Bug #8893

[Crunch] Invalid `docker run` syntax when crunchrunner is not installed

Added by Brett Smith over 5 years ago. Updated over 5 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Brett Smith
Category:
-
Target version:
Start date:
04/06/2016
Due date:
% Done:

50%

Estimated time:
(Total: 0.00 h)
Story points:
0.5

Description

If crunch-job tries to run a Docker job on a compute node that doesn't have crunchrunner installed, it passes an empty string as an argument to docker run. That causes the job to fail like this:

2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr Running [docker.io run --name=qr2hi-ot0gb-shrdsi503141h6h-0 --attach=stdout --attach=stderr --attach=stdin -i --cidfile=/tmp/crunch-job/qr2hi-ot0gb-shrdsi503141h6h-0.cid --sig-proxy --memory=3610756k --memory-swap=3610756k --volume=/tmp/crunch-job/src:/tmp/crunch-job/src:ro --volume=/tmp/crunch-job/opt:/tmp/crunch-job/opt:ro --volume=/tmp/crunch-job/task/compute10.1.keep/by_pdh:/keep:ro --volume=/tmp/crunch-job/task/compute10.1.keep/tmp:/keep_tmp --volume=/tmp  --volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt --env=CRUNCH_JOB_BIN=/usr/local/arvados/src/services/crunch/crunch-job --env=TASK_SEQUENCE=0 --env=TASK_KEEPMOUNT=/keep --env=JOB_PARAMETER_SAMPLE-NAMES=Unstimulated,LPS_6h --env=CRUNCH_SRC_COMMIT=766af589846b703e39bc1bd4fd7051fffb6069c8 --env=JOB_PARAMETER_RSEM-CONTROL-FDR-ARGS= --env=TASK_QSEQUENCE=0 --env=CRUNCH_INSTALL=/tmp/crunch-job/opt --env=CRUNCH_GIT_ARCHIVE_HASH=4049a8b0f3d36eb5de13b929902148be --env=CRUNCH_REFRESH_TRIGGER=/tmp/crunch_refresh_trigger --env=ARVADOS_API_TOKEN=1u5pnwcp0ns12zzooyvvhm9wvhw80f9qfczyshofaj2z47vmew --env=CRUNCH_WORK=/tmp/crunch-job/work --env=CRUNCH_TMP=/tmp/crunch-job --env=TASK_TMPDIR=/tmp/crunch-job-task-work/compute10.1 --env=JOB_UUID=qr2hi-8i9sb-qjzfzlu629zm7ux --env=JOB_PARAMETER_FDR=0.05 --env=CRUNCH_JOB_UUID=qr2hi-8i9sb-qjzfzlu629zm7ux --env=TASK_SLOT_NUMBER=1 --env=CRUNCH_SRC_URL=/var/lib/arvados/internal.git --env=TASK_SLOT_NODE=compute10 --env=JOB_PARAMETER_INPUT=a0d8315f3545588599deba590e0bd1aa+958 --env=JOB_SCRIPT=run_ebseq.py --env=CRUNCH_NODE_SLOTS=1 --env=TASK_WORK=/tmp/crunch-job-task-work/compute10.1 --env=TASK_KEEPMOUNT_TMP=/keep_tmp --env=ARVADOS_API_HOST=qr2hi.arvadosapi.com --env=JOB_WORK=/tmp/crunch-job-work --env=TASK_UUID=qr2hi-ot0gb-shrdsi503141h6h --env=CRUNCH_SRC=/tmp/crunch-job/src --env=HOME=/tmp/crunch-job-task-work/compute10.1 a1b9ed39b2a59d6e76164d66467c0912afcee3d40d622b103cb7e4d8cca2d5c3 /bin/sh -c python -c "from pkg_resources import get_distribution as get; print \"Using Arvados SDK version\", get(\"arvados-python-client\").version">&2 2>/dev/null; mkdir -p "/tmp/crunch-job-work" "/tmp/crunch-job-task-work/compute10.1" && if which stdbuf >/dev/null ; then   exec  stdbuf --output=0 --error=0  \/tmp\/crunch\-job\/src\/crunch_scripts\/run_ebseq\.py ; else   exec \/tmp\/crunch\-job\/src\/crunch_scripts\/run_ebseq\.py ; fi]
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr Usage:\011docker run [OPTIONS] IMAGE [COMMAND] [ARG...]
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr Run a command in a new container
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -a, --attach=[]                 Attach to STDIN, STDOUT or STDERR
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --add-host=[]                   Add a custom host-to-IP mapping (host:ip)
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --blkio-weight=0                Block IO (relative weight), between 10 and 1000
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -c, --cpu-shares=0              CPU shares (relative weight)
2016-04-04_15:28:16 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cap-add=[]                    Add Linux capabilities
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cap-drop=[]                   Drop Linux capabilities
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cgroup-parent=                Optional parent cgroup for the container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cidfile=                      Write the container ID to the file
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cpu-period=0                  Limit CPU CFS (Completely Fair Scheduler) period
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cpu-quota=0                   Limit CPU CFS (Completely Fair Scheduler) quota
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cpuset-cpus=                  CPUs in which to allow execution (0-3, 0,1)
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --cpuset-mems=                  MEMs in which to allow execution (0-3, 0,1)
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -d, --detach=false              Run container in background and print container ID
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --device=[]                     Add a host device to the container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --disable-content-trust=true    Skip image verification
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --dns=[]                        Set custom DNS servers
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --dns-search=[]                 Set custom DNS search domains
