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EOSC-LOFAR / prefactor-cwl

CWL version of prefactor
MIT License
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make run-singularity on fs5 on DAS5 gives "cwltool: error: unrecognized arguments: --singularity" #27

Closed HannoSpreeuw closed 5 years ago

HannoSpreeuw commented 5 years ago

On fs5 on DAS5 (CentOS 7.4.1708) make small module load singularity make run-singularity gives ..... ..... cwltool: error: unrecognized arguments: --singularity make: *** [run-singularity] Error 2

HannoSpreeuw commented 5 years ago

make slurm-singularity gives the same error.

mr-c commented 5 years ago

@HannoSpreeuw What is the output of .virtualenv/bin/pip show cwltool and cwltool --version ?

HannoSpreeuw commented 5 years ago

pip show cwltool gives blank Thanks! After pip install cwltool cwltool --version gives /home/hspreeuw/anaconda3/bin/cwltool 1.0.20180923172926

HannoSpreeuw commented 5 years ago

But the error persists. For run-singularity cwltool: error: unrecognized arguments: --singularity make: *** [run-singularity] Error 2

For make slurm-singularity toil-cwl-runner: error: unrecognized arguments: --singularity

mr-c commented 5 years ago

@HannoSpreeuw Yes, because it uses the copy of cwltool or toil-cwl-runner inside the virtualenv.

I recommend deleting .virtualenv and pulling down the changes I just pushed: https://github.com/EOSC-LOFAR/prefactor-cwl/pull/28

HannoSpreeuw commented 5 years ago

So I did. Different error:

Successfully built dill scandir networkx googleapis-common-protos
Installing collected packages: six, webencodings, html5lib, atomicwrites, more-itertools, pluggy, attrs, scandir, pathlib2, py, funcsigs, pytest, urllib3, idna, chardet, certifi, requests, dill, subprocess32, future, psutil, coverage, pytest-cov, websocket-client, backports.ssl-match-hostname, ipaddress, docker-pycreds, docker, python-dateutil, ruamel.ordereddict, ruamel.yaml, avro, pyparsing, isodate, rdflib, rdflib-jsonld, typing, typing-extensions, lockfile, mistune, CacheControl, schema-salad, bagit, mypy-extensions, lxml, decorator, networkx, prov, shellescape, cwltool, docutils, pyyaml, galaxy-lib, protobuf, googleapis-common-protos, pytz, futures, pyasn1, pyasn1-modules, cachetools, rsa, google-auth, google-api-core, google-cloud-core, google-resumable-media, google-cloud-storage, apache-libcloud, retry-decorator, httplib2, oauth2client, enum34, pycparser, cffi, asn1crypto, cryptography, pyOpenSSL, boto, SocksiPy-branch, gcs-oauth2-boto-plugin, toil, pycrypto
Successfully installed CacheControl-0.11.7 SocksiPy-branch-1.1 apache-libcloud-2.2.1 asn1crypto-0.24.0 atomicwrites-1.2.1 attrs-18.2.0 avro-1.8.1 backports.ssl-match-hostname-3.5.0.1 bagit-1.7.0 boto-2.49.0 cachetools-2.1.0 certifi-2018.8.24 cffi-1.11.5 chardet-3.0.4 coverage-4.5.1 cryptography-2.3.1 cwltool-1.0.20180820141117 decorator-4.3.0 dill-0.2.7.1 docker-2.5.1 docker-pycreds-0.3.0 docutils-0.14 enum34-1.1.6 funcsigs-1.0.2 future-0.16.0 futures-3.2.0 galaxy-lib-17.9.3 gcs-oauth2-boto-plugin-1.14 google-api-core-0.1.4 google-auth-1.5.1 google-cloud-core-0.28.1 google-cloud-storage-1.6.0 google-resumable-media-0.3.1 googleapis-common-protos-1.5.3 html5lib-1.0.1 httplib2-0.11.3 idna-2.6 ipaddress-1.0.22 isodate-0.6.0 lockfile-0.12.2 lxml-4.2.5 mistune-0.7.4 more-itertools-4.3.0 mypy-extensions-0.4.1 networkx-2.2 oauth2client-4.1.3 pathlib2-2.3.2 pluggy-0.7.1 protobuf-3.6.1 prov-1.5.1 psutil-3.0.1 py-1.6.0 pyOpenSSL-18.0.0 pyasn1-0.4.4 pyasn1-modules-0.2.2 pycparser-2.19 pycrypto-2.6.1 pyparsing-2.2.2 pytest-3.7.4 pytest-cov-2.5.1 python-dateutil-2.7.3 pytz-2018.5 pyyaml-3.13 rdflib-4.2.2 rdflib-jsonld-0.4.0 requests-2.18.4 retry-decorator-1.1.0 rsa-4.0 ruamel.ordereddict-0.4.13 ruamel.yaml-0.15.51 scandir-1.9.0 schema-salad-2.7.20180905124720 shellescape-3.4.1 six-1.11.0 subprocess32-3.5.2 toil-3.18.0 typing-3.6.6 typing-extensions-3.6.6 urllib3-1.22 webencodings-0.5.1 websocket-client-0.53.0
mkdir -p /home/hspreeuw/prefactor-cwl/runs/run_2018-10-08-12-04-50
.virtualenv/bin/cwltool \
    --singularity \
    --leave-tmpdir \
    --cachedir cache \
    --outdir /home/hspreeuw/prefactor-cwl/runs/run_2018-10-08-12-04-50/results \
    prefactor.cwl \
    jobs/job_20sb.yaml > >(tee /home/hspreeuw/prefactor-cwl/runs/run_2018-10-08-12-04-50/output) 2> >(tee /home/hspreeuw/prefactor-cwl/runs/run_2018-10-08-12-04-50/log >&2)
.virtualenv/bin/cwltool 1.0.20180820141117
Resolved 'prefactor.cwl' to 'file:///home/hspreeuw/prefactor-cwl/prefactor.cwl'
/home/hspreeuw/prefactor-cwl/.virtualenv/lib/python2.7/site-packages/ruamel/yaml/constructor.py:266: DuplicateKeyFutureWarning: while constructing a mapping
  in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 1, column 1
found duplicate key "cwlVersion" with value "v1.0" (original value: "v1.0")
  in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 4, column 1

