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MMM Hub Young

Young is the UK National Tier 2 High Performance Computing Hub in Materials and Molecular Modelling, and replacement for Thomas. Young went into pilot on 3 Aug 2020.

Applying for an account§

Young 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 and 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.

Logging in§

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 mmmxxxx (where xxxx is a number) and UCL users will use their central username.

You ssh directly to:

young.rc.ucl.ac.uk

SSH timeouts§

Idle ssh sessions will be disconnected after 7 days.

Using the system§

Young 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§

Young 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 Young has should be listed on this page.

Submitting a job§

Create a jobscript for non-interactive use and submit your jobscript using qsub. Jobscripts must begin #!/bin/bash -l in order to run as a login shell and get your login environment and modules.

A job on Young must also specify what type of job it is (Gold, Free, Test) and the project it is being submitted for. (See Budgets and allocations below.)

Memory requests§

Note: the memory you request is always per core, not the total amount. If you ask for 192GB RAM and 40 cores, that may run on 40 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.

Young also has high memory nodes, where a job like this may run.

Monitoring a job§

In addition to qstat, nodesforjob $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 Eqw status.

Useful utilities§

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 --hours=100 for example.
  • scriptfor $JOB_ID - show the script that was submitted for the given job.

These utilities live in GitHub at https://github.com/UCL-RITS/go-clustertools and https://github.com/UCL-RITS/rcps-cluster-scripts

Software§

Young 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 avail shows all modules available.
  • module list shows modules currently loaded.

Access to licensed software may vary based on your host institution and project.

Loading and unloading modules§

Young has a newer version of modulecmd which tries to manage module dependencies automatically by loading or unloading prerequisites for you whenever possible.

If you get an error like this:

[uccaxxx@login01 ~]$ module unload compilers mpi
Unloading compilers/intel/2018/update3
  ERROR: compilers/intel/2018/update3 cannot be unloaded due to a prereq.
    HINT: Might try "module unload default-modules/2018" first.

Unloading mpi/intel/2018/update3/intel
  ERROR: mpi/intel/2018/update3/intel cannot be unloaded due to a prereq.
    HINT: Might try "module unload default-modules/2018" first.

You can use the -f option to force the module change. It will carry it out and warn you about modules it thinks are dependent.

[uccaxxx@login01 ~]$ module unload -f compilers mpi
Unloading compilers/intel/2018/update3
  WARNING: Dependent default-modules/2018 is loaded

Unloading mpi/intel/2018/update3/intel
  WARNING: Dependent default-modules/2018 is loaded

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.

Licensed software§

Reserved application groups exist for software that requires them. The group name will begin with leg or lg. After we add you to one of these groups, the central group change will happen overnight. You can check your groups with the groups command.

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 legcryst group.
  • 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 lgdlp408.
  • 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 legvasp5 or legvasp6 reserved 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 lgmolpro reserved application group.

Suggested job sizes§

The target job sizes for Young are 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§

Cores Max wallclock
5120 48hrs

These are numbers of physical cores: multiply by two for virtual cores with hyperthreads.

On Young, interactive sessions using qrsh have the same wallclock limit as other jobs.

Jobs on Young do not share nodes. This means that if you request less than 40 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 40 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 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.

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.

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Node types§

Young has three types of node: standard nodes, big memory nodes, and really big memory nodes. Note those last have only 36 cores per node, not 40.

Type Cores per node RAM per node tmpfs Nodes Memory request necessary
C 40 192G None 576 Any
Y 40 1.5T None 3 mpi: mem >=19G, smp: >186G total
Z 36 3.0T None 3 mpi: mem >=42G, smp: >1530G total

These are numbers of physical cores: multiply by two for virtual cores with hyperthreading.

The 'memory request necessary' column shows what memory requests a job needs to make to be eligible for that node type. For MPI jobs it looks at the memory per slot requested. For SMP jobs they will go on the node that their total memory request (slots * mem) fits on.

Here are the processors each node type has:

  • C: Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz
  • Y: Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz
  • Z: Intel(R) Xeon(R) Gold 6240M CPU @ 2.60GHz

(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).

Restricting to one node type§

The scheduler will schedule your job on the relevant nodetype based on the resources you request, but if you really need to specify the nodetype yourself, use:

# Only run on Z-type nodes
#$ -ac allow=Z

Hyperthreading§

Young has hyperthreading enabled and you can choose on a per-job basis whether you want to use it.

Hyperthreading lets you use two virtual cores instead of one physical core - some programs can take advantage of this.

If you do not ask for hyperthreading, your job only uses one thread per core as normal.

