Stream: crucible
Topic: Local Deployment
Shreshta Balachandar (Dec 07 2020 at 15:20):
Hey everyone :wave: ! I'm new to FHIR and just got started with exploring Crucible.
When doing a local deployment on Docker (on WSL), I keep getting the error "Task runner waiting for crucible web app to load on port 3000". I don't have any other local applications running on Port 3000. Has anyone else seen this issue and had luck resolving it?
I also noticed that the package was last updated in July 2019 and there were a number of deprecation warnings when I installed. Could this also be why?
Thanks,
Shreshta
Robert Scanlon (Dec 09 2020 at 21:20):
Hi @Shreshta Balachandar -- thanks for letting us know. I am getting what looks to be the same error on my machine, which is using Docker on a Mac. If you run the following command: docker-compose up mongo are you getting something that looks like the following?
mongo_1 | mongod --help for help and startup options
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=4c61d4f2b0fb
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] db version v2.6.12
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] git version: d73c92b1c85703828b55c2916a5dd4ad46535f6a
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] build info: Linux build5.ny.cbi.10gen.cc 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 BOOST_LIB_VERSION=1_49
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] allocator: tcmalloc
mongo_1 | 2020-12-09T21:17:58.672+0000 [initandlisten] options: {}
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] journal dir=/data/db/journal
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] recover : no journal files present, no recovery needed
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten]
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] ERROR: Insufficient free space for journal files
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] Please make at least 3379MB available in /data/db/journal or use --smallfiles
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten]
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] exception in initAndListen: 15926 Insufficient free space for journals, terminating
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] dbexit:
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: going to close listening sockets...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: going to flush diaglog...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: going to close sockets...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: waiting for fs preallocator...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: lock for final commit...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: final commit...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] shutdown: closing all files...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] closeAllFiles() finished
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] journalCleanup...
mongo_1 | 2020-12-09T21:17:58.673+0000 [initandlisten] removeJournalFiles
mongo_1 | 2020-12-09T21:17:58.674+0000 [initandlisten] shutdown: removing fs lock...
mongo_1 | 2020-12-09T21:17:58.675+0000 [initandlisten] dbexit: really exiting now
Robert Scanlon (Dec 09 2020 at 21:21):
Also, are you using WSL2 (I assume if you are using Docker?)
Shreshta Balachandar (Dec 09 2020 at 21:35):
Hi @Robert Scanlon - Yes I am on WSL2.
I followed the instructions found on GitHub here: https://github.com/fhir-crucible/crucible#docker-installation.
I ran the commands in the following order:
docker-compose build
docker-compose up (Getting the error: "Task runner waiting for crucible web app to load on port 3000")
and then again in this order:
docker-compose build
docker-compose up mongo (this exited with code 139 quickly)
docker-compose up (Getting the error: "Task runner waiting for crucible web app to load on port 3000", and the mongo instance also shut down immediately here)
I did not see the same error that you showed above.
However a new error I noticed this time said: "Could not connect to a primary node for replica set" with an error marked ConnectionFailure. Is this because the Mongo instance isn't staying attached?
Robert Scanlon (Dec 09 2020 at 21:38):
It is likely an issue with the Mongo container, since that is what is happening on my machine, but I just wanted to verify that. Could you provide the last 25 lines or so of docker-compose logs mongo?
Shreshta Balachandar (Dec 09 2020 at 22:15):
Tried the command and the only thing I see is: "Attaching to crucible_mongo_1"
Robert Scanlon (Dec 15 2020 at 22:14):
I took a look and it seems that the mongo container we are referencing is hopelessly old and shouldn't be used. If you update docker-compose.yml and change the line that says "mongo:2.6" to "mongo:3.6", that seemed to work on my WSL2 machine (then docker-compose up again). The only thing that appears to not work for the 3.6 version of mongo is some roll-up stats on the main page, which doesn't affect its ability to run or display test results.
Robert Scanlon (Dec 15 2020 at 22:14):
Could you give that a shot?
Brian Postlethwaite (Jan 05 2021 at 22:11):
I assume this isn't on the docker hub registry?
Robert Scanlon (Jan 06 2021 at 15:05):
Crucible itself? It wasn't, but in case it is useful I just linked it up so that it is published here: https://hub.docker.com/repository/docker/projectcrucible/crucible
Shreshta Balachandar (Jan 12 2021 at 12:38):
Hey Robert, thanks for your note! Apologies for the delay. I have tested it out against a sample server and everything works well. Really appreciate it!
Last updated: Apr 12 2022 at 19:14 UTC
