Interactive work on the compute nodes¶

• Rackham/Pelle: uppmax2025-2-360
• Kebnekaise: hpc2n2025-151
• Cosmos: lu2025-2-94
• Tetralith: naiss2025-22-934
• Dardel: naiss2025-22-934
• Alvis: naiss2025-22-934

Overview of the UPPMAX systems¶

Overview of the HPC2N system¶

Overview of the LUNARC system¶

Overview of the NSC system¶

General¶

In order to run interactively, you need to have compute nodes allocated to run on, and this is done through the batch system.

R “interactively” on the compute nodes¶

To run interactively, you need to allocate resources on the cluster first. You can use the command salloc/interactive to allow interactive use of resources allocated to your job. When the resources are allocated, if you are using HPC2N and salloc you need to preface commands with srun in order to run on the allocated nodes instead of the login node.

• First, you make a request for resources with interactive/salloc, like this:

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

$ salloc -n <tasks> --time=HHH:MM:SS -A hpc2n2024-025 

interactive -A lu2025-2-94 -t HHH:MM:SS

interactive -A naiss2025-22-934

salloc --time=HHH:MM:SS -A naiss2025-22-934 -p [partition]

srun -A NAISS2025-22-934 -p alvis --gpus-per-node=T4:1 --pty bash

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 (or login to the compute node with ssh on PDC). The commands you run with srun will then be executed on the resources your job has been allocated. If you do not preface with srun the command is run on the login node!

You can now run R 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 R script or perhaps figure out which parameters are best.

Example¶

Requesting 4 cores for 10 minutes, then running R

[bjornc@pelle2 ~]$ interactive -A uppmax2025-2-360 -n 4 -t 10:00
This is a temporary version of interactive-script for Pelle
Most interactive-script functionality is removed
salloc: Pending job allocation 82050
salloc: job 82050 queued and waiting for resources
salloc: job 82050 has been allocated resources
salloc: Granted job allocation 82050
salloc: Waiting for resource configuration
salloc: Nodes p102 are ready for job
[bjornc@p102 ~]$

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

[~]$ salloc -n 4 --time=00:30:00 -A hpc2n2024-025
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 GCC/12.2.0  OpenMPI/4.1.4 R/4.2.2
[~]$ 

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

Running a script

The script

Adding two numbers from user input (serial_sum.R)

• You will find it in the exercise directory exercises/r/ so go there with cd.
• Otherwise, use your favourite editor and add the text below and save as serial_sum.R.

# This program will add two numbers that are provided by the user
args = commandArgs(trailingOnly = TRUE)
res = as.numeric(args[1]) + as.numeric(args[2])
print(paste("The sum of the two numbers is", res))

Running the script

• Note that the commands are the same for both HPC2N and UPPMAX!

Running a R script in the allocation we made further up. Notice that since we asked for 4 cores, the script is run 4 times, since it is a serial script

$ srun Rscript serial_sum.R 3 4
[1] "The sum of the two numbers is 7"
[1] "The sum of the two numbers is 7"
[1] "The sum of the two numbers is 7"
[1] "The sum of the two numbers is 7"

Without the srun command, R won’t understand that it can use several cores. Therefore the program is run only once.

$ Rscript serial_sum.R 3 4
[1] "The sum of the two numbers is 7"

Running R with workers

• First start R and check available workers with future.
• Create a R script called `script-workers.R`` with the following content:

library(future)
availableWorkers()
availableCores()

• Execute the code with srun -n 1 -c 4 Rscript script-workers.R

Exit¶

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

Don’t do it now!

• We shall test RStudio first in the next session!

[bjornc@p102 ~]$ exit

exit
[screen is terminating]
Connection to p102 closed.

[bjornc@pelle2 ~]$

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