https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422018-02-28T17:59:29ZArvadosArvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=605082018-02-28T17:59:29ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>In Progress</i></li></ul> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=605092018-02-28T17:59:55ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Subject</strong> changed from <i>[CWL] Update cwltool</i> to <i>[CWL] Update cwltool for latest cwl conformance tests</i></li></ul> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=605102018-02-28T18:00:26ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Description</strong> updated (<a title="View differences" href="/journals/60510/diff?detail_id=57736">diff</a>)</li></ul> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=605542018-02-28T20:55:04ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>In Progress</i> to <i>New</i></li><li><strong>Assigned To</strong> set to <i>Peter Amstutz</i></li></ul> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=606542018-03-02T21:21:09ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>Just to keep the record of what we already chatted:</p>
<p>Tried to run the conformance tests on arvbox and got errors similar to:</p>
<pre>
Test [13/127]
Test failed: /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmp0wBPwn --quiet v1.0/cat4-tool.cwl v1.0/cat-job.json
Test command execution in Docker with stdin and stdout redirection
Returned non-zero
2018-03-02 16:04:26 cwltool ERROR: Workflow error, try again with --debug for more information:
v1.0/cat4-tool.cwl:7:5: 'module' object has no attribute 'get_image'
</pre>
<p>There are also some tests failing, don't know if they're related: <a class="external" href="https://ci.curoverse.com/job/developer-run-tests/626/">https://ci.curoverse.com/job/developer-run-tests/626/</a></p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=606572018-03-02T21:55:58ZPeter Amstutzpeter.amstutz@curii.com
<ul></ul><p>Thanks.</p>
<p>Updated with fix 13140-cwl-conformance @ <a class="changeset" title="13140: Fix call to docker.get_image() Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@ver..." href="https://dev.arvados.org/projects/arvados/repository/arvados/revisions/cde5fc115a5d543eb6522fdad6e651dfbe857656">cde5fc115a5d543eb6522fdad6e651dfbe857656</a></p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=606832018-03-05T15:05:28ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>I'm having problems when trying to run the conformance tests on arvbox:</p>
<pre>
(venv) lucas@veritas:~/common-workflow-language$ ./run_test.sh RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse"
--- Running conformance test v1.0 on /home/lucas/venv/bin/arvados-cwl-runner ---
/home/lucas/venv/bin/arvados-cwl-runner 1.0.20180302211217, arvados-python-client 0.1.20180223161544, cwltool 1.0.20180225105849
Test [1/127]
Test timed out: /home/lucas/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --outdir=/tmp/tmp_fJ2Wz --quiet v1.0/bwa-mem-tool.cwl v1.0/bwa-mem-job.json
General test of command line generation
Test [2/127]
</pre>
<p>Maybe it's a local issue, I tried resetting the arvbox instance from scratch, re-building the image, but it's not working for me. On workbench the jobs appear as Queued and are kept that way after the timeout.</p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=606922018-03-05T19:04:41ZLucas Di Pentimalucas.dipentima@curii.com
<ul></ul><p>As suggested by Peter I asked for the <code>crunch-dispatch-local</code> logs and I'm seeing this error:</p>
<pre>
[...]
2018-03-05_19:01:10.61051 # git.curoverse.com/arvados.git/services/crunch-run
2018-03-05_19:01:10.61054 src/git.curoverse.com/arvados.git/services/crunch-run/crunchrun.go:1777: cannot use docker (type *client.Client) as type ThinDockerClient in argument to NewContaine
rRunner:
2018-03-05_19:01:10.61055 *client.Client does not implement ThinDockerClient (wrong type for ContainerAttach method)
2018-03-05_19:01:10.61055 have ContainerAttach("github.com/docker/docker/vendor/golang.org/x/net/context".Context, string, types.ContainerAttachOptions) (types.HijackedResponse
, error)
2018-03-05_19:01:10.61055 want ContainerAttach("golang.org/x/net/context".Context, string, types.ContainerAttachOptions) (types.HijackedResponse, error)
[...]
</pre> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=607922018-03-07T15:46:56ZPeter Amstutzpeter.amstutz@curii.com
<ul></ul><p>Lucas Di Pentima wrote:</p>
<blockquote>
<p>As suggested by Peter I asked for the <code>crunch-dispatch-local</code> logs and I'm seeing this error:</p>
<p>[...]</p>
</blockquote>
<p>arvbox has "reset" and "destroy". The "reset" option only deletes arvados data (database, keep, git repos, etc) whereas the "destroy" option deletes the whole thing including the package caches. This looks like a problem in your go libraries (maybe arvbox isn't using govendor properly? not sure) you can try deleting ~/.arvbox/arvbox/gopath or using "arvbox destroy" to wipe out the whole thing.</p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=607942018-03-07T15:49:15ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>New</i> to <i>Feedback</i></li></ul><p>Also I think our cwltest package needs to be updated, I believe that is why it is failing on some clusters but not others.</p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=608672018-03-12T20:53:28ZPeter Amstutzpeter.amstutz@curii.com
<ul><li><strong>Status</strong> changed from <i>Feedback</i> to <i>Resolved</i></li></ul><p>Finally everything is blue again.</p> Arvados - Bug #13140: [CWL] Update cwltool for latest cwl conformance testshttps://dev.arvados.org/issues/13140?journal_id=648232018-07-23T19:22:41ZTom Morristfmorris@veritasgenetics.com
<ul><li><strong>Release</strong> set to <i>17</i></li></ul>