SIMPLEG-WBM coupling

Current status

• Now you can run a series of Singularity containers automatically by submitting a job script from Terminal.
• The script runs four Singularity containers sequentially and uses previous stage’s outputs
• Current workflow assumes some convergence conditions. Workflow orchestration will be changed to alternative approach proposed by Iman.

There are some minor changes but Jungha should be able to create the shocks for SIMPLEG using the code:
Spin-up:
We need an initial run of WBM for 2000-2005
Then we calculate the shocks for SIMPLEG using WBMtoSIMPLE_v3. The new R script takes the “sim.year1” (here 2004) and “sim.length” (here 4) as inputs. After the test run, the year will be updated at each run.
Then we solve SIMPLEG. It will create a new land area to be sent to WBM. for the test run, I like to label it with the “2005” run.
Consecutive WBM-SIMPLEG runs:
Here we need to run WBM only for the next year (the year 2005).
Then we calculate the shocks for SIMPLEG (for 2005). It creates a new land area to be sent to WBM for the next year, it will be labeled with the next year (here as 2006).
Then we repeat (a) and (b) for all the required years.

Submit workflows and inputs/outputs. Most recent status document is available at WBM-SIMPLEG coupling status

Set up an environment to run coupled models

Singularity containers and their inputs are available at /depot/ssg/geoshare/data/GLASS/INFEWS/SIMPLEG_WBM_COUPLING directory.
Please make sure you have privilege to read that directory. Otherwise the following script will fail.
The script will copy all necessary files to your Brown’s scratch space, namely /scratch/brown/$USER/SIMPLEG_WBM_COUPLING.
Here $USER stands for your account.

wooj@brown-fe02:~$ /depot/ssg/geoshare/data/GLASS/INFEWS/setup_wbm_simpleg_env.sh

Please copy and paste this command to the terminal and execute it.
This may take long as it copies about 40GB zip files and uncompress them.
Once the set up is done, you will see SIMPLEG_WBM_COUPLING directory in /scratch/brown/$USER/

Subdirectories under SIMPLEG_WBM_COUPLING folder

Submit a job

Log and error files are created at the directory where the submit executable is called.
Please look into “slurm-jobid.out” file for investigating errors.

wooj@brown-fe02:~$ sbatch /scratch/brown/wooj/SIMPLEG_WBM_COUPLING/submit/simpleg-wbm.sub
Submitted batch job 12837875

You can use alternative submit file for running the workflow two times.

wooj@brown-fe02:~$ sbatch /scratch/brown/wooj/SIMPLEG_WBM_COUPLING/submit/simpleg-wbm-r2.sub

Checking status of a job

Job status is shown as 'Running' or 'R' at the ST (Status) column

Submit file

The sequence submit file executes containers

One iteration consist of four steps. The script finishes after a single iteration.
Multiple iterations can be done by modifying for loop in the script later.
For example, to run three iterations, script can be updated to

    for i in 1 2 3

1. WBM Singularity container
   • WBM container’s output is written under wbm_output directory, not job-specific directory.
2. WBM to SIMPLEG Singularity container
   • It reads daily files and aggregates them into yearly resolution.
   • Default Start year and end year are set to 2000-2004. Users can supply start and end year when running container. These are specified from the submit file.
3. SIMPLEG Singularity container
   • Each iteration’s output is written to job specific directory such as Iteration_1_S3 or Iteration_2_S3 …
4. SIMPLEG to WBM container
   • Its output is directly written to WBM’s input directory

A submit file executing four containers sequentially. If you want to run a specific step only, comment out the others with '#' at the beginning of the line

Editing submit file

• If you want to execute a certain Singularity only, comment out the other steps.
• DO NOT forget to replace the $SLURM_ID with the actual job id you want to refer to.
• Please contact Jungha Woo (wooj@purdue.edu) for any questions.

Container recipes

Four Singularity recipes are available at GitHub https://github.com/junghawoo/simpleg-wbm-coupling, but they are private repositories at this moment. Please contact Jungha Woo ( wooj@purdue.edu).

Container 101

Created on 19 Oct 2021, Last modified on 11 Jan 2022