Working with Fortran

The tutorial assumes you have already worked through the Execute a Job Tutorial. Therefore, the instructions here are abbreviated but will follow the same format so you may easily consult the extended tutorial.

Table of Contents

• Step 1: Access the Onyx HPC

• Step 2: Create an sbatch Script

  • Example sbatch Script

  • sbatch Procedure

• Step 3: Compile the Fortran Program from Source

  • MPI Hello World Source Code

  • Fortran Procedure

• Step 4: Run the Job

📝 Note: Do not execute jobs on the login nodes; only use the login nodes to access your compute nodes. Processor-intensive, memory-intensive, or otherwise disruptive processes running on login nodes will be killed without warning.

Step 1: Access the Onyx HPC

1. Open a Bash terminal (or MobaXterm for Windows users).

2. Execute ssh [e-mail].

3. When prompted, enter your password.

Step 2: Create an sbatch Script

Example sbatch Script

Here is an example sbatch script for running a batch job on an HPC like Onyx.

#!/bin/bash

#SBATCH -n 16
#SBATCH -o test_%A.out
#SBATCH --error test_%A.err
#SBATCH --mail-user $CHANGE_TO_YOUR_EMAIL
#SBATCH --mail-type ALL

module purge
module load gnu/5.4.0
module load openmpi
module list
mpirun hello_world_f

sbatch Procedure

1. Use nano or Vim (we use Vim here) to create and edit your sbatch script.

   vim slurm_f90_example.job

2. Create your sbatch script within Vim by typing i for insert mode or paste the contents of your sbatch script into Vim.

3. Save your file by typing :wq! and return to the Bash shell.

Step 3: Compile the Fortran Program from Source

MPI Hello World Source Code

program helloworld
use mpi
integer ierr, numprocs, procid

call MPI_INIT(ierr)

call MPI_COMM_RANK(MPI_COMM_WORLD, procid, ierr)
call MPI_COMM_SIZE(MPI_COMM_WORLD, numprocs, ierr)

print *, "Hello world! I am process ", procid, "out of", numprocs, "!"

call MPI_FINALIZE(ierr)

stop
end

Fortran Procedure

1. Use Vim (vim) to create your Fortran source file.

   vim hello_world.f90

2. Save your file and return to the Bash shell.

3. Load the MPI compiler using the openmpi module.

   module load openmpi

4. Compile the Fortran source into a binary executable file.

   mpifort -o hello_world_f hello_world.f90

5. Use ls -al to verify the presence of the hello_world_f binary in your working directory.

Step 4: Run the Job

1. Before proceeding, ensure that you are still in your working directory (using pwd) and that you still have the PE-gnu module loaded (using module list).

   • We need to be in the same path/directory as our sbatch script and our Fortran binary. Use ls -al to confirm their presence.

2. Use sbatch to schedule your batch job in the queue.

   sbatch slurm_f90_example.job

   This command will automatically queue your job using slurm and produce a job number. You can check the status of your job at any time with the squeue command.

   squeue --job <jobnumber>

   You can also stop your job at any time with the scancel command.

   scancel --job <jobnumber>

3. View your results. You can view the contents of these files using the less command followed by the file name.

   less test_<jobnumber>.out

   Your output should look something like this (the output is truncated.):

   Hello world! I am process            3 out of          20 !
   Hello world! I am process            0 out of          20 !
   Hello world! I am process            1 out of          20 !
   Hello world! I am process            7 out of          20 !
   Hello world! I am process            8 out of          20 !
   Hello world! I am process            2 out of          20 !
   Hello world! I am process            6 out of          20 !
   Hello world! I am process           11 out of          20 !
   .
   .
   .

4. Download your results (using the scp command or an SFTP client) or move them to persistent storage. See our moving data section for help.

Additional Examples

• Working with C
• Working with C++
• Working with Python
• Working with Makefiles