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other:available_servers [2026/08/19 17:20] – [Common sense reminders] Added new sections jypeterother:available_servers [2026/08/25 16:19] (current) – [IPSL servers] Added some IPSL content jypeter
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   * You can do what you want on **your local laptop/desktop** (except get viruses)   * You can do what you want on **your local laptop/desktop** (except get viruses)
  
-  * Be **careful** when you use **remote interactive servers shared with other users** +  * **Be very careful when you use remote interactive servers shared with other users** 
-    * Others should not even notice that you(r processes) are there!\\ Yes, you can use computing resources cleanly and efficiently...+    * Others should not even notice that you(r processes) are there!\\ Yes, **you** can use computing resources cleanly and efficiently... 
 +    * Note: notebook servers are shared servers!
     * If you have some heavy duty processing to do:     * If you have some heavy duty processing to do:
       * Use shared interactive servers only for quick tests (ideally with a subset of your huge dataset)       * Use shared interactive servers only for quick tests (ideally with a subset of your huge dataset)
-        * note: notebook servers are shared servers! 
       * Use dedicated batch/computing clusters for //heavy// processing       * Use dedicated batch/computing clusters for //heavy// processing
         * //heavy// =         * //heavy// =
-          * will run for a long time +          * will run for a **long** time 
-          * and/or use a lot of CPU (one or many CPUs) +          * and/or use a **lot** of CPU (one or many CPUs) 
-          * and/or use a lot of RAM +          * and/or use a **lot** of RAM 
-          * and/or do a lot of disk reading/writing,+          * and/or do a **lot** of disk reading/writing,
           * ...           * ...
         * resources you use in High Performance Computing centers will probably be deducted from a (shared) //project//         * resources you use in High Performance Computing centers will probably be deducted from a (shared) //project//
  
   * **Disk space (and backup space) is also an important resource!**   * **Disk space (and backup space) is also an important resource!**
-    * When possible, avoid duplicating data, and run your computations //near// the data +    * When possible, **avoid duplicating data**, and run your computations //near// the data 
-      * e.g. use the ''/bdd/'' //[[https://mesocentre.ipsl.fr/jeux-de-donnees/|mirror data]]// on the ''spirit[x]'' servers +      * e.g. use the //[[https://mesocentre.ipsl.fr/jeux-de-donnees/|mirror data]]// stored in ''/bdd/'' on the ''spirit[x]'' servers 
-    * Use //scratch// disks, when available, for temporary data and do not forget to remove temporary data+    * Use //scratch// disks, when available, for **temporary data** and do not forget to remove temporary data
       * LSCE: ''/home/scratch01/$USER''       * LSCE: ''/home/scratch01/$USER''
       * spiritx: ''/scratchx/$USER''       * spiritx: ''/scratchx/$USER''
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   * **Learn how to monitor resources usage**:   * **Learn how to monitor resources usage**:
     * CPU and RAM: ''[[other:newppl:starting#determining_the_load_of_a_linux_server|top]]''     * CPU and RAM: ''[[other:newppl:starting#determining_the_load_of_a_linux_server|top]]''
-    * Disk: ''df'', ''du''+    * Disk: ''[[other:newppl:starting#quota_command|quota]]'', ''[[other:newppl:starting#du_disk_usage_command|du]]'', ''[[other:newppl:starting#df_command|df]]'' 
 +    * Listing and killing processes: ''[[other:newppl:starting#listing_processes_with_ps|ps]]'', ''[[other:newppl:starting#terminating_processes_will_kill|kill]]'' 
 +    * ... 
 + 
 +  * **Read (some of) the //local// documentation**\\ <wrap hi>[[https://en.wikipedia.org/wiki/RTFM|RTFM]]</wrap> (Read The Fine Manual) 
 +    * [[other:newppl:starting#useful_documentation_for_beginners|Some Linux related documents]] (by JYP) 
 +      * Learn at least how to use the ''[[other:newppl:starting#the_man_command|man]]''(ual) command !! 
 +    * [[https://intranet.lsce.ipsl.fr/informatique/en/|LSCE documentation]] 
 +    * [[https://documentations.ipsl.fr/MESO_User/|IPSL Computing and Data Center documentation]] 
 +    * [[https://www-hpc.cea.fr/tgcc-public/en/html/tgcc-public.html|TGCC documentation]] 
 +    * [[http://www.idris.fr/en/docs/jean-zay/nouvel-utilisateur/|Jean Zay @ IDRIS documentation]]
     * ...     * ...
  