To suppress this check see:
    http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors
by default when using the new API.

  warnings.warn(DuplicateKeyFutureWarning(*args))
/home/hspreeuw/prefactor-cwl/.virtualenv/lib/python2.7/site-packages/ruamel/yaml/constructor.py:266: DuplicateKeyFutureWarning: while constructing a mapping
  in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 251, column 3
found duplicate key "s:person.url" with value "https://orcid.org/0000-0001-5125-9539" (original value: "http://orcid.org/0000-0002-6136-3724")
  in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 252, column 3

To suppress this check see:
    http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors
by default when using the new API.

  warnings.warn(DuplicateKeyFutureWarning(*args))
Workflow checker warning:
prefactor.cwl:181:7: 'dclock_1st' is not an input parameter of
                     file:///home/hspreeuw/prefactor-cwl/steps/plots.cwl, expected amplitude_array,
                     dclock_1st_sm, dtec_1st_sm
[workflow ] start
[workflow ] starting step ndppp_prep_cal
[step ndppp_prep_cal] start
[job ndppp_prep_cal] Output of job will be cached in /home/hspreeuw/prefactor-cwl/cache/187eef3d15e77102e21a6feb47bb8d9f
['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor']
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
Docker image path: index.docker.io/kernsuite/prefactor:latest
Cache folder set to /home/hspreeuw/.singularity/docker
Importing: base Singularity environment
Importing: /home/hspreeuw/.singularity/docker/sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913.tar.gz
Importing: /home/hspreeuw/.singularity/docker/sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6.tar.gz
Importing: /home/hspreeuw/.singularity/docker/sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67.tar.gz
Importing: /home/hspreeuw/.singularity/docker/sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418.tar.gz
Importing: /home/hspreeuw/.singularity/docker/sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2.tar.gz
Importing: /home/hspreeuw/.singularity/docker/sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz

gzip: /home/hspreeuw/.singularity/docker/sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz: not in gzip format
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
Cleaning up...
ERROR: pulling container failed!
Workflow error, try again with --debug for more information:
Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Command '['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor']' returned non-zero exit status 2.
make: *** [run-singularity] Error 1

but similar to #24

mr-c commented 5 years ago

@HannoSpreeuw Progress? :-) What is your Singularity version?

singularity pull --force --name kernsuite-prefactor.img docker://kernsuite/prefactor

works for me with

$ singularity --version
2.5.2-dist
HannoSpreeuw commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ singularity --version 2.4-master.g718360b

mr-c commented 5 years ago

@HannoSpreeuw Feels like a Singularity issue to me. Can you try a new version?

