Permission Denied Error whenever Create/Edit/Save Files using Atom - Windows Subsystem for Linux - WSL 1

[hyeom-wisc]

Hello,
I have worked on tutorial #1 and moved forward by your help. Thanks a lot.

One thing I noticed was that there has been "Permission denied" error whenever I created, edited, and saved input files and source codes using ATOM. So far, I have provided the permission to each file using "chmod +rw" command manually. As you expected, it is time consuming. Is there any way to give the permission to files created/modified by ATOM easily?

Sincerely,
Sung

[cticenhour]

The first thing that comes to my mind - do you launch atom using sudo? If opened as root, even once, a given file (or project directory) could have screwed up permissions like this. Changing a single file back to the proper permissions wouldn't fix an entire directory tree that is screwed up in this way.

Alternatively, do you install packages using the apm install command on the command line? This is mentioned in the Atom Editor Setup page on the MOOSE website. I am wondering if you accidentally used sudo apm install which might have screwed up permissions in your Atom installation, and is spilling down to what you edit using it. Though that's a bit more far-fetched, perhaps.

[cticenhour]

Do you store your source code and input files within a MOOSE app that you created? If so, could you give the output of ls -la when you cd to that location in your Terminal? I am wondering now if it's not Atom at all, but how that application was made in the first place.

[hyeom-wisc]

Please see the output in the terminal when I typed ls -la in the MOOSE app.
(moose) hyeom@ERB914-7920:~$ ls -la
total 90900
drwxr-xr-x 1 hyeom hyeom 4096 Dec 10 15:33 .
drwxr-xr-x 1 root root 4096 Nov 16 16:00 ..
-rw------- 1 hyeom hyeom 14453 Dec 10 16:46 .bash_history
-rw-r--r-- 1 hyeom hyeom 220 Nov 16 16:00 .bash_logout
-rw-r--r-- 1 hyeom hyeom 4331 Nov 27 10:57 .bashrc
drwxr-xr-x 1 hyeom hyeom 4096 Nov 27 11:13 .cache
drwxr-xr-x 1 hyeom hyeom 4096 Nov 16 16:16 .conda
-rw-r--r-- 1 hyeom hyeom 52 Nov 23 10:35 .condarc
drwxr-xr-x 1 hyeom hyeom 4096 Nov 27 11:13 .config
-rw-r--r-- 1 hyeom hyeom 26 Nov 24 12:23 .gitconfig
drwxr-xr-x 1 hyeom hyeom 4096 Nov 16 16:02 .landscape
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 10:26 .local
-rw-r--r-- 1 hyeom hyeom 0 Dec 11 09:16 .motd_shown
-rw-r--r-- 1 hyeom hyeom 807 Nov 16 16:00 .profile
drwx------ 1 hyeom hyeom 4096 Nov 28 15:14 .ssh
-rw-r--r-- 1 hyeom hyeom 0 Nov 16 16:04 .sudo_as_admin_successful
-rw-r--r-- 1 hyeom hyeom 478 Nov 16 16:36 .zshrc
-rw-r--r-- 1 hyeom hyeom 93052469 Nov 16 16:31 Miniconda3-latest-Linux-x86_64.sh
drwxr-xr-x 1 hyeom hyeom 4096 Nov 16 16:16 miniconda3
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 projects

[cticenhour]

Thank you for the output. Instead of the home directory (~), I wanted you to run this in your projects directory (or even in the application you've been developing within projects). so cd ~/projects and then ls -la. But I do see something interesting here in your home directory. You do have a .sudo_as_admin_successful file dated on November 16th, around the same time you installed conda. This file is created after using sudo so that the system knows not to show a bunch of warnings about the dangers of sudo to you after you've used the command once. I am still wondering if this is a general permissions issue that you only see when using Atom. Could you give me that second set of Terminal output in your projects directory?

[cticenhour]

One more question - did you use sudo to install Miniconda?

[hyeom-wisc]

Please check the outputs when I typed ls -la in projects folder and my application folder. I don't remember I used sudo for Miniconda.

(moose) hyeom@ERB914-7920:~/projects$ ls -la
total 0
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 .
drwxr-xr-x 1 hyeom hyeom 4096 Dec 11 10:08 ..
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 10:05 babbler
drwxr-xr-x 1 hyeom hyeom 4096 Dec 10 15:59 babbler2
drwxr-xr-x 1 hyeom hyeom 4096 Nov 24 11:58 hyeom
drwxr-xr-x 1 hyeom hyeom 4096 Nov 16 16:47 moose
drwxr-xr-x 1 hyeom hyeom 4096 Nov 28 14:03 practice
drwxr-xr-x 1 hyeom hyeom 4096 Nov 17 16:49 your_app_name

