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Submit a job for the serial version of the project

This section put everything that has been discussed previously together in order to submit a job running the serial version of the project.

Prepare your environment

Once we are logged in to NIC5, we will load the module that set up the environment for the project. The module name Info0939Tools and we load it with

module load Info0939Tools

Loading this module gives us access to the get_info0939_project command. We can use this command to get starting point source code and example inputs for the project.

 $ get_info0939_project
Project copied in the project_info0939 directory

Next, we use the cd command to move to the project_info0939 directory.

cd project_info0939

Compile your code

Now that we have the source code, we can compile it to produce an executable. Here, we will put the executable in a directory with name bin. For that, we create a directory with mkdir and then we use gcc to compile the code.

mkdir -p bin
gcc -O3 -Wall -o bin/shallow shallow.c -lm

In the table below, a summary of the options used and their meaning.

Meaning
-O3 enable optimization at the O3 level
-Wall enable all compiler warnings
-o bin/shallow specify the name and location of the executable after compilation
shallow.c the source file
-lm link with the math library (libm)

Submit a job

Now that we have an executable, we will create a directory from which we will submit a job. 

mkdir -p workdir/serial
cd workdir/serial

Good practice

It's considered good practice to create a new directory for each job you submit.

To submit the job, we will create a text file with name shallow_serial.sh

nano shallow_serial.sh

and copy the content of the code block below.

Source code for this example

shallow_serial.sh
#!/bin/bash
#SBATCH --job-name="shallow serial"
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=05:00
#SBATCH --output=shallow_serial_%j.out

# define some variables
PROJECT_DIR="${HOME}/project_info0939"
EXEC_DIR="${PROJECT_DIR}/bin"
INPUT_DIR="${PROJECT_DIR}/example_inputs/simple"
PARAM_FILE="param_simple.txt"

# copy all files from the input directory to
# the directory from which we submitted the job
cp ${INPUT_DIR}/* ${SLURM_SUBMIT_DIR}

# move to the directory from which we submitted the job
cd ${SLURM_SUBMIT_DIR}

# run the simulation
${EXEC_DIR}/shallow ${PARAM_FILE}

To save the changes to the file, press the Ctrl+X keys then press Y to confirm you want to save the change and finally, press Enter to confirm the name of the file you want to write.

Additional details about the job batch script

  • The following line for the Slurm output specification:

    #SBATCH --output=shallow_serial_%j.out

    means that the job ID will be inserted in the name of the output file. %j will be automatically replaced by Slurm and set to the job ID.

  • In the script we use variables to define various paths. A variable is defined with

    VARIABLE_NAME=VARIABLE_VALUE

    Once a variable is defined it can be used using $VARIABLE_NAME or ${VARIABLE_NAME}.

  • In the script, we use the HOME environment variable. The value of the variable is the path to your home directory. If run the following command

     $ echo $HOME
/home/ulg/info0939/USERNAME
    the output will be the path to your home directory.

  • The expression ${INPUT_DIR}/* use a wildcard. In the context of our script, the wildcard (*) means "match any files". If we use

    ${INPUT_DIR}/in_*

    then, the expression will match any file starting with in_.

The next step is to submit the job to the queue

 $ sbatch shallow_serial.sh
Submitted batch job 5980715

and check the status of the job using the squeue command

 $ squeue --me
  JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
7721015     batch shallow   olouant  R       0:30      1 nic5-w070

Once the job is finished, the output should contain

 $ cat shallow_serial_7721015.out
Parameters:
 - grid spacing (dx, dy): 5 m, 5 m
 - time step (dt): 0.05 s
 - maximum time (max_t): 200 s
 - gravitational acceleration (g): 9.81 m/s^2
 - dissipation coefficient (gamma): 2e-05 1/s
 - source type: 1
 - sampling rate: 40
 - input bathymetry (h) file: 'h_simple.dat'
 - output elevation (eta) file: 'eta_simple'
 - output velocity (u, v) files: 'u_simple', 'v_simple'
 - grid size: 4000 m x 4000 m (800 x 800 = 640000 grid points)
 - number of time steps: 4000
Computing step 3600/4000 (ETA: 9.46492 seconds)
Done: 95.0937 seconds (26.9208 MUpdates/s)