Thomas is the UK National Tier 2 High Performance Computing Hub in Materials and Molecular Modelling.
Thomas end of life
The Thomas cluster is being retired. Notable dates are:
- Monday 1 March 2021: Job submission will be switched off this morning. Jobs already in the queue may still run. Access to the login nodes will remain for one month so you can retrieve data.
- Friday 5 March 2021: Queues will be drained. Any jobs left will never run.
- Thursday 1 April 2021: Access to the login nodes will be removed and all data will be deleted.
Thomas has now been retired as an MMM Hub machine. A portion of Thomas is running for UCL users only until the end of 2021.
7 June 2021: Thomas is now inside the UCL firewall, use VPN, Socrates or ssh.rc.ucl.ac.uk to access.
Applying for an account§
UCL users can contact David Scanlon or Scott Woodley for access to the post-retirement portion of Thomas.
Thomas accounts belong to you as an individual and are applied for through your own institution's Point of Contact. You will need to supply an SSH public key, which is the only method used to log in.
Creating an ssh key pair§
An ssh key consists of a public and a private part, typically named
id_rsa.pub by default. The public part is what we need. You
must not share your private key with anyone else. You can copy it onto
multiple machines belonging to you so you can log in from all of them
(or you can have a separate pair for each machine).
Creating an ssh key in Linux/Unix/Mac OS X§
ssh-keygen -t rsa
The defaults should give you a reasonable key. If you prefer to use ed25519 instead, and/or longer keys, you can. You can also tell it to create one with a different name, so it doesn't overwrite any existing key.
- Do not use DSA as OpenSSH 7.0 has deprecated it and does not use it by default on client or server. We no longer accept DSA keys.
You will be asked to add a passphrase for your key. A blank passphrase is not recommended; if you use one please make sure that no one else ever has access to your local computer account. How often you are asked for a passphrase depends on how long your local ssh agent keeps it.
You may need to run
ssh-add to add the key to your agent so you can
use it. If you aren't sure what keys your agent can see, running
ssh-add -L will show all the public parts of the keys it is aware of.
Creating an ssh key in Windows§
Have a look at Key-Based SSH Logins With PuTTY which has step-by-step instructions. You can choose whether to use Pageant or not to manage your key. You can again pick RSA, ED25519, ECDSA etc but do not pick SSH-1 as that is a very old and insecure key type. As above, DSA is no longer accepted. The key must be at least 2048-bit.
If you are using Windows 10, then you probably have OpenSSH installed and could instead run ssh-keygen in a terminal per the Linux instructions and use the ssh command to log in instead of PuTTY.
Information for Points of Contact§
Points of Contact have some tools they can use to manage users and allocations, documented at MMM Points of Contact.
You will be assigned a personal username and your SSH key pair will be
used to log in. External users will have a username in the form
xxxx is a number) and UCL users will use their central username.
You ssh directly to:
From inside the UCL VPN you can ssh directly into the above but from outside you can do the following:
ssh -o ProxyJump=<UCL_user_ID>@socrates.ucl.ac.uk <thomas_user_ID>@thomas.rc.ucl.ac.uk
Idle ssh sessions will be disconnected after 7 days.
Using the system§
Thomas is a batch system. The login nodes allow you to manage your files, compile code and submit jobs. Very short (\<15mins) and non-resource-intensive software tests can be run on the login nodes, but anything more should be submitted as a job.
Full user guide§
Thomas has the same user environment as RC Support's other clusters, so the User guide is relevant and is a good starting point for further information about how the environment works. Any variations that Thomas has should be listed on this page.
Submitting a job§
Jobs no longer need to specify what type of job it is (Gold, Free, Test) or the project it is being submitted for. (See Budgets and allocations below.)
Note: the memory you request is always per core, not the total amount. If you ask for 128GB RAM and 24 cores, that will run on 24 nodes using only one core per node. This allows you to have sparse process placement when you do actually need that much RAM per process.
Monitoring a job§
In addition to qstat,
$JOB_ID can be useful to see what proportion of cpu/memory/swap is
being used on the nodes a certain job is running on.
qexplain $JOB_ID will show you the full error for a job that is in
As well as
nodesforjob, there are the following utilities which can
help you find information about your jobs after they have run.
jobhist- shows your job history for the last 24hrs by default, including start and end times and the head node it ran on. You can view a longer history by specifying
scriptfor $JOB_ID- show the script that was submitted for the given job.