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -e, --env=[]                    Set environment variables
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --entrypoint=                   Overwrite the default ENTRYPOINT of the image
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --env-file=[]                   Read in a file of environment variables
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --expose=[]                     Expose a port or a range of ports
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --group-add=[]                  Add additional groups to join
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -h, --hostname=                 Container host name
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --help=false                    Print usage
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -i, --interactive=false         Keep STDIN open even if not attached
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --ipc=                          IPC namespace to use
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -l, --label=[]                  Set meta data on a container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --label-file=[]                 Read in a line delimited file of labels
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --link=[]                       Add link to another container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --log-driver=                   Logging driver for container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --log-opt=[]                    Log driver options
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --lxc-conf=[]                   Add custom lxc options
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -m, --memory=                   Memory limit
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --mac-address=                  Container MAC address (e.g. 92:d0:c6:0a:29:33)
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --memory-swap=                  Total memory (memory + swap), '-1' to disable swap
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --memory-swappiness=-1          Tuning container memory swappiness (0 to 100)
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --name=                         Assign a name to the container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --net=default                   Set the Network mode for the container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --oom-kill-disable=false        Disable OOM Killer
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -P, --publish-all=false         Publish all exposed ports to random ports
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -p, --publish=[]                Publish a container's port(s) to the host
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --pid=                          PID namespace to use
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --privileged=false              Give extended privileges to this container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --read-only=false               Mount the container's root filesystem as read only
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --restart=no                    Restart policy to apply when a container exits
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --rm=false                      Automatically remove the container when it exits
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --security-opt=[]               Security Options
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --sig-proxy=true                Proxy received signals to the process
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -t, --tty=false                 Allocate a pseudo-TTY
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -u, --user=                     Username or UID (format: <name|uid>[:<group|gid>])
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --ulimit=[]                     Ulimit options
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --uts=                          UTS namespace to use
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -v, --volume=[]                 Bind mount a volume
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --volume-driver=                Optional volume driver for the container
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   --volumes-from=[]               Mount volumes from the specified container(s)
2016-04-04_15:28:17 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr   -w, --workdir=                  Working directory inside the container
2016-04-04_15:28:22 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 stderr crunchstat: error reading cid file: /tmp/crunch-job/qr2hi-ot0gb-shrdsi503141h6h-0.cid
2016-04-04_15:28:22 qr2hi-8i9sb-qjzfzlu629zm7ux 10164 0 child 10661 on compute10.1 exit 0 success=
varexp.sh (200 Bytes) varexp.sh Brett Smith, 04/08/2016 02:58 PM

Subtasks

Task #8895: Review 8893-crunch-job-crunchrunner-quoting-wipResolvedBrett Smith

Task #8921: Review 8893-crunch-job-volumes-array-wipResolvedBrett Smith

Associated revisions

Revision 9c3a1a10
Added by Brett Smith over 5 years ago

Merge branch '8893-crunch-job-crunchrunner-quoting-wip'

Closes #8893, #8895.

