Jetstream+Tutorial+for+New+Students

Click here to return to Miscellaneous Documentation page

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 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): code cp ~hbuckley/.cshrc.new-student ~/.cshrc

emacs ~/.cshrc !-- edit .cshrc; !-- replace  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 code

2. Login to scinet and update .bashrc file: code cp /home/z/zingg/hbuckley/.bashrc.new-student ~/.bashrc

emacs ~/.bashrc !-- edit .bashrc; !-- replace  with your !-- oddjob username

source ~/.bashrc

code

3. Setup SSH keys

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

When prompted, enter a passphrase.

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

code ssh-copy-id @oddjob.utias.utoronto.ca code

On your local machine code ssh-copy-id @login.scinet.utoronto.ca code

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

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

6. Compile Jetstream: code 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 code

7. Check to see that the jetstream executable has been created code ls -l ~/bin/jetstream_x86_64 code 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 code 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 code

9. Visualize a flow solution with Tecplot code 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

code

On oddjob account: code 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 code