Thomas mounts the RC Systems software stack.
Have a look at Software Guides for specific information on running some applications, including example scripts. The list there is not exhaustive.
Access to software is managed through the use of modules.
module availshows all modules available.
module listshows modules currently loaded.
Access to licensed software may vary based on your host institution and project.
Requesting software installs§
To request software installs, email us at the support address below or open an issue on our GitHub. You can see what software has already been requested in the Github issues and can add a comment if you're also interested in something already requested.
Installing your own software§
You may install software in your own space. Please look at Compiling for tips.
Maintaining a piece of software for a group§
It is possible for people to be given central areas to install software that they wish to make available to everyone or to a select group - generally because they are the developers or if they wish to use multiple versions or developer versions. The people given install access would then be responsible for managing and maintaining these installs.
Reserved application groups exist for software that requires them. The
group name will begin with
lg. After we add you to one of
these groups, the central group change will happen overnight. You can
check your groups with the
Please let us know your username when you ask to be added to a group.
- CASTEP: You/your group leader need to have
signed up for a CASTEP license.
Send us an acceptance email, or we can ask them to verify you have a
license. You will then be added to the reserved application group
lgcastep. If you are a member of UKCP you are already covered by a license and just need to tell us when you request access.
- CRYSTAL: You/your group leader need to have signed up for an
Academic license. Crystal Solutions will send an email saying an
account has been upgraded to "Academic UK" - forward that to us
along with confirmation from the group leader that you should be in
their group. You will be added to the
- DL_POLY: has individual licenses for specific versions.
Sign up at DL_POLY's website
and send us the acceptance email they give you. We will add you to
the appropriate version's reserved application group, eg
- Gaussian: not currently accessible for non-UCL institutions. UCL having a site license and another institute having a site license does not allow users from the other institute to run Gaussian on UCL-owned hardware.
- VASP: When you request access you need to send us the email
address you are named on a VASP license using. You can also send
name and email of the main VASP license holder along with the license
number if you wish. We will then check in the VASP portal if we can
add you. We will add you to the
legvasp6reserved application groups depending on which versions you are licensed for. You may also install your own copy in your home, and we provide a simple build script on Github (tested with VASP 5.4.4, no patches). You need to download the VASP source code and then you can run the script following the instructions at the top.
- Molpro: Only UCL users are licensed to use our central copy and
can request to be added to the
lgmolproreserved application group.
Suggested job sizes§
The target job sizes for Thomas are 48-120 cores (2-5 nodes). Jobs larger than this may have a longer queue time and are better suited to ARCHER, and single node jobs may be more suited to your local facilities.
Maximum job resources§
On Thomas, interactive sessions using qrsh have the same wallclock limit as other jobs.
Nodes in Thomas are 24 cores, 128G RAM. The default maximum jobsize is 864 cores, to remain within the 36-node 1:1 nonblocking interconnect zones.
Jobs on Thomas do not share nodes. This means that if you request less than 24 cores, your job is still taking up an entire node and no other jobs can run on it, but some of the cores are idle. Whenever possible, request a number of cores that is a multiple of 24 for full usage of your nodes.
There is a superqueue for use in exceptional circumstances that will allow access to a larger number of cores outside the nonblocking interconnect zones, going across the 3:1 interconnect between blocks. A third of each CU is accessible this way, roughly approximating a 1:1 connection. Access to the superqueue for larger jobs must be applied for: contact the support address below for details.
Some normal multi-node jobs will use the superqueue - this is to make it easier for larger jobs to be scheduled, as otherwise they can have very long waits if every CU is half full.
On Thomas, users do not submit directly to queues - the scheduler assigns your job to one based on the resources it requested. The queues have somewhat unorthodox names as they are only used internally, and do not directly map to particular job types.
Preventing a job from running cross-CU§
If your job must run within a single CU, you can request the parallel environment as
-pe wss instead of
-pe mpi (
wss standing for 'wants single switch'). This will increase your queue times. It is suggested you only do this for benchmarking or if performance is being greatly affected by running in the superqueue.
