tacc / rgc Goto Github PK

https://github.com/cea-hpc/modules

If something like libcuda is detected in the container, run with --nv, OR always use --nv if running on a GPU node.

https://docs.python.org/3/library/dbm.html

Should be something like

depends_on("tacc-singularity")
prereq("tacc-singularity")

Some people may want compilers exposed, so add an option to exclude all the compiler binaries that conda may install. This may require a custom target.

A problematic example is fastqtl.

Example Command:

rgc -M /apps/modulefiles/containers -I /apps/singularity-3/containers -S biocontainers/bwa:0.7.15

Resulting Modulefile line:

set_shell_function("bwa",'singularity exec /home/jhrogers/apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $@','singularity exec /home/jhrogers/apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $*')

Expected Line:

set_shell_function("bwa",'singularity exec /apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $@','singularity exec /apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $*')

Further Information:

If I use the --prefix without the --imagedir, the modulefile comes out mostly correct, but the needed image isn't stored.

Example:
rgc -M /apps/modulefiles/containers -P /apps/singularity-3 -S biocontainers/bwa:0.7.15

Results:
Modulefile:
set_shell_function("bwa",'singularity exec /apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $@','singularity exec /apps/singularity-3/containers/bwa/bwa-0.7.15.sif bwa $*')
note: it adds "containers" to the path, which is strange.

ls -l /apps/singularity-3/containers
total 0

Expected Results:
ls -l /apps/singularity-3/containers/
total 0
drwxr-x--- 2 jhrogers admin 36 Aug 11 16:25 bwa

Correctly handle shub:// urls

http://gregoryzynda.com/python/developer/logging/2019/09/26/multiple-python-logs.html

Should include something like this

if (myShellName() == "bash") then
        execute{cmd="export -f funcs", modeA={"load"}}
        execute{cmd="unset funcs", modeA={"unload"}}
end

Images should be pulled once to make sure it works, but other tests should either hit a cache or skip the pulling step.

with something like qemu

This will allow for faster downloads of target images.

Before substituting strings into the lmod modulefile template whatis functions, check for double-quotes in the string.

Either remove line breaks or encode them.