Issue with ./manage_externals/checkout_externals

[hbrodsky]

I'm trying to download CESM on my personal computer. I downloaded it but when I go to checkout the model components and enter the command ./manage_externals/checkout_externals, my output has the errors below. I checked the manage_externals.log file to see what errors were being reported but couldn't see anything obvious. I'm assuing that because of this issue, I don't have any files in my components directory. Any recommendations on how to address this issue?

 

[sacks]

Based on this output, it looks like you have some changes in components/clm. I'd suggest going into that directory and running git status and git diff. If these are changes you made, then commit them or save them in some other way. Otherwise, if they are unintentional, you can either undo them with git commands or simply remove that whole directory (from the top level: rm -rf components/clm). Then you should be able to rerun checkout_externals.

 

[hbrodsky]

Thanks for your quick response!

Hm, the odd thing is that I just downloaded a clone of the 'original' CESM file and the components directory and haven't made any changed to that original version, so there shouldn't be any changes in components/clm

I tried doing the rm -rf components/clm command and re-running ./manage_externals/checkout_externals, but am getting the same errors as before (see below)

 

[sacks]

I'm sorry you're running into this issue. Your latest post makes me see that there is some issue with cloning the CTSM repository (which goes in components/clm), related to our use of git-lfs (large file support) in that repository. I think what's supposed to happen with git lfs is that, if you don't have it installed, git simply ignores the git lfs attributes in the repository. But in your case, that doesn't seem to be happening.

Can you please tell me:

• What version of git are you using? (run git --version)
• Can you please attach the contents of your .gitconfig file in your home directory (i.e., $HOME/.gitconfig), if any? I'm especially wondering if you have anything about lfs in that file. (I'm wondering if you might have had git-lfs installed at some point, which would add some lfs-related configuration to that file, but then later uninstalled git-lfs. I believe that could cause this issue.)

 

[hbrodsky]

I'm running git version 2.15.1, and my terminal says "no such file or directory" when I run /.gitconfig (see below)

 

[sacks]

Sorry, let me try again with respect to .gitconfig: can you do:

cd ~
cat .gitconfig

 

[hbrodsky]

Thanks, here's the output

 

[sacks]

Ah, thanks. This confirms what I suspected. And I'm guessing that, if you run git-lfs, you'll get "command not found". If so, you have two options: (1) Install git lfs (https://docs.github.com/en/github/managing-large-files/installing-git-large-file-storage); (2) edit your .gitconfig file to remove everything from [filter "lfs"] to the bottom. It looks like you had git lfs installed on your system at one point but it's not there anymore, so you're getting errors due to the fact that git thinks it should run git lfs (based on your config file) but it can't find the program to run.

 

[hbrodsky]

Mm okay, yes- when I run git-lfs my output is indeed 'command not found'. I followed the instructions for your option (1) and installed git lfs (see pictures below)

Unfortately I think I'm still having the same problem (below)

 

[sacks]

So now if you run "git-lfs" it gives you some output (probably a help message)?

If so, please repeat the command to rm -rf components/clm (because it is still in a dirty / incomplete state) then rerun checkout_externals. Or did you already do that after reinstalling git lfs?

 

[hbrodsky]

Ah yes now git-lfs gives me a help message. I just ran rm -rf components/clm, too.

When I run ./manage_externals/checkout_externals i think I'm still missing some components, though:

 

[hbrodsky]

I realize my message above was unclear: when I run git-lfs I get the following:

 

[hbrodsky]

Oh yay actually I just closed my terminal and reopened it and ran checkout_externals again and it worked! Thanks so much for all your help!

 

[sacks]

Okay, glad you got this working. I'm sorry it was painful!