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institute_lorentz:gnulinux_workstations [2017/08/24 12:35]
lenocil [Compilers and libraries]
institute_lorentz:gnulinux_workstations [2018/10/08 07:43] (current)
lenocil [Local disks]
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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 ​25)]], 64-bit. The workstations ​+The standard Lorentz Institute workstation runs the GNU/Linux operating system [[https://​getfedora.org/​en/​workstation/​|(Fedora ​27)]], 64-bit. The workstations ​
 are configured to host a variety of scientific and non-scientific software to maximize your productivity. are configured to host a variety of 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.+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''​.
  
-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. One of the immediate advantages of this configuration is that +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 
 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  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 
 not accessible, such as in the event of a network disruption. not accessible, such as in the event of a network disruption.
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 ===== The home disk ===== ===== The home disk =====
 The home disk is `automounted'​ on boot.  The home disk is `automounted'​ on boot. 
-<​code>​+<​code ​bash>
 $ df /home $ df /home
 Filesystem ​        ​1K-blocks ​      ​Used ​ Available Use% Mounted on Filesystem ​        ​1K-blocks ​      ​Used ​ Available Use% Mounted on
 home:/​export/​home 3170555392 1260111360 1910444032 ​ 40% /home home:/​export/​home 3170555392 1260111360 1910444032 ​ 40% /home
 </​code>​ </​code>​
-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 quota settings type +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 quota settings type 
-<​code>​+<​code ​bash>
 $ quota -s $ quota -s
 Disk quotas for user xxxxxx (uid 999x99): ​ Disk quotas for user xxxxxx (uid 999x99): ​
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                  ​12344K ​  ​4786M ​  ​4883M ​            ​279 ​      ​0 ​      ​0 ​       ​                  ​12344K ​  ​4786M ​  ​4883M ​            ​279 ​      ​0 ​      ​0 ​       ​
 </​code>​ </​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.+:!: 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 To compile a list of the ten largest files in a directory execute
-<​code>​+<​code ​bash>
 du -h /​home/​your_username/​some_directory | sort -rh | head du -h /​home/​your_username/​some_directory | sort -rh | head
 </​code>​ </​code>​
-Then clean up responsibly.+Then clean up responsibly.  
 + 
 +==== Home disk data availability ==== 
 + 
 +The IL 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 
 +other words, we should be able to revert to a version of your files that is 16 days old.
 ===== Local disks ===== ===== Local disks =====
 Each workstation could have  one or more local hard disks among which one is  used to host the operating system files. ​ Each workstation could have  one or more local hard disks among which one is  used to host the operating system files. ​
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 /​dev/​md0 ​      ​1922599800 27092644 1797821652 ​  2% /data2 /​dev/​md0 ​      ​1922599800 27092644 1797821652 ​  2% /data2
 </​code>​ </​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 failures. Note 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.+In most cases, **but not always**, ​/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 failures. Note however, that 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.**
  
-To check if a RAID configuration ​is used on your workstation ​type+To check if any of your workstation'​s disks are arranged in a RAID configuration type
 <​code>​ <​code>​
 $ cat /​proc/​mdstat ​ $ cat /​proc/​mdstat ​
-Personalities : +Personalities : [raid1]  
 +md127 : active raid1 sdd[2] sdc[0] 
 +      1953383488 blocks super 1.2 [2/2] [UU] 
 +      bitmap: 0/15 pages [0KB], 65536KB chunk 
 unused devices: <​none>​ unused devices: <​none>​
 +
 </​code>​ </​code>​
-In the example above there are no disks arranged ​in RAID.+The example above shows that two disks are arranged ​into RAID1 configuration. Check the output of ''​df -l | grep md127''​ to retrieve its mount point information. 
 + 
 +:!: The backup of any of the data you might have on the ''/​data[1,​n]''​ falls under your responsibility.
 ===== The shell interpreter ===== ===== The shell interpreter =====
 The Lorentz workstations come with a set of pre-installed shell interpreters. Your login shell can be chosen upon registration of your Lorentz account (HL 409b). Alternatively,​ it is possible to use a different The Lorentz workstations come with a set of pre-installed shell interpreters. Your login shell can be chosen upon registration of your Lorentz account (HL 409b). Alternatively,​ it is possible to use a different
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 csh  csh 
 </​code>​ </​code>​
 +or change your default interpreter by invoking ''​chsh''​.
 ===== Access to other workstation disks ===== ===== 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+All data disks named data//​1//,​...,​data//​n//​ are 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>​ <​code>​
 /​net/<​workstation>/​data<​n>​ /​net/<​workstation>/​data<​n>​
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 Here we only give a summary of useful commands. Here we only give a summary of useful commands.
-<​code>​+<​code ​bash>
 # shows which environment modules are available # shows which environment modules are available
 module avail module avail
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 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.1503578144.txt.gz · Last modified: 2017/08/24 12:35 by lenocil