Story #17755

Test singularity support on a cloud cluster by running some real workflows

Added by Peter Amstutz 6 months ago. Updated 11 days ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
Crunch
Target version:
Start date:
09/03/2021
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-
Release relationship:
Auto

Description

On a cloud cluster with singularity enabled (requires new compute image + config changes), run the the WGS workflow with small chr19 inputs, eg pirca-xvhdp-m4r8n9qmoh5ggra


Subtasks

Task #17796: ReviewResolvedLucas Di Pentima


Related issues

Related to Arvados - Story #17296: Singularity proof of conceptResolved05/27/2021

Related to Arvados Epics - Story #16305: Singularity supportResolved01/01/202109/30/2021

Related to Arvados - Bug #18027: [crunch-run] upload failed (singularity)Resolved09/03/2021

Related to Arvados - Bug #18026: [singularity] crunch-run image cache race conditionResolved08/24/2021

Blocked by Arvados - Bug #17816: singularity not setting working directoryResolved07/14/2021

Associated revisions

Revision 6ef187b8 (diff)
Added by Ward Vandewege 4 months ago

Singularity requires squashfs-tools to build images.

refs #17755

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision d59079ca
Added by Peter Amstutz 3 months ago

Merge branch '17755-singularity-race' into main refs #17755

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

Revision 9695271c
Added by Ward Vandewege 3 months ago

Merge branch '17755-add-singularity-to-compute-image'

closes #17755

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

History

#1 Updated by Peter Amstutz 6 months ago

  • Status changed from New to In Progress

#2 Updated by Peter Amstutz 6 months ago

  • Status changed from In Progress to New
  • Tracker changed from Bug to Story

#3 Updated by Peter Amstutz 6 months ago

  • Category set to Crunch

#4 Updated by Peter Amstutz 6 months ago

  • Description updated (diff)

#5 Updated by Peter Amstutz 6 months ago

  • Description updated (diff)
  • Subject changed from Test singularity support on 9tee4 by running some real workflows to Test singularity support on a cloud cluster by running some real workflows

#6 Updated by Peter Amstutz 6 months ago

  • Assigned To set to Ward Vandewege

#7 Updated by Ward Vandewege 6 months ago

  • Status changed from New to In Progress

#8 Updated by Ward Vandewege 6 months ago

  • Related to Story #17296: Singularity proof of concept added

#9 Updated by Ward Vandewege 6 months ago

I have built a new compute node image for ce8i5 that has the singularity binary 3.5.2 (that's an old version) in it, cf. commit: 784a3f24d37819186a52ea2c67e15e5bd8639076 on branch 17755-add-singularity-to-compute-image. That commit builds singularity from source while creating the packer image which seems suboptimal (it requires a lot of build-time dependencies, and it takes a while).

I've run the diagnostics workflow with it at ce8i5-xvhdp-el23s4fjsrp1mjb.

Observations:
  • the conversion of a ~240MiB docker tar file took over 5 minutes (ouch!!), about 4 of which seem to be in the invocation of `mksquashfs`
  • this conversion is invisible to the user, it's part of the "loading the image" stage so it's not considered when (e.g.) workbench shows workflow step durations.
  • the `hasher3` step ran on the same node as the `hasher1` step, but it repeated the singularity import step. Ouch.

ce8i5-xvhdp-ia0zn3njn6lwbdj: docker: 0m9s(6m queued)
ce8i5-xvhdp-el23s4fjsrp1mjb: singularity: 0m7s(11m queued)

#10 Updated by Ward Vandewege 5 months ago

I upgraded the ce8i5 compute image to use singularity 3.7.4 and switched ce8i5 over to singularity again. The amount of time it takes to convert the docker image to a singularity image seems unchanged (i.e. it's very slow).

The CWL tests were running, and all the jobs started failing because they are trying to write to a read-only filesystem. E.g. ce8i5-xvhdp-6aj1g0l31rae2y4, ce8i5-xvhdp-x95gwpw2gdf3113, etc. See https://ci.arvados.org/job/run-cwl-test-ce8i5/387/. I filed #17816 for this problem.

I then switched ce8i5 back to use docker.

Further testing on this ticket is probably pointless until we fix #17816.

#11 Updated by Ward Vandewege 5 months ago

  • Related to Bug #17816: singularity not setting working directory added

#12 Updated by Ward Vandewege 5 months ago

  • Related to deleted (Bug #17816: singularity not setting working directory)

#13 Updated by Ward Vandewege 5 months ago

  • Blocks Bug #17816: singularity not setting working directory added

#14 Updated by Ward Vandewege 5 months ago

  • Blocks deleted (Bug #17816: singularity not setting working directory)

#15 Updated by Ward Vandewege 5 months ago

  • Blocked by Bug #17816: singularity not setting working directory added

#16 Updated by Peter Amstutz 5 months ago

  • Target version changed from 2021-06-23 sprint to 2021-07-07 sprint

#17 Updated by Tom Clegg 5 months ago

  • Target version changed from 2021-07-07 sprint to 2021-07-21 sprint

#18 Updated by Peter Amstutz 4 months ago

  • Target version changed from 2021-07-21 sprint to 2021-08-04 sprint

#19 Updated by Ward Vandewege 4 months ago

Revisiting this with latest main (which has the fix from #17816).

I built a new compute image for ce8i5 with main + my 17755-add-singularity-to-compute-image branch at c2aceca339ec3a6f3d853865cebd0efe348ff518, image id: ce8i5-compute-v1627063559

The diagnostics workflow worked fine, as before: https://workbench.ce8i5.arvadosapi.com/container_requests/ce8i5-xvhdp-6f6xwvqpjhusey0

Re-running one of the cwl tests that failed last time succeeded:

https://workbench.ce8i5.arvadosapi.com/container_requests/ce8i5-xvhdp-wqwktdy4ijpvrgx#Log

I kicked off the cwl tests workflow at https://ci.arvados.org/job/run-cwl-test-ce8i5/420/

It failed (errors to be checked), and it took 14 hours (!) as opposed to the normal 3+ hours.

