Matlab on Baobab with OpenOnDemand

HPC Technical
1

Dear HPC team,

I’m contacting you because I’m having an issue using Matlab on Baobab with OpenonDemand.

All my files/scripts are located on my $HOME/scratch.

I chose the public iterative cpu partition, with 1 node and 6 cores, for 8 hours to run a Matlab script.
However, when I attempt to run it, it constantly crashes with the message: “session in a bad state”. The data file I am using is 1.7 GB, and the script performs several iterations with this data. The last session I tried was job ID 10209205 .

I have also tried using other partitions, but the webpage TurboVNC disconnects every time.

FYI, I also tried to run the same script reducing the data (47.8MB) and using the public iterative cpu partition, with 1 node and 4 cores, for 8 hours, and it worked perfectly well ( job ID 10208383 if it’s useful).

I guess the problem could come from the data size then? I am wondering if I am selecting the correct partition, number of cores, or the appropriate amount of memory per job.

Any guidance would be very appreciated.

Thank you in advance for your help!!

Best,
Jade

2

Hi @Jade.Awada

You have exceeded your memory allocation (OUT_OF_MEMORY)

(baobab)-[root@login2 ~]$ sacct -X -o Jobid%15,jobname,account,user,nodelist,ReqCPUS,ReqMem,ntask,start,end,Elapsed,state%20  -j 10209205
          JobID    JobName    Account      User        NodeList  ReqCPUS     ReqMem   NTasks               Start                 End    Elapsed                State 
--------------- ---------- ---------- --------- --------------- -------- ---------- -------- ------------------- ------------------- ---------- -------------------- 
       10209205 sys/dashb+    sinanaj     awada          cpu007        4     12000M          2024-05-23T18:13:57 2024-05-23T18:21:51   00:07:54        OUT_OF_MEMORY

You need to ask more memory (you can try with 16GB)

I invite you to read this Best Pratice about resource allocations, to help you :

https://doc.eresearch.unige.ch/hpc/best_practices?s[]=resource#stop_wasting_resources

PS: At some point, using the interactive session has its limits, and it is preferable to run jobs asynchronously with sbatch (slurm batch).

Example:

  1. Writte your Matlab script
(baobab)-[alberta@login2 Matlab_project]$ cat simple_script.m
% simple_script.m
n = 5;
result = sum((1:n).^2);
fileID = fopen('output.txt', 'w');
fprintf(fileID, 'The sum of the squares of the first %d integers is : %d\n', n, result);
fclose(fileID);
exit;
  1. Write your sbatch, specifying the necessary resources, loading the required modules, then run the command with slurm.
(baobab)-[alberta@login2 Matlab_project]$ cat simple_script.sbatch
#!/bin/bash
#SBATCH --job-name=simple_matlab_job
#SBATCH --output=simple_matlab_job.out
#SBATCH --error=simple_matlab_job.err
#SBATCH --time=00:05:00
#SBATCH --partition=debug-cpu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G

module load MATLAB
srun matlab -nodisplay -nosplash -nodesktop -r "simple_script; exit"
  1. Add your job in the queue:
(baobab)-[alberta@login2 Matlab_project]$ sbatch simple_script.sbatch
Submitted batch job 10235116
  1. wait the result drinking your favorite coffee (for me it’s roasted hazelnut latte)

Job pending → Preparing my Latte

(baobab)-[alberta@login2 Matlab_project]$ sac -j 10236031
          JobID    JobName    Account      User        NodeList   NTasks               Start                 End      State 
--------------- ---------- ---------- --------- --------------- -------- ------------------- ------------------- ---------- 
       10236031 simple_ma+      burgi   alberta   None assigned                      Unknown             Unknown    PENDING

Job Running → Drinking my Latte

(baobab)-[alberta@login2 Matlab_project]$ sac -j 10236031
          JobID    JobName    Account      User        NodeList   NTasks               Start                 End      State 
--------------- ---------- ---------- --------- --------------- -------- ------------------- ------------------- ---------- 
       10236031 simple_ma+      burgi   alberta          cpu001          2024-05-24T11:32:48             Unknown    RUNNING

Job Completed → FInish my Latte and read my result

(baobab)-[alberta@login2 Matlab_project]$ sac -j 10236031
          JobID    JobName    Account      User        NodeList   NTasks               Start                 End      State 
--------------- ---------- ---------- --------- --------------- -------- ------------------- ------------------- ---------- 
       10236031 simple_ma+      burgi   alberta          cpu001          2024-05-24T11:32:48 2024-05-24T11:33:14  COMPLETED

(baobab)-[alberta@login2 Matlab_project]$ cat output.txt 
The sum of the squares of the first 5 integers is : 55

Best Regards

3

Hi @Adrien.Albert,

Thank you for your reply and your help!

It’s all good then!!!

Best,
Jade

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