INCA with MATLAB¶

These are the steps to get INCA to work with MATLAB on Kebnekaise.

Note

You need to get your own license for INCA!

Get a license for INCA from http://mfa.vueinnovations.com/licensing
Wait for license acceptance. It can take more than a day.
Then go to download “Your premium content” while logged in: MFA Suite 2.3
Transfer the zip file to Kebnekaise (filezilla is a good option - use sftp). There is a Guide for file transfers here.
Login to Kebnekaise. It is recommended you use ThinLinc.
Open a terminal:
- In the ThinLinc menu: “Applications” -> “System Tools” -> “MATE Terminal”
Unzip the downloaded zip file in your project folder (if you did not unzip it first and just transferred the folder).
- You should use this folder: /proj/nobackup/<your-project>/<your-directory> - change the <your-project> to the name your project storage folder has, and then put it in <your-directory> under it, if it is a shared folder.
- The command to unzip is: unzip incax.y.zip (change the name of the zip file if it is not as here).
Use the terminal you just opened, or open a new terminal and configure MATLAB for parallel runs (DO ONCE PER VERSION of MATLAB!)
- Opening a terminal: “Applications” -> “System Tools” -> “MATE Terminal”
- For MATLAB 2023a: type ml MATLAB/2023a.Update4 and press Enter
- Type configCluster.sh and press Enter
Start MATLAB. It should preferrably be done from the INCA folder so the working path of INCA is recognized
- Can either be done from menu:
  - In ThinLinc this can be done from “Applications” -> “Programming” -> “MATLAB 2023a” (change to preferred version, same as you ran configCluster.sh for)
  - Set the working directory path to the INCA folder inside MATLAB
- Or you can do it from a terminal. Two ways to get a terminal and change to directory:
  - Start a terminal from the menu and change to INCA directory then load the MATLAB module and start matlab:
    - “Applications” -> “System Tools” -> “MATE Terminal”
    - Then switch to inca directory by typing cd /proj/nobackup/<your-project>/<path/to/inca> and press enter.
    - Then type ml MATLAB/2023a.Update4 and enter, then type matlab -singleCompThread and press “enter” to start MATLAB version 2023a
  - OR use the filebrowser (shortcut to your home folder on ThinLinc desktop) to find the folder and open a terminal from there, then load MATLAB and start it:
    - Double-left-click on “YOURUSERNAME’s Home” on the ThinLinc desktop
    - Click around in the file finder until you have the inca directory open
    - Right-click in that window and pick “Open in Terminal”
    - and then start MATLAB there by typing ml MATLAB/2023a.Update4 and enter, then type matlab -singleCompThread and press “enter” to start MATLAB version 2023a
    - NOTE that your project directory is found under “File System” -“proj” -> “nobackup” -> “directory-you-picked-for-project” in the file browser.
Transfer the network .mat file to a subfolder in this INCA root folder to avoid the “rungui” error.

Set job parameters for the batch system:

>> c = parcluster;

>> % account name is your project id
>> c.AdditionalProperties.AccountName = 'account-name';

>> % Ask for some time, here 5 hours
>> c.AdditionalProperties.WallTime = '05:00:00';

>> % How many processors per node you want - here 20
>> c.AdditionalProperties.ProcsPerNode=20;

>> % save the profile 
>> c.saveProfile

You can check your settings with c.AdditionalProperties
You can clear a job setting by giving an empty value, like this: c.AdditionalProperties.WallTime = '';
Always save the settings after you have changed them, with c.saveProfile
Inside MATLAB, set path to where you put INCA with addpath '/path/to/inca' and also do this for your data directory.
- Example for me:
```
>> addpath '/pfs/stor10/projects/projnb10/support-hpc2n/bbrydsoe/inca2.3/inca2.3'
>> addpath '/home/b/bbrydsoe/Downloads'
```
  NOTE: if there are problems with the path, one solution is to start MATLAB from the inca directory, as describe further up on the page
Start a parpool, here in this example for 16 workers
```
>> parpool(16) 
```
Wait for it to have resources. Start inca by typing this inside MATLAB: inca
INCA should automatically use the parallel pool of workers when available, i.e. the ones we just asked for.
Job monitoring:
- You can start a terminal and look there to see which jobs you have running (and get job-ids) with
```
squeue --me
```
  and then do
```
scontrol show job <jobid-you-got-from-above>
```
  You can also monitor the job with
```
job-usage <jobid-you-got-from-above>
```