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OCF User Manual for University of Aberdeen Maxwell HPC Cluster OCF plc. Rotunda Business Centre, Thorncliffe Park, Chapeltown, Sheffield S35 2PG T: 0114 257 2200 F: 0114 257 0022 W: www.ocf.co.uk Company Reg Number: 4132533 VAT Number: GB 780 6803 14

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Page 1: OCF User Manaul - Aberdeen - Maxwell - v0 · 2019. 10. 17. · ô r K & h D v µ o r D Æ Á o o ,W o µ o µ Z } µ ï X ð ^ o µ u W ] ] } v W ] } ] ]

OCF User Manual

for

University of Aberdeen Maxwell HPC Cluster

OCF plc. Rotunda Business Centre, Thorncliffe Park, Chapeltown, Sheffield S35 2PG T: 0114 257 2200 F: 0114 257 0022 W: www.ocf.co.uk Company Reg Number: 4132533 VAT Number: GB 780 6803 14

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2

Table of Contents – OCF User Manual – Maxwell HPC Cluster OCF Document Control ................................................................................................................... 4

1.1 Latest ............................................................................................................................................................ 4

1.2 History........................................................................................................................................................... 4

1.3 Notes ............................................................................................................................................................. 4

Cluster Summary ............................................................................................................................ 5

Cluster Resources ........................................................................................................................... 6

3.1 Physical Resources ........................................................................................................................................ 6

3.2 Storage Resources ........................................................................................................................................ 6

3.3 Slurm Resources ........................................................................................................................................... 7

3.4 Slurm Partition Priorities .............................................................................................................................. 8

Cluster Access ................................................................................................................................. 9

4.1 University of Aberdeen Users ..................................................................................................................... 10

Command Line ................................................................................................................................ 10

Graphical ......................................................................................................................................... 12

4.2 National Decommissioning Centre Users ................................................................................................... 13

Command Line ................................................................................................................................ 13

Graphical ......................................................................................................................................... 13

4.3 File Transfers............................................................................................................................................... 14

Standard Linux Utilities ................................................................................................................... 14

WinSCP ............................................................................................................................................ 15

Remote Cluster Access ................................................................................................................... 16

4.3.3.1 Command Line Access .................................................................................................................... 16

4.3.3.2 Graphical ......................................................................................................................................... 17

4.3.3.3 File Transfers ................................................................................................................................... 18

Cluster Applications ...................................................................................................................... 19

5.1 Loadable Applications ................................................................................................................................. 19

5.2 Installed Applications ................................................................................................................................. 19

5.3 Galaxy ......................................................................................................................................................... 21

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Workload Manager - Slurm ........................................................................................................... 23

6.1 Common Slurm Commands ........................................................................................................................ 23

6.2 Common Slurm Parameters ....................................................................................................................... 26

6.3 Submitting Compute Jobs ........................................................................................................................... 27

6.4 Submitting GPU Jobs .................................................................................................................................. 29

Getting Help ................................................................................................................................. 31

Index ............................................................................................................................................ 32

8.1 Tables .......................................................................................................................................................... 32

8.2 Images ......................................................................................................................................................... 32

8.3 Code Samples ............................................................................................................................................. 33

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OCF Document Control

1.1 Latest

Company: University of Aberdeen OCF Deal Number: 4755

Date Submitted: 16/10/2019 Last Updated by: Matthew Brazier

Document Owner: Chris Devine Version No: 0.3

Table 1 - version control - latest

1.2 History

Version Date Author Changes Approved by

0.1 11/10/19 Matthew Brazier Initial version

0.2 15/10/19 Matthew Brazier Add GPU placement table, added support section and corrected a few minor spelling mistakes.

0.3 16/10/19 Matthew Brazier Added remote cluster access sections

Table 2 - version control - history

1.3 Notes

This document will refer to University of Aberdeen as UoA and National Decommissioning Centre as NDC.

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Cluster Summary

The cluster is built up of Lenovo hardware. The cluster has a 10G management backbone and a 100G InfiniBand high speed interconnect between each node. The cluster is accessible using command line or graphical interfaces.

The cluster comprises of 30 nodes with a mixture of different memory capacities. Six nodes are equipped with consumer grade GPUs suitable for single precision workloads and one node is equipped with an enterprise grade GPU optimised for double precision workloads.