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 ==== Connecting to the servers ==== ==== Connecting to the servers ====
  
 +  * We use **''[[other:ssh|ssh]]''** and //ssh clients// to connect securely to the servers we work with
 +    * Use the [[other:putty_conf|PuTTY]] ssh //client// to easily open a terminal on a remote server from a Windows computer
 +
 +  * Some computing resources can also be accessed with a web browser and a [[https://jupyter.org/|JupyterHub server]]
 ==== Transferring data ==== ==== Transferring data ====
  
 +  * Servers can usually only access data on local (in the same computer room) disks. If you need to work locally on data available on a remote server, you first have to download the remote data
 +    * Notable exceptions :
 +      * ''spirit**x**'' servers in Palaiseau campus can access ''spirit'' servers disks at Sorbonne Université, in //read-only// mode, and the other way around ([[https://documentations.ipsl.fr/MESO_User/|details]])
 +      * some of the data available in ''/bdd'' on the ''spirit[x]'' servers are actually distributed from HPC centers
 +    * Reminder: when possible, **avoid duplicating data**, and **perform the data analysis near the (original) data**
 +    * When possible, **//reduce// the data** before download, in order to transfer only the subset you need: e.g. select only the regions and variables you need, pre-compute spatial or temporal means, etc...\\ You can easily reduce NetCDF data with:
 +      * [[https://code.mpimet.mpg.de/projects/cdo/wiki|cdo]] (Climate Data Operators)
 +      * [[https://nco.sourceforge.net/|NCO]] (netCDF Operators)
 +    * It is of course a good idea to document (in a simple text file) where the files come from, how they were pre-processed, ...
  
 +  * We use transfer programs based on the //ssh protocol// to move data securely
 +    * [[other:ssh#copying_files_with_scp|scp]] (secure copy): **easily** copy files and directories recursively
 +      * Use the [[other:win10apps#winscp|WinSCP]] //scp client// to easily copy files to/from a Windows computer
 +    * [[other:ssh#mirroring_directories_with_rsync|rsync]]: mirror directories (more complex)
 +
 +
 +==== Checking data integrity ====
 +
 +If you need to check that a (potentially big) file is identical to its remote version, you can first check that the file sizes are identical, and then **check data integrity** by comparing the //checksum// (with ''sha256sum'' or ''[[https://en.wikipedia.org/wiki/Md5sum|md5sum]]'') of the original and copied files. It is more efficient and secure to compare this unique fingerprint than to transfer a file again (and use ''diff'')
 +
 +e.g. with a 14 Gb file on spirit:
 +
 +<code>$ cd /bdd/CMIP6/CMIP/IPSL/IPSL-CM6A-LR/piControl/r1i1p1f1/Omon/thetao/gn/latest
 +
 +$ ls -l thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +[...] 14293466154 [...] thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +
 +$ ls -lh thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +[...] 14G [...] thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +
 +$ md5sum thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +5378634e97136d75e4517cb72e0cda9a  thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +
 +$ sha256sum thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc
 +90cf48c540216897bf4d9841acd7034f85cc10e233eed74b1aa27fd77a8da1e6  thetao_Omon_IPSL-CM6A-LR_piControl_r1i1p1f1_gn_185001-194912.nc</code>
 ===== LSCE servers ===== ===== LSCE servers =====
 +
 +
 +==== The LSCE gateway ====
 +
 +''ssh1.lsce.ipsl.fr''
 +    * Use ''ssh ssh1.lsce.ipsl.fr'' when you are **outside the LSCE wired network**, before accessing any other LSCE server:
 +      * By **//outside LSCE//**, we mean that your computer is:
 +        * connected to the LSCE WiFi network (instead of the wired network)
 +        * or physically outside LSCE
 +    * You can also use ''ssh1'' when you are **copying files to/from outside LSCE** with ''scp'' or ssh-based tools
 +    * <wrap hi>The ''ssh1'' gateway can **only** be used for copying files or accessing the LSCE interactive servers</wrap>!
 +      * **You have to** connect to an ''obelix//NN//'' interactive server before doing any real work
 +
 +
 +==== The LSCE interactive servers ====
 +
 +''obelix//NN//'' (''obelix2'' to ''obelix5'')
 +    * Use ''ssh obelix'' to access the LSCE servers from **inside LSCE**.\\ The //load balancing// system will send you to the ''obelix//NN//'' server that has currently the smallest load.
 +      * By **//inside LSCE//**, we mean that:
 +        * your computer is connected to the LSCE **wired** network
 +        * or you are using the [[https://intranet.lsce.ipsl.fr/informatique/fr/vpn-forticlient.php#vpnlsce|LSCE VPN]]
 +        * or you have a //terminal// connected to the ''ssh1'' gateway
 +    * <wrap hi>Never forget that you are **sharing** these interactive 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 !
 +    * You can use one of the following commands if you want to know on which ''obelixNN'' you are
 +      * <code>$ ssh obelix
 +Last login: Mon Jun  3 08:49:53 2019 from somewhere
 +$ echo $HOST
 +obelix5
 +$ 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>
 +
 +
 +==== The LSCE cluster ====
 +
 +  * **[[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 LSCE JupyterHub notebook server ====
 +
 +    * Read the [[other:python:starting#using_jupyterhub_servers|Using JupyterHub servers]] section of the //Working with Python// page
  
  
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 +
 +  * **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://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]]
 +    * [[https://documentations.ipsl.fr/spirit/getting_started/support.html|Getting help]]
 ===== HPC centers ===== ===== HPC centers =====
  
other/available_servers.1787152820.txt.gz · Last modified: by jypeter
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