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Your First Program on Hopper

From Logging in to Submitting a Job

In order to follow this page, you will need an account, a username and a password. If you do not have all of these things please visit the Accounts Page.

Logging in

% ssh -l username

When you successfully log in you will land in your $HOME directory.

First Program Code: Parallel Hello World

Open a new file called helloWorld.f90 with a text editor such as emacs or vi. Paste the contents of the below code into the file.

program helloWorld
implicit none
include "mpif.h"
integer :: myPE, numProcs, ierr
call MPI_INIT(ierr)
call MPI_COMM_SIZE(MPI_COMM_WORLD, numProcs, ierr)
print *, "Hello from Processor ", myPE
call MPI_FINALIZE(ierr)
end program helloWorld

Compile the program

Use the compiler "wrappers" to compile codes on Hopper: use ftn for Fortran, cc for C, and CC for C++.

% ftn -o helloWorld helloWorld.f90

Create a Batch Script

Open a file called my_batch_script with a text editor like vi or emacs and paste in the contents below. (Use the "view source" button Copy Icon that will appear in the upper right hand corner of the batch script example when you move your cursor there.)  The batch script is used to tell the Hopper system to reserve compute node resources for your job and how it should launch your application on the compute nodes it has reserved.

Contents of file: my_batch_script

#PBS -q debug 
#PBS -l mppwidth=24
#PBS -l walltime=00:10:00
#PBS -N my_job
#PBS -j oe

aprun -n 24 ./helloWorld

Submit Your Job to the Queue

The qsub command is used on the login nodes to submit your batch script so your job will run on the Hopper compute nodes.

% qsub my_batch_script

A jobid will be returned, such as 15674.sdb

Monitor Your Job in the Queue

After you submit your job, the system scheduler will check to see if there are compute nodes available to run the job. If there are compute nodes available, your job will start running. If there are not, your job will wait in the queue until there are enough resources to run your application. You can monitor your position in the queue using several different commands, such as:

hopper% qs
hopper% qstat -u username
hopper% showq

Examine Your Job's Output

When your job has completed you should see a file called my_job.o[jobid]

Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell. Hello from Processor            20
 Hello from Processor            18
 Hello from Processor             8
 Hello from Processor            16
 Hello from Processor             4
 Hello from Processor             2
 Hello from Processor            21
 Hello from Processor            12
 Hello from Processor            10
 Hello from Processor             0
 Hello from Processor            14
 Hello from Processor            22
 Hello from Processor            11
 Hello from Processor             5
 Hello from Processor            17
 Hello from Processor            19
 Hello from Processor             1
 Hello from Processor            23
 Hello from Processor             6
 Hello from Processor             3
 Hello from Processor             9
 Hello from Processor             7
 Hello from Processor            15
 Hello from Processor            13

Application 189782 resources: utime 0, stime 0

Note: If you see messages such as "Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell" in your batch output, just ignore them!