OAR tips¶

This page collect some tips and tricks for managing jobs using the OAR system of GRICAD.

Submit Jobs with Dependencies¶

You can submit jobs with dependencies using the following example. Assuming that you have two job scripts, job1.sh and job2.sh, and that you wish to submit job2.sh after job1.sh is done.

Submit job1.sh and capture its job ID:

job1_id=`oarsub -S ./job1.sh |grep OAR_JOB_ID|awk -F'=' '{print $2}'`

Submit job2.sh so that it starts only after the completion of job1.sh:
```
oarsub -S ./job2.sh  -a $job1_id
```

In this example, job2.sh will wait for job1.sh to complete before starting, using the job ID (job1_id).

Cancel All Your Jobs at Once¶

You can cancel all your jobs at once by typing:

oarstat -u username | awk '{print $1}' | xargs -n 1 oardel

where username should be replaced by your ID.

Record the last Job ID and state¶

It can be useful to record the ID of the last launched job.

oarsub -S ./myjob.sh
oarstat -u username | awk '{print $1}' | tail -n 1 > last_job_id.txt

where username should be replaced by your ID. The file last_job_id.txt will contain the ID of the last launched job. You can also record the entire state of the job:

last_job_id=$(oarstat -u username | awk '{print $1}' | tail -n 1)
oarstat -u username -j "$last_job_id" > last_job_state.txt

Launch Multiple Jobs¶

Here, tips to efficiently launch multiple jobs are provided.

#!/bin/bash
...
#OAR --array 50

id=`echo "$OAR_JOB_ID - $OAR_ARRAY_ID + 2" | bc -l`  # <---- This id runs from 0 to 50, each job gets one, with which you can e.g. index a bash array
temperatures=(0.25 0.5 1 .... )
T=${temperatures[${id}]}

Measure the CPU Usage per User¶

This script runs oarstat, and then calculates the CPU cores per user. The output will list each user along with the total number of CPU cores they are using (Running and waiting).

Create a Bash Script (for instance named cpu_usage.sh), and copy the following lines into the file:

#!/bin/bash

oarstat | awk '
    /^[0-9]+/ {
        # $3 is the user, $2 is the job status, and we look for "R=" to get the core count
        job_status = $2
        user = $3

        # Find the core count for the job
        for (i=1; i<=NF; i++) {
            if ($i ~ /^R=[0-9]+/) {
                # Extract the core count from the "R=" field
                split($i, core_count, "=")

                # Increment cores based on job status (R for running, W for waiting)
                if (job_status == "R") {
                    running_cores[user] += core_count[2]
                } else if (job_status == "W") {
                    waiting_cores[user] += core_count[2]
                }
            }
        }
    }
    # After processing all lines, print the total cores for each user for running and waiting jobs
    END {
        printf "%-10s %-15s %-15s\n", "User", "Running Cores", "Waiting Cores"
        for (user in running_cores) {
            printf "%-10s %-15d %-15d\n", user, running_cores[user], waiting_cores[user]
        }
    }
' | sort

Run the following command to give execution permissions to the script:

chmod +x cpu_usage.sh
./cpu_usage.sh

It will return something like:

calvof     102             0
farutial   2               0
gravells   100             24
joyeuxm    280             0
jungg      114             0
mhirizn-   4               0
nagasawt   2               0
ozawam     50              0
quilliec   2               0
User       Running Cores   Waiting Cores