Total cluster nodes: 30 nodes comprising of Lenovo ThinkSystem SD530, Lenovo ThinkSystem SR650 and Lenovo ThinkSystem SR850

Total cluster cores: 1240 using Intel Xeon Gold 6138 2.00Ghz processors

Total cluster memory: 10.5T using TruDDR4 2666MHz RDIMM

Total cluster storage: 991T block storage using 8T and 10T 7.2K near line SAS disk drives

Cluster interconnect: Mellanox InfiniBand HDR 100G

High performance shared file system: BeeGFS

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Cluster Resources

3.1 Physical Resources

The cluster has the following computational resources available to users:

Node Type Node Name Cores Useable

Memory

GPU

Resources

High Memory hmem[01-11] 40 (2x Intel Xeon Gold 6138 2.00Ghz) 380G

Consumer GPU cgpu[01-11] 40 (2x Intel Xeon Gold 6138 2.00Ghz) 185G 2 x NVIDIA 2080Ti (12G GPU Memory)

Compute node[01-11] 40 (2x Intel Xeon Gold 6138 2.00Ghz) 185G

Very High Memory vhmem01 80 (4x Intel Xeon Gold 6138 2.00Ghz) 3000G

Enterprise GPU egpu01 40 (2x Intel Xeon Gold 6138 2.00Ghz) 185G 2 x NVIDIA V100

(32G GPU Memory)

Table 3 - cluster resources - physical resources

All nodes are running CentOS 7.61 and have 1 x Mellanox InfiniBand HDR 100G.

3.2 Storage Resources

The cluster has the following storage resources available to users:

User

Organisation

Home Directory Scratch Directory

Storage Limit File Limit Storage Limit File Limit

UoA 64G 200K 1T 200K

NDC 64G 200K 1T 200K

Table 4 - cluster resources - storage resources

Note: These limitations are the defaults on the cluster. Higher limits could be made to specific users with appropriate justification.

1 CentOS 7.6 installed as of 10/10/2019. Operating systems will be updated on a regular basis when updates are stable.

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Cluster Resources

3.3 Slurm Resources

Note: All standard user accounts will have a limit of 200 allocated cores. If this limit is reached jobs will be queued until enough resources are available.

Primary User

Organisation

Slurm

Partition Nodes

Notes

(default)

UoA uoa-compute hmem[01-11]

UoA uoa-gpu cgpu[01-06]

NDC ndc-compute node[01-11]

NDC ndc-gpu egpu01

NDC ndc-hmem vhmem01

UoA spot-compute hmem[01-11]

cgpu[01-11]

node[01-11]

egpu01

vhmem01

Default partition for jobs unless a partition is specified at submission.

UoA spot-gpu egpu01 Active jobs will be requeued if a job submitted to ndc-gpu requires resource.

UoA spot-vhmem vhmem01 Active jobs will be requeued if a job submitted to ndc-hmem requires resource.

UoA uoa-teaching node[01-05] Max nodes per job = 2

Max CPUs per node = 10

Max memory per node = 20G

Users must be a member of “maxwell-users-teach”

Table 5 - cluster resources - Slurm resources

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Cluster Resources

3.4 Slurm Partition Priorities

Slurm partitions are setup with priority tiers allowing a flexible and timely approach to usage of the cluster. Jobs submitted to higher priority tiers will cause lower priority jobs to be re-queued if resources are required to run the higher priority job.

Priority Tier Partitions

6 uoa-teaching

5 ndc-hmem | ndc-compute | ndc-gpu | ocf-benchmark

4 not in use

3 uoa-gpu | uoa-compute

2 spot-gpu | spot-vhmem

1 spot-compute

Table 6 - cluster resources - Slurm partition priorities

[root@maxmgmt1 ~]# sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST uoa-gpu up infinite 6 idle cgpu[01-06] spot-vhmem up infinite 1 mix vhmem01 ndc-gpu up infinite 1 idle egpu01 ndc-hmem up infinite 1 mix vhmem01 ocf-benchmark up infinite 22 idle hmem[01-11],node[01-11] spot-compute* up infinite 1 mix vhmem01 spot-compute* up infinite 29 idle cgpu[01-06],egpu01,hmem[01-01],node[01-11] spot-gpu up infinite 1 idle egpu01 ndc-compute up infinite 11 idle node[01-11] uoa-compute up infinite 11 idle hmem[01-11] uoa-teaching up infinite 5 idle node[01-05]

