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.
% ssh -l username hopper.nersc.gov
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.
integer :: myPE, numProcs, ierr
call MPI_COMM_RANK(MPI_COMM_WORLD, myPE, ierr)
call MPI_COMM_SIZE(MPI_COMM_WORLD, numProcs, ierr)
print *, "Hello from Processor ", myPE
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 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% qstat -u username
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!