Interactive RStudio

Opening RStudio Form

The first step is to select the Interactive apps and then click the RStudio Server in the Open OnDemand dashboard.
Then you will see a form which needs to be filled to launch the RStudio Server on the compute nodes.

Partition

Partitions are work queues that has computational nodes in it to run the jobs. The partitions available in Discovery are interactive,normal, gpu, backfill, class, epscor, iiplab, cfdlab, so on.
However, you will see only the list of authorized partitions available for your Discovery account and hence, you won’t see the partitions which you don’t have authorization in the select dropdown.
Select one of the partitions where you want to submit your job. Refer to the page → Partitions in Discovery to select the ideal partition for your job.
By Default, partition is set to interactive.

Walltime(Hours)

Sets the Walltime for your job. The job gets killed if the Walltime you set gets elapsed.

Parameter #Hours

Min Limit

1 hour

Max Limit

24 hours

Default

1 hour

Parameter	#Hours
Min Limit	1 hour
Max Limit	24 hours
Default	1 hour

CPUs(Threads)

Sets the Number of CPUs(Threads) for the job. The below table shows the maximum limit for CPU threads for each partition. The default and minimum value is 1 CPU thread.

Partition Max Limit

interactive

16

normal

44

gpu

28

epscor

124

iiplab

52

cfdlab

52

class

60

Partition	Max Limit
interactive	16
normal	44
gpu	28
epscor	124
iiplab	52
cfdlab	52
class	60

Memory (GB/Gigabytes)

Sets the memory for the job in terms of GB. The memory you select is available to all assigned threads for the job. The below table shows the maximum memory limit for each partition which can be requested for the job. The default and minimum value is 1 GB.

Partition	Max Memory Limit(GB)
interactive	64
normal	240
gpu	50
epscor	3000
iiplab	175
cfdlab	175
class	490

GPUs

To enable the GPU selection, you need to choose one of the following partitions: interactive, class, gpu, epscor, iiplab, cfdlab. Only these partitions have GPUs and if you select any of the partitions, you can see the GPUs dropdown enabled.

Parameter #GPU

Min Limit

0

Max Limit

2

Parameter	#GPU
Min Limit	0
Max Limit	2

Partition normal don’t have GPUs.

Email Address

If you want to get notified via email when the job starts/fails/ends, enter the email address associated with the Discovery account.
You can leave the text field blank if you don’t want job notifications.

Singularity Image File

RStudio uses Apptainer/Singularity Container to launch the RStudio Server on the compute node.
The default singularity image points to the /software/singularity/ondemand/singularity-rstudio.simg path location for all the users.
If you want to change the singularity image file, use the Select Path Button.

The singularity file selection allows for files with the .simg, .sif format only.

Launching the Interactive Session

Once all the form fields are set, you can click the Launch button. The interactive session will be launched and you will see the below output.

The above output shows that the interactive RStudio session has been launched successfully. You will see the Connect to RStudio Server button only if the resources you have requested becomes available. Else, you might need to wait for some more minutes for the resources allocation and then the Connect to RStudio Server button appears.
After it appears, click it.

The interactive session won’t be launched if you try to submit your job to the partition that you don’t have access to. You will get the following error message → Batch job submission failed: User’s group not permitted to use this partition. Also, the page gets reloaded and you need to select the value for the form fields again since the form gets reset.

Opening RStudio Server

The RStudio Server opens up in a new tab.

You can now run your R scripts, install packages, restart session, so on.

Change Working Directory

To change your working directory to other directories like /scratch or /project, click the Go to Directory button(pointed by the arrow symbol) like below.

It opens a popup to enter the path of the destination folder.

For example, to switch to your /scratch account, enter the following path in the popup:

/scratch/<username>

On Clicking OK, your working directory will be changed.

Killing the Interactive Session

After the work is done, it’s important to kill the session. Go to My Interactive sessions tab and select the Delete button of the current interactive session.

A confirmation pop-up will appear and press Confirm to delete the session.

Whenever you are done with the work, it’s always recommended to kill/delete the interactive session running on the compute nodes and free the resources.