Hi there, first thank you guys for all your work and efforts in driving this project.
We are implementing Alma Linux in our HPC and the rest of our infrastructure replacing CentOS 7 in the research institution where I work.
We have encountered an issue running Java applications. When a user runs it in an owned directory, like their home directory, Java complains about the user rights in that folder:
Exception in thread "main" java.lang.ExceptionInInitializerError at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:312) Caused by: java.lang.IllegalArgumentException: Output dir /mnt/user-home/singularity/test/temp1 doesn't exist or isn't writeable at uk.ac.babraham.FastQC.FastQCConfig.<init>(FastQCConfig.java:52) at uk.ac.babraham.FastQC.FastQCConfig.<clinit>(FastQCConfig.java:26) ... 1 more
To give you more details about the context, the users have their home director in an Isilon mount that is meant to be multi-protocol, accessed from Linux and Windows.
If you do a chmod +s and then chmod -s on the directory the users are able to run the software without issues
We have tracked the error down to the “Delete subfolders and files” permission.
The same setup worked for CentOS 7. However, both Alma 8 and 9 don’t like it. We are in conversations with Dell to check if there is a setup on the Isilon mounts that can be changed. Also, we have created a preload on the HPC that corrects this behaviour.
However, we would like to check if there is a security feature on the new builds that is active by default and triggers this response when CentOS 7 did not.
We are suspecting that this could affect more pieces of software and we would like to anticipate it.
Thanks in advance