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allegrouserguide:computers [2020/12/15 09:45] – immerallegrouserguide:computers [2024/11/21 10:46] (current) – alma
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 ==== Desktop Machines ==== ==== Desktop Machines ====
  
-At Allegro, we have five computers that are dedicated to high-performance work with ALMA data:+At Allegro we have five compute servers that are dedicated to high-performance work with ALMA data:
  
 ^name       ^processor                ^speed  ^memory  ^alias^ ^name       ^processor                ^speed  ^memory  ^alias^
 |tulor      |40x Intel Xeon E5-2640 v4|2.4GHz|512GiB |TU   | |tulor      |40x Intel Xeon E5-2640 v4|2.4GHz|512GiB |TU   |
 |helada     |32x Intel Xeon E5-2640 v3|2.6GHz|512GiB |HE   | |helada     |32x Intel Xeon E5-2640 v3|2.6GHz|512GiB |HE   |
-|chaxa      |32x Intel Xeon E5 2665   |2.4GHz|256GiB |CX   | +|miscanti   |48x Intel Xeon Gold 6226 |2.7GHz|512GiB |MI   |
-|cejar      |16x Intel Xeon E5 2650   |2.0GHz| 32GiB |CE   | +
-|tebinquiche|12x Intel Xeon E5645     |2.4GHz| 48GiB |TQ   |+
  
-<note>**#HUIB: ADD MISCANTI**</note> +All these machines except tebinquiche are running on a stable Linux operating system **Red Hat Enterprise Linux Server release 7.9 (Maipo)**. tebinquiche still runs 6.10 (Santiago) and is intended for legacy purposes (e.g., CASA version 4).
- +
-All these machines except tebinquiche are running **Red Hat Enterprise Linux Server release 7.5 (Maipo)**. tebinquiche still runs 6.10 (Santiago) and is intended for legacy purposes. +
- +
-Logging in to any of these machines works through e.g. :+
  
 +Logging into any of these computers works through e.g. :
 <code bash> <code bash>
-$ ssh -X username@chaxa+$ ssh -X username@helada
 </code> </code>
-From outside the STRW network, you cannot reach these machines directly: you first need to ssh to a normal Sterrwacht machine, and from there to one of the Allegro ones.+From outside the Leiden Observatory network these computers are not directly accessible, except for almaportal (almaportal.strw.leidenuniv.nl). To access any computer, you first need to ssh to almaportal and from there to one of the other Allegro computers.
  
 ==== Filesystem ==== ==== Filesystem ====
  
-<note>**#HUIB: NEEDS UPDATING - NSF SYSTEM**</note>+The data at Allegro is stored on the almastorage [[https://en.wikipedia.org/wiki/Network_File_System|NFS]] file system. This storage is accessible from all Allegro compute servers through a dedicated high-speed network. From other Linux computers at Leiden Observatory this storage is accessible via ''/net/chaxa/allegro1'' through ''/net/chaxa/allegro6'' at reduced speed. Note that the ''/allegro'' storages have different sizes and purposes, so please consult the Allegro staff before using one of these storages.
  
-Our data is stored on several filesystems - three at last count. Two of these (''%%/lustre1%%'' and ''%%/lustre2%%'') are [[http://en.wikipedia.org/wiki/Lustre_%28file_system%29|Lustre]] systems, but the third (''%%/allegro1%%'') is mounted via the more standard [[https://en.wikipedia.org/wiki/Network_File_System|NFS]]. Whether Lustre or NFS should be transparent to the user. Currently, these three are mounted on all 5 Allegro compute nodes under the names given above, but ''%%/lustre1%%'' and ''%%/lustre2%%'' at least can be accessed from all STRW computers via ''%%/net/chaxa/lustre1%%'' or ''%%net/chaxa/lustre2%%'' (at reduced speed).+You may come accross references to [[http://en.wikipedia.org/wiki/Lustre_%28file_system%29|Lustre]] file systems at Allegro. These are the previous storages that have been replaced. Because of backward compatibiliy, the ''/lustre2'' storage name is still in use, but is in fact a virtual storage that physically lives on the ''almastorage'' storage.
  
 <note warning> <note warning>
-Although your files on the Sterrewacht home area are backed up on a daily basis, there is **no backup scheme** in place for your files on the Allegro data disks. You are therefore advised NOT to store irreplaceable files on these disk systems.+Although your files on the Leiden Observatory home area are backed up on a daily basis, there is **no backup scheme** in place for your files on the Allegro storages. You are therefore advised NOT to store single irreplaceable files on these file systems. Allegro-provided software and the data archive are replicated on all file systems, but actual data is not.
 </note> </note>
- 
-Such things as Allegro-provided software and the data archive are replicated on all file systems, but actual data is not. 
  
