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institute_lorentz:gnulinux_workstations

GNU/Linux Workstations

The standard Lorentz Institute workstation runs the GNU/Linux operating system (Fedora 27), 64-bit. The workstations 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 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 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 not accessible, such as in the event of a network disruption.

The home disk

The home disk is `automounted' on boot.

$ df /home
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 quota settings type

$ 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       0       0        

:!: 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

du -h /home/your_username/some_directory | sort -rh | head

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

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].

$ 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

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 any of your workstation's disks are arranged in a RAID configuration type

$ cat /proc/mdstat 
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>

The example above shows that two disks are arranged into a 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 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 shell interpreter at any time by just invoking it, e.g.

csh 

or change your default interpreter by invoking chsh.

Access to other workstation disks

All data disks named data1,…,datan 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

/net/<workstation>/data<n>

Note that in the example above <workstation> can either be bingo or bingo.lorentz.leidenuniv.nl with no difference. TIP: The `mounting' of these network file systems 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).

Compilers and libraries

A variety of compilers and libraries are available on your workstation. Please refer to the following manual pages for more info.

Here we only give a summary of useful commands.

# shows which environment modules are available
module avail
# load module 
module load <modulename>
# unload module
module unload <modulename>

NOTE: If 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 sfinx.

Help

Should you need assistance operating your workstation, please do not hesitate to request help via our helpdesk application. You can also visit our offices in the Huygens Laboratory Room 409b at any time during working hours.

institute_lorentz/gnulinux_workstations.txt · Last modified: 2018/10/08 07:43 by lenocil