Code 1 - cluster resources - Slurm sinfo

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Cluster Access

Access to the cluster will vary based on the organisation you are part of. All access to the cluster for standard users is based on your Windows credentials used to access any University computer. To access the cluster, you must be a member of one of the HPC user groups. If you need to become a member of a group or are not sure whether you are already a member speak to your local HPC administration team. UoA users must be part of the “maxwell-users” or “maxwell-users-teach” to be able to access the cluster. NDC users must be part of the “ndc-hpc-users” group to be able to access the cluster.

In addition to being able to log on to the cluster you must also have a Slurm account to be able to submit jobs for processing. Slurm accounts are setup by your local HPC administration team and they will be your first point of contact should you find you do not have a Slurm account or your account is not working. See section 6.3 - Workload Manager - Slurm - Submitting compute jobs for more detail about the usage of Slurm.

There are two dedicated login nodes for each organisation for gaining access to the cluster. All login nodes can be accessed using SSH or x2go graphical client. To access the cluster you will need an SSH client on your computer. If you are a Windows user Putty is the recommended application.

X2GO client is required for accessing the graphical client and can be installed by IT Services if not already present on your computer. Supported session types for X2GO are XFCE, KDE and MATE. Other desktop window systems are not currently installed on the cluster due to incompatibility or insufficient justification.

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Cluster Access

4.1 University of Aberdeen Users

Login node addresses:

maxlogin1.abdn.ac.uk maxlogin2.abdn.ac.uk

Command Line

SSH access to the cluster is the most straight forward from a Linux/Mac/Terminal emulator.

Code 2 - cluster access - UoA maxlogin1

Code 3 - cluster access - UoA maxlogin2

[ocf-engineer@OCF ~]$ ssh [email protected] [email protected]'s password: [USERNAME@maxlogin1 ~]$

[ocf-engineer@OCF ~]$ ssh [email protected] [email protected]'s password: [USERNAME@maxlogin1 ~]$

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Cluster Access

If using Putty simply open Putty and enter the desired login node address into the Host Name box.

Image 1 - cluster access - UoA Putty

Image 2 - cluster access - UoA Putty logged in

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Cluster Access

Graphical

The following X2GO session server options are required to connect to a graphical instance. Remember the session type must be XFCE, KDE or MATE.

Host: maxlogin1.abdn.ac.uk or maxlogin2.abdn.ac.uk Login: Your usersname SSH Port: 22

Code 4 - cluster access - UoA x2go server settings

You will be prompted for your password after the session has been setup.

Image 3 - cluster access - UoA x2go XFCE desktop

Image 4 - cluster access - UoA x2go session preferences

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Cluster Access

4.2 National Decommissioning Centre Users

Login node addresses:

ndc1.abdn.ac.uk ndc2.abdn.ac.uk

Command Line

SSH access to the cluster is the most straight forward from a Linux/Mac/Terminal emulator.

Code 5 - cluster access - NDC ndc1

Code 6 - cluster access - NDC ndc2

Please refer to section 4.1.1 Putty for Putty screenshots.

Graphical

The following X2GO session server options are required to connect to a graphical instance. Remember the session type must be XFCE, KDE or MATE.

Host: ndc1.abdn.ac.uk or ndc2.abdn.ac.uk Login: Your usersname SSH Port: 22

Code 7 - cluster access - NDC x2go server settings

Please refer to section 4.1.2 for x2go client screenshots.

[ocf-engineer@OCF ~]$ ssh [email protected] [email protected]'s password: [USERNAME@ndc1 ~]$

[ocf-engineer@OCF ~]$ ssh [email protected] [email protected]'s password: [USERNAME@ndc2 ~]$

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Cluster Access

4.3 File Transfers

Data can be transferred in and out of the cluster using standard Linux tools, such as “scp” or “rsync”. Windows users can use WinSCP to transfer data using a graphical application.

