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M&CS big memory compute (mastodont)

Documentation by M&CS

This section of the documentation is maintained by M&CS. For suggestions to these pages, please contact Hub MetaForum.

Introduction

mastodont.win.tue.nl is a Linux system designed to support long-running computations that require a large amount of RAM. It was not designed to support CPU-bound or parallel computations. For such computations, please consider the HPC cluster . The mastodont server is not part of a cluster.

Documentation

Technical specifications

Resource Specification
CPU 4 x Intel(R) Xeon(R) Gold 6136 CPU @ 3.00GHz (96 processors)
RAM 3 TB (3169407968 KB)
Storage swap space: 4 x 2.9 TB (SSD, equal priority, parallel)
/home: 50 GB SSD in RAID 1
/scratch: 33 TB HDD in RAID 6

Operating system

mastodont runs Ubuntu Server 20.04 LTS.

For security reasons, users will not be granted root permissions. Software is installed and upgraded by LIS-CSS, see also the section below.

Security updates are applied automatically every night. Reboots only happen after communication with users, so as not to disturb long-running processes.

User accounts

To get access to mastodont, please contact Hub MetaForum and also contact the key user of the system (see this page). The FSA cluster is the biggest consumer of the machine and can help determine when and whether there is capacity available on the machine for your research.

For security reasons, SSH access is only allowed from the campus or VPN (vpn2 and vpn3 both have access to the machine). Login using SSH with your TU/e user name and password. It is highly recommended that you setup and use public key authentication.

User account names starting with a digit

Starting with Ubuntu 20, obstacles were raised by the service manager systemd for user names starting with a digit. These usernames violate the default NAME_REGEX on Ubuntu systems ("^[a-z][-a-z0-9]*\$"), but these usernames were already introduced at TU/e (as part of central IAM - identity and access management) before systemd introduced these obstacles.

Relevant obstacles are mentioned below:

  • The obstacles mostly concern desktop applications that you will probably not use on mastodont. Such applications will complain that they cannot connect to the dbus.

  • In case you are working with uid/gid (for example in order to set the owner of a file using chown), this can cause some confusion.
    You can enforce interpretation as those IDs by prepending the IDs with a +. This is relevant if the uid overlaps with an existing username.

  • The environment variable XDG_RUNTIME_DIR will not be set. $XDG_RUNTIME_DIR will normally point to the process environment directory. Typically, it is set to /run/user/[uid], but this fails for numeric user IDs. This may concern applications that you do use on mastodont.
    Sometimes this can be resolved by setting this variable in your .bashrc.

Disk space

All disk space is local, not shared with other systems.

Data transfer to/from other data solutions

On this page, some tips can be found on how to transfer data to and from TU/e long-term data solutions.

Path Storage space Purpose
/home/[username] 50 GB (shared with all users) Your home directory
Mostly intended for configuration files. We do not provide a backup service, so keep your files safe elsewhere. Disk space is limited, and quota are not enforced; please be considerate of other users and keep your use as limited as possible.
/scratch 33 TB (shared with all users) Scratch space for temporary files
Use it for files you can afford to lose. We reserve the right to clean it up when required! There is plenty of disk space, but please be considerate of other users and regularly remove files you no longer need.

No backup

There is no backup service available for home directories. Please check the Storage Finder for available options to store your data for long term!

Disk error protection is provided by the RAID levels as mentioned in the Hardware specifications section. Note that this does not protect against disk controller failures.

Software

To obtain a list of available software packages and versions, please log in to the machine and run apt list --installed. This list is not documented here because of the volatile nature of a package list. However, you can expect common software tools to be available. In case you want to know if a specific package is available, please contact the key user (see this page).

Packages from the Ubuntu repositories can be installed by submitting a request through TOPdesk SSP. LIS-CSS will check the requested packages for security and side-effects for other users and install them if there are no issues. Sometimes this review may take longer, for example in case the key user or the Security Operations team needs to be contacted.