Cartblanche22 Build Instructions - Revision history

Jocastanon at 19:41, 18 June 2024

2024-06-18T19:41:03Z

2024-06-18T19:40:53Z

2024-06-18T19:33:29Z

← Older revision		Revision as of 19:33, 18 June 2024
Line 109:		Line 109:

	* 0.0.0.0:5068 refers to the port that points to the application.		* 0.0.0.0:5068 refers to the port that points to the application.

			[[Category:Cartblanche]]
			[[Category:Docker]]
			[[Category:Mar]]

2024-06-18T19:32:11Z

Deployment Information

← Older revision		Revision as of 19:32, 18 June 2024
Line 20:		Line 20:

	The first stage will build/update the current docker image to the gitlab server running on n-9-22. On the web interface, this is in the cartblanche repo under 'Packages & Registries'.		The first stage will build/update the current docker image to the gitlab server running on n-9-22. On the web interface, this is in the cartblanche repo under 'Packages & Registries'.

	~~The second stage tests the new container and runs tests for~~
	~~- ZincID Search~~
	~~- Supplier Code Search~~
	~~- SMILES Search~~

	Finally, the docker image is pulled in each of the three servers and restarted.		Finally, the docker image is pulled in each of the three servers and restarted.

2023-11-16T18:49:03Z

Deployment Information

← Older revision		Revision as of 18:49, 16 November 2023
Line 29:		Line 29:

	'''Useful Commands''' (Use these in the respective server to debug):		'''Useful Commands''' (Use these in the respective server to debug):
	docker restart ~~molecule-shopping-cart~~ (restart the docker container)		sudo docker restart cartblanche22 (restart the docker container)
	docker logs ~~molecule-shopping-cart~~ (view app logs)		sudo docker logs cartblanche22 (view app logs)

	'''Some troubleshooting tips:'''		'''Some troubleshooting tips:'''

2023-08-17T19:05:36Z

Setting up Auto-Deployment

← Older revision		Revision as of 19:05, 17 August 2023
Line 97:		Line 97:
	- cartblanche-dev'''		- cartblanche-dev'''
	script:		script:
	- docker ~~build~~ -~~t "~~${~~CI_PROJECT_NAME~~}:${~~CI_COMMIT_REF_NAME~~}-~~0.1.~~${~~CI_JOB_ID~~}~~" .~~		- docker login ${GITLAB_REGISTRY_URL} -u ${GITLAB_REGISTRY_USER} -p ${GITLAB_REGISTRY_PASS}
			- docker pull ${GITLAB_REGISTRY_URL}/mar/cartblanche22
	- docker stop ${CI_PROJECT_NAME}		- docker stop ${CI_PROJECT_NAME}
	~~- docker rm ${CI_PROJECT_NAME}~~
	~~- docker stop redis~~
	~~- docker rm redis~~
	- docker run --net cartblanche --name redis -d redis		- docker run --net cartblanche --name redis -d redis
	- docker run --net cartblanche -v /nfs/db2/smallworld_anon_21Q4:/nfs/db3/private_smallworld_4th_gen/anon		- docker run --net cartblanche -v /nfs/db2/smallworld_anon_21Q4:/nfs/db3/private_smallworld_4th_gen/anon

2023-08-17T19:04:19Z

Deployment Information

← Older revision		Revision as of 19:04, 17 August 2023
Line 12:		Line 12:

	== Deployment Information ==		== Deployment Information ==
			'''Gitlab Deployment Stages'''

	Production builds are distributed among 3 machines		Production builds are distributed among 3 machines
	- epyc2		- epyc2
	- n-9-38		- n-9-38
	- n-1-18		- n-1-18

			The first stage will build/update the current docker image to the gitlab server running on n-9-22. On the web interface, this is in the cartblanche repo under 'Packages & Registries'.

			The second stage tests the new container and runs tests for
			- ZincID Search
			- Supplier Code Search
			- SMILES Search

			Finally, the docker image is pulled in each of the three servers and restarted.

	'''Useful Commands''' (Use these in the respective server to debug):		'''Useful Commands''' (Use these in the respective server to debug):
	docker restart molecule-shopping-cart (restart the docker container)		docker restart molecule-shopping-cart (restart the docker container)
	docker logs molecule-shopping-cart (view app logs)		docker logs molecule-shopping-cart (view app logs)
	~~docker exec -it molecule-shopping-cart /bin/bash (open a shell inside of the docker container, useful for making quick minimal changes without having to redeploy)~~

	'''Some troubleshooting tips:'''		'''Some troubleshooting tips:'''

2023-08-17T18:41:28Z

Deployment Information

← Older revision		Revision as of 18:41, 17 August 2023
Line 19:		Line 19:
	'''Useful Commands''' (Use these in the respective server to debug):		'''Useful Commands''' (Use these in the respective server to debug):
	docker restart molecule-shopping-cart (restart the docker container)		docker restart molecule-shopping-cart (restart the docker container)
	docker logs molecule-shopping-cart (view app logs~~, only stdout~~)		docker logs molecule-shopping-cart (view app logs)
	docker exec -it molecule-shopping-cart /bin/bash (open a shell inside of the docker container, useful for making quick minimal changes without having to redeploy)		docker exec -it molecule-shopping-cart /bin/bash (open a shell inside of the docker container, useful for making quick minimal changes without having to redeploy)

	~~'''To view error logs (stderr)'''~~
	~~docker exec -it molecule-shopping-cart /bin/bash~~
	~~cat std.log~~

	'''Some troubleshooting tips:'''		'''Some troubleshooting tips:'''
Line 35:		Line 31:

	For search errors (zincid, smiles, vendor), the docker app logs are usually very informative.		For search errors (zincid, smiles, vendor), the docker app logs are usually very informative.

			It is also useful to see the status of the redis and redis-sentinel services on each of those machines.

			There are three redis databases, one main and two backups. If the main db goes down, one of the backups becomes main. When the old main goes back up, it becomes a backup database.

	== Deployment Process ==		== Deployment Process ==

2023-08-17T18:39:13Z

Deployment Information

← Older revision		Revision as of 18:39, 17 August 2023
Line 12:		Line 12:

	== Deployment Information ==		== Deployment Information ==
	~~Live site runs on~~ n-9-~~22:5067. Pushing to master branch will deploy here.~~		Production builds are distributed among 3 machines
	~~Dev server runs on~~ n-1-~~17:5068. Pushing to the dev branch will deploy to this server.~~		- epyc2
			- n-9-38
			- n-1-18

	'''Useful Commands''' (Use these in the respective server to debug):		'''Useful Commands''' (Use these in the respective server to debug):

2023-08-17T18:37:48Z

Local environment

← Older revision		Revision as of 18:37, 17 August 2023
Line 1:		Line 1:
	== ~~Local~~ environment ==		== Development environment inside cluster==

	* Clone repo		* Clone repo
Line 7:		Line 7:
	conda env create -f environment.yml		conda env create -f environment.yml
	conda activate cartblanche		conda activate cartblanche

	* Open ssh tunnel to machines, [https://sshuttle.readthedocs.io/en/stable/installation.html sshuttle] is a good tool to avoid having to open the tunnel to each tin/antimony machine individually.
	~~sudo sshuttle --auto-hosts --dns -v -vvvv -r jcastanon@gimel.ucsf.bkslab.org:22 -x gimel.ucsf.bkslab.org:22 0/0~~

	* Start application		* Start application