Matlab interactively

Learning outcomes for today

  • Be able to start interactive sessions with several cores
  • Be able to run MATLAB and seae the available workers
Instructor note
  • Intro 5 min
  • Lecture and 10 min

Notes

  • It is possible to run MATLAB directly on the login (including ThinLinc) nodes.
  • But this should only be done for shorter jobs or jobs that do not use a lot of resources, as the login nodes can otherwise become slow for all users.
  • If you want to work interactively with your code or data, you should start an interactive session.
  • If you rather will run a script which won’t use any interactive user input while running, you can instead start a batch job, see next session.

General

In order to run interactively with more memory or more threads/processes, you need to have compute nodes allocated to run on, and this is done through the Slurm system.

Interactive sessions at NSC, PDC, HPC2N, UPPMAX and LUNARC

Here we define an interactive session as a session with direct access to a compute node. Or alternatively: an interactive session is a session, in which there is no queue before a command is run on a compute node.

This differs between HPC2N and UPPMAX :

  • HPC2N: the user remains on a login node. All commands can be sent directly to the compute node using srun
  • UPPMAX: the user is actually on a computer node. Whatever command is done, it is run on the compute node
  • LUNARC: the user is actually on a computer node if the correct menu option is chosen. Whatever command is done, it is run on the compute node
  • NSC: the user is actually on a computer node if the correct menu option is chosen. Whatever command is done, it is run on the compute node
  • PDC: the user is actually on a computer node if the correct menu option is chosen. Whatever command is done, it is run on the compute node

Start an interactive session

To start an interactive session, one needs to allocate resources on the cluster first.

The command to request an interactive node differs per HPC cluster:

Cluster interactive salloc GfxLauncher Open OnDemand
HPC2N Works Recommended N/A Recommended
UPPMAX Recommended Works N/A N/A
LUNARC Works N/A Recommended N/A
NSC Recommended N/A N/A N/A
PDC N/A Recommended Possible N/A

Example, HPC2N vs. UPPMAX (also valid for NSC, PDC and LUNARC):

graph TD subgraph uppmax[UPPMAX] subgraph login_node[Login nodes] user_on_login_node[User on login node] end subgraph compute_node[Compute nodes] user_on_computer_node[User on compute node] job_on_compute_node[Job on compute node] end end subgraph hpc2n[HPC2N] subgraph hpc2n_login_node[Login nodes] hpc2n_user_on_login_node[User on login node] hpc2n_user_in_interactive_mode[User on login node in interactive session] end subgraph hpc2n_compute_node[Compute nodes] hpcn2_job_on_compute_node[Job on compute node] end end user_on_login_node --> |interactive| user_on_computer_node user_on_login_node --> |sbatch| job_on_compute_node user_on_computer_node --> |exit| user_on_login_node user_on_computer_node --> |srun| user_on_computer_node hpc2n_user_on_login_node --> |salloc| hpc2n_user_in_interactive_mode hpc2n_user_in_interactive_mode --> |exit| hpc2n_user_on_login_node hpc2n_user_on_login_node --> |sbatch| hpcn2_job_on_compute_node hpc2n_user_in_interactive_mode --> |srun| hpcn2_job_on_compute_node
  • First, you make a request for resources with interactive/salloc, like this:

Interactive jobs

Short serial example for running on different clusters.

$ interactive -n <tasks> --time=HHH:MM:SS -A naiss2025-22-934

$ salloc -n <ntasks> --time=HHH:MM:SS -A naiss2025-22-934 -p <partition>

Where is shared, main or gpu

  • We recommend shared
  • Wait until you get the node
  • ssh to the node given and then work there

    • Example:

      $ ssh nid001057

$ interactive -n <tasks> --time=HHH:MM:SS -A uppmax2025-2-360

$ interactive -n <tasks> --time=HHH:MM:SS -A lu2025-2-94

$ salloc -n <tasks> --time=HHH:MM:SS -A hpc2n2025-151

where is the number of tasks (or cores, for default 1 task per core), time is given in hours, minutes, and seconds (maximum T168 hours), and then you give the id for your project.

  • Your request enters the job queue just like any other job, and interactive/salloc will tell you that it is waiting for the requested resources.
  • When salloc tells you that your job has been allocated resources, you can interactively run programs on those resources with srun.
  • The commands you run with srun will then be executed on the resources your job has been allocated.

On HPC2N

  • If you do not preface with srun the command is run on the login node!
  • You can now run Matlab scripts on the allocated resources directly instead of waiting for your batch job to return a result.
  • This is an advantage if you want to test your Matlab script or perhaps figure out which parameters are best.

End an interactive session

When you have finished using the allocation, either wait for it to end, or close it with exit

$ exit
logout

Documentation at the centers

Exercise

Run from ThinLinc (web or client!)

