other:newppl:starting
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other:newppl:starting [2024/03/20 10:27] jypeter [Determining the load of a Linux server] Added details about TIME and mem usage |
other:newppl:starting [2024/09/13 14:28] (current) jypeter [Available servers] Updated the IPSL account request link |
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| <WRAP center round important 60%> | <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! | + | 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> | </WRAP> | ||
| - | === Finding your phone number === | + | === Finding YOUR phone number === |
| - | Use the following sequence of keys on the //Mitel// phone in your office: | + | Use the following sequence of keys on the phone in your office: |
| - | - Select **MENU** (use the downward arrow) | + | - Select **MENU** (then use the downward arrow) |
| - Select **PARAMETRES** (use the downward arrow) | - Select **PARAMETRES** (use the downward arrow) | ||
| - Select **GENERAL** (use the downward arrow) | - Select **GENERAL** (use the downward arrow) | ||
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| * You can be called from outside with ''01 69 08 NN NN'' | * You can be called from outside with ''01 69 08 NN NN'' | ||
| - | === Updating your entry in the directory === | + | === Updating YOUR entry in the phone directory === |
| - | - Find your name in the [[https://intranet.lsce.ipsl.fr/en/Phocea/Membres/Annuaire/index.php|phone directory]] | + | - Find your name in the [[https://intranet.lsce.ipsl.fr/en/Phocea/Membres/Annuaire/index.php|intranet phone directory]] |
| - Click on **Modifier mes coordonnées** (in blue on the right side) | - Click on **Modifier mes coordonnées** (in blue on the right side) | ||
| - Click on **Informations dans l'annuaire** and update the different fields | - Click on **Informations dans l'annuaire** and update the different fields | ||
| - Click on **Envoyez votre demande** | - Click on **Envoyez votre demande** | ||
| + | - Wait (for someone to validate your request) | ||
| ===== The LSCE mailing lists ===== | ===== The LSCE mailing lists ===== | ||
| Line 220: | Line 221: | ||
| $ hostname | $ hostname | ||
| obelix5</code> | obelix5</code> | ||
| + | * In a python script, you can use the following to get some information | ||
| + | * <code>>>> import os | ||
| + | >>> os.getlogin(), os.getenv('HOST') | ||
| + | ('mylogin', 'obelix5')</code> | ||
| * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//)\\ Use this cluster for **//heavy duty// programs**, rather than killing the multi-users interactive servers | * **[[https://intranet.lsce.ipsl.fr/informatique/en/calcul/batch.php|The LSCE cluster]]** (aka the //batch system//)\\ Use this cluster for **//heavy duty// programs**, rather than killing the multi-users interactive servers | ||
| * //Heavy duty// programs are programs that will prevent other users from working on the same server because these programs use a lot of CPU and/or memory for more than a few minutes. Ask your advisor, if you are not sure | * //Heavy duty// programs are programs that will prevent other users from working on the same server because these programs use a lot of CPU and/or memory for more than a few minutes. Ask your advisor, if you are not sure | ||
| + | |||
| + | * The **''JupyterHub'' notebook servers**: | ||
| + | * Read the [[other:python:starting#using_jupyterhub_servers|Using JupyterHub servers]] section of the //Working with Python// page | ||
| + | |||
| * **The [[https://documentations.ipsl.fr/spirit/|IPSL Computing and Data Center]]**, aka //Mésocentre ESPRI// (''Spirit'' / ''SpiritX'' / ''HAL'') | * **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) | * 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! | * 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/getting_started/account.html|Requesting an IPSL account]] |
| * [[https://documentations.ipsl.fr/spirit/|IPSL ESPRI Mesocenter documentation]] | * [[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/spirit_clusters/head_nodes.html|spirit clusters]] | ||
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| ==== Using module to access optional programs ==== | ==== Using module to access optional programs ==== | ||
| - | Main ''module'' options: | + | Most useful ''[[https://modules.readthedocs.io/|module]]'' options: |
| * ''module list'': list the currently loaded modules | * ''module list'': list the currently loaded modules | ||
| - | * ''module avail'': list the available modules | + | * ''module avail [mod_name]'': list the available modules (or only the ones with a name starting with ''mod_name'') |
| * ''module load module_a ... module_n'': load modules (automatically including dependencies) | * ''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'': load default version of //module_a// | ||
| Line 460: | Line 469: | ||
| No Modulefiles Currently Loaded. | No Modulefiles Currently Loaded. | ||
| - | > module avail | + | > module avail ncview |
| - | [...] | + | ncview/2.1.7 |