(moose) hyeom@ERB914-7920:~/projects/babbler2$ ls -la
total 476
drwxr-xr-x 1 hyeom hyeom 4096 Dec 10 15:59 .
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 ..
-rw-r--r-- 1 hyeom hyeom 738 Dec 7 09:39 .clang-format
drwxr-xr-x 1 hyeom hyeom 4096 Dec 11 10:21 .git
-rw-r--r-- 1 hyeom hyeom 3266 Dec 7 09:39 .gitignore
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:45 .libs
-rw-r--r-- 1 hyeom hyeom 7848 Dec 7 09:46 .previous_test_results.json
-rw-r--r-- 1 hyeom hyeom 26530 Dec 7 09:39 LICENSE
-rw-r--r-- 1 hyeom hyeom 2061 Dec 7 09:39 Makefile
-rw-r--r-- 1 hyeom hyeom 196 Dec 7 09:56 README.md
-rwxr-xr-x 1 hyeom hyeom 435696 Dec 10 15:59 babbler2-opt
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 12:05 build
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 doc
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 11:59 include
drwxr-xr-x 1 hyeom hyeom 4096 Dec 10 15:59 lib
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 12:22 problems
-rwxr-xr-x 1 hyeom hyeom 471 Dec 7 09:39 run_tests
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 scripts
drwxr-xr-x 1 hyeom hyeom 4096 Dec 10 15:56 src
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:45 test
-rw-r--r-- 1 hyeom hyeom 87 Dec 7 09:39 testroot
drwxr-xr-x 1 hyeom hyeom 4096 Dec 7 09:39 unit

[GiudGiud]

If you need a quick fix I reckon you should un-install and re-install Atom.
Avoid using sudo in that process.

[GiudGiud]

I mean Atom installed in WSL, ran from WSL
I mean maybe you'll like VIM, but it's pretty minimal.

[hyeom-wisc]

All,
After I opened the input files using Vim or Notepad ++ in Windows 10 and saved them, I lost the permission to the files in Ubuntu. This is the same thing when I used Atom in Windows 10. Was my approach wrong?

[GiudGiud]

Please try opening the input files from a text editor in Ubuntu / WSL. Any text editor opened on the windows side will change the permissions.

[cticenhour]

Also I do want to suggest you give a try to @dschwen's suggestion below as well. I'll try to remember the steps without having Windows in front of me (but feel free to correct me Daniel!). To find the virtual network share he mentions, open a new Atom window, click "Add project folder" in the drop down menus. In the Open Folder prompt that Atom provides, look on the left hand side of the window (you might have to scroll down the menu panel), select "Network", then "Ubuntu-##.##", then you should have your Linux file system and can navigate to your projects/moose directory. That would allow a Windows workflow for your code writing, while you compile and run inside of WSL.

[hyeom-wisc]

All,
Thanks. I have decided to use vim to edit text files through WSL. There is no permission issue now.

[cticenhour]

For those who come across this later, the answer to this issue was that Atom in Windows was being used to edit files within Windows Subsystem for Linux. Windows does not do a great job handling the transition between the two OS environments and often causes issues related to corrupted files, file permissions, or other incompatibilities. Therefore, it is recommended that a Linux native editor is used. We recommend vim and emacs since many members of the MOOSE development ecosystem use these, as well as other lightweight editors like nano. Tutorials for vim can be found in the threads in this discussion, as well as via a Google search.

[dschwen]

No @cticenhour , see below.

[cticenhour]

I have no knowledge of WSL2, so thanks for the additional information @dschwen :)

This answer would still apply for WSL1 users though.

[dschwen]

The solution is to use WSL2 and access files through a virtual network share located at \\wsl$\distribution\path. I have gone through the effort of enabling autocompletion with native Atom on Windows with WSL2 based MOOSE installations.

[dschwen]

[dschwen]

From our FY 2020 report:

WSL2 promised better performance and we investigated building MOOSE and MOOSE-based applications on this improved system. Besides having to build the MPI mpich2 from scratch, we were able to follow the Linux build instructions very closely and ended up with fully featured MOOSE app executables.
To improve the user experience, the MOOSE integration for autocompletion[2] in the Atom editor[3] was improved to work on Windows allowing the native Windows version of Atom to be used to edit files inside the WSL2 container. WSL2 files are made available in Windows through a virtual network share located at \\wsl$\distribution\path. The moose-autocomplete plugin for Atom obtains a description of valid application syntax by running a MOOSE app using the --json commandline switch. This causes the app to output JSON data describing all valid parameters for all available objects for the given app — rather than statically supplying a syntax description which would quickly go out of date as soon as objects in a MOOSE-based application are added or modified.
The MOOSE-autocomplete plugin detects whenever a file is located within a WSL2 container and uses the Windows wsl command to discover and execute a MOOSE app executable within the WSL2 container. The entire process is seamless to the user. Figure 6.2 shows a screenshot of a native Atom editor being used to edit a MOOSE inputfile within a WSL2 container with working autocompletion. We believe WSL2 to be a suitable avenue for making MOOSE available on Windows systems as it very closely maps to our current Linux based testing and development infrastructure.

[cticenhour]

We really should integrate this into our current documentation for Windows 10, especially since users can still choose WSL1 or WSL2.