In this activity, you will verify that you can run a job on the compute resources, Comet and Bridges, that we are using for hands-on sessions. Directions are given below for logging into each resource and running a job by submitting a simple batch script. You do not need to write the batch script, one that runs a trivial simulation will be provided. 

Important Note: Before you try to run a job, please check the user portal front page, you should see "Comet" and "Bridges" listed under "My XSEDE Resources", and "International HPC Summer School 2018", Charge # TG-ASC170029 listed under "My Projects".  If you do not see those, check back later, we are propagating add-user requests through the system which may take a couple of days.

Important Note #2: If you had not yet registered for the hands-on training computer access, please go to https://portal.xsede.org, create a portal account (if you have not yet done so), and then register for the session at:

https://portal.xsede.org/course-calendar/-/training-user/class/609

This session requires a password: IHPCSS2018


Run a Job on Bridges

Step 1: Log into Bridges

You will need your XSEDE username and password to log into Bridges.  Log in using the following command:

$ ssh -p 2222 <your_xsede_username>@bridges.psc.edu
Password: <your_xsede_password>

Note: If you encounter ssh connection problems like No route to host or Connection refused, please try to login into comet first (ssh <your_comet_username>@comet.sdsc.edu). From there you should be able to ssh into bridges.

Note: If you set up Duo multi-factor authentication in the XSEDE user portal, you will be prompted to use it when connecting to Bridges.

Step 2: Submit the batch script

The default environment will work for this job without modification. You can verify this with the module list command:

$ module list
Currently Loaded Modulefiles:
  1) psc_path/1.1      2) slurm/default   3) intel/17.4

(If you want to learn more about using modules, see Section 4 Environment Modules in the CI-Tutor course XSEDE: Customizing your Computing Environment.)

Get the provided batch script, shallow-ihpcss.sb, by copying it to your home directory:

$ cp ~alameda/shallow-ihpcss.sb .

Submit the batch script using the sbatch command:

$ sbatch shallow-ihpcss.sb
Submitted batch job 1192054

After the job runs, inspect the output file using the cat command:

$ cat shallow.*.out

The last 7 - 8 lines of output from a successful run should look something like this: 

Cycle number  1000    Model time in days   1.04
   Potential energy    21561.033  Kinetic Energy    26439.463
   Total Energy        48000.496  Pot. Enstrophy     1.805456e-27

Mon Jun  5 16:06:36 EDT 2017
r442.pvt.bridges.psc.edu
alameda

 

Run a Job on Comet

Step 1: Log into Comet

You will need your Comet username and XSEDE password to log into Comet. You can find your Comet username at https://portal.xsede.org/group/xup/accounts

$ ssh <your_comet_username>@comet.sdsc.edu
Password: <your_xsede_password>

Step 2: Submit the batch script

The default environment for Comet is correct for this particular job:

$ module list
Currently Loaded Modulefiles:
  1) intel/2013_sp1.2.144   2) mvapich2_ib/2.1        3) gnutools/2.69

Copy the provided batch script to your home directory:

$ cp ~ux400689/shallow-ihpcss.sb .

Submit the batch script:

$ sbatch shallow-ihpcss.sb
Submitted batch job 1192054

After the job runs, inspect the output file:

$ cat shallow.*.out

A successful run will show output that ends with:

Cycle number  1000    Model time in days   1.04
   Potential energy    21560.932  Kinetic Energy    26439.541
   Total Energy        48000.473  Pot. Enstrophy     2.288422e-27

IBRUN: Job ended with value 0
Mon Jun  5 13:32:33 PDT 2017
comet-05-09.sdsc.edu
ux400689

 

A note about project charge codes:

These exercises will charge the allocation provided for the 2018 International HPC Summer School which corresponds to the charge code TG-ASC170029 on Comet, and ac560tp on Bridges. The batch scripts already have these charge codes added.

Last modified: Friday, June 29, 2018, 3:56 PM