Remember the hostname will be one of the following:

maxlogin1.abdn.ac.uk maxlogin2.abdn.ac.uk ndc1.abdn.ac.uk ndc2.abdn.ac.uk

Standard Linux Utilities

SCP or rsync directly to your home directory and then work on the data when it is on the cluster.

scp jobdata.tar.gz USERNAME@maxlogin1:~/ rsync -avzh ./jobName/ USERNAME@maxlogin1:~/

Code 8 - cluster access - scp and rsync

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Cluster Access

WinSCP

Login to the cluster using the same connection details as you would use for logging into the command line or graphical interface. Once logged in you will be able to drag and drop files to the cluster.

Image 5 - cluster access - WinSCP login

Image 6 - cluster access - WinSCP logged in

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Cluster Access

Remote Cluster Access Access to the cluster can be obtained from outside the University allowing you to access the cluster from non-university computers or when not connected to university WiFi. Remote access to the cluster must be enabled for your account by the HPC team and does not come as part of a standard user account.

Remote access is possible via any of the access methods described above and will require a proxy or jump host to be specified when connecting to the cluster. The proxy connection must use:

Hostname: ssh-gateway.abdn.ac.uk Port: 22 Proxy/connection type: ssh tunnel Credentials: same as you would use to login to the cluster from within the University network

4.3.3.1 Command Line Access Log on to the SSH gateway prior to logging on to your login nodes as per sections 4.1.1 and 4.2.1.

[ocf-engineer@OCF ~]$ ssh [email protected] -sh-4.2$ ssh maxlogin1.abdn.ac.uk [USERNAME@ndc1 ~]$ Code 9 - cluster access - remote command line access

Image 7 - cluster access - remote access Putty remote Image 8 - cluster access - remote access Putty

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Cluster Access

4.3.3.2 Graphical

Image 9 - cluster access - remote x2go

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Cluster Access

4.3.3.3 File Transfers

Image 10 - cluster access - SSH tunnel WinSCP

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Cluster Applications

5.1 Loadable Applications

All applications available on the cluster are installed as loadable modules. Loadable modules allows a vast array of software to be installed on the cluster without causing compatibility between applications that have dependencies on the same applications but of different versions.

Available modules can be displayed using “module avail”. At the time of writing the following applications are available on the cluster.

5.2 Installed Applications

See https://www.abdn.ac.uk/it/documents/Maxwell-Software.pdf for a list of applications and the “Loadable Module” identifier. Modules are loaded by issuing the command “module load <Loadable Module>”.

Parameter Description Example

module load <Loadable Module> Load a module module load intel-19.0.4.243

module list List loaded modules module list

module unload <Loadable Module> Unload a loaded module module unload intel-19.0.4.243

module spider <search term> Search available modules module spider intel

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Cluster Applications

By default “slurm/19.05.1-2” or a newer version will be loaded and must be loaded to allow jobs to be submitted to Slurm.

[root@maxlogin1 ~]# module load intel-19.0.4.243 [root@maxlogin1 ~]# module list Currently Loaded Modules: 1) slurm/19.05.1-2 2) intel-19.0.4.243 [root@maxlogin1 ~]# module spider intel ------------ intel: ------------ Versions: intel/imkl-2019 intel/impi-2019 intel/2017.3 intel/2019.3 Other possible modules matches: ffmpeg-4.1.1-intel-19.0.4.243 intel-19.0.4.243 intel-mpi-09.01.04.03r-ce intelconda3 mothur-1.39.5-intel-19.0.4.243 mothur-1.40.5-intel-19.0.4.243 netcdf-4.7.0-intel-19.0.4.243 ... ------------ To find other possible module matches execute: $ module -r spider '.*intel.*' ------------ For detailed information about a specific "intel" module (including how to load the modules) use the module's full name. For example: $ module spider intel/impi-2019 ------------ [root@maxlogin1 ~]# module unload intel-19.0.4.243 [root@maxlogin1 ~]# module list Currently Loaded Modules: 1) slurm/19.05.1-2

Code 10 - cluster applications - lmod

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Cluster Applications

5.3 Galaxy

A Galaxy server is available on Maxwell. The Galaxy server uses the same login credentials as you would use to login to the command line or graphical desktop. Galaxy server is accessible by visiting:

https://maxgalaxy.abdn.ac.uk

Image 11 - workload manager - Galaxy login

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Cluster Applications

Image 12 - workload manager - Galaxy logged in Galaxy computation submits jobs to the Slurm cluster. All data used by Galaxy must be available on the cluster the same as any other Slurm job run on the cluster.