The next batch of singularity fixes (#17813) has been merged, which includes the fix to do the image conversion just once. The cwl tests are running against it at https://ci.arvados.org/job/run-cwl-test-ce8i5/423/. That run completed at 2 hours and 31 minutes, about 35 minutes faster than with Docker (!). One test failure remains, because we do not support the Docker ENTRYPOINT feature yet.

#20 Updated by Peter Amstutz 4 months ago

#21 Updated by Ward Vandewege 4 months ago

Preparing to run pirca-xvhdp-m4r8n9qmoh5ggra. The costanalyzer says these node types were used in that run on pirca:

m5.2xlarge
m5.4xlarge
m5.large
m5.xlarge
t3.small

Our quota on ce8i5 (azure) is tiny, so maybe we'll move this testing over to tordo (aws) where we have a bit more room. Building compute image with singularity for tordo at https://ci.arvados.org/view/Packer%20Images/job/packer-build-compute-image/138/...

That image built, I've reconfigured tordo to use Singularity with it. I'm gathering the files needed to run this workflow at https://workbench.tordo.arvadosapi.com/projects/tordo-j7d0g-q56odvtnbo37ajt.

#22 Updated by Peter Amstutz 4 months ago

  • Target version changed from 2021-08-04 sprint to 2021-08-18 sprint

#23 Updated by Ward Vandewege 4 months ago

Ward Vandewege wrote:

Preparing to run pirca-xvhdp-m4r8n9qmoh5ggra. The costanalyzer says these node types were used in that run on pirca:

m5.2xlarge
m5.4xlarge
m5.large
m5.xlarge
t3.small

Our quota on ce8i5 (azure) is tiny, so maybe we'll move this testing over to tordo (aws) where we have a bit more room. Building compute image with singularity for tordo at https://ci.arvados.org/view/Packer%20Images/job/packer-build-compute-image/138/...

That image built, I've reconfigured tordo to use Singularity with it. I'm gathering the files needed to run this workflow at https://workbench.tordo.arvadosapi.com/projects/tordo-j7d0g-q56odvtnbo37ajt.

Hmm, tordo seems to be having problems running its usual diag jobs because `singularity build` requires mksquashfs, from the squashfs-tools package (cf. https://ci.arvados.org/view/Arvados%20build%20pipeline/job/diagnostics-tordo/259/console). I've added that dependency to the 17755-add-singularity-to-compute-image branch and am building a new image with it for Tordo in https://ci.arvados.org/view/Packer%20Images/job/packer-build-compute-image/139/console. Curious I didn't see that on ce8i5. I suppose the azure Debian base image includes that package, and the AWS one does not.

New AMI for tordo is ami-0d9c1d43a4700db01, the config has been updated, and the diagnostics job succeeded at https://ci.arvados.org/view/Arvados%20build%20pipeline/job/diagnostics-tordo/260/console with singularity.

Good. Now, the actual chromosome 19 workflow.

The gist of it is to check out https://github.com/arvados/arvados-tutorial and then something like arvados-cwl-runner cwl/wgs-processing-wf.cwl yml/wgs-processing-wf-chr19.yml

I copied all the collections referenced in wgs-processing-wf-chr19.yml to my 17755 test project at tordo-j7d0g-q56odvtnbo37ajt.

And then:

arvados-cwl-runner --project-uuid tordo-j7d0g-q56odvtnbo37ajt ./cwl/wgs-processing-wf.cwl ./yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 2.3.0.dev20210729201354, arvados-python-client 2.3.0.dev20210726143205, cwltool 3.0.20210319143721
INFO Resolved './cwl/wgs-processing-wf.cwl' to 'file:///home/ward/arvados-tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Using cluster tordo (https://workbench2.tordo.arvadosapi.com/)
INFO Upload local files: "head.html" "generatereport.py" "tail.html" 
INFO Uploaded to 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-9p4undcuyh75qot)
INFO ['docker', 'pull', 'broadinstitute/gatk:4.1.7.0']
4.1.7.0: Pulling from broadinstitute/gatk
9ff7e2e5f967: Pull complete 
59856638ac9f: Pull complete 
6f317d6d954b: Pull complete 
a9dde5e2a643: Pull complete 
f7e0d1ec4184: Pull complete 
8ec82ad80803: Pull complete 
Digest: sha256:192fedf9b9d65809da4a2954030269e3f311d296e6b5e4c6c7deec12c7fe84b2
Status: Downloaded newer image for broadinstitute/gatk:4.1.7.0
docker.io/broadinstitute/gatk:4.1.7.0
INFO Uploading Docker image broadinstitute/gatk:4.1.7.0
2021-08-06 21:12:40 arvados.arv_put[16368] INFO: Creating new cache file at /home/ward/.cache/arvados/arv-put/6e8880e401836b16215bb738675fcb39
4022M / 4022M 100.0% 2021-08-06 21:13:48 arvados.arv_put[16368] INFO: 

2021-08-06 21:13:48 arvados.arv_put[16368] INFO: Collection saved as 'Docker image broadinstitute gatk:4.1.7.0 sha256:e7b5b'
tordo-4zz18-bc2qarec0qvov3i
2021-08-06 21:13:49 cwltool[16368] INFO: ['docker', 'pull', 'curii/clinvar-report']
Using default tag: latest
Error response from daemon: pull access denied for curii/clinvar-report, repository does not exist or may require 'docker login': denied: requested access to the resource is denied
2021-08-06 21:13:49 cwltool[16368] ERROR: Workflow error, try again with --debug for more information:
cwl/helper/gvcf-to-vcf.cwl:7:5: Command '['docker', 'pull', 'curii/clinvar-report']' returned
                                non-zero exit status 1. (X-Request-Id: req-lqjx8gknsk1uif6s7g0m)

Hmmm, looks like I missed that one.

