Computer Cluster for Analysis of Data from SLS and SwissFEL Facilities
The official cluster name is Ra and the cluster will be referenced below by this name.
Current status - Planned maintenance
Current status: OPERATIONAL
Schedule of maintenance: See table
|2020-04-27 08:00||2020-04-27 17:00||ra-l-001||update (OS, Nomachine, OFED, GPFS)|
|2020-04-29 08:00||2020-04-29 17:00||ra-l-002||update (OS, Nomachine, OFED, GPFS)|
To be able to use Ra cluster you need :
- PSI account
- authorisation to use the Ra cluster.
If you don't have PSI account, please follow this procedure
Authorisation for the Ra cluster
Please contact your beamline manager and provide the following information:
- your PSI account
- data identifier (Proposal ID or e-account used to collect the data) for the data you need to access.
Getting Connection to Ra Cluster
The names of the login nodes are
From the PSI subnet, you can connect to login nodes directly via ssh or with NoMachine using
ra-nx.psi.ch as target host. From outside the PSI subnet, you may use one of the two way for a remote access to Ra cluster:
Option one: connect to the hop.psi.ch system and from there go via ssh to the one of the Ra login node
$ ssh <PSI_account>@hop.psi.ch $ Password: <password> AFTER login $ssh ra-l-003.psi.ch $ Password: <password>
For further details see
Option two: (recommended) NoMachine Connection via Remote Access Server
Please follow these instructions
- Set the display preferences of the NoMachine (
"Resize remote screen". This will provide a better default resolution matching your monitor to the remote desktop on the Ra login node.
- In case of heavy graphic application try to run it prepending vglrun before the application name. See yourself the difference by running "
glxgears" vs. "
- If a NoMachine sessions is not being accessed for 5 days it gets automatically terminated.
Login nodes usage limits
Login nodes are the entry point to the Ra cluster and they are the common place for every user. For this reason please avoid to overload the login nodes with CPU or memory intensive job, since for that ones the batch system should be used instead.
Currently a limit of 100GB maxmimum memory usage per user is enforced.
There are several file systems for different purposes on the Ra cluster:
|File system||Path||Default Quota||Access rights||Access mode||Used for|
|HOME||/mnt/das-gpfs/home/$USER||5 GB||user only||read-write||user home directory, code, private data, etc.|
|SLS raw data||/sls/$BEAMLINE||-||the PI* group only||read-only||SLS data|
|work data||/das/work/$PGR/$PGROUP||4 TB||the PI* group only||read-write||derived data|
*) PI -- principal investigator or Main Proposer
/sls/X06SA/Data10/e15874 # contains the raw data for the PI group 15874 /das/work/p15/p15874 # contains the derived data for the PI group 15874
To see the group members for a given group use the getent group command, e.g.:
getent group p15874
To check the quota for home, use homequota command being on one of the login node:
The p-groups inside the work area are split between the so called internal and external area. The default quota per p-group only applies to the external p-groups. The internal ones are members of one and only one unit, that provides a certain amount of space on the work area to all its p-groups. The p-group of a unit don't have a default quota so a single p-group could fill up all the space on the work area for its unit.
To see to which unit a pgroup is member of and if is internal or external:
[talamo_i@ra-l-002 ~]$ /das/support/users/space_usage/pgroup_info p17277 Name: p17277 Unit: tomcat Kind: internal Used: 63 GB Members: ozerov_d,talamo_i,gsell Unit quota: 500 TB
Files permission and ownership
All files inside a specific p-group directory are considered to be owned by the specific pgroup, meaning that the unix group of the files should be the p-group and that the group should have read-write access, ie. all its members have read-write access. For this reason a regular process checks the files permission and ownership and fixes them.
The fix happens automatically every hour, but in case you would need to change permission/ownership sooner, you can run the following commands for a file:
chmod g+w file chgrp your-p-group file
And in case you want to do it recursively on a directory:
chmod -R g+ws dir chgrp -R your-p-group dir
The data analysis and advanced development software is available via PSI Environment Modules (Pmodules) system. Use the following commands to manage your environment:
module list # show the loaded modules module avail # show the available modules module search # show all modules in hierarchy module help # if you do not remember what to do module add module_name # add module_name module rm module_name # remove module_name
module load matlab/2015b # load Matlab 2015b
There are MX-beamline specific environment configuration files in the
/etc/scripts/mx_sls.sh- the default configuration for the analysis of SLS data
/etc/scripts/mx_fel.sh- the default configuration for the analysis of data from FEL sources
Source the corresponding configuration file to use the predefined settings, for example:
The environment settings done with the module are effective only in the current shell and all its children processes.