HannoSpreeuw commented 5 years ago

This is the latest available singularity on fs5. I'll ask fs5 maintenance for an update.

HannoSpreeuw commented 5 years ago

System management installed Singularity 3.0.0. The latest, allegedly. rm -rf .virtualenv make run-singularity gives " .... .... Resolved 'prefactor.cwl' to 'file:///home/hspreeuw/prefactor-cwl/prefactor.cwl' /home/hspreeuw/prefactor-cwl/.virtualenv/lib/python2.7/site-packages/ruamel/yaml/constructor.py:266: DuplicateKeyFutureWarning: while constructing a mapping in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 1, column 1 found duplicate key "cwlVersion" with value "v1.0" (original value: "v1.0") in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 4, column 1

To suppress this check see: http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors by default when using the new API.

warnings.warn(DuplicateKeyFutureWarning(*args)) /home/hspreeuw/prefactor-cwl/.virtualenv/lib/python2.7/site-packages/ruamel/yaml/constructor.py:266: DuplicateKeyFutureWarning: while constructing a mapping in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 251, column 3 found duplicate key "s:person.url" with value "https://orcid.org/0000-0001-5125-9539" (original value: "http://orcid.org/0000-0002-6136-3724") in "file:///home/hspreeuw/prefactor-cwl/prefactor.cwl", line 252, column 3

To suppress this check see: http://yaml.readthedocs.io/en/latest/api.html#duplicate-keys

Duplicate keys will become an error in future releases, and are errors by default when using the new API.

warnings.warn(DuplicateKeyFutureWarning(*args)) Workflow checker warning: prefactor.cwl:181:7: 'dclock_1st' is not an input parameter of file:///home/hspreeuw/prefactor-cwl/steps/plots.cwl, expected amplitude_array, dclock_1st_sm, dtec_1st_sm [workflow ] start [workflow ] starting step ndppp_prep_cal [step ndppp_prep_cal] start [job ndppp_prep_cal] Output of job will be cached in /home/hspreeuw/prefactor-cwl/cache/187eef3d15e77102e21a6feb47bb8d9f ['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor'] Error: unknown flag: --name Usage: singularity [global options...] pull [pull options...]

Workflow error, try again with --debug for more information: Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Command '['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor']' returned non-zero exit status 1. make: *** [run-singularity] Error 1 "

mr-c commented 5 years ago

That was a quick upgrade! And 3.0.0 is very new, it came out two days ago. Looks like they broke some of the command line interface, and re-wrote their entire codebase (!!)

This will need a lot of testing by the cwltool developers (myself and others), so I'll get back to you.

In the meantime, the system administrators could downgrade to Singularity 2.6.0 which should work with cwltool and toil-cwl-runnet as is.

mr-c commented 5 years ago

I've reported the break in Singularity's command line interface at https://github.com/sylabs/singularity/issues/2214

HannoSpreeuw commented 5 years ago

System management also installed 2.5.2 for me: [hspreeuw@fs5 prefactor-cwl]$ singularity --version 2.5.2-dist

make run-singularity [workflow ] start [workflow ] starting step ndppp_prep_cal [step ndppp_prep_cal] start [job ndppp_prep_cal] Output of job will be cached in /home/hspreeuw/prefactor-cwl/cache/187eef3d15e77102e21a6feb47bb8d9f ['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor'] WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/kernsuite/prefactor:latest Cache folder set to /home/hspreeuw/.singularity/docker Importing: base Singularity environment Exploding layer: sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913.tar.gz Exploding layer: sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6.tar.gz Exploding layer: sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67.tar.gz Exploding layer: sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418.tar.gz Exploding layer: sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2.tar.gz Exploding layer: sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz ERROR : Error applying layer whiteouts ABORT : Retval = 255 Cleaning up... ERROR: pulling container failed! Workflow error, try again with --debug for more information: Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Command '['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor']' returned non-zero exit status 255. make: *** [run-singularity] Error 1

gijzelaerr commented 5 years ago

does running $ singularity pull --force --name kernsuite-prefactor.img docker://kernsuite/prefactor work? (for 2.5.2)

HannoSpreeuw commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ singularity --version 2.5.2-dist [hspreeuw@fs5 prefactor-cwl]$ singularity pull --force --name kernsuite-prefactor.img docker://kernsuite/prefactor WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/kernsuite/prefactor:latest Cache folder set to /home/hspreeuw/.singularity/docker Importing: base Singularity environment Exploding layer: sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913.tar.gz Exploding layer: sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6.tar.gz Exploding layer: sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67.tar.gz Exploding layer: sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418.tar.gz Exploding layer: sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2.tar.gz Exploding layer: sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz ERROR : Error applying layer whiteouts ABORT : Retval = 255 Cleaning up... ERROR: pulling container failed!

