Setting up the Deployment Environment
Requirements:
WUSTL key is required to access both RIS Compute Cluster and Azure Devops
Access to the RDC git repository in devops
A ssh client like Windows cmd/powershell ssh, WSL linux shell on Windows, Git Bash shell, Mac (Debian ssh) shell or Putty SSH
Setting up user's home environment
- create pgpass file for PostgreSQL credentials, !!! be careful if you have an already exiting .pgpass file
touch ~/.ssh/.pgpass
chmod 600 ~/.ssh/.pgpass
# copy pgpass template info
echo "# host:port:database:username:password" >> ~/.ssh/.pgpass
- Add new bash prompt to users existing .bash_profile file
cat bash_profile >> ~/.bash_profile
# you may need to manually remove any older PS1 export from the bash profile
- Add bashrc docker environment update to users existing .bashrc file
cat bashrc >> ~/.bashrc
- create new psqlrc file with new prompt and extras, !!! be careful if you have an already exiting .psqlrc file
# add new ,psqlrc file for users
cp psqlrc ~/.psqlrc
# to append to users existing .psqlrc file
cat psqlrc >> ~/.psqlrc
- launching the lsub job for postgres
Example output from RIS compute cluster:
warrenth@BB000WL-FTC36D3:~$ ssh -l warren.thomas compute1-client-2.ris.wustl.edu
You are connecting to RIS Compute services.
Membership in a compute-* AD group is required.
Users are responsible for acting in accordance with
policies applicable to Washington University St. Louis.
https://confluence.ris.wustl.edu/display/RSUM/RIS+Compute+%3A+User+Agreement
warren.thomas@compute1-client-2.ris.wustl.edu's password:
Last failed login: Thu Dec 19 08:38:23 CST 2024 from 10.224.31.105 on ssh:notty
There were 2 failed login attempts since the last successful login.
Last login: Tue Dec 17 08:41:17 2024 from 10.224.30.7
[warren.thomas@compute1-client-2i: ~] $ repos/ris-etl-deployments/rdc_scripts/get-interactive-job.sh
Job <958462> is submitted to queue <ohids-interactive>.
<<Waiting for dispatch ...>>
<<Starting on compute1-exec-391.ris.wustl.edu>>
v1: Pulling from indraniel/bolton-db-toolkit
8740c948ffd4: Pull complete
de070776c313: Pull complete
93346d961b28: Pull complete
8287e6c66390: Pull complete
Digest: sha256:b9b062f1625700670dbc293cac5efca49aac290519554efe778f7528c9d7fe70
Status: Downloaded newer image for indraniel/bolton-db-toolkit:v1
docker.io/indraniel/bolton-db-toolkit:v1
Supported Environments:
-----------------------
prod
qa
dev
local
What environment is to be used? prod
Valid Connections:
------------------
0. rdcadmin@i2rdc3-dev-pg-flex-config.dev.i2rdc3.wustl.edu:postgres
1. rdcadmin@i2rdc3-qa-pg-flex-config.qa.i2rdc3.wustl.edu:postgres
2. rdcadmin@i2rdc3-prod-pg-flex-config.prod.i2rdc3.wustl.edu:postgres
3. rdc_etl_user@postgresql.prod.i2rdc3.wustl.edu:omop_dw
4. rdc_etl_user@postgresql.qa.i2rdc3.wustl.edu:omop_dw
5. rdc_etl_user@postgresql.dev.i2rdc3.wustl.edu:omop_dw
6. mdc_etl_user@postgresql.prod.i2rdc3.wustl.edu:omop_dw
7. mdc_etl_user@postgresql.qa.i2rdc3.wustl.edu:omop_dw
8. mdc_etl_user@postgresql.dev.i2rdc3.wustl.edu:omop_dw_mdclone
9. postgres@postgresql.qa.i2rdc3.wustl.edu:postgres
10. postgres@postgresql.dev.i2rdc3.wustl.edu:postgres
[warren.thomas@compute1-exec-391i:prod ~] $ show_rdc_env
${CONNECTION} =
${PG_STRING} =
${PGPASSFILE} = /home/warren.thomas/.ssh/.pgpass
${RDC_LOGS} = /storage1/fs1/I2/Active/rdc2_etl/prod/logs
${RDC_REPOS} = /storage1/fs1/I2/Active/rdc2_etl/prod/repos
${RDC_HOME} = /storage1/fs1/I2/Active/rdc2_etl/prod
${RDC_ETL} = /storage1/fs1/I2/Active/rdc2_etl/prod/repos/rdc_etl
${ENVIRONMENT} = prod
${USER} = warren.thomas
${RDC_BACKUPS} = /storage1/fs1/I2/Active/rdc2_etl/prod/backups
${RDC_DEVOPS} = /storage1/fs1/I2/Active/rdc2_etl/prod/devops