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easybuilders / easybuild-easyconfigs

A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
https://easybuild.io
GNU General Public License v2.0
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missing executable permissions on Julia wrapper script #20978

Open tbeason opened 4 months ago

tbeason commented 4 months ago

I tried to install Julia 1.10 via the easyconfig. I used curl to download the current easyconfig file and the new julia.wrapper file. The sanity checks fail saying

== 2024-07-08 16:06:47,294 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/software/tinkercliffs-rome/EasyBuild/4.9.2/lib/python3.6/site-packages/easybuild/base/exceptions.py:126 in __init__): Build of /home/beasont/Julia-1.10.0-linux-x86_64.eb failed (err: 'build failed (first 300 chars): Sanity check failed: sanity check command julia --help exited with code 126 (output: /bin/bash: /home/beasont/easybuild/software/tinkercliffs-rome/Julia/1.10.0-linux-x86_64/bin/julia: Permission denied\n)') (at easybuild/software/tinkercliffs-rome/EasyBuild/4.9.2/lib/python3.6/site-packages/easybuild/main.py:178 in build_and_install_software)

Here is what ends up in the bin folder

[beasont@tinkercliffs1 ~]$ ls -l /home/beasont/easybuild/software/tinkercliffs-rome/Julia/1.10.0-linux-x86_64/bin/
total 32
-rw-rw-r-- 1 beasont beasont   100 Jul  8 16:06 julia
-rwxr-xr-x 1 beasont beasont 23352 Dec 25  2023 julia.bin

I can execute julia.bin manually but the file named julia is simply the julia.wrapper file from this repo. Is there some symbol linking that is missing?

tbeason commented 4 months ago

FWIW I tried again after adding && chmod +x julia to the end of the post install commands and then things worked fine.

lexming commented 4 months ago

I cannot reproduce this issue. The permissions of julia.wrapper in the repo are correct and have executable permissions. After installation, the installed julia file (formerly julia.wrapper) has executable permissions as well.

$ ls -la ~/easybuild/install/zen4/software/Julia/1.10.0-linux-x86_64/bin/
rwxr-xr-x 100 4 Jul 11:13 julia
rwxr-xr-x 23k 25 Dec 2023 julia.bin

Is there anything special about your setup that could be removing the executable permissions of that file?

update: reading your first comment again, probably it is the use of curl to get the files instead of cloning the repo with git