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Workload Manager - Slurm

The cluster resources are managed by SchedMD Slurm. All computational jobs run on the cluster must be submitted via Slurm. There is no direct access to nodes jobs are not running on. Job data must be present in your home or scratch directory depending on dataset size. Jobs must be submitted via a login node. The environment on the login node is the same as what must be loaded on a compute node. For example, if you load a module using “module load” this must be in your submission script so it can be loaded by the node running the job.

6.1 Common Slurm Commands

Command Description Example

sbatch [args] ./script Slurm batch script submission sbatch -p spot-compute \ ./script.sh

squeue Show job queue squeue

scontrol show partition <name> Show partition details scontrol show partition \ spot-compute

scontrol show job <ID> Show job information scontrol show job 205295

sinfo Show summary information sinfo

scancel <ID> Cancel a running job scancel 205295

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Workload Manager - Slurm

[root@maxlogin1 ~]# squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 205295 uoa-gpu fmnist_c USER1 R 19:31 1 cgpu01 205294 spot-gpu fmnist_c USER1 R 19:50 1 egpu01 205298 spot-comp MR125P5x USER2 R 12:37 1 vhmem01 205297 spot-comp MaR4P5nX USER2 R 16:01 1 vhmem01 205296 spot-comp MR125P4x USER2 R 19:01 1 vhmem01 205291 spot-comp MaR1P3nX USER2 R 25:01 1 vhmem01 Code 11 - workload manager - squeue

[root@maxlogin1 ~]# scontrol show partition spot-compute PartitionName=spot-compute AllowGroups=maxwell-users,OCF-Admin-Users,galaxy AllowAccounts=ALL AllowQos=ALL AllocNodes=ALL Default=YES QoS=N/A DefaultTime=41-15:00:00 DisableRootJobs=NO ExclusiveUser=NO GraceTime=0 Hidden=NO MaxNodes=UNLIMITED MaxTime=UNLIMITED MinNodes=0 LLN=NO MaxCPUsPerNode=UNLIMITED Nodes=node[01-11],cgpu[01-06],hmem[01-11],vhmem[01-01],egpu[01-01] PriorityJobFactor=1 PriorityTier=1 RootOnly=NO ReqResv=NO OverSubscribe=NO OverTimeLimit=NONE PreemptMode=REQUEUE State=UP TotalCPUs=1240 TotalNodes=30 SelectTypeParameters=NONE JobDefaults=(null) DefMemPerNode=UNLIMITED MaxMemPerNode=UNLIMITED

Code 12 - workload manager - scontrol show partition

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Workload Manager - Slurm

[root@maxmgmt1 H2O-64]# scontrol show job 205290 JobId=205290 JobName=cp2k_h20_64_1_node UserId=root(0) GroupId=root(0) MCS_label=N/A Priority=6013 Nice=0 Account=root QOS=normal JobState=RUNNING Reason=None Dependency=(null) Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=00:00:07 TimeLimit=41-15:00:00 TimeMin=N/A SubmitTime=2019-10-11T16:11:21 EligibleTime=2019-10-11T16:11:21 AccrueTime=2019-10-11T16:11:21 StartTime=2019-10-11T16:11:36 EndTime=2019-11-22T06:11:36 Deadline=N/A PreemptEligibleTime=2019-10-11T16:11:36 PreemptTime=None SuspendTime=None SecsPreSuspend=0 LastSchedEval=2019-10-11T16:11:36 Partition=spot-compute AllocNode:Sid=maxmgmt1:204311 ReqNodeList=(null) ExcNodeList=(null) NodeList=cgpu01 BatchHost=cgpu01 NumNodes=1 NumCPUs=36 NumTasks=36 CPUs/Task=1 ReqB:S:C:T=0:0:*:* TRES=cpu=36,mem=150G,node=1,billing=36 Socks/Node=* NtasksPerN:B:S:C=36:0:*:* CoreSpec=* MinCPUsNode=36 MinMemoryNode=150G MinTmpDiskNode=0 Features=(null) DelayBoot=00:00:00 OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null) Command=./h2o_64_1_node.sh WorkDir=/opt/software/benchmarking/cp2k/inputs/H2O-64 StdErr=/opt/software/benchmarking/cp2k/inputs/H2O-64/slurm.205290.err StdIn=/dev/null StdOut=/opt/software/benchmarking/cp2k/inputs/H2O-64/slurm.205290.out Power= Code 13 - workload manager - scontrol show job [root@maxlogin1 ~]# sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST uoa-gpu up infinite 1 mix cgpu01 uoa-gpu up infinite 5 idle cgpu[02-06] spot-vhmem up infinite 1 mix vhmem01 ndc-gpu up infinite 1 mix egpu01 ndc-hmem up infinite 1 mix vhmem01 ocf-benchmark up infinite 22 idle hmem[01-11],node[01-11] spot-compute* up infinite 3 mix cgpu01,egpu01,vhmem01 spot-compute* up infinite 27 idle cgpu[02-06],hmem[01-11],node[01-11] spot-gpu up infinite 1 mix egpu01 ndc-compute up infinite 11 idle node[01-11] uoa-compute up infinite 11 idle hmem[01-11] uoa-teaching up infinite 5 idle node[01-05] Code 14 - workload manager - sinfo

