Execute a Job: Fortran Example

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

📝 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 Your Allocation

If you need to request an allocation, see instructions here.

  1. Open a Bash terminal (or PuTTY for Windows users).
  2. Execute ssh username@or-condo-login.ornl.gov.
  3. Replace "username" with your XCAMS or UCAMS ID.
  4. When prompted, enter your XCAMS or UCAMS password.

Step 2: Create a PBS Script

Example PBS Script

Here is an example PBS script for running a batch job on a SHPC Condo allocation.

#!/bin/bash

#PBS -N mpi_hello_world_f
#PBS -M your_email@ornl.gov
#PBS -l nodes=1:ppn=16
#PBS -l walltime=0:00:6:0
#PBS -W group_list=cades-birthright
#PBS -A birthright
#PBS -l qos=burst
#PBS -V

module purge
module load PE-gnu
module list
cd $PBS_O_WORKDIR
pwd
mpirun hello_world_f

PBS Procedure

  1. From the login node, change your working directory to the desired file system. We are going to use our Lustre allocation for this example. If Lustre storage is not available, you may complete this tutorial from within your home directory on NFS.
cd /lustre/or-scratch/cades-birthright/username

Replace "username" with your UCAMS/XCAMS user ID.

  1. Use Vi to create and edit your PBS script.
vi hello_world_f.pbs
  1. Create your PBS script within Vi or paste the contents of your PBS script into Vi.
  2. Save your file 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. Ensure that you are still in your working directory (/lustre/or-scratch/cades-birthright/username) using pwd.
  2. Use Vi (vi) to create your Fortran source file within your working directory.
vi hello_world.f90
  1. Save your file and return to the Bash shell.
  2. Load the MPI compiler using the PE-gnu module.
module load PE-gnu
  1. Compile the Fortran source into a binary executable file.
mpifort -o hello_world_f hello_world.f90
  1. 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).

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

  3. PE-gnu also loads OpenMPI, GCC, and XALT. Use module list to confirm their presence. If necessary, use module load PE-gnu to reload the module(s).

  4. Use qsub to schedule your batch job in the queue.

qsub hello_world_f.pbs

This command will automatically queue your job using Torque and produce a six-digit job number (shown below).

143295.or-condo-pbs01

You can check the status of your job at any time with the checkjob command.

checkjob 143295

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

qdel 143295
  1. View your results.
    You can view the contents of these files using the more command followed by the file name.
more mpi_hello_world_f.o143295

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 !
.
.
.
  1. 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