use [[other:win7apps#putty|Putty]] if you just need text windows, 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**. | + | ==== Working directly on your desktop ==== |
+ | |||
+ | Always remember that **your local LSCE desktop/laptop can [[#accessing_remote_disks|access remote disks on the LSCE servers]]**. | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ==== 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 | ||
- | Otherwise, use the appropriate Linux servers. The load balancing system will send you to the server that has currently the smallest load | + | * **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]] | ||
- | * 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) | + | * **The ''asterix//NN//'' servers**\\ Some wise LSCE elders may mention these servers, but they don't exist any more! |
- | * 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 | + | |
==== Which shell are you using? ==== | ==== Which shell are you using? ==== | ||
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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 | 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 | 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 | Tasks: 324 total, 2 running, 320 sleeping, 2 stopped, 0 zombie | ||
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PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | ||
- | 10193 mpeau 20 0 302m 4336 2272 R 100.0 0.0 7033:08 emacs | + | 10193 john 20 0 302m 4336 2272 R 100.0 0.0 7033:08 emacs |
- | 16504 mpeau 20 0 110m 2008 1228 S 0.7 0.0 0:00.13 tcsh | + | 16504 john 20 0 110m 2008 1228 S 0.7 0.0 0:00.13 tcsh |
- | 26344 dzhu 20 0 1635m 20m 3880 S 0.3 0.1 0:44.90 ipython | + | 26344 jane 20 0 1635m 20m 3880 S 0.3 0.1 0:44.90 ipython |
1 root 20 0 21448 1108 892 S 0.0 0.0 0:01.61 init | 1 root 20 0 21448 1108 892 S 0.0 0.0 0:01.61 init | ||
[...] | [...] | ||
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<code> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | <code> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | ||
- | 16092 jchang 20 0 8488m 8.1g 7912 R 99.6 25.9 1:41.38 idl | + | 16092 bob 20 0 8488m 8.1g 7912 R 99.6 25.9 1:41.38 idl |
- | 23256 pvait 20 0 232m 70m 2632 S 0.0 0.2 0:01.36 R | + | 23256 john 20 0 232m 70m 2632 S 0.0 0.2 0:01.36 R |
- | 26344 dzhu 20 0 1635m 20m 3880 S 0.0 0.1 0:44.87 ipython | + | 26344 jane 20 0 1635m 20m 3880 S 0.0 0.1 0:44.87 ipython |
- | 10619 astege 20 0 954m 9292 2664 S 0.0 0.0 0:40.67 gedit | + | 10619 bob 20 0 954m 9292 2664 S 0.0 0.0 0:40.67 gedit |
1362 nslcd 20 0 442m 6056 2208 S 0.0 0.0 2:13.98 nslcd | 1362 nslcd 20 0 442m 6056 2208 S 0.0 0.0 2:13.98 nslcd | ||
- | 16238 twang 20 0 128m 5068 2076 S 0.0 0.0 0:00.05 gconfd-2 | + | 10193 john 20 0 302m 4336 2272 R 99.9 0.0 7024:13 emacs |
- | 10193 mpeau 20 0 302m 4336 2272 R 99.9 0.0 7024:13 emacs | + | |
[...]</code> | [...]</code> | ||
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<note warning> | <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 | * It is very important to use the correct directories and make it easy for your advisor to find things after you have left | ||
- | * **Put the source codes, scripts and papers you are writing on a backed up disk** | + | * <wrap em>**Put the source codes, scripts and papers you are writing on a backed up disk**</wrap> |
- | * Put temporary files on a scratch disk | + | * 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 |
- | * Do NOT put (big) data files on a backed up disk | + | * 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) | * Do not forget to clean your directories before you leave (ask your advisor what should be kept or cleaned) | ||
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==== Accessing remote disks ==== | ==== 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''\\ {{ :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 ==== | ==== The home directory ==== | ||
* **Location**: the location depends on the machine you are connected to in the current terminal | * **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: | * 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) | * 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) | ||
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* bash shell users: ''.profile'' and ''.bashrc'' | * bash shell users: ''.profile'' and ''.bashrc'' | ||
* emacs text editor: ''.emacs'' | * 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 | * **Backup of the home directory on the LSCE servers**: YES! Every night | ||
- | * More details on the [[https://intranet.lsce.ipsl.fr/informatique/en/orme/nsr/index.php|backup system]] page | + | * More details on the [[https://intranet.lsce.ipsl.fr/informatique/en/nsr/index.php|LSCE backup system]] page |
- | * Put the most important sources/scripts/data/papers in this directory | + | * <wrap em>Put the most important sources/scripts/data/papers in this directory</wrap> |
- | * Do not put temporary files, or big data files that are available somewhere else in this directory! | + | * **Do not** use the //home// directory to store: |
- | * Your home directory will also be archived when your account is closed | + | * 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! | * **Backup of the TGCC home directory**: YES! | ||
