Permission denied in git status command

[hyeom-wisc]

Hello,
I am a new user in Moose code and moving forward step by step by asking questions in this forum. Thank you so much all!

I am working on tutorial01. I was able to run a new input file and see the output through peacock. It took a week for me to get this stage. However, unfortunately, I have some issue to run "git status" It shows:

(moose) hyeom@ERB914-7920:~/projects/babbler$ git status
fatal: .git/index: index file open failed: Permission denied

In GitHub desktop, it says "last fetched just now on" but I cannot Pull in Git tab in Atom. I think I messed it up somehow. Can you please provide some clues to resolve this? Thanks. Sung

[milljm]

Permission denied errors usually are the result of running commands with sudo.
Can you perform a long listing while 'babbler'?

ls -latrh ~/projects/babbler

Thanks!

[hyeom-wisc]

Guillaume,
Thanks. Now I can run "git status" after changing the ownership of .git folder. After then I typed "git add problems" and it showed another error. There are many permission issues... Sung

(moose) hyeom@ERB914-7920:~/projects/babbler$ git add problems
error: insufficient permission for adding an object to repository database .git/objects
error: problems/pressure_diffusion.i: failed to insert into database
error: unable to index file 'problems/pressure_diffusion.i'
fatal: updating files failed

[GiudGiud]

Maybe try changing the permissions recursively, for all files in the folder at once.
So 'chmod +rw --recursive ~/projects/babbler'

[hyeom-wisc]

Guillaume,
Thanks. I run it but it showed many "cannot access" error messages.

(moose) hyeom@ERB914-7920:~/projects/babbler$ chmod +rw --recursive ~/projects/babbler
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/01/6580497728634160a6541a6342e2ba07000696': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/02/ae105e1a8d4370e00d1ce6bba5a072e299ad19': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/03/f7cb153298d959ee5bbc4493ad80c87341a684': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/0b/3f587194e53ab2c855ea66dac23662289fec90': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/17/b27300a29aad760be364281469b72f0ff4d1d7': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/34/154808f950bd18324a8b5ed914fc737c4dd931': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/34/58c0efe9c0fe75be67df29bac8601f8a28c927': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/3a/13df19eef2cc5b3df81d920175b31c411ca88c': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/3d/ffbd86b56f30d464d543ac4542443a1fc0a04e': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/47/d8ee3d8a753c186f5aed84296b42661f9e3028': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/62/c62ed143f8a6868635ac82eef6a66791957e03': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/79/201b6137aa03fe34b8c5867044a2f187fb6eea': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/87/249798ab181373d276a068dd3aec85d6d8ac4d': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/8c/aaf328a9718c6057e7f587a824f05af242d2e2': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/96/027c6336b3aecb7b9eea2a09a81f5df08e3efb': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/a3/2d71723da2ea0f4273943acd5192fbe1a717c0': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/b5/52b8e3d4fc5f233a5c9e8bf0d8e9bb400ed992': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/b5/6d12faeae50810d231b12b1f6b7b37cf9b0d0e': Permission denied
chmod: cannot access '/home/hyeom/projects/babbler/.git/objects/e1/8a5a2ec524dee700af30333b153710d391f471': Permission denied

[GiudGiud]

I'm not sure you need permission on those files.
Can you git add problems now?

If not, you may want to sudo chmod, but double check that the permissions are actually given to you

[GiudGiud]

As Jason stated, you've probably run git with sudo at some point, changing the ownership of some internal git files to root. You can fix that by doing

sudo chown -R hyeom:hyeom ~/projects/babbler

and then never use sudo again when working with MOOSE :-)

Actually this should work

[hyeom-wisc]

Guillaume,
I am frustrated... I tried two things again.
1)
(moose) hyeom@ERB914-7920:~/projects/babbler$ sudo chown -R hyeom:hyeom /projects/babbler
[sudo] password for hyeom:
2)
(moose) hyeom@ERB914-7920:/projects/babbler$ sudo chmod +rw --recursive /projects/babbler
3)
(moose) hyeom@ERB914-7920:/projects/babbler$ git add problems
error: insufficient permission for adding an object to repository database .git/objects
error: problems/pressure_diffusion.i: failed to insert into database
error: unable to index file 'problems/pressure_diffusion.i'
fatal: updating files failed

It still showed the error message. It is not easy.

[GiudGiud]

If fixing the permissions is becoming too time consuming, I recommend you re-create the application, and only move the files that you modified to the new application.
If this is your first commit, it should not take too long.

[hyeom-wisc]

Guillaume,
Please see the two ls -latrh commands. Can you see something strange?
1)
(moose) hyeom@ERB914-7920:~/projects/babbler$ ls -latrh /projects/babbler
total 476K
-rw-r--r-- 1 hyeom hyeom 26K Nov 24 12:17 LICENSE
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 include
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 scripts
-rw-r--r-- 1 hyeom hyeom 183 Nov 24 12:17 README.md
-rw-r--r-- 1 hyeom hyeom 2.1K Nov 24 12:17 Makefile
-rwxr-xr-x 1 hyeom hyeom 470 Nov 24 12:17 run_tests
-rw-r--r-- 1 hyeom hyeom 86 Nov 24 12:17 testroot
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 unit
-rw-r--r-- 1 hyeom hyeom 738 Nov 24 12:17 .clang-format
-rw-r--r-- 1 hyeom hyeom 3.2K Nov 24 12:17 .gitignore
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:25 build
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:26 test
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:26 .libs
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 27 11:51 ..
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 28 15:06 src
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 28 15:07 lib
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 28 15:08 .
-rwxr-xr-x 1 hyeom hyeom 426K Nov 28 15:08 babbler-opt
-rw-r--r-- 1 hyeom hyeom 7.7K Nov 28 15:09 .previous_test_results.json
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 30 09:53 doc
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 30 11:18 problems
drwxr-xr-x 1 hyeom hyeom 4.0K Dec 1 11:29 .git
2)
(moose) hyeom@ERB914-7920:/projects/babbler$ ls -latrh ~/projects/babbler/.git
total 8.0K
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 branches
-rw-r--r-- 1 hyeom hyeom 73 Nov 24 12:17 description
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 hooks
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:17 info
-rw-r--r-- 1 hyeom hyeom 23 Nov 24 12:17 HEAD
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:23 logs
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 24 12:25 refs
-rw-r--r-- 1 hyeom hyeom 41 Nov 28 14:32 ORIG_HEAD
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 28 14:37 objects
-rw-r--r-- 1 hyeom hyeom 262 Nov 28 15:02 config
drwxr-xr-x 1 hyeom hyeom 4.0K Nov 28 15:08 ..
-rw-r--r-- 1 hyeom hyeom 0 Nov 30 11:29 FETCH_HEAD
-rw-r--r-- 1 hyeom hyeom 2.7K Dec 1 10:26 index
-rw-r--r-- 1 hyeom hyeom 1.4K Dec 1 10:39 COMMIT_EDITMSG
drwxr-xr-x 1 hyeom hyeom 4.0K Dec 1 11:29 .

[hyeom-wisc]

I agree. I may remove the whole babbler directory (should I do that in github website?) and restart the tutorial again.

Sincerely,
Sung

[GiudGiud]

The permissions look fine. You are the owner of the files (thanks to chown) and you have read/write access on all these files (first set of rw- is for the owner).

You can worry about removing the directory later (from both your github account and your computer). For now, maybe try restarting the tutorial without using sudo.

[hyeom-wisc]

Guillaume,
Thanks. I will restart the tutorial with a new directory (e.g., babbler2) and see what happens.

Sincerely,
Sung