Scientific analysis servers

Intro  

The scientific analysis (sci) servers are provided for general purpose use by all users with the jasmin-login access role. The sci servers are not directly accessible outside the firewall of the STFC network (JASMIN’s host organisation) so most* users will need to access them via a login server.

Users inside the STFC network (e.g. STFC staff on site, or remotely using the STFC VPN) should be able to access them directly.

Available sci servers  

The following sci servers are available:

Server name	Virtual/Physical	Processor model	CPU Cores	RAM (GB)	/tmp max per user	/tmp size	slurm cluster
sci-vm-01	virtual	Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz	8	32 GB	512 MB	80 GB virtual disk	new
sci-vm-02	virtual	Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz	8	32 GB	512 MB	80 GB virtual disk	new
sci-vm-03	virtual	Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz	8	32 GB	512 MB	80 GB virtual disk	new
sci-vm-04	virtual	Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz	8	32 GB	512 MB	80 GB virtual disk	new
sci-vm-05	virtual	Intel(R) Xeon(R) Gold 6348 CPU @ 2.60GHz	8	32 GB	512 MB	80 GB virtual disk	new
sci-ph-01	physical	AMD EPYC 74F3	48	2 TB	20 GB	2 x 446 GB SATA SSD	new
sci-ph-02	physical	AMD EPYC 74F3	48	2 TB	20 GB	2 x 446 GB SATA SSD	new
sci-ph-03	physical	AMD EPYC 9654	48	1.5 TB	20 GB	480 GB SATA SSD + 800 GB NvMe SSD	new

Notes  

1. Access  

Sci servers are not exposed outside the STFC network, so from external locations you need to access them via a login server.

For users within the STFC network, there is no longer any reverse DNS restriction, so all should be accessible directly within that network without need to go via a login node.

See connecting to a sci server via a login server for some alternative methods of connecting.

2. Physical servers  

Physical servers are actually re-configured nodes within the LOTUS cluster and as such have different a network configuration from the virtual sci servers, with limited outward connectivity.

Outbound internet access (via NAT) is only for HTTP(S), so outbound SSH will not work (to hosts outside of JASMIN) on these machines. This also applies to SSH-based transfer methods (scp, ftp, rsync) which anyway should be done instead on a transfer server. If you try to git pull/clone from external repositories e.g. Github using ssh, the operation will timeout with error fatal: Could not read from remote repository. The solution in this case is to access git pull/clone over HTTPS instead (check the repo for alternative access details).

3. /tmp on VMs  

The local /tmp of the virtual sci servers is not available (N/A) for users as this is used by the VM itself. It also provides no performance advantage as it is not local to the server.

4. Arbiter  

A monitoring utility Arbiter is used across all sci machines to control CPU and memory usage. This utility records the activity on the node, automatically sets limits on the resources available to each user. Users’ processes are thus capped from using excessive resources, and can be slowed or have memory reduced in response to repeated violations.

5. Privileges  

Users are not permitted to execute commands which require administrative privileges. This applies to all hosts in the managed part of JASMIN where users have SSH login access (for example login, nx-login, sci, xfer and hpxfer machines). In other words, the use of su or sudo is not permitted. Please be careful when typing commands, particularly if you have multiple terminal windows open on your own computer, that you do not accidentally attempt sudo on a JASMIN machine: expect some follow-up from the JASMIN team if you do!

See also software installed, below.

Purpose  

Scientific analysis servers are designed for interactive and ad-hoc analysis of data in group workspaces, the CEDA archive, and users’ home directories. For long-running and resource-intensive jobs, users are required to use the LOTUS cluster which offers better I/O performance, parallelism, and fair-share scheduling.

The following guidelines should be considered when using the scientific analysis servers:

• Check available resources before your process starts and choose a sci server that is suitable (check average load in the list displayed at the login screen on the login servers, or by using the Linux monitoring commands: top, or free -h )
• Execution/processing time should be less than 1 hour
• Serial jobs only
• High memory jobs should be executed on the physical servers which have more memory (labelled P in above table).
• Monitor your process on a sci server using top or ps Linux commands
• Report if there is a user’s process affecting the performance of a scientific server

Software installed  

Each sci server has the following features:

• Rocky 9 operating system with development tools.
• Software packages that make up the JASMIN Analysis Platform are all installed - providing commonly-used open-source analysis tools. These packages include NCO, CDO, Python (with netCDF4, matplotlib, numpy etc.,) and R.
• Access to proprietary tools, e.g. IDL and Intel Fortran, through the module system.
• Editors: emacs, vim, nedit, geany and nano are installed.
• For a more richly-featured editor or Integrated Development Environment (IDE), consider using a remote editor locally, for example VSCode  or PyCharm  : these can be installed and customised on your own machine rather than needing central installation and management on JASMIN. Watch this space for further advice about how to configure and use VSCode in this way.
• Ability to run graphical applications: use the NX graphical desktop service for best performance.

See [Note 4] above about privileges: you can only install software for yourself if it can be done with user-level privileges.

Access to storage  

Each sci server has:

• Access to the LOTUS /work/scratch-pw* and /work/scratch-nopw2 volumes.
• Read access to the CEDA Archive according to permissions on your CEDA account.
• Read/Write access to Group Workspaces according to membership.