Revision 86996de8 (diff)
Added by Peter Amstutz over 5 years ago

Remove over-quoting from crunchrunner and certificate volume mounts. refs #8893

Revision f044dbbc
Added by Brett Smith over 5 years ago

Merge branch '8893-crunch-job-volumes-array-wip'

Closes #8893, #8921.

History

#1 Updated by Brett Smith over 5 years ago

(11:28:21 AM) tetron_: brett: #8893 LGTM

#2 Updated by Brett Smith over 5 years ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 100

Applied in changeset arvados|commit:9c3a1a10b702ec7ee79bb0aa1beb3c227bec95dd.

#3 Updated by Peter Amstutz over 5 years ago

  • Status changed from Resolved to In Progress

Bad news. I tried the latest master in arvbox and it looks like trying to pass the quoting through doesn't work:

016-04-07_01:59:27 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 stderr starting: ['bash','-c','if [ -e \\/tmp\\/crunch0\\/task\\/localhost\\.1 ]; then rm -rf \\/tmp\\/crunch0\\/task\\/localhost\\.1; fi; mkdir -p \\/tmp\\/crunch0 \\/tmp\\/crunch0\\/work \\/tmp\\/crunch0\\/task\\/localhost\\.1 \\/tmp\\/crunch0\\/task\\/localhost\\.1\\.keep && cd \\/tmp\\/crunch0 && MEM=$(awk \'($1 == "MemTotal:"){print $2}\' /dev/null ; then VOLUME_CRUNCHRUNNER=\\"--volume=$(which crunchrunner):/usr/local/bin/crunchrunner\\" ; fi && if test -f /etc/ssl/certs/ca-certificates.crt ; then VOLUME_CERTS=\\"--volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt\\" ; elif test -f /etc/pki/tls/certs/ca-bundle.crt ; then VOLUME_CERTS=\\"--volume=/etc/pki/tls/certs/ca-bundle.crt:/etc/arvados/ca-certificates.crt\\" ; fi && exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other  \\/tmp\\/crunch0\\/task\\/localhost\\.1\\.keep --exec crunchstat -cgroup-root=\\/sys\\/fs\\/cgroup -cgroup-parent=docker -cgroup-cid=/tmp/crunch0/3d0ga-ot0gb-k9kg4a81t0e8l5y-0.cid -poll=10000 docker run  --name=3d0ga-ot0gb-k9kg4a81t0e8l5y-0 --attach=stdout --attach=stderr --attach=stdin -i \\-\\-user\\=crunch --cidfile=/tmp/crunch0/3d0ga-ot0gb-k9kg4a81t0e8l5y-0.cid --sig-proxy --memory=${MEMLIMIT}k --memory-swap=${SWAPLIMIT}k --volume=\\/tmp\\/crunch0\\/src\\:\\/tmp\\/crunch0\\/src\\:ro --volume=\\/tmp\\/crunch0\\/opt\\:\\/tmp\\/crunch0\\/opt\\:ro --volume=\\/tmp\\/crunch0\\/task\\/localhost\\.1\\.keep\\/by_pdh\\:\\/keep\\:ro --volume=\\/tmp\\/crunch0\\/task\\/localhost\\.1\\.keep\\/tmp\\:\\/keep_tmp --volume=/tmp $VOLUME_CRUNCHRUNNER $VOLUME_CERTS --env=TASK_TMPDIR\\=\\/tmp\\/crunch\\-job\\-task\\-work\\/localhost\\.1 --env=JOB_SCRIPT\\=crunchrunner --env=TASK_SLOT_NODE\\=localhost --env=JOB_PARAMETER_TASKS\\=ARRAY\\(0x33c3c08\\) --env=JOB_UUID\\=3d0ga\\-8i9sb\\-g77fcbtmrvwbq39 --env=CRUNCH_JOB_BIN\\=\\/usr\\/src\\/arvados\\/sdk\\/cli\\/bin\\/crunch\\-job --env=JOB_WORK\\=\\/tmp\\/crunch\\-job\\-work --env=CRUNCH_NODE_SLOTS\\=1 --env=TASK_QSEQUENCE\\=0 --env=TASK_WORK\\=\\/tmp\\/crunch\\-job\\-task\\-work\\/localhost\\.1 --env=CRUNCH_SRC_COMMIT\\=94f5be8c86ad975ee7aa9f3df87be23fbc154dec --env=ARVADOS_API_HOST\\=172\\.17\\.0\\.2\\:8000 --env=TASK_SLOT_NUMBER\\=1 --env=TASK_KEEPMOUNT_TMP\\=\\/keep_tmp --env=CRUNCH_SRC_URL\\=\\/var\\/lib\\/arvados\\/internal\\.git --env=CRUNCH_INSTALL\\=\\/tmp\\/crunch0\\/opt --env=TASK_UUID\\=3d0ga\\-ot0gb\\-k9kg4a81t0e8l5y --env=CRUNCH_GIT_ARCHIVE_HASH\\=1de71538fa6973760966cbaaa6a8e91e --env=CRUNCH_REFRESH_TRIGGER\\=\\/tmp\\/crunch_refresh_trigger --env=CRUNCH_JOB_DOCKER_BIN\\=docker --env=TASK_KEEPMOUNT\\=\\/keep --env=TASK_SEQUENCE\\=0 --env=ARVADOS_API_HOST_INSECURE\\=1 --env=CRUNCH_TMP\\=\\/tmp\\/crunch0 --env=CRUNCH_WORK\\=\\/tmp\\/crunch0\\/work --env=CRUNCH_JOB_UUID\\=3d0ga\\-8i9sb\\-g77fcbtmrvwbq39 --env=ARVADOS_API_TOKEN\\=[...] --env=CRUNCH_SRC\\=\\/tmp\\/crunch0\\/src --env=HOME\\=\\/tmp\\/crunch\\-job\\-task\\-work\\/localhost\\.1 b067ef33063eaa1e74b985a4cce725f800342227da656bc1d1f65e0c2481c437 /bin/sh -c \'python -c "from pkg_resources import get_distribution as get; print \\"Using Arvados SDK version\\", get(\\"arvados-python-client\\").version">&2 2>/dev/null; mkdir -p "/tmp/crunch-job-work" "/tmp/crunch-job-task-work/localhost.1" && if which stdbuf >/dev/null ; then   exec  stdbuf --output=0 --error=0  \\/tmp\\/crunch0\\/src\\/crunch_scripts\\/crunchrunner ; else   exec \\/tmp\\/crunch0\\/src\\/crunch_scripts\\/crunchrunner ; fi\'']
2016-04-07_01:59:27 3d0ga-8i9sb-g77fcbtmrvwbq39 5652  status: 0 done, 1 running, 0 todo
2016-04-07_01:59:27 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 stderr Running [docker run --name=3d0ga-ot0gb-k9kg4a81t0e8l5y-0 --attach=stdout --attach=stderr --attach=stdin -i --user=crunch --cidfile=/tmp/crunch0/3d0ga-ot0gb-k9kg4a81t0e8l5y-0.cid --sig-proxy --memory=11571744k --memory-swap=22856220k --volume=/tmp/crunch0/src:/tmp/crunch0/src:ro --volume=/tmp/crunch0/opt:/tmp/crunch0/opt:ro --volume=/tmp/crunch0/task/localhost.1.keep/by_pdh:/keep:ro --volume=/tmp/crunch0/task/localhost.1.keep/tmp:/keep_tmp --volume=/tmp "--volume=/usr/local/bin/crunchrunner:/usr/local/bin/crunchrunner" "--volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt" --env=TASK_TMPDIR=/tmp/crunch-job-task-work/localhost.1 --env=JOB_SCRIPT=crunchrunner --env=TASK_SLOT_NODE=localhost --env=JOB_PARAMETER_TASKS=ARRAY(0x33c3c08) --env=JOB_UUID=3d0ga-8i9sb-g77fcbtmrvwbq39 --env=CRUNCH_JOB_BIN=/usr/src/arvados/sdk/cli/bin/crunch-job --env=JOB_WORK=/tmp/crunch-job-work --env=CRUNCH_NODE_SLOTS=1 --env=TASK_QSEQUENCE=0 --env=TASK_WORK=/tmp/crunch-job-task-work/localhost.1 --env=CRUNCH_SRC_COMMIT=94f5be8c86ad975ee7aa9f3df87be23fbc154dec --env=ARVADOS_API_HOST=172.17.0.2:8000 --env=TASK_SLOT_NUMBER=1 --env=TASK_KEEPMOUNT_TMP=/keep_tmp --env=CRUNCH_SRC_URL=/var/lib/arvados/internal.git --env=CRUNCH_INSTALL=/tmp/crunch0/opt --env=TASK_UUID=3d0ga-ot0gb-k9kg4a81t0e8l5y --env=CRUNCH_GIT_ARCHIVE_HASH=1de71538fa6973760966cbaaa6a8e91e --env=CRUNCH_REFRESH_TRIGGER=/tmp/crunch_refresh_trigger --env=CRUNCH_JOB_DOCKER_BIN=docker --env=TASK_KEEPMOUNT=/keep --env=TASK_SEQUENCE=0 --env=ARVADOS_API_HOST_INSECURE=1 --env=CRUNCH_TMP=/tmp/crunch0 --env=CRUNCH_WORK=/tmp/crunch0/work --env=CRUNCH_JOB_UUID=3d0ga-8i9sb-g77fcbtmrvwbq39 --env=ARVADOS_API_TOKEN=1xx0lcakio9oc7qt71e3qpyo94r43tc9p11swqnc4o24rmwteh --env=CRUNCH_SRC=/tmp/crunch0/src --env=HOME=/tmp/crunch-job-task-work/localhost.1 b067ef33063eaa1e74b985a4cce725f800342227da656bc1d1f65e0c2481c437 /bin/sh -c python -c "from pkg_resources import get_distribution as get; print \"Using Arvados SDK version\", get(\"arvados-python-client\").version">&2 2>/dev/null; mkdir -p "/tmp/crunch-job-work" "/tmp/crunch-job-task-work/localhost.1" && if which stdbuf >/dev/null ; then   exec  stdbuf --output=0 --error=0  \/tmp\/crunch0\/src\/crunch_scripts\/crunchrunner ; else   exec \/tmp\/crunch0\/src\/crunch_scripts\/crunchrunner ; fi]
2016-04-07_01:59:27 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 stderr Unable to find image '"--volume=/usr/local/bin/crunchrunner:/usr/local/bin/crunchrunner":latest' locally
2016-04-07_01:59:27 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 stderr repository name component must match "[a-z0-9](?:-*[a-z0-9])*(?:[._][a-z0-9](?:-*[a-z0-9])*)*" 
2016-04-07_01:59:32 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 stderr crunchstat: error reading cid file: /tmp/crunch0/3d0ga-ot0gb-k9kg4a81t0e8l5y-0.cid
2016-04-07_01:59:33 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 child 6281 on localhost.1 exit 1 success=
2016-04-07_01:59:33 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 ERROR: Task process exited 1, but never updated its task record to indicate success and record its output.
2016-04-07_01:59:33 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 failure (#1, permanent) after 5 seconds
2016-04-07_01:59:33 3d0ga-8i9sb-g77fcbtmrvwbq39 5652 0 task output (0 bytes):

#4 Updated by Brett Smith over 5 years ago

Shell programming: You want to do the right thing? WELL TOO BAD SCREW YOU.

#5 Updated by Brett Smith over 5 years ago

Peter Amstutz wrote:

Bad news. I tried the latest master in arvbox and it looks like trying to pass the quoting through doesn't work:

Thanks for cleaning that up. A generalized fix is now up for review in 8893-crunch-job-volumes-array-wip. I've also attached the test script that I wrote to prove to myself this method does what we want: each time showvars is called, the number of arguments, and their expansion, is correct.

#6 Updated by Brett Smith over 5 years ago

#7 Updated by Peter Amstutz over 5 years ago

675ae7b LGTM (tested on Arvbox)

#8 Updated by Brett Smith over 5 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 100

Applied in changeset arvados|commit:f044dbbcab5f4fcefaf2952fa1b71eb68aba7999.

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