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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
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 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
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
du -h /home/your_username/some_directory | sort -rh | head
Then clean up responsibly.
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.
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 sdc 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 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.
Partitions named data1,…,datan 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
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).
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.
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.
Comments and suggestions to improve this guide are welcome.