We should probably publish that container on dockerhub...

ward@shell:~/arvados-tutorial/WGS-processing$ arv-copy pirca-4zz18-rn8581yvkk73lmc --project-uuid tordo-j7d0g-q56odvtnbo37ajt
pirca-4zz18-rn8581yvkk73lmc: 1067M / 1067M 100.0% 
2021-08-06 21:16:19 arvados.arv-copy[16704] INFO: 
2021-08-06 21:16:19 arvados.arv-copy[16704] INFO: Success: created copy with uuid tordo-4zz18-4zqcmpzmobikh0w

Take 2:

ward@shell:~/arvados-tutorial/WGS-processing$ arvados-cwl-runner --project-uuid tordo-j7d0g-q56odvtnbo37ajt ./cwl/wgs-processing-wf.cwl ./yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 2.3.0.dev20210729201354, arvados-python-client 2.3.0.dev20210726143205, cwltool 3.0.20210319143721
INFO Resolved './cwl/wgs-processing-wf.cwl' to 'file:///home/ward/arvados-tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Using cluster tordo (https://workbench2.tordo.arvadosapi.com/)
INFO Upload local files: "head.html" "generatereport.py" "tail.html" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-9p4undcuyh75qot)
INFO ['docker', 'pull', 'curii/bwa-samtools']
Using default tag: latest
Error response from daemon: pull access denied for curii/bwa-samtools, repository does not exist or may require 'docker login': denied: requested access to the resource is denied
ERROR Workflow error, try again with --debug for more information:
cwl/helper/bwamem-samtools-view.cwl:7:5: Command '['docker', 'pull', 'curii/bwa-samtools']'
                                         returned non-zero exit status 1.

Jeez. More copying:

ward@shell:~/arvados-tutorial/WGS-processing$ arv-copy pirca-4zz18-mjt3nkmmuuo4uos --project-uuid tordo-j7d0g-q56odvtnbo37ajt
pirca-4zz18-mjt3nkmmuuo4uos: 999M / 999M 100.0% 
2021-08-06 21:21:46 arvados.arv-copy[17076] INFO: 
2021-08-06 21:21:46 arvados.arv-copy[17076] INFO: Success: created copy with uuid tordo-4zz18-8r0gqxll14jcpfv

And one more try:

ward@shell:~/arvados-tutorial/WGS-processing$ arvados-cwl-runner --project-uuid tordo-j7d0g-q56odvtnbo37ajt ./cwl/wgs-processing-wf.cwl ./yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 2.3.0.dev20210729201354, arvados-python-client 2.3.0.dev20210726143205, cwltool 3.0.20210319143721
INFO Resolved './cwl/wgs-processing-wf.cwl' to 'file:///home/ward/arvados-tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Using cluster tordo (https://workbench2.tordo.arvadosapi.com/)
INFO Upload local files: "generatereport.py" "tail.html" "head.html" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-9p4undcuyh75qot)
INFO ['docker', 'pull', 'biocontainers/fastqc:v0.11.9_cv6']
v0.11.9_cv6: Pulling from biocontainers/fastqc
9ff7e2e5f967: Already exists 
59856638ac9f: Already exists 
6f317d6d954b: Already exists 
a9dde5e2a643: Already exists 
675cac559d07: Pull complete 
0e6dd20ee818: Pull complete 
374c558e71da: Pull complete 
0df3c64bb19a: Pull complete 
e936d7784cf9: Pull complete 
4dfd8d164cc5: Pull complete 
473490461998: Pull complete 
8f5e491552e6: Pull complete 
a66ab3a674d9: Pull complete 
18f922275a6f: Pull complete 
ef8214645dd0: Pull complete 
Digest: sha256:c740cf547548689724bf43b3e923fea6a7588c17d59b7cbd76fa9ac7544102c5
Status: Downloaded newer image for biocontainers/fastqc:v0.11.9_cv6
docker.io/biocontainers/fastqc:v0.11.9_cv6
INFO Uploading Docker image biocontainers/fastqc:v0.11.9_cv6
2021-08-06 21:24:52 arvados.arv_put[17135] INFO: Creating new cache file at /home/ward/.cache/arvados/arv-put/28720ca8e76a2892c0ea812e2e0e0ab6
1001M / 1001M 100.0% 2021-08-06 21:25:06 arvados.arv_put[17135] INFO: 

2021-08-06 21:25:06 arvados.arv_put[17135] INFO: Collection saved as 'Docker image biocontainers fastqc:v0.11.9_cv6 sha256:33755'
tordo-4zz18-h6aj03stuegf0hu
2021-08-06 21:25:08 cwltool[17135] INFO: Using collection cache size 256 MiB
2021-08-06 21:25:10 arvados.cwl-runner[17135] INFO: [container WGS processing workflow scattered over samples] submitted container_request tordo-xvhdp-4dc27lh513rh7ai
2021-08-06 21:25:10 arvados.cwl-runner[17135] INFO: Monitor workflow progress at https://workbench2.tordo.arvadosapi.com/processes/tordo-xvhdp-4dc27lh513rh7ai

It's running now. I should have used --no-wait, but I'm in screen so it's all right.

#24 Updated by Ward Vandewege 4 months ago

That almost worked. One step got stuck in the 'Queued' state:

https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-iwwdqh2w5wyprix#Log

Looks like the container was restarted twice. The third copy appears just stuck.