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Workload Manager - Slurm

6.2 Common Slurm Parameters

Parameter Description Example

-N

--nodes

Number of nodes to run a job on #SBATCH -N 1

-n

--ntasks

Number of tasks to allocate #SBATCH -n 36

--mem Amount of memory required specified as M, G or T

#SBATCH --mem 150G

--mail-user Send an email upon a state change #SBATCH [email protected]

-o

--output

Output file name #SBATCH -o slurm.%j.out

-e

--error

Error file #SBATCH -e slurm.%j.out

%j Job ID %j

%s Step ID %s

%J Job ID.Step ID (eg 2001.0) %J

%x Job name %x

--gres=TYPE:X Generic resources - GPUs

Type=gtx2080ti or v100

X = 1 or 2

#SBATCH --gres=gtx2080ti:1 #SBATCH --gres=v100:1

Table 7 - workload manager - common Slurm parameters

All commands are available on https://slurm.schedmd.com/sbatch.html

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Workload Manager - Slurm

6.3 Submitting Compute Jobs

The basic steps to submitting a compute job are:

1. Determine what application you are using 2. Write a job script similar to below. The job script will need to contain:

a. Number of nodes b. Number of tasks or cores c. Tasks per node d. Amount of memory

3. Copy your data set to your home directory or scratch directory 4. Submit the job using “sbatch” 5. After submission you will get a job ID. The job ID can be used to monitor the job using “squeue” or

“scontrol”. Alternatively, if you specified “--mail-user” you will receive an email when the job begins and ends

Here is an example compute Slurm script.

#!/bin/bash #SBATCH -N 1 # number of nodes #SBATCH -n 36 # number of cores #SBATCH --mem 150G # memory pool for all cores #SBATCH -o slurm.%j.out # STDOUT #SBATCH -e slurm.%j.err # STDERR #SBATCH --ntasks-per-node=36 #SBATCH --job-name=cp2k_h20_64_1_node cd ${SLURM_SUBMIT_DIR} module load openmpi/3.1.4-intel-19.0.4.243-ocf module load cp2k/cp2k-6.1-gcc-4.8.5-vsc5ptz mpirun --allow-run-as-root cp2k.popt -i ./H2O-64.inp >> ./ocf_uat_1.6_hmem_cp2k_h2o_64.out-${SLURM_JOB_ID}

Code 15 - workload manager - Slurm script

[root@maxmgmt1 H2O-64]# sbatch --partition=spot-compute ./h2o_64_1_node.sh [root@maxmgmt1 H2O-64]# squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 205290 spot-comp cp2k_h20 root R 0:03 1 cgpu01