 ===== Directory Structure ===== ===== Directory Structure =====
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   * ''%%allegro_staff%%'': Only accessible for Allegro members   * ''%%allegro_staff%%'': Only accessible for Allegro members
   * ''%%bin%%'': binaries/executables   * ''%%bin%%'': binaries/executables
-    * ''%%data%%'': ALMA data+  * ''%%data%%'': ALMA data
     * ''%%projects%%'': Projects     * ''%%projects%%'': Projects
-  * ''%%public_data_archive%%'': Public data that is accessible for everyone+    * ''%%public_data_archive%%'': Public data that is accessible for everyone
   * ''%%doc%%'': Documentation (e.g., ALMA handbooks, ...)   * ''%%doc%%'': Documentation (e.g., ALMA handbooks, ...)
   * ''%%etc%%'': Startup scripts, etc.   * ''%%etc%%'': Startup scripts, etc.
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 </note> </note>
  
-<note>**#HUIB: This should be directly done by Huib not by the user**</note> +Rather than sourcing this script manually, it is advised to add a small statement to your shell rc-file. The following line will alias the startup scripts if needed:
- +
-Rather than sourcing this script manually, it is advised to add a small statement to your shell rc-file. The following lines will check for the computer you are currently logged in, and source the startup scripts if needed:+
  
   * **Bash** users should add these lines to their ''%%~/.bashrc%%'':<code bash>   * **Bash** users should add these lines to their ''%%~/.bashrc%%'':<code bash>
-lustreroot_file='/home/alma/etc/lustre_root' +alias allegro-setup 'source /almastorage/allegro/bin/allegro-user-setup.sh'
-if [[ -r $lustreroot_file ]]; then +
-  lustreroot=`cat $lustreroot_file` +
-else +
-  lustreroot='/lustre1' +
-fi +
-alg_user_setup=$lustreroot/allegro/bin/bashrc_user.sh +
-if [[ -r $alg_user_setup ]]; then +
-    . $alg_user_setup +
-fi+
 </code> </code>
 +
   * **C-Shell** (i.e. tcsh) users should add these lines to their ''%%~/.cshrc%%'':<code bash>   * **C-Shell** (i.e. tcsh) users should add these lines to their ''%%~/.cshrc%%'':<code bash>
-set lustre_root_file="/home/alma/etc/lustre_root" +alias allegro-setup 'source /almastorage/allegro/bin/allegro-user-setup.csh'
-if ( -r $lustre_root_file ) then +
-  set lustreroot=`cat $lustre_root_file` +
-else +
-  set lustreroot="/lustre1" +
-endif +
-set alg_user_setup=$lustreroot/allegro/bin/cshrc_user.csh +
-if ( -r $alg_user_setup ) then +
-    source $alg_user_setup +
-endif+
 </code> </code>
  
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 </note> </note>
  
 +Every time you log in to an Allegro computer, you need to type ''allegro-setup'' in order to have all of the correct paths and CASA versions available. 
  
 === CASA setup === === CASA setup ===
 +
 +<note>#HUIB: These changes to init.py etc should be done by Huib not the user.</note>
 +
 +<note>**#HUIB: NEEDS UPDATE: see https://trello.com/c/zxQMCTST/100-allegro-users-guide**</note>
  
 To access the user-provided CASA tasks and other modules when you work on the Allegro computers, simply add the following lines to your ''%%~/.casa/init.py%%'': To access the user-provided CASA tasks and other modules when you work on the Allegro computers, simply add the following lines to your ''%%~/.casa/init.py%%'':
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 <code bash> <code bash>
-casapy-54+nice +10 casapy-580
 </code> </code>
-at the command line (on all machines but tebinquiche, which doesn't have it). Typing simply:+for (t)csh or 
 + 
 +<code bash> 
 +nice -n 10 casapy-580 
 +</code> 
 +for bash 
 + 
 +at the command line. Typing simply:
  
 <code bash> <code bash>
 casapy casapy
 </code> </code>
-will start up the Allegro default version. NOTE however that this is not necessarily the latest version of CASA.+will start up the Allegro default version. NOTE however that this is not necessarily the latest version of CASA and does not use the nice command, which you should use as these are shared resources. 
 + 
 +For CASA 6 and later, type 
 +<code bash> 
 +nice -n 10 env -u PYTHONPATH -u LD_LIBRARY_PATH casapy-641p 
 +</code> 
 + 
 +for bash or for (t)csh: 
 +<code bash> 
 +nice +10 env -u PYTHONPATH -u LD_LIBRARY_PATH casapy-641p 
 +</code> 
 + 
 +<note>**#HUIB: ADD CASA VERSIONS ON DIFFERENT COMPUTERS: see https://trello.com/c/L0BWiAf6/101-casa-versions-on-various-computers**</note>
  
 ==== ALMA Projects ==== ==== ALMA Projects ====
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 ==== non-ALMA Projects ==== ==== non-ALMA Projects ====
 +
 +<note>**#HUIB: UPDATE /lustre1/ PATH**</note>
  
 You can also use the Allegro computing facilities to perform other, non-ALMA related work. Your dedicated workspace for that is ''%%/lustre1/username%%'' (feel free to create a directory with your username). However, the general terms of using the Allegro computing facility apply. You can also use the Allegro computing facilities to perform other, non-ALMA related work. Your dedicated workspace for that is ''%%/lustre1/username%%'' (feel free to create a directory with your username). However, the general terms of using the Allegro computing facility apply.
allegrouserguide/computers.1608021908.txt.gz · Last modified: by immer
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