Arvados

Now that 9tee4 is "crunch2" only, I am now checking how running processes fares in that environment.

I pulled the latest arvados from master and build it. Also pulled the latest cwl code and built it.

It created a container_request and ran it. According to the CR, it completed successfully, but I saw this error in my console window saying that there was error while setting container output.

Two issues here: (1) Why did writing the output to container failed and what needs to be done, (2) Shouldn't the container_requests/9tee4-xvhdp-szqhn2nfh0tei5d say it failed, not success (green complete)?

(venv)radhika@shell.9tee4:~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml
/home/radhika/venv/bin/arvados-cwl-runner 0d2a561091b777dfb7735d842a88f8529f4f982a 1.0.20161107220300, arvados-python-client 0.1.20160826210445, cwltool 1.0.20161107145355
2016-11-08 14:25:31 arvados.arv-run[15513] INFO: Upload local files: "bwa-mem.cwl" 
2016-11-08 14:25:31 arvados.arv-run[15513] INFO: Using collection 9tee4-4zz18-1om5a5o9jxspigw
2016-11-08 14:25:31 arvados.cwl-runner[15513] INFO: Container request bwa-mem.cwl (9tee4-xvhdp-szqhn2nfh0tei5d) state is Committed with container 9tee4-dz642-nn4zaf01plu4p8z Queued
2016-11-08 14:26:16 arvados.cwl-runner[15513] INFO: Job bwa-mem.cwl (9tee4-dz642-nn4zaf01plu4p8z) is Running
2016-11-08 14:26:47 arvados.cwl-runner[15513] INFO: Container bwa-mem.cwl (9tee4-dz642-nn4zaf01plu4p8z) is Complete
2016-11-08 14:26:48 arvados.cwl-runner[15513] INFO: Overall process status is success
2016-11-08 14:26:51 arvados.cwl-runner[15513] INFO: Final output collection cea84304a6c2346e7f876f9dcdf8e4f8+154 "Output of bwa-mem.cwl" (9tee4-4zz18-n475zqj8ux1x3sl)
2016-11-08 14:26:51 arvados.cwl-runner[15513] INFO: Setting container output: <HttpError 404 when requesting https://9tee4.arvadosapi.com/arvados/v1/containers/current?alt=json returned "Token is not associated with a container.">
{   
    "aligned_sam": {
        "class": "File",
        "location": "keep:cea84304a6c2346e7f876f9dcdf8e4f8+154/HWI-ST1027_129_D0THKACXX.1_1.sam" 
    }
}

The bug is that arvados-cwl-runner thinks it is running in a container and trying to set the container output. However, there is an optimization to not schedule a cwl-runner container when running a single tool (as opposed to a workflow). It should not try to set container output when it is not running in a container.