Code 16 - workload manager - sbatch and squeue

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Workload Manager - Slurm

[root@maxmgmt1 H2O-64]# scontrol show job 205290 JobId=205290 JobName=cp2k_h20_64_1_node UserId=root(0) GroupId=root(0) MCS_label=N/A Priority=6013 Nice=0 Account=root QOS=normal JobState=RUNNING Reason=None Dependency=(null) Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0 RunTime=00:00:07 TimeLimit=41-15:00:00 TimeMin=N/A SubmitTime=2019-10-11T16:11:21 EligibleTime=2019-10-11T16:11:21 AccrueTime=2019-10-11T16:11:21 StartTime=2019-10-11T16:11:36 EndTime=2019-11-22T06:11:36 Deadline=N/A PreemptEligibleTime=2019-10-11T16:11:36 PreemptTime=None SuspendTime=None SecsPreSuspend=0 LastSchedEval=2019-10-11T16:11:36 Partition=spot-compute AllocNode:Sid=maxmgmt1:204311 ReqNodeList=(null) ExcNodeList=(null) NodeList=cgpu01 BatchHost=cgpu01 NumNodes=1 NumCPUs=36 NumTasks=36 CPUs/Task=1 ReqB:S:C:T=0:0:*:* TRES=cpu=36,mem=150G,node=1,billing=36 Socks/Node=* NtasksPerN:B:S:C=36:0:*:* CoreSpec=* MinCPUsNode=36 MinMemoryNode=150G MinTmpDiskNode=0 Features=(null) DelayBoot=00:00:00 OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null) Command=./h2o_64_1_node.sh WorkDir=/opt/software/benchmarking/cp2k/inputs/H2O-64 StdErr=/opt/software/benchmarking/cp2k/inputs/H2O-64/slurm.205290.err StdIn=/dev/null StdOut=/opt/software/benchmarking/cp2k/inputs/H2O-64/slurm.205290.out Power= Code 17 - workload manager - scontrol job

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Workload Manager - Slurm

6.4 Submitting GPU Jobs

GPU jobs are very similar to compute jobs with the exception of an additional required Slurm parameter. When submitting GPU jobs “--gres” must be used to allow a GPU resource to be allocated. GPU jobs must be submitted to one of the GPU partitions. If a GPU job is submitted to a non-gpu partition it will not run and likely fail when being submitted and give an error or sit in the queue waiting for resources.

To determine which GPU type you are best using see the following table:

Job requirements Slurm Attributes

Org. Application

Precision

GPU

Memory

Job

Interru-ptible?

GRES

Attributes

Recommended

Partition Notes

UoA Single <12G No gtx2080ti:1 uoa-gpu

UoA Single <12G Yes gtx2080ti:1 spot-gpu

Job could be interrupted if uoa-gpu partition becomes busy.

UoA Single <24G No gtx2080ti:2 uoa-gpu Application must be able to run on multiple GPUs.

UoA Single <24G Yes gtx2080ti:2 spot-gpu Job could be requeued if uoa-gpu partition becomes busy.

UoA Single >24G No gtx2080ti:X uoa-gpu

X denotes the amount of GPUs required. Each GPU has 12G memory.

UoA Double <32G Yes v100:1 spot-gpu Job could be requeued if an NDC user submits a GPU job.

UoA Double <64G Yes v100:2 spot-gpu Job could be requeued if an NDC user submits a GPU job.

NDC Single/Double <32G N/A v100:1 ndc-gpu

NDC Single/Double <64G N/A v100:2 ndc-gpu

Table 8 - workload manager - GPU placement

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Workload Manager - Slurm

It is important to remember the NVIDIA GeForce GTX 2080ti are not optimised for double precision workloads but are still capable of running them. Use sinfo to determine if there are any jobs running on spot-gpu partition to see if you can run your job there quicker than using a GTX 2080ti GPU. NDC users have priority access to V100 GPUs and can only submit jobs to this resource type.

Submitting a job to a consumer GPU node:

#!/bin/bash #SBATCH -N 1 # number of nodes #SBATCH -n 2 # number of cores #SBATCH --mem 50G # memory pool for all cores #SBATCH -o slurm.%j.out # STDOUT #SBATCH -e slurm.%j.err # STDERR #SBATCH --ntasks-per-node=2 #SBATCH --gres=gtx2080ti:1 #SBATCH --partition=uoa-gpu module load cudatoolkit-10.1.168 nvidia-smi # show GPU status ./cuda-program

Code 18 - workload manager - consumer GPU job

Submitting a job to an enterprise GPU node:

#!/bin/bash #SBATCH -N 1 # number of nodes #SBATCH -n 2 # number of cores #SBATCH --mem 50G # memory pool for all cores #SBATCH -o slurm.%j.out # STDOUT #SBATCH -e slurm.%j.err # STDERR #SBATCH --ntasks-per-node=2 #SBATCH --gres=v100:1 #SBATCH --partition=spot-gpu module load cudatoolkit-10.1.168 nvidia-smi # show GPU status ./cuda-program

Code 19 - workload manager - enterprise GPU job

If the job is from an NDC user the job should be submitted to “ndc-gpu” to use the V100 GPU and start the job with higher priority than any UoA jobs running on egpu01 node.