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> quota -s | > 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 | Filesystem blocks quota limit grace files quota limit grace | ||
prolix3:/users/ 4658M 4883M 4981M 23503 0 0</code> | 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'' | * **Location**: ''/home/scratch01/your_lsce_login'' | ||
Line 228: | Line 339: | ||
* **Backup**: NO | * **Backup**: NO | ||
* Use this directory for temporary and big data files | * 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 | * **Quota**: NO | ||
Line 234: | Line 346: | ||
==== 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) | ||
+ | |||
+ | \\ 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'' | * **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 | * 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 | * **Backup**: ask your advisor | ||
Line 246: | Line 363: | ||
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'' | 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 | ||
+ | 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 ===== | ===== Useful documentation for beginners ===== | ||
Line 255: | Line 442: | ||
- A tutorial | - A tutorial | ||
* Useful Linux commands for working with (potentially big) text files ({{:other:newppl:houchesa4_updated.pdf}}) | * 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** | ||
+ | * 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! Some text editors (e.g ''nano'') fortunately display some help at the bottom of the screen | ||
+ | |||
+ | * 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> | ||
+ | |||
+ | |||
+ | |||
+ | === 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? | * What are binary ({{:other:newppl:binaire_jyp.pdf}}) and NetCDF ({{:other:newppl:netcdf_jyp.pdf}}) files? | ||
Line 268: | Line 483: | ||
* 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 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 | * 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) ===== | ===== Getting help (from the LSCE system administrators) ===== | ||
- | Send a mail to: [[help-lsce@lsce.ipsl.fr]] | + | Send a mail to //help-lsce// |
==== Describing your problem ==== | ==== Describing your problem ==== | ||
Line 289: | Line 522: | ||
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// !) | 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// | + | 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 asterix | + | <code> >ssh -v obelix |
- | OpenSSH_6.4, OpenSSL 1.0.1e-fips 11 Feb 2013 | + | OpenSSH_7.4p1, OpenSSL 1.0.2k-fips 26 Jan 2017 |
- | debug1: Reading configuration data /homel/jypisthebest/.ssh/config | + | debug1: Reading configuration data /home/users/johndoe/.ssh/config |
debug1: Reading configuration data /etc/ssh/ssh_config | debug1: Reading configuration data /etc/ssh/ssh_config | ||
- | debug1: /etc/ssh/ssh_config line 20: Applying options for * | + | debug1: /etc/ssh/ssh_config line 58: Applying options for * |
- | debug1: Connecting to asterix [132.166.72.26] port 22. | + | debug1: Connecting to obelix [157.136.72.75] port 22. |
debug1: Connection established. | debug1: Connection established. | ||
- | debug1: identity file /homel/jypisthebest/.ssh/id_rsa type -1 | + | debug1: key_load_public: No such file or directory |
- | debug1: identity file /homel/jypisthebest/.ssh/id_rsa-cert type -1 | + | debug1: identity file /home/users/johndoe/.ssh/id_rsa type -1 |
- | debug1: identity file /homel/jypisthebest/.ssh/id_dsa type 2 | + | |
[...] | [...] | ||
debug1: Entering interactive session. | 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: Requesting X11 forwarding with authentication spoofing. | ||
- | debug1: Requesting authentication agent forwarding. | ||
debug1: Sending environment. | debug1: Sending environment. | ||
debug1: Sending env LANG = en_US | debug1: Sending env LANG = en_US | ||
- | Last login: Tue Mar 22 15:25:36 2016 from lsce3046.extra.cea.fr | + | Last login: Thu Mar 1 15:52:44 2018 from lsce4078.lsce.ipsl.fr |
- | Disk quotas for user jypisthebest (uid 6369): | + | |
- | Filesystem blocks quota limit grace files quota limit grace | + | > |
- | prolix3:/users/ 4726M 4883M 4981M 23586 0 0 | + | </code> |
- | jypisthebest@asterix3 ></code> | + | |
==== Taking a screenshot ==== | ==== Taking a screenshot ==== | ||
Line 320: | Line 552: | ||
{{ :other:newppl:screenshot_xfce.jpg?200 |Click to get a larger version}} | {{ :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}} | {{ :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 **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) | + | |
- | + | ||
- | - Send a mail to [[help-lsce@lsce.ipsl.fr]], and request an access to the idefix1 server | + | |
- | - 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: add the following line to your ''~/.bashrc'' configuration file\\ ''alias iasterix='ssh -A -X your_lsce_login@idefix1.extra.cea.fr -t ssh -A asterix.lscelb''' | + | |
- | - 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 ==== | + | |
- | + | ||
- | 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! | + | |
- | + | ||
- | * Example from a Linux/mac desktop: ''scp -p file_outside_lsce your_lsce_login@idefix1.extra.cea.fr:/home/scratch01/your_lsce_login/'' | + | |
- | * From a Windows desktop: use [[other:win7apps#winscp|winscp]] | + | |
+ | Check the [[https://mesocentre.ipsl.fr/contacts//|Contacts]] page | ||
===== What next? ===== | ===== What next? ===== | ||