Maris is a small computational cluster at the Lorentz Institute, financed by external research grants. Access is primarily for those research groups who have purchased the machines, but there may well be computing time available for others. If you would like to use the Maris cluster, please get in touch with the local contact persons at the Lorentz Institute to see what resources can be made available for your needs. You can then request access by sending an email to Carlo Beenakker.

The cluster is optimised for multithreading applications and embarrassingly parallel problems.

Once you have been granted access to the cluster, you must login on to its head node to access it. Whitin the IL network, Maris' head node is reachable at novamaris.lorentz.leidenuniv.nl or trough its aliases maris and mariscluster. For connections from outside the IL network, an ssh tunnel into the IL ssh server (styx.lorentz.leidenuniv.nl) is needed.

Note that ssh.lorentz.leidenuniv.nl is an alias of styx.

Direct ssh access to any computation node is disabled. To open an interactive session to one of the nodes use for example

srun <whatever srun options you'd like> --pty bash

Any calculation must be submitted to slurm for execution. If not, the associated process will be terminated without any notice.

A summary of the current cluster load/usage is available on here (only within the IL network).

Maris' head node and nodes run the GNU/Linux OS Fedora 27. Currently there are seventy-two (73) nodes available for calculations. The latter are organized in groups according to their specs and configuration as the table below shows

Note that the resources allocatable by slurm might be slightly lower to those in the table above because of the resources necessary to run a node's OS.

The nodes have been configured in a similar way to your workstation to maximize productivity although there are substantial differences worth noting. One of these is the home directory. In order to keep the network traffic at a low rate, the /home directory on the Maris cluster is different from the one of your Lorentz GNU/Linux Workstation. In order to access the latter from the head node you can use

cd /lorentz/your_username

In a similar fashion, you can access all data[1,..,n] on each Lorentz Institute workstation using for instance

/net/workstation_name/data1

Also novamaris and all maris nodes mount at boot two storage devices one available under the /clusterdata mount point and the other under /marisdata. The former is an old storage device which will be retired upon failure, the latter is a newly installed (as of 17/05/2016) storage device which you are encouraged to use.

NOTE: Some devices get mounted upon access by autofs. Do not get surprised if the command df does not show the desired output.

Maris home directories are mounted under /home. This is a dedicated 5.5TB storage system which keeps hourly, daily and weekly snapshots of the home disk. Should you need to access one of the snapshots in the event of a lost file, then access the directory .snapshot and recover the file you need, for instance

$ ls /home/.snapshot
daily.2016-05-16_0010  hourly.2016-05-17_0405  hourly.2016-05-17_0605  hourly.2016-05-17_0805  weekly.2016-05-08_0015 daily.2016-05-17_0010  hourly.2016-05-17_0505  hourly.2016-05-17_0705 hourly.2016-05-17_0905  weekly.2016-05-15_0015
$ cd /home/.snapshot/hourly.2016-05-17_0805/<username>

10 GB quotas are enforced on the home disk. Please use /marisdata to temporarily store large datafiles.

Maris has currently two storage disks mounted respectively under /clusterdata and /marisdata.

The plan is to gradually replace /clusterdata with its newer counterpart /marisdata. As of 17/05/2016 you are encouraged to use ONLY /marisdata to store your data because /clusterdata is no longer maintained and all data on it will get permanently lost in case of hardware failure. In fact, you are encouraged to move all data you deem important from /clusterdata to /marisdata as soon as possible. /marisdata has 37TB available.

Please remember that /marisdata is supposed to act as a temporary storage device during your calculations. You are encouraged not to use it as an archive disk.

We try to minimize the differences between your Lorentz workstation and Maris so you can be as productive as possible. A variety of compilers and libraries are available for you to use in a similar fashion to your workstation. Explore which modules are available by typing module avail. For extra information take also a look at this page and read the manual pages: man module.

All calculations must be executed via slurm. A typical pseudo session would look like

ssh into novamaris
write a slurm batch script in which you request all needed computation resources
submit the batch script to slurm for execution

An overview of maris' slurm configuration is given here.

A rough guide to slurm is here.

NOTE that calculations executed outside slurm's control will be terminated without notice.

Maris has a large list of pre-installed python modules available for you to use. Nonetheless, it is possible to install new modules or hack existing ones as long as they are (re)installed in a location for which you have writing credentials. You can find an extensive guide with examples here.

Further readings: virtualenv and conda.

Help with cluster issues can be requested through the helpdesk. It is strongly advised you discuss your problem also with other Maris users because they might have helpful tips. Here follows a list of Lorentz Institute members that could be consulted for tips

* Thomas O'Brien (Office 259, Telephone: 5534)
* IT Support (HL 40[7-9], Telephone:8484)