CWLScatter) that do no computation but are needed. And the second concept is: what is the maximum number of jobs (running and waiting ) that are allowed to be in the batch scheduler's queue?
--maxLocalJobsis about the 1st concept; and the second concept has no command line parameter.
I believe we have different versions of the code, I'm using 3.19, and my line which compares based on cores:
sum(self.allocatedCpus.values()) < int(self.boss.maxCores)):
seems to have been changed in your version to a comparison based on job count:
len(self.runningJobs) < int(self.boss.config.maxLocalJobs):
toil/docker/Docker.pyspecifies python 3.6 as a dependency. I can successfully make and run the docker image, and verify that versions of python exist. However toil is installed in the python 2
dist-packages, and does not play nicely with python 3. I am probably missing something elementary ...
docker-py, and creates a docker client using
client = docker.from_env(version='auto')where
dockeris imported from the
timeoutkeyword argument to toil's
Failed to set loop flags on loop device: Resource temporarily unavailablefrom Singularity. To debug this I'd like to be able to extract the singularity command and containers that toil uses - how can I tell toil to nut clean up those temporary files?
btw cwl is:
cwlVersion: v1.0 class: CommandLineTool baseCommand: echo stdout: output.txt hints: - class: DockerRequirement dockerPull: busybox:latest inputs: message: type: string inputBinding: position: 1 outputs: output: type: stdout
and example-job.cwl is
message: Hello world!
Failed to set loop flags on loop device: Resource temporarily unavailableis a Singularity error. Literally you need more