Arvados: Issueshttps://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422021-06-30T19:27:42ZArvados
Redmine Arvados - Bug #17846 (Duplicate): [tutorial] inconsistencies/roadbumpshttps://dev.arvados.org/issues/178462021-06-30T19:27:42ZWard Vandewegeward@curii.com
<p>This is about <a class="external" href="https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html">https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html</a>:</p>
<ul>
<li>the tutorial says to search for the “PGP UK FASTQs” collection, but that collection does not exist, there is "PGP UK FASTQs (one genome)" and "PGP UK FASTQs (ten genomes)". Which of these 2 collections should the tutorial to refer to?</li>
</ul>
<ul>
<li>the tutorial says to search for the "WGS Processing Workflow” registered workflow. There is a project with that name at <a class="external" href="https://workbench.pirca.arvadosapi.com/projects/pirca-j7d0g-chdv0xwrzxngtfn">https://workbench.pirca.arvadosapi.com/projects/pirca-j7d0g-chdv0xwrzxngtfn</a>, which contains the workflow "WGS processing workflow scattered over samples". It would be better to point directly at that workflow from the tutorial docs (i.e. change the search term), if that is indeed the intended one. We don't explain that one needs to navigate from the project to the registered workflow in it, and in any case, that is an unnecessary step.</li>
</ul>
<ul>
<li>Confusingly for the user, there is also that visible run <a class="external" href="https://workbench.pirca.arvadosapi.com/container_requests/pirca-xvhdp-0ipx8626jkb7qob#Status">https://workbench.pirca.arvadosapi.com/container_requests/pirca-xvhdp-0ipx8626jkb7qob#Status</a> which is called "(start here) Example WGS processing workflow" and shows up in the same search query. Should we rename the latter to something less confusing if we do <strong>not</strong> actually want people to start there? As far as I can tell that visible run is (only?) intended to make reuse work (but, see <a class="issue tracker-1 status-3 priority-4 priority-default closed" title="Bug: [tutorial] reuse is not working (Resolved)" href="https://dev.arvados.org/issues/17845">#17845</a>).</li>
</ul>
<ul>
<li>The tutorial says "The input Directory of paired FASTQ files will need to be set. " but that is not true, it defaults to "keep:a146a06222f9a66b7d141e078fc67660+376237". The registered workflow should be updated to make that input field empty.</li>
</ul>
<ul>
<li>Customer feedback - "Hi all - I'm going through the users guide and discovered a discrepency in steps. Specifically <a class="external" href="https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html">https://doc.arvados.org/v2.2/user/tutorials/wgs-tutorial.html</a>, from step 3a setting up a new project to step 3b working with collections. There is no transition.<br />EDIT: Nevermind, its there, just wasn't clear as II was reading it."</li>
</ul> Arvados - Bug #17845 (Resolved): [tutorial] reuse is not workinghttps://dev.arvados.org/issues/178452021-06-30T19:27:21ZWard Vandewegeward@curii.com
<p>We've seen a couple runs of the WGS tutorial now where reuse did not work, e.g. <a href="https://arvadosapi.com/pirca-xvhdp-gk39gqtkxmw7qcp">pirca-xvhdp-gk39gqtkxmw7qcp</a>.</p>
<p>From discussion: shell quoting changed at one point with arvados-cwl-runner which would have caused commands that use "sh -c" (ShellCommandRequirement) to change.</p>
<p>Confirm that with the new run, reuse still works. Also want to share the new project so that other users will reuse the containers.</p> Arvados - Bug #8953 (Resolved): [Node manager] can not shut down nodes anymorehttps://dev.arvados.org/issues/89532016-04-12T21:56:19ZWard Vandewegeward@curii.com
<p>Node manager version 0.1.20160410021132-1 (with the drain fix from <a class="issue tracker-1 status-3 priority-4 priority-default closed parent" title="Bug: [Node manager] nodes in slurm drained state are counted as "up" but not candidates for shut down (Resolved)" href="https://dev.arvados.org/issues/8799">#8799</a>) appears to have a shutdown loop...</p>
<pre>
2016-04-12_21:55:42.54948 2016-04-12 21:55:42 ComputeNodeShutdownActor.01df952eda4b.compute-q74ljtuggvufc9l-su92l[46608] INFO: Draining SLURM node compute19
2016-04-12_21:55:42.63657 2016-04-12 21:55:42 ComputeNodeShutdownActor.01df952eda4b.compute-q74ljtuggvufc9l-su92l[46608] INFO: Waiting for SLURM node compute19 to drain
2016-04-12_21:55:42.71020 2016-04-12 21:55:42 ComputeNodeShutdownActor.01df952eda4b.compute-q74ljtuggvufc9l-su92l[46608] INFO: Shutdown cancelled: shutdown window closed.
