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institute_lorentz:gnulinux_workstations [2018/01/29 13:06] – [GNU/Linux Workstations] lenocilinstitute_lorentz:gnulinux_workstations [2022/11/08 08:34] (current) – [Data storage disk] lenocil
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 ====== GNU/Linux Workstations ====== ====== GNU/Linux Workstations ======
-The standard Lorentz Institute workstation runs the GNU/Linux operating system [[https://getfedora.org/en/workstation/|(Fedora 27)]], 64-bit. The workstations  +The standard Lorentz Institute workstation runs the [[https://getfedora.org/en/workstation/|Fedora]] GNU/Linux operating system. The workstations  
-are configured to host a variety of scientific and non-scientific software to maximize your productivity. +are configured with pre-installed scientific and non-scientific software to maximize your productivity. 
-You are allowed to install and/or build packages locally (directories to which you have access), but for system-wide installations you must file a request through our [[https://helpdesk.lorentz.leidenuniv.nl/|helpdesk]] application or via email at ''support@lorentz.leidenuniv.nl''.+You are allowed to install and/or build packages locally (directories to which you have writing access), but for system-wide installations you must file a request through our [[https://helpdesk.lorentz.leidenuniv.nl/|helpdesk]] or via email at <support@lorentz.leidenuniv.nl>.
  
-Although the workstations might differ in their hardware specifications, they are set so that you can switch from one to the other flawlessly. For instance, the home directories are not local to a particular  machine, but they are `mounted'  as a network file system on each workstation. One of the immediate advantages of this configuration is that  +We perform upgrades of the operating system of all workstations once a year usually starting in December. This is crucial for both security and latest software availability. 
-you can access you home files upon login no matter the workstation you are working on. On the other hand, having the home directories mounted over the network can result in problems if the home file system is + 
 +Although the workstations might differ in their hardware specifications, they are set so that you can switch from one to the other flawlessly. For instance, the home directories are not local to a particular  machine, but they are hosted on remote server and served as network file system (NFS) to all workstations. One of the immediate advantages of this configuration is that  
 +you can access any files in your home directory no matter the workstation you are working on. On the other hand, having the home directories mounted over the network can result in problems if the home file system is 
 not accessible, such as in the event of a network disruption. not accessible, such as in the event of a network disruption.
  
-===== The home disk ===== +===== Home disk ===== 
-The home disk is `automounted' on boot.  + 
-<code> +^Mount Point^ User Space^ Redundancy^Notes^ 
-$ df /home +|/home/home/<username>| RAID, 12:00 PM Daily Snapshots with 7 day expiration |NFS, automounted, quota| 
-Filesystem         1K-blocks       Used  Available Use% Mounted on + 
-home:/export/home 3170555392 1260111360 1910444032  40% /home +Each user has an **__allocated quota__** on the home disk depending on their role within the Lorentz Institute. The standard quota is 4GB, nonetheless it is possible to request extra space. To check your home disk usage type ''quota -s''. Use ''du -h /home/<username> | sort -rh | head'' to compile a list of the ten largest files in your home directory. 
-</code+ 
-Each user has an **allocated quota**__Underlined Text__ on the home disk depending on their role within the Lorentz Institute. The standard quota is 4GB, nonetheless it is possible to request extra space. To check your quota settings type +We advise you do not store large files in your home directory. 
-<code> + 
-quota -s +
-Disk quotas for user xxxxxx (uid 999x99):  +
-     Filesystem   space   quota   limit   grace   files   quota   limit   grace +
-home:/export/home +
-                 12344K   4786M   4883M             279                     +
-</code> +
-:!: TIP: Regularly check that you are below your assigned quota. Your workstation will stop working correctly if softwares cannot write temporary files in your home folder any more.+
  
-To compile a list of the ten largest files in a directory execute 
-<code> 
-du -h /home/your_username/some_directory | sort -rh | head 
-</code> 
-Then clean up responsibly. 
  
 ==== Home disk data availability ==== ==== Home disk data availability ====
  
-The IL home directories are hosted on a iSCSI array of disks arranged in a RAID +The Lorentz Institute home directories are hosted on a iSCSI array of disks arranged in a RAID 
-configuration. Automatic snapshots (a sort of incremental backup) of the whole home disk are performed __everyday at midnight__The total number of snapshots stored on our system at any time is __16 snapshots__. In +configuration. Automatic snapshots (a sort of incremental backup) of the whole home disk are performed __everyday at around 12:00 PM__Each snapshot has a 7-day expiration and as such the total number of snapshots stored on our system at any time is __7__
-other words, we should be able to revert to a version of your files that is 16 days old+===== Data disks ===== 
-===== Local disks ===== +Each workstation could have  one or more local disks to offer large-data storageThe data disks of one workstation are also accessible from any other workstation
-Each workstation could have  one or more local hard disks among which one is  used to host the operating system files.  +
-The remaining space can be used to store relatively large files and will be accessible through the +
-mount points /data1, /data2,...,/data[n]. +
-<code> +
-$ df /data[0-9]* +
-Filesystem      1K-blocks     Used  Available Use% Mounted on +
-/dev/sda7      1838137644 67915552 1676827048   4% /data1 +
-/dev/md0       1922599800 27092644 1797821652   2% /data2 +
-</code> +
-Usually /data2 is configured as the mount point of a RAID[1|5] stack, meaning that data in it have a certain level of redundancy which can protect against disk failuresNote however, that storing all of your data on /data2 will not prevent loss if all disks in the array configuration `die' and/or  your computer tower gets destroyed by a fire  or any other disastrous event.+
  
