Another pull request from johnoel/stock-synthesis

[johnoel]

Concisely describe what has been changed/addressed in the pull request.

• Resolves issue #

What tests have been done?

Where are the relevant files?

What tests/review still need to be done?

Is there an input change for users to Stock Synthesis?

Additional information (optional).

[johnoel]

Thanks Rick for letting me know. I will just wait for Elizabeth and work on other Docker improvements.

[e-perl-NOAA]

@johnoel Thank you for working on this! I'm finally back after being in and out for the past 2 weeks. I'll try this out this week and get back to you with any problems I have (hopefully I won't have any).

[johnoel]

Did you get a chance to review changes? I will be on break soon.

[e-perl-NOAA]

Hi Johnoel, I have been working on testing it and getting it working with our ss3-build workflow using the admb-docker-images branch. Running into some issues getting that workflow successfully running but I'm hoping that I can clear that up on my own.

[e-perl-NOAA]

@johnoel I'm running into a couple different issues depending on the operating system - see workflow run fail here. In all of them it's say that the admb command is not found though.

[johnoel]

Add "--admb docker" to Make...sh arguments

[e-perl-NOAA]

I did that and it's working for mac but not for linux for some reason, see here

[e-perl-NOAA]

@johnoel I think that I'm close to solving the problem (i'm pretty sure I solved the linux problem...the windows might be a bit more difficult). It's end of day for me right now so I'm going to work on it more tomorrow.

[johnoel]

okay, see the file changes it works.

[e-perl-NOAA]

@johnoel, I don't know why all of the actions here have failed. I did get the image working with the ss3-build workflow. Apparently just using make docker will run it, the trouble is just finding where it put the executables after to be able to move them which I eventually found (see successful workflow run here). I am now working on making sure that the image works with the rest of the workflows, first starting off with build-ss3-warnings but that seems to be failing for some reason that I can't figure out (see failed workflow run here)

[e-perl-NOAA]

Also, a question that came up in a meeting with someone else who is not trying to use admb for stock synthesis, is what would be the best way to add admb to your path when using the docker image?

[e-perl-NOAA]

@johnoel The windows image worked yesterday but now it isn't working on the github action, codespaces, or locally. The kubectl get nodes -o wide is returning:

E1208 14:44:47.611644   30608 memcache.go:265] couldn't get current server API group list: Get "http://localhost:8080/api?timeout=32s": dial tcp 127.0.0.1:8080: connectex: No connection could be made because the target machine actively refused it.
Unable to connect to the server: dial tcp 127.0.0.1:8080: connectex: No connection could be made because the target machine actively refused it.

and then docker pull johnoel/admb:windows is returning:

image operating system "windows" cannot be used on this platform: operating system is not supported

[johnoel]

seems to be working now

[johnoel]

admb is already installed and configured in the docker container. the host computer that uses the container does not need any additional configuration for admb.

please see windows quick start

https://github.com/admb-project/admb/blob/main/scripts/docker/quickstart-windows.md

[e-perl-NOAA]

@johnoel I tried it again this morning using both make docker and sh Make_SS_330_new.sh --admb docker --safe but neither of them works for windows in the github action, it's also not working for me locally. You can see the failed workflow runs using just make docker here and using sh Make_SS_330_new.sh --admb docker --safe here. Can you please help me figure out why the windows image isn't working?

[johnoel]

Take a look at the changes for Make.sh

https://github.com/nmfs-ost/ss3-source-code/pull/530/files

Works for me in the forked respository

[e-perl-NOAA]

@johnoel, please see the admb-docker-images branch where I have been making changes and running the github actions. Specifically, the build-ss3.yml file which is where the windows docker image is failing (see failed action here but a whole list of failed actions is available when you click on the actions tab). I copied all of the changes you made in the GNUmakefile, the Make_SS_330_new.sh, the build-ss3-warnings.yml, and the SS_write_report.tpl so everything should be the same there. Can you please look at that build-ss3.yml file and failed action to see if you can determine why it is failing? I have tried a million different things but it still isn't working.

[e-perl-NOAA]

@johnoel, I added a comment to the code, but the reason that the actions are passing is because build-ss3.yml still contains the original code to get the admb release from GitHub. If you take those lines out, build.ss3 will not pass with the changes that you have made.

[e-perl-NOAA]

@johnoel, have you been able to dive into this more recently to see what the issue is? I would like to get this mostly solved this month so we are sure to have it wrapped up before March. Thank you!

[johnoel]

Back from vacation, I will look at this today.

[johnoel]

Hi Elizabeth (@e-perl-NOAA), can you review changes?

[e-perl-NOAA]

@johnoel please see my draft PR #550, there are some weird c++ errors now and the windows docker image still isn't working.

[johnoel]

See Pull Request #552