mr-c commented 5 years ago

hmm.. works for me using the Debian packaged version of Singularity: https://packages.debian.org/buster/singularity-container

Maybe they included patches that were part of the Singularity 2.6 release? https://github.com/sylabs/singularity/releases/tag/2.6.0

HannoSpreeuw commented 5 years ago

Thanks for all your good help, but I am giving up attempts on this cluster. Will try my own laptop (Manjaro = Arch) and if that does not work an Ubuntu 18.04 VM.

gijzelaerr commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ singularity --version 2.5.2-dist [hspreeuw@fs5 prefactor-cwl]$ singularity pull --force --name kernsuite-prefactor.img docker://kernsuite/prefactor WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/kernsuite/prefactor:latest Cache folder set to /home/hspreeuw/.singularity/docker Importing: base Singularity environment Exploding layer: sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913.tar.gz Exploding layer: sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6.tar.gz Exploding layer: sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67.tar.gz Exploding layer: sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418.tar.gz Exploding layer: sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2.tar.gz Exploding layer: sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz ERROR : Error applying layer whiteouts ABORT : Retval = 255 Cleaning up... ERROR: pulling container failed!

there seems to be something wrong with that singularity configuration/installation on that node or cluster.

HannoSpreeuw commented 5 years ago

Okay. Let me contact system maintenance.

HannoSpreeuw commented 5 years ago

Problem solved by fs5 maintenance: disk quota problem on my account.

gijzelaerr commented 5 years ago

zal ik m dan ook nog ff openen en sluiten

HannoSpreeuw commented 5 years ago

Sorry, I was confused. After I was allocated additional disk quota, I could run make run-udocker up to #23 I also could run e.g. singularity pull docker://flatironinstitute/triqs:unstable with singularity 2.5.2-dist However make run-singularity still gives

[job calib_cal_20] Using cached output in /home/hspreeuw/prefactor-cwl/cache/06aded945abf766882d0daeaf876b148 [step calib_cal] completed success [workflow ] starting step do_magic [step do_magic] start [job do_magic] Output of job will be cached in /home/hspreeuw/prefactor-cwl/cache/beb5265705eeddf4aed154aa5c85cfb8 ['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor'] WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/kernsuite/prefactor:latest Cache folder set to /home/hspreeuw/.singularity/docker Importing: base Singularity environment Exploding layer: sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913.tar.gz Exploding layer: sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6.tar.gz Exploding layer: sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67.tar.gz Exploding layer: sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418.tar.gz Exploding layer: sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2.tar.gz Exploding layer: sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c.tar.gz ERROR : Error applying layer whiteouts ABORT : Retval = 255 Cleaning up... ERROR: pulling container failed! Workflow error, try again with --debug for more information: Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Command '['singularity', 'pull', '--force', '--name', 'kernsuite-prefactor.img', 'docker://kernsuite/prefactor']' returned non-zero exit status 255. make: *** [run-singularity] Error 1

mr-c commented 5 years ago

@HannoSpreeuw Can you work with your colleagues to get singularity pull --force --name kernsuite-prefactor.img docker://kernsuite/prefactor working? Once that works, then toil-cwl-runner & cwltool will work.

One piece of information that would be helpful, what filesystem is /home/hspreeuw/prefactor-cwl/cache ? stat -f -c %T /home/hspreeuw/ should have the answer

HannoSpreeuw commented 5 years ago

Okay.

xfs

mr-c commented 5 years ago

@HannoSpreeuw Thanks. I don't see any know issues with XFS & Singularity (there are some with BeeGFS)

My advice remains to work with your colleagues to get singularity pull docker://kernsuite/prefactor working? Once that works, then toil-cwl-runner & cwltool will work.

