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other:newppl:starting [2020/07/23 12:41] jypeter [Which disks should you use?] |
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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 ===== | ===== Miscellaneous information ===== | ||
- | A few useful links that have nothing to do with science and software resources! | + | A few useful links. Some have nothing to do with science and LSCE hardware/software resources! |
+ | |||
+ | * [[#accessing_the_lsce_intranet|LSCE intranet]] | ||
* [[other:newppl:pub_transport|LSCE-related public transport]] | * [[other:newppl:pub_transport|LSCE-related public transport]] | ||
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* [[https://intranet.lsce.ipsl.fr/Phocea/Page/index.php?id=97|Survival kit and other information for CDD and interns]] (LSCE intranet) | * [[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// | * [[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://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://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/|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}} | * {{:other:newppl:uvsq-guide-du-personnel-nov2019.pdf|Guide du Personnel UVSQ}} | ||
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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 //obelix// LSCE servers from the wifi network. You first have to connect to ''ssh1.lsce.ipsl.fr'', and then to ''obelix'' | + | **Warning!** You **can't** connect directly to the //obelix// LSCE servers from the wifi network. You first have to connect to the ''ssh1.lsce.ipsl.fr'' //gateway// server, and then to ''obelix''. More details in [[other:ssh#lsce_servers|LSCE servers]] |
===== Accessing the LSCE intranet ===== | ===== Accessing the LSCE intranet ===== | ||
<WRAP center round tip 60%> | <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 | + | 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> | </WRAP> | ||
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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]] | ||
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===== 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 computer ==== | ==== Windows computer ==== | ||
Read the [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows 10// section | Read the [[other:index#windows_10_notes|Windows 10 notes]], especially the //Configuring Windows 10// 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 === | ||
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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 Windows cluster from a Linux computer ===== | + | 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]] | ||
- | 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 Windows cluster from a Linux computer ===== |
- | ===== Accessing the Linux servers from your LSCE deskop ===== | + | 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. |
- | ==== Linux or mac 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. |
- | Just open a terminal and [[#which_linux_servers_should_you_use|use ssh to connect to the appropriate server]] | + | ===== Accessing the LSCE Linux servers ===== |
- | ==== Windows desktop ==== | + | 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]] |
- | 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 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**! |
- | 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? ===== | ||
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==== Working directly on your desktop ==== | ==== Working directly on your desktop ==== | ||
- | Always remember that **your local LSCE desktop can [[#accessing_remote_disks|access remote disks on the LSCE servers]]**. | + | 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** Windows 10 or Linux desktop (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 desktop, than by using ''evince'' on the server. | + | 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 ==== | ==== 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.\\ Never forget that you are sharing these servers with other users! Do not use too much CPU and/or memory for a long time. Heavy computation should be done on the obelix cluster | + | * **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 | * <code>$ ssh obelix | ||
Last login: Mon Jun 3 08:49:53 2019 from somewhere | Last login: Mon Jun 3 08:49:53 2019 from somewhere | ||
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obelix5</code> | obelix5</code> | ||
- | * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//). Use this for really heavy duty programs | + | * **[[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 |
- | * **[[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 | + | |
+ | * **The [[http://mesocentre.ipsl.fr/|IPSL/ESPRI Mesocenter servers/clusters]]** (''ciclad'' / ''climserv'' / etc...)\\ You will need an account (different from your //LSCE// account) to access these servers and use data files that are already available/mirrored there (e.g. **''CMIPn'' data**). **Do not duplicate** at LSCE data that is already available on IPSL servers and that you can process there! | ||
* [[http://mesocentre.ipsl.fr/account-opening/|Requesting a new account]] | * [[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! | + | * [[https://documentations.ipsl.fr/MESO_User/|IPSL ESPRI Mesocenter documentation]] (//English//) |
+ | * [[https://mesocentre.ipsl.fr/quick-start/|Utilisation du Mésocentre IPSL]] (//French//, the //English// documentation link above has more information) | ||
+ | |||
+ | * **The ''asterix//NN//'' servers**\\ Some wise LSCE elders may mention these servers, but they don't exist any more! | ||
==== Which shell are you using? ==== | ==== 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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==== 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 computer\\ (//local// = a computer on the LSCE ethernet/wired network) | + | It is possible to **directly** access some disks on the LSCE servers from: |
- | * Example path on the LSCE Linux server: ''/home/scratch01/your_lsce_login'' | + | * a Linux or Windows computer connected directly to the LSCE ethernet/wired network |
- | * Accessing the path above from a //local// computer: | + | * or a remote computer using the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php#vpnlsce|LSCE VPN]] |
- | * Linux computer: ''/home/scratch01/your_lsce_login'' | + | |
- | * Windows computer: ''\\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 ==== | ||
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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> | ||
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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>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 |
58M GLAC1DHiceF26.nc | 58M GLAC1DHiceF26.nc | ||
47M dashboard | 47M dashboard | ||
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- 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? | ||
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* 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) ===== | ||
Line 459: | Line 523: | ||
<code> >ssh -v obelix | <code> >ssh -v obelix | ||
OpenSSH_7.4p1, OpenSSL 1.0.2k-fips 26 Jan 2017 | 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: Reading configuration data /etc/ssh/ssh_config | ||
debug1: /etc/ssh/ssh_config line 58: Applying options for * | debug1: /etc/ssh/ssh_config line 58: Applying options for * | ||
Line 465: | Line 529: | ||
debug1: Connection established. | debug1: Connection established. | ||
debug1: key_load_public: No such file or directory | 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. | debug1: Entering interactive session. | ||
Line 474: | Line 538: | ||
debug1: Sending env LANG = en_US | debug1: Sending env LANG = en_US | ||
Last login: Thu Mar 1 15:52:44 2018 from lsce4078.lsce.ipsl.fr | 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> | </code> | ||
Line 487: | Line 549: | ||
{{ :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 **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/'' | + | |
+ | Check the [[https://mesocentre.ipsl.fr/contacts//|Contacts]] page | ||
===== What next? ===== | ===== What next? ===== | ||