Interactive session

Requesting 4 cores for 10 minutes, and load Matlab

[sm_bcarl@tetralith3 ~]$ interactive -n 4 -t 0:30:0 -A naiss2025-22-934
salloc: Pending job allocation 43071298
salloc: job 43071298 queued and waiting for resources
salloc: job 43071298 has been allocated resources
salloc: Granted job allocation 43071298
salloc: Waiting for resource configuration
salloc: Nodes n760 are ready for job

[bjornc@n760 ~]$ module load MATLAB/2023b-bdist

Let us check that we actually run on the compute node:

[sm_bcarl@n760 ~]$ srun hostname
n760
n760
n760
n760

We are. Notice that we got a response from all four cores we have allocated.

claremar@login1:~> salloc --ntasks=4 -t 0:30:00 -p shared --qos=normal -A naiss2025-22-934
salloc: Pending job allocation 9102757
salloc: job 9102757 queued and waiting for resources
salloc: job 9102757 has been allocated resources
salloc: Granted job allocation 9102757
salloc: Waiting for resource configuration
salloc: Nodes nid001057 are ready for job

claremar@login1:~> module load PDC/23.12 matlab/r2024b

Let us check that we actually run on the compute node. This has to be done differently

claremar@login1:~> srun hostname
nid001064
nid001063
nid001064
nid001063

Now, it seems that Dardel allows for “hyperthreading”, that is 2 threads per core.

claremar@login1:~> srun -n 8 hostname
nid001064
nid001064
nid001063
nid001063
nid001064
nid001064
nid001063
nid001063

We are. Notice that we got a response from all four cores we have allocated.

[bjornc@pelle ~]$ interactive -A uppmax2025-2-360 -n 4 -t 0:30:00
You receive the high interactive priority.
There are free cores, so your job is expected to start at once.

Please, use no more than 6.4 GB of RAM.

Waiting for job 29556505 to start...
Starting job now -- you waited for 1 second.

[bjornc@p102 ~]$ module load MATLAB/2023b-update4

Let us check that we actually run on the compute node:

[bjornc@p102 ~]$ srun hostname
r483.uppmax.uu.se
r483.uppmax.uu.se
r483.uppmax.uu.se
r483.uppmax.uu.se

We are. Notice that we got a response from all four cores we have allocated.

[bjornc@sens2017625-bianca ~]$ interactive -A sensXXXX -p core -n 4 -t 0:30:00
You receive the high interactive priority.
There are free cores, so your job is expected to start at once.

Please, use no more than 6.4 GB of RAM.

Waiting for job 29556505 to start...
Starting job now -- you waited for 1 second.

[bjornc@p102 ~]$ module load MATLAB/2023b-update4

Let us check that we actually run on the compute node:

[bjornc@p102 ~]$ srun hostname
r483.uppmax.uu.se
r483.uppmax.uu.se
r483.uppmax.uu.se
r483.uppmax.uu.se

We are. Notice that we got a response from all four cores we have allocated.

[~]$ salloc -n 4 --time=00:30:00 -A hpc2n2025-151
salloc: Pending job allocation 20174806
salloc: job 20174806 queued and waiting for resources
salloc: job 20174806 has been allocated resources
salloc: Granted job allocation 20174806
salloc: Waiting for resource configuration
salloc: Nodes b-cn0241 are ready for job
[~]$ module load MATLAB/2023b
[~]$

Let us check that we actually run on the compute node:

[~]$ srun hostname
b-cn0241.hpc2n.umu.se
b-cn0241.hpc2n.umu.se
b-cn0241.hpc2n.umu.se
b-cn0241.hpc2n.umu.se

We are. Notice that we got a response from all four cores we have allocated.

[bjornc@cosmos1 ~]$ interactive -A lu2025-2-94 -n 4 -t 30:00
Cluster name: COSMOS
Waiting for JOBID 930844 to start

[bjornc@cn050 ~]$ module load matlab/2024b

Let us check that we actually run on the compute node:

[bjornc@cn050 ~]$ echo $SLURM_CPUS_ON_NODE
4

We are, because the $SLURM environment variable gives an output. Notice that we got 4, which is not the size of the physcial node but the allocation size.

Check from Matlab

  • Start matlab (same for all clusters)
matlab &
  • In MATLAB test how big parpool you can make (should be limited by the allocated resources above)
p=parpool("local")
p.NumWorkers
Output of parpool command on UPPMAX

According to the below output 

Starting parallel pool (parpool) using the 'Processes' profile ...
Connected to parallel pool with 4 workers.

p =

 ProcessPool with properties:

            Connected: true
            NumWorkers: 4
            Busy: false
      Cluster: Processes (Local Cluster)
       AttachedFiles: {}
    AutoAddClientPath: true
    FileStore: [1x1 parallel.FileStore]
   ValueStore: [1x1 parallel.ValueStore]
  IdleTimeout: 30 minutes (30 minutes remaining)
  SpmdEnabled: true

Quit MATLAB

End Matlab by closing the GUI.

Exit interactive session

When you have finished using the allocation, either wait for it to end, or close it with exit

[sm_bcarl@n134 ~]$ exit
logout
srun: error: n134: task 0: Exited with exit code 130
srun: Terminating StepId=43071803.interactive
salloc: Relinquishing job allocation 43071803
salloc: Job allocation 43071803 has been revoked.
[sm_bcarl@tetralith3 ~]$

claremar@login1:~> exit
exit
salloc: Relinquishing job allocation 9103056
claremar@login1:~>

[bjornc@r483 ~]$ exit

exit
[screen is terminating]
Connection to r483 closed.

[bjornc@rackham2 ~]$

[~]$ exit
exit
salloc: Relinquishing job allocation 20174806
salloc: Job allocation 20174806 has been revoked.
[~]$

[~]$ exit
exit
[screen is terminating]
Connection to cn050 closed.

[~]$