| - | 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 load ncview netcdf/4 | ||
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| There are **lots of text editors available** on Linux computers/servers (''emacs'', ''nano'', ''vi'', ''vim'', ''gvim'', ''gedit'', ...). You can use them: | 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** | * 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 | + | * **If you only need to read a text file**, use a //pager// like [[http://www.greenwoodsoftware.com/less|less]] (or ''more''): ''less my_text_file.txt'' |
| - | * you should know the basic commands and shortcuts! Some text editors (e.g ''nano'') fortunately display some help at the bottom of the screen | + | * ''SPACE'' goes down one page |
| + | * ''b'' (//back//) goes back one page | ||
| + | * ''/STRING'' looks for ''STRING'' in the text (then ''n''ext, ''p''revious, ''q''uit) | ||
| + | * ''q'' exits | ||
| + | * **[[#gnu_nano|nano]] is probably the easiest editor in text mode** to use! | ||
| + | * 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! | ||
| * With a **full Graphical User Interface** (aka //GUI//) allowing you to use the mouse+menus/buttons/etc... | * With a **full Graphical User Interface** (aka //GUI//) allowing you to use the mouse+menus/buttons/etc... | ||
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| <note important>Read the **dedicated [[other:emacs_doc|Using emacs]] page**, and become a power user!</note> | <note important>Read the **dedicated [[other:emacs_doc|Using emacs]] page**, and become a power user!</note> | ||
| + | === Gnu nano === | ||
| + | <note tip>Gnu [[https://www.nano-editor.org/|nano]] is probably the easiest text editor in text mode to use!</note> | ||
| + | |||
| + | You can easily view/edit a file by just typing ''nano my_text_file.txt'' in a terminal, and looking at the instructions displayed at the bottom of the screen (e.g. ''^X Exit'' means that you can exit the editor by typing ''CTRL-X'') | ||
| === vi (vim, gvim) === | === vi (vim, gvim) === | ||
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| * 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? | ||
| + | * A reminder about [[other:python:misc_by_jyp#numerical_values|numerical precision]] | ||
| * [[http://www.unidata.ucar.edu/software/netcdf/|Network Common Data Form (NetCDF)]] official page | * [[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) | * [[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) | ||
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| * 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 | * 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 (//h_eader// of the file) |
| - | * ''ncdump -h some_climate_data_file.nc'': only display the metadata | + | * ''ncdump some_climate_data_file.nc | less'': dump the **full** content to text, and use ''less'' to display it page by page |
| + | * Maybe it is time to learn how to {{:other:newppl:houchesa4_updated.pdf|work efficiently with big text files}} | ||
| * You can use [[other:win7apps#panoply|Panoply]] and [[http://meteora.ucsd.edu/~pierce/ncview_home_page.html|ncview]] for quickly visualizing NetCDF files | * 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: | * Manipulating NetCDF files: | ||
| * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] (''cdo'') | * [[https://code.zmaw.de/projects/cdo/wiki/Cdo#Documentation|Climate Data Operators]] (''cdo'') | ||
| + | * Use ''[[#using_module_to_access_optional_programs|module]] load cdo'' on the LSCE and IPSL servers | ||
| * [[http://nco.sourceforge.net/#RTFM|netCDF Operator]] (//NCO// operators) | * [[http://nco.sourceforge.net/#RTFM|netCDF Operator]] (//NCO// operators) | ||
| + | * Use ''[[#using_module_to_access_optional_programs|module]] load cdo'' on the LSCE and IPSL servers | ||
| === NetCDF related Conventions === | === NetCDF related Conventions === | ||
| + | |||
| + | * [[http://cfconventions.org/|NetCDF CF (Climate and Forecast) Metadata Conventions]] | ||
| * [[https://arxiv.org/abs/1911.08638|Gridspec: A standard for the description of grids used in Earth System models]] | * [[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! | * 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 | * [[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 | * [[http://sgrid.github.io/sgrid/|SGRID Conventions]] for storing staggered data on structured grids that are consistent with the UGRID conventions | ||
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| {{ :other:newppl:xnview_capture.jpg?200 |Click to get a larger version}} | {{ :other:newppl:xnview_capture.jpg?200 |Click to get a larger version}} | ||
| - | ===== Getting help, when using the IPSL Mesocenter ===== | + | ===== Getting help, when using the IPSL Mesocenter (ESPRI) ===== |
| - | Check the [[https://mesocentre.ipsl.fr/contacts//|Contacts]] page | + | Check the [[https://documentations.ipsl.fr/spirit/getting_started/support.html|ESPRI User Support]] page |
| ===== What next? ===== | ===== What next? ===== | ||
other/newppl/starting.1710930460.txt.gz · Last modified: 2024/03/20 10:27 by jypeter