Thomas has one type of node.
|Type||Cores per node||RAM per node||tmpfs||Nodes|
Here are the processors each node type has:
- K: Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
(If you ever need to check this, you can include
cat /proc/cpuinfo in your jobscript so
you get it in your job's .o file for the exact node your job ran on. You will get an entry
for every core).
Quotas were enabled on Thomas on 29 May 2019. You have one per-user quota, with a default amount of 250GB - this is the total across home and Scratch.
lquotashows you your quota and total usage (twice).
request_quotais how you request a quota increase.
If you go over quota, you will no longer be able to create new files and your jobs will fail as they cannot write.
Quota increases may be granted without further approval, depending on size and how full the filesystem is. Otherwise they may need to go to the Thomas User Group for approval.
Budgets and allocations§
There is no more Gold on Thomas. Jobs should now be submitted without specifying
-A entries in your jobscript.
1 Gold unit is 1 hour of using 1 processor core.
Troubleshooting: Unable to verify membership in project / Uninitialized value§
Unable to run job: Rejected by policyjsv Reason:Unable to verify sufficient material worth to submit this job: Unable to verify membership of mmmxxxx in the UCL_Example project
This error from
qsub can mean that you aren't in the project you are trying to
submit to, but also happens when the Gold daemon is not running.
-A lines from your jobscript and submit jobs without any
Use of uninitialized value in print at /opt/gold/bin/mybalance line 60, <GBALANCE> line 1. Failed sending message: (Unable to connect to socket (Connection refused)).
The Gold database is uncontactable.
-A lines from your jobscript and submit jobs without any
The Tier 2 SAFE§
SAFE is a service administration platform used by ARCHER and various of the Tier 2 sites. As a user, you can use it to do some management of your details and view your usage across all systems that send data to SAFE.
See your usage data in SAFE§
If you wish, you can claim your Thomas account as belonging to you in the Tier 2 SAFE. This lets you view some individual usage reports, and if you have other Tier 2 accounts that also use SAFE, you use the same login information.
- You need to login at https://safe.epcc.ed.ac.uk or create a new Tier2 SAFE account if you do not have one.
- If creating a new account, you will be asked to create a password - this is for the SAFE login only and has no link to your Thomas account.
- On Thomas, run
hashclaim. This will give you a link to claim your Thomas username's usage data.
- Visit this link when logged in to SAFE and it will tell you this account has been added to your SAFE account, and username@Thomas will now be visible in the 'Login accounts' menu at the top.
- Choosing that account will take you to a page where you can view your individual usage reports.
If you do not claim your account, then SAFE only contains username/job usage information with no information about who owns that username. Points of Contact can use it to allocate Gold to your budgets.
Update your SSH key via SAFE§
SAFE also gives you a second mechanism for changing your SSH key - changing the key you have associated with your SAFE account will automatically create a request for us to add that key to your Thomas account. (We still need to act on it, so it won't update immediately).
Email email@example.com with any support queries. It will be helpful to include Thomas in the subject along with some descriptive text about the type of problem, and you should mention your username in the body.
EPSRC contributed to the hardware, so there are two numbers to use for notional costs:
- Cost per core hour excluding hardware (to be charged on EPSRC grants): 0.6 pence / core hour
- Cost per core hour including hardware cost (to be charged on non-EPSRC grants): 1.5 pence / core hour
Non-grant-funded projects should use the second figure.
Acknowledging the use of Thomas in publications§
All work arising from this facility should be properly acknowledged in presentations and papers with the following text:
"We are grateful to the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1 and EP/T022213/1)"
When publishing work that benefited from resources allocated by the MCC: please include the following acknowledgment:
"Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the UK Materials and Molecular Modelling Hub for computational resources, MMM Hub, which is partially funded by EPSRC (EP/P020194 and EP/T022213)"
When publishing work that benefited from resources allocated by UKCP, please include:
"We are grateful for computational support from the UK Materials and Molecular Modelling Hub, which is partially funded by EPSRC (EP/P020194 and EP/T022213), for which access was obtained via the UKCP consortium and funded by EPSRC grant ref EP/P022561/1"