search

common-workflow-language / cwltool

Common Workflow Language reference implementation
https://cwltool.readthedocs.io/
Apache License 2.0
335 stars 231 forks source link

bind source path does not exist - cwltool keeps waiting / running does not stop #1887

Open jjkoehorst opened 1 year ago

jjkoehorst commented 1 year ago

Expected Behavior

The cwltool execution should stop Ticket is in a way related to https://github.com/common-workflow-language/cwltool/issues/1433

Actual Behavior

It just hangs

Workflow Code

Any kind of system that can cause a Error response from daemon: invalid mount config for type "bind": bind source path does not exist

Full Traceback

INFO [job fastqc.cwl] /Volumes/Git/m-unlock/cwl/tests/quality/TEMPsni_4q21$ docker \
    run \
    -i \
    --mount=type=bind,source=/Volumes/Git/m-unlock/cwl/tests/quality/TEMPsni_4q21,target=/UGPAAz \
    --mount=type=bind,source=/Volumes/Git/m-unlock/cwl/tests/quality/TEMPzo3plhh_,target=/tmp \
    --mount=type=bind,source=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpbjuirt14,target=/var/lib/cwl/stga89df90a-6e44-4402-b5f1-c31fe009096c/forward.fastq.gz,readonly \
    --mount=type=bind,source=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpl03c7t5g,target=/var/lib/cwl/stga1bc4c48-0a08-41e4-b81a-605af80f6c6c/reverse.fastq.gz,readonly \
    --workdir=/UGPAAz \
    --read-only=true \
    --net=none \
    --user=501:20 \
    --rm \
    --cidfile=/Volumes/Git/m-unlock/cwl/tests/quality/TEMP3vfjc209/20230817154231-366180.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/UGPAAz \
    docker-registry.wur.nl/m-unlock/docker/fastqc:0.11.9 \
    fastqc \
    --outdir \
    FASTQC \
    --threads \
    1 \
    /var/lib/cwl/stga89df90a-6e44-4402-b5f1-c31fe009096c/forward.fastq.gz \
    /var/lib/cwl/stga1bc4c48-0a08-41e4-b81a-605af80f6c6c/reverse.fastq.gz
docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist: /host_mnt/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpbjuirt14.
See 'docker run --help'.

Your Environment

simaattar2003 commented 1 year ago

Hey! I have the same issue! any luck?

mikeloomans1999 commented 1 year ago

It is a Docker problem: https://forums.docker.com/t/bind-source-path-does-not-exist-but-it-does-exist/124250/8

The solution for me (Ubuntu 20.04.3, cwl version 3.1.20220224085855) involved removing docker: 

sudo apt remove docker* 
sudo snap remove docker

and reinstalling docker using these instructions: https://docs.docker.com/engine/install/ubuntu/