# request hyperthreading in this job
#$ -l threads=1

# request the number of virtual cores
#$ -pe mpi 160

# request 2G RAM per virtual core
#$ -l mem=2G

# set number of OpenMP threads being used per MPI process
export OMP_NUM_THREADS=2

This job would be using 80 physical cores, using 80 MPI processes each of which would create two threads (on Hyperthreads).

Note that memory requests are now per virtual core with hyperthreading enabled. If you asked for #$ -l mem=4Gon a node with 80 virtual cores and 192G RAM then you are requiring 320G RAM in total which will not fit on that node and so you would be given a sparse process layout across more nodes to meet this requirement.

# request hyperthreading in this job
#$ -l threads=1

# request the number of virtual cores
#$ -pe mpi 160

# request 2G RAM per virtual core
#$ -l mem=2G

# set number of OpenMP threads being used per MPI process
# (a whole node's worth)
export OMP_NUM_THREADS=80

This job would still be using 80 physical cores, but would use one MPI process per node which would create 80 threads on the node (on Hyperthreads).

Diskless nodes§

Young nodes are diskless (have no local hard drives) - there is no $TMPDIR available, so you should not request -l tmpfs=10G in your jobscripts or your job will be rejected at submit time.

If you need temporary space, you should use somewhere in your Scratch.

Disk quotas§

You have one per-user quota, with a default amount of 250GB - this is the total across home and Scratch.

  • lquota shows you your quota and total usage (twice).
  • request_quota is 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 MMM Hub User Group for approval.

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Budgets and allocations§

We have enabled Gold for allocation management. Jobs that are run under a project budget have higher priority than free non-budgeted jobs. All jobs need to specify what project they belong to, whether they are paid or free.

To see the name of your project(s) and how much allocation that budget has, run the command budgets.

budgets  
Project  Machines Balance   
-------- -------- --------  
UCL_Test ANY      22781.89

Pilot users temporarily have access to a project for their institution, eg. Imperial_pilot. These will be deactivated after the pilot and no longer show up.

Info

1 Gold unit is 1 hour of using 1 virtual processor core (= 0.5 physical core).

Since Young has hyperthreading, a job asking for 40 physical cores and one asking for 80 virtual cores with hyperthreading on both cost the same amount: 80 Gold.

Subprojects§

You might be in a subproject that does not itself have an allocation, but instead takes allocation from a different project:

Project       Machines Balance
--------      -------- --------
UCL_physM        ANY   474999.70  
UCL_physM_Bowler ANY        0.00

In this case, you submit jobs using the subproject (UCL_physM_Bowler here) even though it says it has 0 budget and it takes Gold from the superproject.

Submitting a job under a project§

To submit a paid job that will take Gold from a particular project budget, add this to your jobscript:

#$ -P Gold
#$ -A MyProject

To submit a free job that will not use up any Gold, use this instead:

#$ -P Free
#$ -A MyProject

You can also submit testing jobs that will not use up any Gold, and will have higher priority than normal free jobs, but are limited to 2 nodes (80 cores) and 1 hour of walltime:

#$ -P Test
#$ -A MyProject

Troubleshooting: Unable to verify membership in policyjsv project§

Unable to run job: Rejected by policyjsv
Unable to verify membership of `<username>` in the policyjsv project

You asked for a Free job but didn't specify #$ -A MyProject in your jobscript.

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.

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)).

If you also get this error from the budgets command, then the Gold daemon is definitely not running and you should contact rc-support.

Gold charging§

When you submit a job, it will reserve the total number of core hours that the job script is asking for. When the job ends, the Gold will move from 'reserved' into charged. If the job doesn't run for the full time it asked for, the unused reserved portion will be refunded after the job ends. You cannot submit a job that you do not have the budget to run.

Troubleshooting: Unable to verify sufficient material worth§

Unable to run job: Rejected by policyjsv
Reason:Unable to verify sufficient material worth to submit this job:
Insufficient balance to reserve job

This means you don't have enough Gold to cover the cores ⨉ wallclock time cost of the job you are trying to submit. You need to wait for queued jobs to finish and return unused Gold to your project, or submit a smaller/shorter job. Note that array jobs have to cover the whole cost of all the tasks at submit time.

Job deletion§

If you qdel a submitted Gold job, the reserved Gold will be made available again. This is done by a cron job that runs every 15 minutes, so you may not see it back instantly.

Reporting Gold usage§

There are a few commands that everyone can run that report Gold usage for their entire project, broken down by user. See Reporting from Gold.

Support§

Email rc-support@ucl.ac.uk with any support queries. It will be helpful to include Young in the subject along with some descriptive text about the type of problem, and you should mention your username in the body.

Acknowledging the use of Young 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)"

MCC§

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)"

UKCP§

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"