This repository pulls national flow data from NWIS for 50 states and all territories. The pipeline pushes to a shared cache in a USGS-internal S3 bucket called ds-pipeline-national-flow-observations (note you need to be logged into the console before this link will work).
As of 2022, the repo is set-up for use on Tallgrass because Yeti will be removed from service in August 2022. The 2022 version of this repo is currently cloned here: /caldera/projects/usgs/water/iidd/datasci/data-pulls/national-flow-observations
These are exact commands for Tallgrass. This is needed only when the image needs to be updated or when we move the repo somewhere other than Tallgrass.
After cloning the repo, pull the docker image from code.chs.usgs.gov:
module load singularity
singularity pull --docker-login docker://code.chs.usgs.gov:5001/wma/wp/national-data-pulls:v0.1
After you run the commands above you will see a prompt for a password. The password it is looking for is your personal access token (PAT). If you do not have a PAT set up you will need to do so.
Two Slurm scripts are included in this repo. If you want to run Rstudio to do development work, run sbatch launch_rstudio.slurm and then follow the instructions in the Slurm output file (shellLog/rstudio.out) to make an SSH tunnel and log in to Rstudio via a browser.
To run the pipeline as a non-interactive batch job, open run_scmake.slurm and modify parameters like job length (--time) and partition (-p) as needed for how long you expect the job to run (see this issue for estimates). Submit the job with sbatch --mail-user=$USER@usgs.gov run_scmake.slurm.
To be able to run the full pipeline, you will need to have AWS credentials setup on your user's home directory on Tallgrass. This will only be possible for USGS users. You need to have the file /home/username/.saml2aws, which looks like this:
[default]
url = https://fs.doi.gov
username = USER@usgs.gov
provider = ADFS
mfa = Auto
skip_verify = false
timeout = 0
aws_urn = urn:amazon:webservices
aws_session_duration = 28800
aws_profile = default
resource_id =
subdomain =
role_arn =
region =
http_attempts_count = 3
http_retry_delay = 1
Be sure to update the username field to match your own email. Before being able to successfully use this file, you will need to install saml2aws (yes, even on HPC). You can follow instructions for doing so in our USGS guide to using saml2aws.
To use the saml2aws setup, you will need to log in either before running scmake() in an interactive session or before you submit your non-interactive batch job. Note that credentials will work for a maximum of 8 hours, which means that you may get a failure and need to re-authenticate for jobs that take longer. Run the following to use the appropriate credentials to authenticate to AWS for this pipeline:
saml2aws login --role=arn:aws:iam::807615458658:role/adfs-wma-developer --region us-west-2