You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 33 Next »

Research Repository for Data and Diagnostics

GitHub repositories:

https://github.com/JCSDA-internal/r2d2-client (R2D2 V3 client: feature/cleanup1)

Related GitHub repositories:

https://github.com/JCSDA-internal/ewok (R2D2 V3: feature/r2d2v3)

Documentation:

R2D2 Planning Meeting Notes:

News Releases:


Table of Contents

About

R2D2 is a lightweight Python API, an SQL schema, and a live, production, cloud-based MySQL database server that Skylab utilizes for data assimilation experiments.

The current R2D2 is version 2 which uses Python MySQL Connector to execute queries directly to the remote, production MySQL database located on us-east-2 on r2d2.jcsda.org on port 3306. 

The new R2D2 is version 3 which uses a standardized client / server architecture using REST HTTP API calls well-defined by an OpenAPI 3.0 specification matching R2D2's SQL schema.

Both the client and REST server APIs for R2D2 V3 are item-based and not function-based as in the R2D2 V2 database connector API.

The SQL schema for V2 and V3 are identical. 

Procedures

Adding Files to EWOK_STATIC_DATA to HPC environments

Requirements:

Access to Orion since files are synced from there, although this can be worked around.

  • Access to jedi-para  or jedipara  or role-jcsda on HPCs

Steps:

  1. Log into Orion and sudo to the role-jcsda  account.
    ssh -Y <user_name>@orion-login.hpc.msstate.edu
sudo -su role-jcsda
  2. Copy static files from staging location to the decided $EWOK_STATIC_DATA location. The staging location is usually given in the work ticket and is the location where the JCSDA team member has placed the data. File names can be renamed if needed. Make sure to match the permissions as the other files in $EWOK_STATIC_DATA directory (hint: chmod 644).
  3. Run the rsync from the other HPCs. There is a script located inside jedipara's ~/bin  directory the can be used to perform the rsync. Make sure the username is yours instead of the most recent team members. If you get an ssh error, you can remove the machine from known hosts and try again. An example of the script on Discover is located at /home/jedipara/bin/rsync-ewok-static-from-orion.sh. Sync to discover example:
    ssh -XY <user_name>@login.nccs.nasa.gov
sudo -iu jedipara
cd bin
vi rsync-ewok-static-from-orion.sh 		# Edit to your Orion username
bash rsync-ewok-static-from-orion.sh
  4. Check off each machine in the R2D2-data ticket as you sync.

Adding Files to EWOK_STATIC_DATA to the AWS bucket

Execute the following line from Orion. Note, this can be done from your own user and aws is a part of our JEDI environment provided by spack-stack.

/path/to/aws s3 sync --size-only --profile=jcsda-usaf-aws-us-east-2 /work2/noaa/jcsda/role-jcsda/static/ s3://r2d2.static.s3.us-east-2/

Adding Files for R2D2 Archive (such as background files)

Requirements:

This procedure requires the use of R2D2 Admin functions, therefore you will need:

  • Recent version of R2D2 on the host the data is located on
  • Make sure your r2d2, solo, and venv directories are accessible by the jedipara user. Hint:
    chmod g+rX jedi-bundle
chmod o+rX jedi-bundle
chmod -R g+rX r2d2
chmod -R g+rX solo
chmod -R g+rX venv

Steps (example using Discover):

