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 2019: Due to our current inability to use port 2222 through our summer school venue we need to use local bridges usernames and passwords to access bridges, and the default port of 22 with ssh.  Two important things to know:

1) You can find your local username for all of your resources at the XSEDE User Portal (https://portal.xsede.org), "My XSEDE>Accounts".

2) Please set your local password on bridges at the following site: https://apr.psc.edu.

Once you have set your local password, you can access bridges using the default port 22, ie, ssh -l local_bridges_username bridges.psc.edu


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>Summary>My XSEDE Resources", and "International HPC Summer School 2019", 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/1507/session/2839

This session requires a password: IHPCSS2019


Run a Job on Bridges

Step 1: Log into Bridges

Follow the steps above for accessing Bridges.  Do NOT use port 2222, it won't work.


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 2019 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: Sunday, July 7, 2019, 9:47 PM