Nothing obviously wrong on the compute node:

root@ip-10-253-254-170:/home/crunch# singularity  --version
singularity version 3.7.4
root@ip-10-253-254-170:/var/log# df -h
Filesystem       Size  Used Avail Use% Mounted on
udev             970M     0  970M   0% /dev
tmpfs            196M   18M  179M   9% /run
/dev/nvme1n1p1   7.7G  3.0G  4.4G  41% /
tmpfs            980M     0  980M   0% /dev/shm
tmpfs            5.0M  4.0K  5.0M   1% /run/lock
tmpfs            980M     0  980M   0% /sys/fs/cgroup
/dev/nvme1n1p15  124M  278K  124M   1% /boot/efi
tmpfs            196M     0  196M   0% /run/user/1000
/dev/mapper/tmp   47G   81M   47G   1% /tmp
tmpfs            196M     0  196M   0% /run/user/1001
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root         2  0.0  0.0      0     0 ?        S    21:26   0:00 [kthreadd]
root         3  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [rcu_gp]
root         4  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [rcu_par_gp]
root         6  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/0:0H-kblockd]
root         8  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [mm_percpu_wq]
root         9  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [ksoftirqd/0]
root        10  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [rcu_sched]
root        11  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [rcu_bh]
root        12  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [migration/0]
root        14  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [cpuhp/0]
root        15  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [cpuhp/1]
root        16  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [migration/1]
root        17  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [ksoftirqd/1]
root        19  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/1:0H-kblockd]
root        20  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [kdevtmpfs]
root        21  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [netns]
root        22  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [kauditd]
root        23  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [khungtaskd]
root        24  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [oom_reaper]
root        25  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [writeback]
root        26  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [kcompactd0]
root        27  0.0  0.0      0     0 ?        SN   21:26   0:00  \_ [ksmd]
root        28  0.0  0.0      0     0 ?        SN   21:26   0:00  \_ [khugepaged]
root        29  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [crypto]
root        30  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kintegrityd]
root        31  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kblockd]
root        32  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [watchdogd]
root        33  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [kworker/1:1-events]
root        34  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [kworker/u4:1-events_unbound]
root        36  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [kswapd0]
root        52  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kthrotld]
root        53  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [ipv6_addrconf]
root        62  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kstrp]
root        67  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [kworker/1:2-mm_percpu_wq]
root       104  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [nvme-wq]
root       105  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [nvme-reset-wq]
root       106  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [nvme-delete-wq]
root       107  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [kworker/u4:2-events_unbound]
root       115  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [ena]
root       184  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [jbd2/nvme1n1p1-]
root       185  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [ext4-rsv-conver]
root       229  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/0:1H-kblockd]
root       257  0.0  0.0      0     0 ?        I    21:26   0:00  \_ [kworker/0:2-events]
root       528  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/1:1H-kblockd]
root       807  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kdmflush]
root      1254  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kdmflush]
root      1259  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kcryptd_io]
root      1260  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kcryptd]
root      1261  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [dmcrypt_write]
root      1263  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/u5:1-kcryptd]
root      1264  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [kworker/u5:2-kcryptd]
root      1347  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfsalloc]
root      1348  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs_mru_cache]
root      1349  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-buf/dm-1]
root      1350  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-data/dm-1]
root      1351  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-conv/dm-1]
root      1352  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-cil/dm-1]
root      1353  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-reclaim/dm-]
root      1354  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-log/dm-1]
root      1355  0.0  0.0      0     0 ?        I<   21:26   0:00  \_ [xfs-eofblocks/d]
root      1356  0.0  0.0      0     0 ?        S    21:26   0:00  \_ [xfsaild/dm-1]
root      3687  0.0  0.0      0     0 ?        I    22:17   0:00  \_ [kworker/0:0-events_power_efficient]
root      6027  0.0  0.0      0     0 ?        I    23:12   0:00  \_ [kworker/0:1-xfs-cil/dm-1]
root      6186  0.0  0.0      0     0 ?        I<   23:13   0:00  \_ [kworker/u5:0-kcryptd]
root         1  0.0  0.5  22116 10224 ?        Ss   21:26   0:02 /sbin/init
root       247  0.0  0.5  42948 11668 ?        Ss   21:26   0:05 /lib/systemd/systemd-journald
root       265  0.0  0.2  20068  4880 ?        Ss   21:26   0:00 /lib/systemd/systemd-udevd
root       381  0.0  0.2   9488  5720 ?        Ss   21:26   0:00 /sbin/dhclient -4 -v -i -pf /run/dhclient.ens5.pid -lf /var/lib/dhcp/dhclient.ens5.leases -I -df /var/lib/dhcp/dhclient6.ens5.leases ens5
root       483  0.0  0.2   9488  5644 ?        Ss   21:26   0:00 /sbin/dhclient -6 -v -pf /run/dhclient6.ens5.pid -lf /var/lib/dhcp/dhclient6.ens5.leases -I -df /var/lib/dhcp/dhclient.ens5.leases -nw ens5
message+   579  0.0  0.2   8808  4132 ?        Ss   21:26   0:00 /usr/bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --systemd-activation --syslog-only
root       581  0.0  0.3  19520  7336 ?        Ss   21:26   0:00 /lib/systemd/systemd-logind
root       582  0.0  0.2 225824  4280 ?        Ssl  21:26   0:01 /usr/sbin/rsyslogd -n -iNONE
root       584  0.0  0.1  10228  2664 ?        Ss   21:26   0:00 /usr/sbin/cron -f
_chrony    590  0.0  0.1   4816  2228 ?        S    21:26   0:00 /usr/sbin/chronyd -F -1
_chrony    594  0.0  0.0   4816   268 ?        S    21:26   0:00  \_ /usr/sbin/chronyd -F -1
root       591  0.0  0.0   5612  1688 tty1     Ss+  21:26   0:00 /sbin/agetty -o -p -- \u --noclear tty1 linux
root       592  0.0  0.1   7136  2052 ttyS0    Ss+  21:26   0:00 /sbin/agetty -o -p -- \u --keep-baud 115200,38400,9600 ttyS0 vt220
root       593  0.0  0.3  15852  6708 ?        Ss   21:26   0:00 /usr/sbin/sshd -D
root       625  0.0  0.3  16612  7828 ?        Ss   21:26   0:00  \_ sshd: admin [priv]
admin      651  0.0  0.2  16612  4848 ?        S    21:26   0:00  |   \_ sshd: admin@notty
root      1268  0.0  0.3  16612  7956 ?        Ss   21:26   0:00  \_ sshd: admin [priv]
admin     1274  0.0  0.2  16784  5348 ?        S    21:26   0:01  |   \_ sshd: admin@notty
root      6025  0.0  0.4  16608  8076 ?        Ss   23:12   0:00  \_ sshd: crunch [priv]
crunch    6043  0.0  0.2  16608  4940 ?        S    23:12   0:00      \_ sshd: crunch@pts/0
crunch    6044  0.0  0.2   9648  4736 pts/0    Ss   23:12   0:00          \_ -bash
root      6058  0.0  0.1  11664  3700 pts/0    S    23:12   0:00              \_ sudo -s
root      6059  0.0  0.1   8716  3632 pts/0    S    23:12   0:00                  \_ /bin/bash
root      6222  0.0  0.1  12512  3204 pts/0    R+   23:14   0:00                      \_ ps auxwf
admin      628  0.0  0.4  21148  9164 ?        Ss   21:26   0:00 /lib/systemd/systemd --user
admin      629  0.0  0.1  22888  2304 ?        S    21:26   0:00  \_ (sd-pam)
root      1315  0.2  2.2 1327060 44344 ?       Sl   21:26   0:14 /var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df -no-detach --detach --stdin-env --runtime-engine=singularity tordo-dz642-xm3fbl5he5o2aul
root      1325  0.1  2.4 1320308 49556 ?       Sl   21:26   0:12  \_ /usr/share/python3/dist/python3-arvados-fuse/bin/python /usr/bin/arv-mount --foreground --allow-other --read-write --storage-classes default --crunchstat-interval=10 --file-cache 268435456 --mount-by-pdh by_id --mount-by-id by_uuid /tmp/crunch-run.tordo-dz642-xm3fbl5he5o2aul.806337907/keep928487990
root      1417  0.1  4.1 1074032 83872 ?       Ssl  21:26   0:09 /usr/sbin/dockerd -H fd:// --default-ulimit nofile=10000:10000 --dns 10.253.0.2
root      1424  0.1  1.6 878344 32680 ?        Ssl  21:26   0:12  \_ docker-containerd --config /var/run/docker/containerd/containerd.toml --log-level info
root      1546  0.0  1.0  32536 21896 ?        Ss   21:27   0:00 /usr/share/python3/dist/arvados-docker-cleaner/bin/python /usr/bin/arvados-docker-cleaner
crunch    6029  0.0  0.4  21160  9120 ?        Ss   23:12   0:00 /lib/systemd/systemd --user
crunch    6030  0.0  0.1  23080  2556 ?        S    23:12   0:00  \_ (sd-pam)

