Differences

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

--- other:newppl:starting [2024/02/05 17:09] – [Determining the space used by directories] jypeter
+++ other:newppl:starting [2025/08/07 13:51] (current) – [Miscellaneous information] Added link to GATE desk jypeter
@@ Line 17: / Line 17: @@
   * [[https://www.science-accueil.org/en/|Science Accueil]]
     * [[https://www.science-accueil.org/en/request-services/|Service request page]]
+  * [[https://gate.paris-saclay.fr/en/|GATE desk]]
   * {{:other:newppl:uvsq-guide-du-personnel-nov2019.pdf|Guide du Personnel UVSQ}}
@@ Line 34: / Line 35: @@
 <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 48: @@
     * 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 222: @@
 $ 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 272: / Line 282: @@
 </code>
-The top lines give you some summary information about the system, but you should monitor the memory usage (''VIRT'' and ''RES''), ''CPU'' and ''TIME'' columns. By default, ''top'' will will put the processes using the more CPU at the top (as shown above). You can see above that the ''emacs'' text editor has clearly crashed, because it should not use 100% CPU for such a long time
+The top lines give you some summary information about the system, but you should monitor the memory usage (''VIRT'' and ''RES''), ''CPU'' and ''TIME+'' columns. By default, ''top'' will will put the processes using the more CPU at the top (as shown above). You can see above that the ''emacs'' text editor has clearly crashed, because it should not use 100% CPU for such a long time
+  * The ''TIME+'' information is in //minutes// (e.g. ''5432:01'' means //5432 minutes and 1 second//, ''25:15.20'' means //25 minutes, 15 seconds and 20% of 1 second//)
+  * Memory usage:
+    * ''%MEM'' (Kb): percentage of the total available **physical memory** used by a process. This is based on ''RES'', the **non-swapped physical memory** used by a process
+    * ''VIRT'' (Kb): total  amount  of **virtual memory** (i.e. memory temporarily swapped/saved to disk) used by a process.  It includes all code, data and shared libraries plus pages that have been swapped out and pages that have been mapped but not used
+    * The ''free'' command can display the memory usage of a server at a given time. ''available'' is an estimation of how much memory is available for starting new applications, without swapping
+      * <code> % free -ht
+              total        used        free      shared  buff/cache   available
+Mem:            62G        1.5G         56G         11M        5.0G         60G
+Swap:           62G        1.7G         60G
+Total:         125G        3.3G        116G</code>
 If you type ''M'', the processes will be sorted my memory usage, as shown below
@@ Line 410: / Line 432: @@
 ===== 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.
+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 ''[[other:newppl:starting#using_module_to_access_optional_programs|module]]'' command to access other programs (or access a specific version of a program).
 ==== Which program am I using? ====
@@ Line 433: / Line 455: @@
 ==== Using module to access optional programs ====
-Main ''module'' options:
+=== Documentation ===
+  * [[https://documentations.ipsl.fr/spirit/common/module_command.html|IPSL Meso documentation]]
+  * [[https://modules.readthedocs.io/|Full and official module documentation]]
+=== Most useful 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 avail -l 2>&1 | grep subname'': list the modules that have ''subname'' in their name, and their installation date
+    * <wrap hi>This only works in a //bash// shell!</wrap> In a //tcsh// shell, start by invoking a //bash// shell with ''bash -l''
   * ''module load module_a ... module_n'': load modules (automatically including dependencies)
     * ''module load module_a'': load default version of //module_a//
@@ Line 441: / Line 471: @@
   * ''module purge'': remove all modules
-Detailed example:
+=== Detailed example ===
 <code> > which ncview
 ncview: Command not found.
@@ Line 448: / Line 479: @@
 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 464: / Line 492: @@
  > which ncdump
-/usr/local/install/netcdf-4.3.2/bin/ncdump</code>
+/usr/local/install/netcdf-4.3.2/bin/ncdump
+ > bash -l
+    $ module avail -l 2>&1 | grep gcc
+binutils/2.43.1-gcc14-acc                            2025/01/27 21:09:36
+gcc/14.2.0-openacc                                   2025/01/24  8:11:14
+gcc/8.3.0                                            2021/04/21  8:27:35
+netcdf/4.9.2-gcc14-acc                               2025/01/27 22:02:57
+netcdf/4.9.2-gcc8                                    2024/06/05 20:49:36
+R/4.0.3-gcc8                                         2022/02/03 12:53:55</code>
 ===== Useful documentation for beginners =====
@@ Line 475: / Line 512: @@
   * 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 485: / Line 524: @@
 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 496: / Line 542: @@
 <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 511: / Line 561: @@
   * 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 520: / Line 571: @@
   * 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 nco'' 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 542: / Line 598: @@
 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 587: / Line 644: @@
 {{ :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? =====