84-add singularity guide

[fdiblen]

Refs: #84 #108 #17

[jspaaks]

super job man

[sverhoeven]

Trying it out with https://github.com/ci-for-research/example-python-1 repo with black check disabled in workflow. The jobs fails with incomplete job log and when I CTRL-C the singularity container, it errors with

---> Removing the runner.
Unhandled exception. System.IO.IOException: No space left on device
   at System.IO.FileStream.WriteNative(ReadOnlySpan`1 source)
   at System.IO.FileStream.FlushWriteBuffer()
   at System.IO.FileStream.FlushInternalBuffer()
   at System.IO.FileStream.Flush(Boolean flushToDisk)
   at System.IO.FileStream.Flush()
   at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder)
   at System.IO.StreamWriter.Flush()
   at System.Diagnostics.TextWriterTraceListener.Flush()
   at GitHub.Runner.Common.HostTraceListener.Write(String message)
   at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id)
   at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message)
   at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message)
   at GitHub.Runner.Common.Tracing.Trace(TraceEventType eventType, String message)
   at GitHub.Runner.Common.HostContext..ctor(String hostType, String logFile)
   at GitHub.Runner.Listener.Program.Main(String[] args)
./config.sh: line 79: 20881 Aborted                 (core dumped) ./bin/Runner.Listener "$@"

And keeps the runner (run.sh) running in the background.

Is this because my tmpfs has 1.6Gb available?

[sverhoeven]

Using temporary mode I get the log of the runner in my terminal. How do I get the log from running instance?

[fdiblen]

added the info.

[sverhoeven]

Why disable? ubuntu-docker/Dockerfile should still be linted.

[jspaaks]

i fiddled with this extensively see #127

Summary:

• one of our Dockerfiles uses the word sudo, to add a user to the sudo group. This seems to trigger the linter who thinks we are sudo doing something.
• disabling of rules is not very extensive in the linter, see https://github.com/github/super-linter/blob/master/docs/disabling-linters.md#dockerfile
• I tried .dockerfilelintrc with rules: sudo_usage: off but that doesnt seem to be used correctly. Possibly due to https://github.com/github/super-linter/pull/384
• I tried the VALIDATE_DOCKER: false option, that disables linting on all files. Perhaps due to the counterintuitive way the defaults switch after adding one that see https://github.com/github/super-linter#environment-variables "However if any one of the variables are set, we default to leaving any unset variable to false"
• I made an issue to revisit this re-enable dockerfile linting after superlinter fix is released #128

Alternative approaches:

• avoid using sudo as a string in the Dockerfile, maybe using an env var or something.
• include all VALIDATE_[LANGUAGE] keys in the workflow file and setting them to true (excpet Docker)

Neither approach seems good, hence I decided to wait.

[fdiblen]

removed sudo command from the Docker file

[sverhoeven]

As you don't have root-permission on the HPC cluster you will need to build the github-actions-runner-singularity.sif file on your own machine and copy it to the cluster. Can a build+copy hint be added?

[fdiblen]

added scp command