  1. Log into the HCP where the data to be ingested is located, become the jedipara or role-jcsda user depending on HPC, and go to the location for R2D2 archive.
    ssh -XY <user_name>@login.nccs.nasa.gov
sudo -iu jedipara 
cd /discover/nobackup/projects/jcsda/s2127
  2. Set up your venv, using setup.sh, that was created in the requirements section. You might need to update $JEDI_ENV.
    vi setup.sh			# Verify JEDI_ENV location
source setup.sh
  3. Log into a screen session so no work will be lost if you get logged out
    screen -S r2d2_ingest
  4. Verify that your venv is still loaded, if not re-load following the same steps as #2.
  5. Check your r2d2 admin utility access. If this does not work make sure you followed the requirements.
    python3
>>> from r2d2.util.admin_util import AdminUtil
  6. Use the "AdminUtil.move_experiment" function to move the experiment given in the r2d2-ingest ticket to oper and the correct data_store. You can refer to the r2d2 code to ceck for arguments needed and how to use them.
    >>> AdminUtil.move_experiment(source_experiment='e8254a', target_experiment='oper', ensemble_data_store_type='geosensemble')
  7. To get the data to the other HPCs, on your origin system you will sync to S3 and then sync the data stores.
    /path/to/aws s3 sync --size-only --profile=jcsda-usaf-aws-us-east-2 /discover/nobackup/projects/jcsda/s2127/r2d2-archive-nccs/ s3://r2d2-archive-jcsda-usaf-aws-us-east-2/

python3
>>> from r2d2.util.admin_util import AdminUtil
>>> AdminUtil.sync_data_stores(source_data_store='r2d2-archive-nccs', target_data_store='r2d2-archive-jcsda-usaf-aws-us-east-2')
  8. Log into MSU's Orion and sync from S3. Then you can proceed to log into the other HPCs and sync NWSC/SSEC systems from MSU using the sync scripts in ~/bin.
    ssh -Y <user_name>@orion-login.hpc.msstate.edu
sudo -su role-jcsda
# Load venv to get aws modules or load modules following jedi-docs
aws s3 sync --size-only --profile=jcsda-usaf-aws-us-east-2 s3://r2d2-archive-jcsda-usaf-aws-us-east-2/ /work2/noaa/jcsda/role-jcsda/r2d2-archive-msu/
  9. Run the rsync from the other HPCs. There is a script located inside jedipara's ~/bin  directory the can be used to perform the rsync. Make sure the username is yours instead of the most recent team members. If you get an ssh error, you can remove the machine from known hosts and try again.
    ssh -XY <user_name>@<hpc>
sudo -iu jedipara
cd bin
vi rsync-r2d2-archive-from-msu-<user-name>.sh        # Edit to your Orion username
bash rsync-r2d2-archive-from-msu-<user-name>.sh

Installing the r2d2 v3 server

This installation process needs to be updated and combined into one standard install. Note: The r2d2 server does NOT require spack-stack or any spack-stack-related dependencies. 

cd r2d2
python3 -m pip install -e .
cd server
python3 -m pip install -e .

Starting the r2d2 v3 server

cd r2d2/server/app
pwd					
# Returns .../r2d2/server/app
run_r2d2_app --port=8080 --debug
# You should see this output. This means that the server is running.
* Serving Flask app 'app.app'
* Debug mode: on
WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
* Running on all addresses (0.0.0.0)
* Running on http://127.0.0.1:8080
* Running on http://192.168.10.66:8080
Press CTRL+C to quit
* Restarting with stat
* Debugger is active! 
* Debugger PIN: 912-946-391

Installing the r2d2 v3 client

cd r2d2-client
python3 -m pip install -e .

How to use the r2d2 v3 client generator

cd r2d2/server/app
python3
>>> from generator import Generator
>>> Generator().generate(client_output_path='/Users/eric2/jedi/jedi-bundle/r2d2-client/src/r2d2_client/r2d2_client.py')
>>> # OR
>>> Generator(selected_item='observation').generate(client_output_path='/Users/eric2/jedi/jedi-bundle/r2d2-client/src/r2d2_client/r2d2_client.py')

Using the r2d2 v3 client

python3
>>> from r2d2_client import R2D2Client
>>> R2D2Client.search_experiment(user='eric')

How to launch the Swagger Editor for editing app.yaml using a localhost Docker container

docker pull swaggerapi/swagger-editor
docker run -d -p 80:8080 swaggerapi/swagger-editor

Important Reference Links

Troubleshooting / FAQ

  • No labels