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Getting Help

For support and assistance or to report a fault with the Maxwell cluster, contact the Digital Research Infrastructure team via email - [email protected]

For urgent matters please email the details of your issue to the address below and follow up with a phone call to ensure the Digital Research Infrastructure team can give the matter the appropriate priority.

[email protected] Naveed Khan: 01224 27-4126 Michael Chung: 01224 27-2750

Where possible, please include the following information to ensure the issue/request can be dealt with as soon as possible:

1. Identify Maxwell HPC in the call 2. Include a description of the problem or request 3. Identify username(s) or groups the call relates to 4. Provide example job output files clearly identifying the issue 5. A method for replicating the problem

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Index

8.1 Tables

Table 1 - version control - latest ................................................................................................................................... 4

Table 2 - version control - history ................................................................................................................................. 4

Table 3 - cluster resources - physical resources ........................................................................................................... 6

Table 4 - cluster resources - storage resources ............................................................................................................ 6

Table 5 - cluster resources - Slurm resources ............................................................................................................... 7

Table 6 - cluster resources - Slurm partition priorities ................................................................................................. 8

Table 7 - workload manager - common Slurm parameters ........................................................................................ 26

Table 8 - workload manager - GPU placement ........................................................................................................... 29

8.2 Images

Image 1 - cluster access - UoA Putty ......................................................................................................................... 11

Image 2 - cluster access - UoA Putty logged in ........................................................................................................... 11

Image 3 - cluster access - UoA x2go XFCE desktop ..................................................................................................... 12

Image 4 - cluster access - UoA x2go session preferences .......................................................................................... 12

Image 5 - cluster access - WinSCP login...................................................................................................................... 15

Image 6 - cluster access - WinSCP logged in ............................................................................................................... 15

Image 7 - cluster access - remote access Putty remote ............................................................................................. 16

Image 8 - cluster access - remote access Putty .......................................................................................................... 16

Image 9 - cluster access - remote x2go ...................................................................................................................... 17

Image 10 - cluster access - SSH tunnel WinSCP .......................................................................................................... 18

Image 11 - workload manager - Galaxy login ............................................................................................................. 21

Image 12 - workload manager - Galaxy logged in ...................................................................................................... 22

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Index

8.3 Code Samples

Code 1 - cluster resources - Slurm sinfo ....................................................................................................................... 8

Code 2 - cluster access - UoA maxlogin1 .................................................................................................................... 10

Code 3 - cluster access - UoA maxlogin2 .................................................................................................................... 10

Code 4 - cluster access - UoA x2go server settings .................................................................................................... 12

Code 5 - cluster access - NDC ndc1 ............................................................................................................................. 13

Code 6 - cluster access - NDC ndc2 ............................................................................................................................. 13

Code 7 - cluster access - NDC x2go server settings .................................................................................................... 13

Code 8 - cluster access - scp and rsync ....................................................................................................................... 14

Code 9 - cluster access - remote command line access ............................................................................................. 16

Code 10 - cluster applications - lmod ......................................................................................................................... 20

Code 11 - workload manager - squeue ...................................................................................................................... 24

Code 12 - workload manager - scontrol show partition ............................................................................................. 24

Code 13 - workload manager - scontrol show job ...................................................................................................... 25

Code 14 - workload manager - sinfo........................................................................................................................... 25

Code 15 - workload manager - Slurm script ............................................................................................................... 27

Code 16 - workload manager - sbatch and squeue .................................................................................................... 27

Code 17 - workload manager - scontrol job ............................................................................................................... 28

Code 18 - workload manager - consumer GPU job .................................................................................................... 30

Code 19 - workload manager - enterprise GPU job .................................................................................................... 30

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2019 Candidate Qualifying List FULL LIST · v ] o Ç W µ o ] ^ À ] } u u ] ] } v Z µ o ] v v o E ] > } W µ o ] ^ À ] } u u ] ] } v Z µ o ] v v o

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µ´t´o»w¼ - paslc.gov

µ´t´o»w¼ - paslc.gov

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