-To check if a RAID configuration is used on your workstation type +^Mount Point^ User Space^ Redundancy^Notes^ 
-<code> +|/data[1,..,n]| /data[1,..,n]| None or RAID. Backups are your resposibility |Local, no quota, mounted at boot| 
-$ cat /proc/mdstat  +|/net/<workstation-name>/data[1,..,n]| /net/<workstation-name>/data[1,..,n]| None or RAID*Backups are your resposibility |NFS, no quota, automounted|
-Personalities :  +
-unused devices: <none> +
-</code> +
-In the example above there are no disks arranged in a RAID.+
  
-:!: The backup of any of the data you might have on the ''/data[1,n]'' falls under your responsibility. +In most cases, **but not always**, /data2 is configured as the mount point of a RAID[1|5] stackmeaning that data in it have certain level of redundancy which can protect against disk failuresNote howeverthat storing all  data on /data2 in RAID configuration will still not prevent data loss if all disks in the array `die',  your computer tower gets destroyed by a fire  or in any other disastrous event**You are strongly encourage to keep your personal backup of any important data.**
-===== The shell interpreter ===== +
-The Lorentz workstations come with set of pre-installed shell interpreters. Your login shell can be chosen upon registration of your Lorentz account (HL 409b)Alternativelyit is possible to use a different +
-shell interpreter at any time by  just invoking  it, e.g. +
-<code> +
-csh  +
-</code> +
-===== Access to other workstation disks ===== +
-Partitions named data//1//,...,data//n// are usually network-shared among all the Lorentz Institute workstations. You can access /data1 on a machine called //bingo//  via /net/bingo/data1. More generally, the pattern to access a data disk on a Lorentz machine is +
-<code> +
-/net/<workstation>/data<n> +
-</code>   +
-Note that in the example above <workstation> can either be //bingo// or //bingo.lorentz.leidenuniv.nl// with no difference.  +
-TIP: The `mountingof these network file systems is managed by autofs. This means that those disks will not be mounted until there is an attempt to access themfor instance by contents listing (ls) or change of working directory (cd) +
-===== Compilers and libraries ===== +
-A variety of compilers and libraries are available on your workstation. Please refer to the following manual [[linux:sfinx|pages]] for more info.+
  
-Here we only give a summary of useful commands. +To check if any of your workstation's disks are arranged in a RAID configuration type ''cat /proc/mdstat''.
-<code> +
-# shows which environment modules are available +
-module avail +
-# load module  +
-module load <modulename> +
-# unload module +
-module unload <modulename> +
-</code> +
  
-NOTE: If [[linux:sfinx|sfinx]]  was not installed under your account, you might see less modules on your workstation. In this case make a backup of your settings (for instance .bashrc, .cshrc, etc...) and install [[linux:sfinx|sfinx]]. +Note that in the table above <workstation-name> can either be a short workstation name or a full name including its domain with no difference. Disk mounting via the ''/net/<workstation-name>'' scheme is managed by autofs. This means that those disks will not be mounted until there is an attempt to access them, for instance by contents listing (ls) or change of working directory (cd).  
 +===== Data storage disk ===== 
 + 
 +Our data-storage disk can be accessed according to the following schema  
 + 
 +^Mount Point^ Total Size ^ Redundancy ^ Notes ^ 
 +|/disks/misc | 5 TB | RAID, 1:00 AM Daily Snapshots with two-day expiration | NFS, no quota, automount| 
 +|[[institute_lorentz:irods_fair_storage|iRODS]] | 20 GB (per user) | iRODS | iCommands, WebDAV, FUSE | 
 + 
 +If you work on [[institute_lorentz:xmaris|xmaris]], there is an extra storage space that you could use while you work on the cluster. For mor einfo, please read [[institute_lorentz:xmaris|here]]. 
 +===== Shell interpreters ===== 
 +The Lorentz Institute workstations come with a set of pre-installed shell interpreters. Your login shell can be chosen upon registration of your Lorentz account (HL 409b) otherwise it will default to ''bash''. In any case, it is possible to use a different 
 +shell interpreter at any time by  just invoking  it, e.g. ''csh''
 + 
 +If you want to change your default interpreter use ''chsh'' and follow the on-screen indications. 
 + 
 +===== Available software ===== 
 +A variety of softwares are available on your workstation. Some software is installed locally on your workstation others are provided  
 +remotely in the form of //modules// from our software disk either via the [[linux:sfinx|sfinx]] environment or via the [[https://easybuild.readthedocs.io/en/latest/|EasyBuild]] framework. 
 + 
 +While locally installed softwares can be launched directly because already loaded in your environment, //sfinx-// and //EasyBuild-// built software must be loaded in your environment first via the ''module'' command. 
 +For more information consult  ''man module''
 + 
 +:!: If [[linux:sfinx|sfinx]] is not installed for your account, you might see less modules available on your workstation. In this case make a backup of your settings (for instance .bashrc, .cshrc, etc...) and install [[linux:sfinx|sfinx]]. 
 ===== Help ===== ===== Help =====
 Should you need assistance operating your workstation, please do not hesitate to request help via our [[https://helpdesk.lorentz.leidenuniv.nl/|helpdesk]] application. You can also visit our offices in the Huygens Laboratory Room 409b at any time during working hours. Should you need assistance operating your workstation, please do not hesitate to request help via our [[https://helpdesk.lorentz.leidenuniv.nl/|helpdesk]] application. You can also visit our offices in the Huygens Laboratory Room 409b at any time during working hours.
    
-Comments and suggestions to improve this guide are welcome.+
  
institute_lorentz/gnulinux_workstations.1517231189.txt.gz · Last modified: 2018/01/29 13:06 by lenocil