Differences

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

--- other:newppl:starting [2024/03/20 11:27] – [Determining the load of a Linux server] Added details about TIME and mem usage jypeter
+++ other:newppl:starting [2025/02/04 14:39] (current) – New section title, link to IDRIS jypeter
@@ Line 34: / Line 34: @@
 <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>
-=== 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 **GENERAL** (use the downward arrow)
@@ Line 47: / Line 47: @@
     * 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 **Informations dans l'annuaire** and update the different fields
   - Click on **Envoyez votre demande**
+  - Wait (for someone to validate your request)
 ===== The LSCE mailing lists =====
@@ Line 220: / Line 221: @@
 $ hostname
 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
     * //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'')
     * 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/getting_started/account.html|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]]
@@ Line 445: / Line 454: @@
 ==== 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 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'': load default version of //module_a//
@@ Line 460: / Line 469: @@
 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
@@ Line 487: / Line 493: @@
   * Useful Linux commands for working with (potentially big) text files ({{:other:newppl:houchesa4_updated.pdf}})
   * Using [[other:ssh|ssh]] and [[other:ssh#copying_files_with_scp|scp]]
+  * See also the //old// [[http://www.idris.fr/formations/utilisation-unix/unix-u-cours.html|IDRIS (advanced) Linux training]] (French tutorial)
 ==== Text editors ====
@@ Line 497: / Line 505: @@
 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
+    * **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...
@@ Line 508: / Line 523: @@
 <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) ===
@@ Line 523: / Line 542: @@
   * 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/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)
@@ Line 532: / Line 552: @@
   * 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
   * Manipulating NetCDF files:
     * [[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)
+      * Use ''[[#using_module_to_access_optional_programs|module]] load cdo'' on the LSCE and IPSL servers
 === 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]]
     * 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
@@ Line 554: / Line 579: @@
 Check the [[other:python:jyp_steps#using_netcdf_files_with_python|dedicated section]] of the //Python// page
-==== Programming languages ====
+==== Programming languages, parallelism, ... ====
   * [[other:index#python_notes|JYP's Python notes]]
+  * [[http://www.idris.fr/eng/formations/supports_de_cours-eng.html|IDRIS classes and tutorials]]
 ===== Getting help (from the LSCE system administrators) =====
@@ Line 599: / Line 625: @@
 {{ :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? =====