Jetstream Tutorial for New Students

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Follow the steps below to quickly get up and running with Jetstream

0. The first thing that you need to do is sign-up for a SciNet account. See document here for instructions. NOTE: The correct address for acct setup is here: http://www.scinethpc.ca/getting-a-scinet-account/
Use the following when asked for a Compute Canada Role Identifier:
syu-780
After completing the above steps, tt takes about 1-2 days to activate your SciNet account. You should be sent an email containing your login credentials when your account has been activated.
1. Update .cshrc file on your CFD lab computer (oddjob account):
cp ~hbuckley/.cshrc.new-student ~/.cshrc
 
emacs ~/.cshrc !-- edit .cshrc;
               !-- replace <your-scinet-username> with your
               !-- scinet username
 
source ~/.cshrc !-- reload updated .cshrc file
 
mkdir ~/bin !-- create a 'bin' directory on oddjob
 
mkdir ~/grid_utils !-- create a directory for grid utility scripts

2. Login to scinet and update .bashrc file:
cp /home/z/zingg/hbuckley/.bashrc.new-student ~/.bashrc
 
emacs ~/.bashrc !-- edit .bashrc;
                !-- replace <your-oddjob-username> with your
                !-- oddjob username
 
source ~/.bashrc
 
 

3. Setup SSH keys

On the HPC system (SciNet, Graham, etc)
ssh-keygen -t rsa

When prompted, enter a passphrase.

Now transfer the public keys to your local machine (and vice versa).
On the HPC system (eg scinet):

ssh-copy-id <username>@oddjob.utias.utoronto.ca

On your local machine
ssh-copy-id <username>@login.scinet.utoronto.ca

4. Create 'bin' directory for the jetstream executable file
mkdir ~/bin

5. Get Jetstream:
git clone -o central <your-oddjob-username>@oddjob.utias.utoronto.ca:/nfs/carv/d1/people/comp-aero/jetstream.git jetstream

6. Compile Jetstream:
gpc1 !-- login to a scinet development node
 
cd ~/jetstream !-- navigate to jetstream directory
 
./make_jetstream !-- run script to compile jetstream executable for the first time

7. Check to see that the jetstream executable has been created
ls -l ~/bin/jetstream_x86_64
The output from the above command should show an executable file created with a date stamp from today and a non-zero size

8. Run a test case
cd $SCRATCH !-- navigate to scratch space...can’t run cases from your home directory
 
cp -r $JSTS/002/ !-- copy test casefrom jetstream test suite
 
cd 002
 
qsub sciSubmit !-- submit job to the scinet queue

9. Visualize a flow solution with Tecplot
scp grid_026.con $SCP_ODDJOB/grid.con !-- copy grid and solution files to oddjob
 
scp grid_026.g $SCP_ODDJOB/grid.g
 
scp results.q $SCP_ODDJOB/results-001.q
 

On oddjob account:
cp ~hbuckley/bin/sol7_3d.eqn ~/bin/. !-- copy tecplot equations file
cp -r ~hbuckley/grid_utils/code ~/grid_utils/.!-- copy scripts for grid manipulation
 
cd ~/grid_utils/code
 
ifort -o gen_surfsym_layout gen_surfsym_layout.f90
 
cd ~/scinet-temp
 
~/grid_utils/code/gen_surfsym_layout
 
tecplot surfsym.lay