From /var/log/auth.log:

Aug  6 21:26:56 ip-10-253-254-170 systemd-logind[581]: New session 3 of user admin.
Aug  6 21:26:56 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/usr/bin/cat /var/run/arvados-instance-secret
Aug  6 21:26:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:26:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:26:56 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/usr/bin/docker ps -q
Aug  6 21:26:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:26:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:26:56 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/usr/bin/sh -c set -e; dstdir="/var/lib/arvados/"; dstfile="/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df"; mkdir -p "$dstdir"; touch "$dstfile"; chmod 0755 "$dstdir" "$dstfile"; cat >"$dstfile" 
Aug  6 21:26:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:26:57 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:26:57 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:26:57 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:26:57 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:26:57 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --detach --stdin-env --runtime-engine=singularity tordo-dz642-xm3fbl5he5o2aul
Aug  6 21:26:57 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:26:57 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:06 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:06 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:06 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:16 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:16 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:16 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:26 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:26 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:26 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:36 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:36 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:36 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:46 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:46 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:46 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 21:27:56 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 21:27:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 21:27:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root

....

and on and on and on

....

Aug  6 23:25:56 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 23:25:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 23:25:56 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root
Aug  6 23:26:06 ip-10-253-254-170 sudo:    admin : TTY=unknown ; PWD=/home/admin ; USER=root ; COMMAND=/var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
Aug  6 23:26:06 ip-10-253-254-170 sudo: pam_unix(sudo:session): session opened for user root by (uid=0)
Aug  6 23:26:06 ip-10-253-254-170 sudo: pam_unix(sudo:session): session closed for user root

Running that command manually shows

root@ip-10-253-254-170:/var/log# /var/lib/arvados/crunch-run~59eb599fd48e090ea6b99794587612df --list
tordo-dz642-xm3fbl5he5o2aul

So we get the uuid of the container back. That's expected.

I guess something happened to the arv-mount process, it got stuck?

root@ip-10-253-254-170:/var/log# v /proc/1325/fd/
total 0
dr-x------ 2 root root  0 Aug  6 21:26 ./
dr-xr-xr-x 9 root root  0 Aug  6 21:26 ../
lr-x------ 1 root root 64 Aug  6 21:26 0 -> /dev/null
l-wx------ 1 root root 64 Aug  6 21:26 1 -> 'pipe:[16552]'
l-wx------ 1 root root 64 Aug  6 21:26 2 -> 'pipe:[16553]'
lrwx------ 1 root root 64 Aug  6 21:26 3 -> /run/lock/crunch-run-tordo-dz642-xm3fbl5he5o2aul.lock*
lrwx------ 1 root root 64 Aug  6 21:26 4 -> 'socket:[17495]'
lrwx------ 1 root root 64 Aug  6 23:34 5 -> /dev/fuse
lrwx------ 1 root root 64 Aug  6 23:34 6 -> 'socket:[17503]'

root@ip-10-253-254-170:/var/log# v /run/lock/crunch-run-tordo-dz642-xm3fbl5he5o2aul.lock
-rwx------ 1 root root 50 Aug  6 21:26 /run/lock/crunch-run-tordo-dz642-xm3fbl5he5o2aul.lock*