HannoSpreeuw commented 5 years ago

This works for singularity 3.0.0, but not for 2.5.2-dist: [hspreeuw@fs5 ~]$ module load singularity/3.0.0 [hspreeuw@fs5 ~]$ singularity pull docker://kernsuite/prefactor WARNING: Authentication token file not found : Only pulls of public images will succeed INFO: Starting build... Getting image source signatures Copying blob sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913 45.41 MiB / 45.41 MiB [====================================================] 0s Copying blob sha256:c59d01a7e4caf1aba785eb33192fec3f96e4ab01975962bcec10f4989a6edcc6 848 B / 848 B [============================================================] 0s Copying blob sha256:41ba73a9054d231e1f555c40a74762276900cc6487f5c6cf13b89c7606635c67 619 B / 619 B [============================================================] 0s Copying blob sha256:f1bbfd495cc1112b503350686641ee4fa2cea8ccd13fb8a8a302c81dae61d418 854 B / 854 B [============================================================] 0s Copying blob sha256:0c346f7223e24b517358f52c4a3f5f9af1c86e5ddeaee5659c8889846e46d1e2 169 B / 169 B [============================================================] 0s Copying blob sha256:760bbf8251916f26631b53355347bcfdc0274d9b455b2ad9017ddc87b5c5a83c 288 B / 288 B [============================================================] 0s Copying blob sha256:d92598cf94b04c7b388143c4ec91a867e415c299d97970f90cbbe0c586afd661 46.24 MiB / 46.24 MiB [====================================================] 0s Copying blob sha256:44bd5d573b1bf3b0c10cd3f4622fb8682abf34e828fddb042bc897b563a3460a 7.58 KiB / 7.58 KiB [======================================================] 0s Copying blob sha256:92c8ae71df9ef968b3f02aa60be0b4b957371120b748b1f54e7fcf5ac769b66e 89 B / 89 B [==============================================================] 0s Copying blob sha256:7c66b3b256d7e54d498dee22b146ce288bac00877272b59ea4c6e1f21c7f1988 92 B / 92 B [==============================================================] 0s Copying blob sha256:a22c18e00204f5f149a7328b37c3473d69019471f0a25daae6925e7f96602b77 295.43 MiB / 295.43 MiB [==================================================] 4s Copying blob sha256:a3a761fd9e05053e844a5b226f290d40e814fe6bccf5bb5428cd4ac2dddfc62b 7.03 MiB / 7.03 MiB [======================================================] 0s Copying config sha256:ae80dffaf8b3e40ebf9878340dc0e88ecb483a44db5ea02fd863a9e41a60cb5b 4.50 KiB / 4.50 KiB [======================================================] 0s Writing manifest to image destination Storing signatures INFO: Creating SIF file... INFO: Build complete: prefactor_latest.sif

mr-c commented 5 years ago

@HannoSpreeuw Interesting! I'll see if I can add Singularity 3.0.0 support soon.

mr-c commented 5 years ago

@HannoSpreeuw While we wait for that, you can make the following local modification to see if it is good enough.

echo $(pip show cwltool | grep Location | awk '{print $2}')/cwltool/singularity.py

And edit the path it produces. Look for and make the following change:

diff --git a/cwltool/singularity.py b/cwltool/singularity.py
index cd1bb9e0..2633e8b9 100644
--- a/cwltool/singularity.py
+++ b/cwltool/singularity.py
@@ -98,7 +98,7 @@ class SingularityCommandLineJob(ContainerCommandLineJob):
         if (force_pull or not found) and pull_image:
             cmd = []  # type: List[Text]
             if "dockerPull" in dockerRequirement:
-                cmd = ["singularity", "pull", "--force", "--name",
+                cmd = ["singularity", "pull", "--force", 
                        str(dockerRequirement["dockerImageId"]),
                        str(dockerRequirement["dockerPull"])]
                 _logger.info(Text(cmd))
HannoSpreeuw commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ echo $(pip show cwltool | grep Location | awk '{print $2}')/cwltool/singularity.py /cwltool/singularity.py [hspreeuw@fs5 prefactor-cwl]$ ls /cwltool/singularity.py ls: cannot access /cwltool/singularity.py: No such file or directory

HannoSpreeuw commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ find . -name singularity.py ./.virtualenv/lib/python2.7/site-packages/cwltool/singularity.py

Got it.

mr-c commented 5 years ago

[hspreeuw@fs5 prefactor-cwl]$ echo $(pip show cwltool | grep Location | awk '{print $2}')/cwltool/singularity.py /cwltool/singularity.py [hspreeuw@fs5 prefactor-cwl]$ ls /cwltool/singularity.py ls: cannot access /cwltool/singularity.py: No such file or directory

oh yeah, you have to activate the virtualenv or call it directly:

echo $(.virtualenv/bin/pip show cwltool | grep Location | awk '{print $2}')/cwltool/singularity.py
HannoSpreeuw commented 5 years ago

Success! Now running into #23