This PR allows an admin to turn on a new feature. In all ToolConfigs, there is a new flag Use short workdirs inside Singularity. Default is off.
When turned on, a task run in a Singularity container will see its workdir remapped to a much shorter path such as "/T12345/" (where 12345 is the task's ID).
The system should normally make sure all data files are properly accessible from that new location. This was needed because some stupid C tools crash when a path provided in argument is too long (e.g. some of the internal programs invoked by FMRIPrep).
As an added feature, an admin can go to the work directory of any Singularity-based task and start a Singularity shell simply by invoking:
bash .science.TOOLNAME.1234-1.sh shell
Basically, the scripts named .science.TOOLNAME* can take the single argument shell to bypass the execution of the tool and boot an interactive shell instead.
This PR allows an admin to turn on a new feature. In all ToolConfigs, there is a new flag
Use short workdirs inside Singularity. Default is off.When turned on, a task run in a Singularity container will see its workdir remapped to a much shorter path such as "/T12345/" (where 12345 is the task's ID).
The system should normally make sure all data files are properly accessible from that new location. This was needed because some stupid C tools crash when a path provided in argument is too long (e.g. some of the internal programs invoked by FMRIPrep).
As an added feature, an admin can go to the work directory of any Singularity-based task and start a Singularity shell simply by invoking:
Basically, the scripts named
.science.TOOLNAME*can take the single argumentshellto bypass the execution of the tool and boot an interactive shell instead.