#25 Updated by Ward Vandewege 4 months ago

Trying to cancel this job, the cancel button in wb doesn't work, this is the error I see in the controller logs:

Aug 06 23:41:16 tordo.arvadosapi.com arvados-controller[13414]: {"PID":13414,"RequestID":"req-3x51wipebp66b8pxx8hg","level":"info","msg":"response","remoteAddr":"127.0.0.1:41130","reqBytes":1982,"reqForwardedFor":"10.253.0.41","reqHost":"tordo.arvadosapi.com","reqMethod":"POST","reqPath":"arvados/v1/container_requests/tordo-xvhdp-iwwdqh2w5wyprix","reqQuery":"","respBody":"{\"errors\":[\"//railsapi.internal/arvados/v1/container_requests/tordo-xvhdp-iwwdqh2w5wyprix: 422 Unprocessable Entity: Mounts cannot be modified in state 'Final' ({\\\"/keep/35d4f4c5720a1e1c7b5c583cc901c3e0+3765\\\"=\\u003e{\\\"kind\\\"=\\u003e\\\"collection\\\", \\\"portable_data_hash\\\"=\\u003e\\\"35d4f4c5720a1e1c7b5c583cc901c3e0+3765\\\"}, \\\"/tmp\\\"=\\u003e{\\\"capacity\\\"=\\u003e1073741824, \\\"kind\\\"=\\u003e\\\"tmp\\\"}, \\\"/var/spool/cwl\\\"=\\u003e{\\\"capacity\\\"=\\u003e1073741824, \\\"kind\\\"=\\u003e\\\"tmp\\\"}}, {\\\"/keep/35d4f4c5720a1e1c7b5c583cc901c3e0+3765\\\"=\\u003e{\\\"capacity\\\"=\\u003e0, \\\"commit\\\"=\\u003e\\\"\\\", \\\"content\\\"=\\u003enil, \\\"device_type\\\"=\\u003e\\\"\\\", \\\"exclude_from_output\\\"=\\u003efalse, \\\"git_url\\\"=\\u003e\\\"\\\", \\\"kind\\\"=\\u003e\\\"collection\\\", \\\"path\\\"=\\u003e\\\"\\\", \\\"portable_data_hash\\\"=\\u003e\\\"35d4f4c5720a1e1c7b5c583cc901c3e0+3765\\\", \\\"repository_name\\\"=\\u003e\\\"\\\", \\\"uuid\\\"=\\u003e\\\"\\\", \\\"writable\\\"=\\u003efalse}, \\\"/tmp\\\"=\\u003e{\\\"capacity\\\"=\\u003e1073741824, \\\"commit\\\"=\\u003e\\\"\\\", \\\"content\\\"=\\u003enil, \\\"device_type\\\"=\\u003e\\\"\\\", \\\"exclude_","respBytes":1618,"respStatus":"Unprocessable Entity","respStatusCode":422,"time":"2021-08-06T23:41:16.438539926Z","timeToStatus":0.018596,"timeTotal":0.018626,"timeWriteBody":0.000030}

This sounds vaguely familiar. This is a second bug, then.

I'll kill the node with a-d-c.

curl -H "Authorization: Bearer $TOKEN" -X GET http://10.253.0.44:9006/arvados/v1/dispatch/instances |jq .
{
  "items": [
    {
      "instance": "i-0321dc62106d21d98",
      "address": "10.253.254.104",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-mitu9yi55h7femh",
      "last_busy": "2021-08-07T00:07:16.063745476Z",
      "worker_state": "running",
      "idle_behavior": "run" 
    },
    {
      "instance": "i-0362e2a61c62cfaf2",
      "address": "10.253.254.170",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-xm3fbl5he5o2aul",
      "last_busy": "2021-08-07T00:07:16.078001157Z",
      "worker_state": "running",
      "idle_behavior": "run" 
    }
  ]
}

tordo:~# curl -H "Authorization: Bearer $TOKEN" -X POST http://10.253.0.44:9006/arvados/v1/dispatch/instances/kill?instance_id=i-0362e2a61c62cfaf2 |jq .

tordo:~# curl -H "Authorization: Bearer $TOKEN" -X GET http://10.253.0.44:9006/arvados/v1/dispatch/instances |jq .
{
  "items": [
    {
      "instance": "i-0321dc62106d21d98",
      "address": "10.253.254.104",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-mitu9yi55h7femh",
      "last_busy": "2021-08-07T00:07:56.023842384Z",
      "worker_state": "running",
      "idle_behavior": "run" 
    },
    {
      "instance": "i-0362e2a61c62cfaf2",
      "address": "10.253.254.170",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-xm3fbl5he5o2aul",
      "last_busy": "2021-08-07T00:07:46.041616399Z",
      "worker_state": "shutdown",
      "idle_behavior": "run" 
    }
  ]
}

A new node was created:

tordo:~# curl -H "Authorization: Bearer $TOKEN" -X GET http://10.253.0.44:9006/arvados/v1/dispatch/instances |jq .
{
  "items": [
    {
      "instance": "i-0321dc62106d21d98",
      "address": "10.253.254.104",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-mitu9yi55h7femh",
      "last_busy": "2021-08-07T00:08:56.02153052Z",
      "worker_state": "running",
      "idle_behavior": "run" 
    },
    {
      "instance": "i-06dd557531f9df013",
      "address": "10.253.254.243",
      "price": 0.0208,
      "arvados_instance_type": "t3small",
      "provider_instance_type": "t3.small",
      "last_container_uuid": "tordo-dz642-xm3fbl5he5o2aul",
      "last_busy": "2021-08-07T00:08:56.047446083Z",
      "worker_state": "running",
      "idle_behavior": "run" 
    }
  ]
}

And this node ran the job without trouble: https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-iwwdqh2w5wyprix#Status.

I think we have a missing error check somewhere early in the singularity docker loading code. There was a (transient?) problem on this particular node, and that made the container get stuck.