You may wish to edit the
.bashrc file in home directory to make permanent changes of your environment: see the comments therein for more details.
The list of the available software includes: Matlab, python, intel and gcc compilers, Fiji, standard MX software like xds, shelx, hkl2map, adxv, CBFlib, ccp4, dials, mosflm, phenix, software used for serial crystallography like crystfel, cheetah .... For the complete list use the following commands:
module use unstable module avail
The Ra login node should be used mainly for development, small and quick tests, and work with the graphical applications.
For CPU intensive work, the compute nodes must be used. There are presently 48 computing nodes in the cluster, each with 256GB of RAM, InfiniBand interconnect, and 10GbE network.
|Computing node||Processor on each node||Number of cores on each node|
|c-001..016||2xIntel Xeon E5-2690v3 (2.60 GHz)||24 (2x12)|
|c-017..032||2xIntel Xeon E5-2697Av4 (2.60 GHz)||32 (2x16)|
|c-033..048||2xIntel Xeon(R) Gold 6140 (2.30GHz )||36 (2x18)|
Access to the compute nodes is controlled by Slurm, a modern workload manager for Linux clusters. You can allocate compute node for interactive use or submit batch jobs using Slurm.
sinfo # view information about Slurm nodes, in particular, idle (free) nodes squeue # view information about jobs in the scheduling queue (useful to find your nodes) salloc # request a job allocation (a set of nodes) for further use srun # allocate compute nodes and run a command inside the allocated nodes sbatch # submit a batch script
The present Slurm configuration at Ra implements two modes of allocation of the resources on the computing node: a) "shared" allocation (partition "shared"): your job will share computing resources with other jobs on the node; b)the "whole node" allocation (partitions "day" and "week"): you will have an exclusive access to the allocated compute nodes (not shared with the other users) within the requested time limits. By default (if you don't specify the partition name) jobs land on the "shared" partition.
|Partition name||shared/exclusive access to computing node||default allocation time||maximum allocation time|
|default||shared||shared||1 hour||8 days|
|hour||exclusive||1 hour||1 hour|
|day||exclusive||8 hours||24 hours|
|week||exclusive||2 days||8 days|
sbatch job.sh # to submit job to the default partition, with allocation time of 1 hour sbatch -p week job.sh # to submit to the partition with longer allocation time (2 days if not specified) sbatch -p week -t 4-5:30:00 job.sh # to submit job with time limit of 4 days, 5 hours and 30 minutes (max. allowed time limit is 8 days)
When the time limit is reached, all the unfinished process will be killed.
Please, do not forget to release the resources you do not need any more, otherwise they will remain unavailable to other users until your allocation expires. Holding on idle nodes will have negative impact on the scheduling priority of your future jobs. The priority of your future Slurm jobs depends on your past usage according to the fair share mechanism.
For interactive use of Ra cluster one can use jupyter notebooks as well.
More examples and details how to use Slurm on Ra cluster, you will find in the Ra help pages.
User Mailing List
To receive announcements about the cluster (downtime, changes in the resource policy etc.) please subscribe to the mailing list
For any problem or further information please contact: firstname.lastname@example.org
NoMachine connection to Ra
From PSI subnet and using PSI-VPN, one need to use ra-nx as target for NoMachine connection, to reduce load on VPN and network infrastructure.
rem-acc is accessible from PSI subnet, but not from PSI-VPN.
My heavy graphical application (coot for example) runs slow via NoMachine
Try to reduce in your NoMachine client settings (
Ctrl+Alt+0, then "Display", then "Settings") the resolution to find a compromise between speed, comfort and network latency
More detailed documentation on use of slurm on Ra, description of NoMachine setup is available in the internal PSI page (accessible from PSI subnet, PSI-VPN or in the NoMachine session (Ra help))