#26 Updated by Peter Amstutz 4 months ago

The first two failures I think are due to a race condition between two crunch-run processes trying to convert and caching the singularity image.

This attempt found the collection, but apparently before the cached image had been created. (not supposed to happen.)

2021-08-06T21:26:16.608212665Z Using Docker image id "sha256:337550d506a3fc77e30292bba95108f1cd34a33719f0dd997d0de0540522def7"
2021-08-06T21:26:16.608240987Z Loading Docker image from keep
2021-08-06T21:26:17.188261275Z building singularity image
2021-08-06T21:26:17.223285265Z [singularity build /tmp/crunch-run.tordo-dz642-pez87oegh5fgbs7.099258167/keep207354666/by_uuid/tordo-4zz18-t0wx4utpwx4ligf/image.sif docker-archive:///tmp/crunch-run-singularity-917581112/image.tar]
2021-08-06T21:26:26.466105517Z INFO: Starting build...
2021-08-06T21:26:26.466105517Z FATAL: While performing build: conveyor failed to get: Error loading tar component 337550d506a3fc77e30292bba95108f1cd34a33719f0dd997d0de0540522def7.json: open /tmp/crunch-run-singularity-917581112/image.tar: no such file or directory
2021-08-06T21:26:26.466234171Z error in Run: While loading container image: exit status 255
2021-08-06T21:26:26.466268708Z error in CaptureOutput: error scanning files to copy to output: lstat "/var/spool/cwl": lstat /tmp/crunch-run.tordo-dz642-pez87oegh5fgbs7.099258167/tmp701045228: no such file or directory
2021-08-06T21:26:26.605452965Z Cancelled

On the second attempt, it tried to create a collection with the same temporary name (down to the exact timestamp?) and that failed.

2021-08-06T21:26:47.149336231Z Executing container 'tordo-dz642-amjt50vnz4qyn4n'
...
2021-08-06T21:26:47.972965997Z error in Run: While loading container image: error creating 'singularity image for sha256:337550d506a3fc77e30292bba95108f1cd34a33719f0dd997d0de0540522def7 2021-08-06T21:26:47Z' collection: request failed: https://tordo.arvadosapi.com/arvados/v1/collections: 422 Unprocessable Entity: //railsapi.internal/arvados/v1/collections: 422 Unprocessable Entity: #<ActiveRecord::RecordNotUnique: PG::UniqueViolation: ERROR: duplicate key value violates unique constraint "index_collections_on_owner_uuid_and_name"
2021-08-06T21:26:47.972965997Z DETAIL: Key (owner_uuid, name)=(tordo-j7d0g-7p82g804nk5l7gx, singularity image for sha256:337550d506a3fc77e30292bba95108f1cd34a33719f0dd997d0de0540522def7 2021-08-06T21:26:47Z) already exists.
2021-08-06T21:26:47.972965997Z : INSERT INTO "collections" ("owner_uuid", "created_at", "modified_by_user_uuid", "modified_at", "portable_data_hash", "updated_at", "uuid", "manifest_text", "name", "properties", "delete_at", "file_names", "trash_at", "current_version_uuid") VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14) RETURNING "id"> (req-8t57dqc95orqsvelydce)
2021-08-06T21:26:48.136224600Z Cancelled

#27 Updated by Peter Amstutz 4 months ago

The 3rd failure is puzzling, if you check stderr it actually did run to the end, but failed the upload. This happened after the intervention of being stuck in queued state and killing the compute node.

2021-08-07T00:08:37.343893355Z Executing container 'tordo-dz642-xm3fbl5he5o2aul'
...
2021-08-07T00:08:39.823076366Z Waiting for container to finish
2021-08-07T00:10:47.551657400Z error in CaptureOutput: error scanning files to copy to output: lstat "/var/spool/cwl": lstat /tmp/crunch-run.tordo-dz642-xm3fbl5he5o2aul.609138299/tmp536330368: no such file or directory
2021-08-07T00:10:47.568368336Z Cancelled

#28 Updated by Peter Amstutz 4 months ago

Was the "queued" container actually "locked"? (probably but would be good to confirm).

Because it didn't get far enough, the container record was reused for the 2nd attempt, all the logs in keep are only the second attempt. Fortunately there are logs stored on the API server:

https://workbench.tordo.arvadosapi.com/containers/tordo-dz642-xm3fbl5he5o2aul#Log

Although they don't tell us very much. It hung sometime after starting arv-mount.

This might be related to the event handling deadlock we've been seeing.

#29 Updated by Ward Vandewege 3 months ago

Peter Amstutz wrote:

Was the "queued" container actually "locked"? (probably but would be good to confirm).

Because it didn't get far enough, the container record was reused for the 2nd attempt, all the logs in keep are only the second attempt. Fortunately there are logs stored on the API server:

https://workbench.tordo.arvadosapi.com/containers/tordo-dz642-xm3fbl5he5o2aul#Log

Although they don't tell us very much. It hung sometime after starting arv-mount.

This might be related to the event handling deadlock we've been seeing.

I'll make a new compute image before doing further testing: ami-0ba36796c859d41a2 has the arv-mount fix built in.

#30 Updated by Ward Vandewege 3 months ago

  • Related to Bug #18027: [crunch-run] upload failed (singularity) added

#31 Updated by Ward Vandewege 3 months ago

  • Related to Bug #18026: [singularity] crunch-run image cache race condition added

#32 Updated by Ward Vandewege 3 months ago

Peter Amstutz wrote:

Was the "queued" container actually "locked"? (probably but would be good to confirm).

Because it didn't get far enough, the container record was reused for the 2nd attempt, all the logs in keep are only the second attempt. Fortunately there are logs stored on the API server:

https://workbench.tordo.arvadosapi.com/containers/tordo-dz642-xm3fbl5he5o2aul#Log

Although they don't tell us very much. It hung sometime after starting arv-mount.

This might be related to the event handling deadlock we've been seeing.

Now that the fix for the arv-mount deadlock has been merged, I've built a new compute image with that fix (ami-0ba36796c859d41a2), and kicked off a new test run with

ward@shell:~/arvados-tutorial/WGS-processing$ arvados-cwl-runner --project-uuid tordo-j7d0g-q56odvtnbo37ajt ./cwl/wgs-processing-wf.cwl ./yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 2.3.0.dev20210813182157, arvados-python-client 2.3.0.dev20210810185721, cwltool 3.0.20210319143721
INFO Resolved './cwl/wgs-processing-wf.cwl' to 'file:///home/ward/arvados-tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Using cluster tordo (https://workbench2.tordo.arvadosapi.com/)
INFO Upload local files: "tail.html" "head.html" "generatereport.py" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-9p4undcuyh75qot)
INFO Using collection cache size 256 MiB
INFO [container WGS processing workflow scattered over samples] submitted container_request tordo-xvhdp-911ekye8xxwcb7r
INFO Monitor workflow progress at https://workbench2.tordo.arvadosapi.com/processes/tordo-xvhdp-911ekye8xxwcb7r
INFO [container WGS processing workflow scattered over samples] tordo-xvhdp-911ekye8xxwcb7r is Final
INFO Overall process status is success
INFO Final output collection 431b75fdad437345c678fe58163ad2ec+1243
INFO Output at https://workbench2.tordo.arvadosapi.com/collections/431b75fdad437345c678fe58163ad2ec+1243
{   
    "gvcf": [
        {   
            "basename": "ERR2122553.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122553.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122553.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122553.g.vcf.gz.tbi" 
                }
            ],
            "size": 100428289
        },
        {   
            "basename": "ERR2122554.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122554.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122554.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122554.g.vcf.gz.tbi" 
                }
            ],
            "size": 83396874
        },
        {   
            "basename": "ERR2122555.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122555.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122555.g.vcf.gz.tbi",
                }
            ],
            "size": 100428289
        },
        {   
            "basename": "ERR2122554.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122554.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122554.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122554.g.vcf.gz.tbi" 
                }
            ],
            "size": 83396874
        },
        {   
            "basename": "ERR2122555.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122555.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122555.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122555.g.vcf.gz.tbi" 
                }
            ],
            "size": 68070153
        },
        {   
            "basename": "ERR2122556.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122556.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122556.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122556.g.vcf.gz.tbi" 
                }
            ],
            "size": 80162449
        },
        {   
            "basename": "ERR2122557.g.vcf.gz",
            "class": "File",
            "format": "http://edamontology.org/format_3016",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122557.g.vcf.gz",
            "secondaryFiles": [
                {   
                    "basename": "ERR2122557.g.vcf.gz.tbi",
                    "class": "File",
                    "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122557.g.vcf.gz.tbi" 
                }
            ],
            "size": 92916518
        }
    ],
    "report": [
        {   
            "basename": "ERR2122553.html",
            "class": "File",
            "format": "http://edamontology.org/format_2331",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122553.html",
            "size": 213477
        },
        {   
            "basename": "ERR2122554.html",
            "class": "File",
            "format": "http://edamontology.org/format_2331",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122554.html",
            "size": 203560
        },
        {   
            "basename": "ERR2122555.html",
            "class": "File",
            "format": "http://edamontology.org/format_2331",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122555.html",
            "size": 224649
        },
        {   
            "basename": "ERR2122556.html",
            "class": "File",
            "format": "http://edamontology.org/format_2331",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122556.html",
            "size": 210935
        },
        {   
            "basename": "ERR2122557.html",
            "class": "File",
            "format": "http://edamontology.org/format_2331",
            "location": "keep:431b75fdad437345c678fe58163ad2ec+1243/ERR2122557.html",
            "size": 225496
        }
    ]
}
INFO Final process status is success

Hmm, that reused everything, not quite what I wanted.

Trying again:

ward@shell:~/arvados-tutorial/WGS-processing$ arvados-cwl-runner --disable-reuse --project-uuid tordo-j7d0g-q56odvtnbo37ajt ./cwl/wgs-processing-wf.cwl ./yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 2.3.0.dev20210813182157, arvados-python-client 2.3.0.dev20210810185721, cwltool 3.0.20210319143721
INFO Resolved './cwl/wgs-processing-wf.cwl' to 'file:///home/ward/arvados-tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Using cluster tordo (https://workbench2.tordo.arvadosapi.com/)
INFO Upload local files: "generatereport.py" "tail.html" "head.html" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-9p4undcuyh75qot)
INFO Using collection cache size 256 MiB
INFO [container WGS processing workflow scattered over samples] submitted container_request tordo-xvhdp-bb8pjmzh93hkzmz
INFO Monitor workflow progress at https://workbench2.tordo.arvadosapi.com/processes/tordo-xvhdp-bb8pjmzh93hkzmz

...

This run completed successfully without obvious issues: https://workbench.tordo.arvadosapi.com/container_requests/tordo-xvhdp-bb8pjmzh93hkzmz.

This container started at 5:09 PM 8/17/2021. It completed in 1h18m at 6:27 PM 8/17/2021.

It has runtime of 1h16m(2mqueued) and used 5h18m of node allocation time (4.2тип scaling).

#33 Updated by Peter Amstutz 3 months ago

  • Target version changed from 2021-08-18 sprint to 2021-09-01 sprint

#34 Updated by Peter Amstutz 3 months ago

  • Target version changed from 2021-09-01 sprint to 2021-09-15 sprint

#35 Updated by Ward Vandewege 3 months ago

17755-add-singularity-to-compute-image is ready for review at 72d7d41944006d1f48f570784dafe56b9812b0c8

It builds singularity from source, it would be nice if there was a better way.

#36 Updated by Lucas Di Pentima 3 months ago

LGTM, thanks!

#37 Updated by Ward Vandewege 3 months ago

  • Status changed from In Progress to Resolved

#38 Updated by Peter Amstutz 11 days ago

  • Release set to 42

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