2016-04-12_21:55:42.71048 2016-04-12 21:55:42 ComputeNodeShutdownActor.01df952eda4b.compute-q74ljtuggvufc9l-su92l[46608] INFO: finished
2016-04-12_21:55:43.14420 2016-04-12 21:55:43 pykka[46608] DEBUG: Registered ComputeNodeShutdownActor (urn:uuid:58d90fdd-7dee-4219-9ebb-429da8a893ef)
2016-04-12_21:55:43.14471 2016-04-12 21:55:43 pykka[46608] DEBUG: Starting ComputeNodeShutdownActor (urn:uuid:58d90fdd-7dee-4219-9ebb-429da8a893ef)
2016-04-12_21:55:43.15100 2016-04-12 21:55:43 ComputeNodeShutdownActor.429da8a893ef.compute-csm26hx92t8pf8o-su92l[46608] INFO: Draining SLURM node compute20
2016-04-12_21:55:43.27655 2016-04-12 21:55:43 ComputeNodeShutdownActor.429da8a893ef.compute-csm26hx92t8pf8o-su92l[46608] INFO: Waiting for SLURM node compute20 to drain
2016-04-12_21:55:43.36943 2016-04-12 21:55:43 ComputeNodeShutdownActor.429da8a893ef.compute-csm26hx92t8pf8o-su92l[46608] INFO: Shutdown cancelled: shutdown window closed.
2016-04-12_21:55:43.36970 2016-04-12 21:55:43 ComputeNodeShutdownActor.429da8a893ef.compute-csm26hx92t8pf8o-su92l[46608] INFO: finished
2016-04-12_21:55:43.87084 2016-04-12 21:55:43 pykka[46608] DEBUG: Registered ComputeNodeShutdownActor (urn:uuid:f1192c0a-dbad-4bd6-9a70-949cb086f5bf)
2016-04-12_21:55:43.87123 2016-04-12 21:55:43 pykka[46608] DEBUG: Starting ComputeNodeShutdownActor (urn:uuid:f1192c0a-dbad-4bd6-9a70-949cb086f5bf)
2016-04-12_21:55:43.87793 2016-04-12 21:55:43 ComputeNodeShutdownActor.949cb086f5bf.compute-1q9g2jmg5askowg-su92l[46608] INFO: Draining SLURM node compute36
2016-04-12_21:55:44.08007 2016-04-12 21:55:44 ComputeNodeShutdownActor.949cb086f5bf.compute-1q9g2jmg5askowg-su92l[46608] INFO: Waiting for SLURM node compute36 to drain
2016-04-12_21:55:44.15134 2016-04-12 21:55:44 ComputeNodeShutdownActor.949cb086f5bf.compute-1q9g2jmg5askowg-su92l[46608] INFO: Shutdown cancelled: shutdown window closed.
2016-04-12_21:55:44.15164 2016-04-12 21:55:44 ComputeNodeShutdownActor.949cb086f5bf.compute-1q9g2jmg5askowg-su92l[46608] INFO: finished
2016-04-12_21:55:44.57382 2016-04-12 21:55:44 pykka[46608] DEBUG: Registered ComputeNodeShutdownActor (urn:uuid:df6d159b-1837-4308-a409-e76748ab7dc6)
2016-04-12_21:55:44.57430 2016-04-12 21:55:44 pykka[46608] DEBUG: Starting ComputeNodeShutdownActor (urn:uuid:df6d159b-1837-4308-a409-e76748ab7dc6)
2016-04-12_21:55:44.58096 2016-04-12 21:55:44 ComputeNodeShutdownActor.e76748ab7dc6.compute-rs1ayc75z1atwki-su92l[46608] INFO: Draining SLURM node compute41
2016-04-12_21:55:44.69442 2016-04-12 21:55:44 ComputeNodeShutdownActor.e76748ab7dc6.compute-rs1ayc75z1atwki-su92l[46608] INFO: Waiting for SLURM node compute41 to drain
2016-04-12_21:55:44.75848 2016-04-12 21:55:44 ComputeNodeShutdownActor.e76748ab7dc6.compute-rs1ayc75z1atwki-su92l[46608] INFO: Shutdown cancelled: shutdown window closed.
2016-04-12_21:55:44.75878 2016-04-12 21:55:44 ComputeNodeShutdownActor.e76748ab7dc6.compute-rs1ayc75z1atwki-su92l[46608] INFO: finished
2016-04-12_21:55:45.13360 2016-04-12 21:55:45 ComputeNodeMonitorActor.1dab685fdd8a.compute-u3ps8tsf7ygy0bw-su92l[46608] DEBUG: Cannot shut down because node is not idle.
2016-04-12_21:55:45.32131 2016-04-12 21:55:45 pykka[46608] DEBUG: Registered ComputeNodeShutdownActor (urn:uuid:955f8a87-54e4-4c11-8dd5-d6359dd39c83)
2016-04-12_21:55:45.32186 2016-04-12 21:55:45 pykka[46608] DEBUG: Starting ComputeNodeShutdownActor (urn:uuid:955f8a87-54e4-4c11-8dd5-d6359dd39c83)
2016-04-12_21:55:45.32826 2016-04-12 21:55:45 ComputeNodeShutdownActor.d6359dd39c83.compute-iaiguf1czbby51n-su92l[46608] INFO: Draining SLURM node compute30
2016-04-12_21:55:45.41042 2016-04-12 21:55:45 ComputeNodeShutdownActor.d6359dd39c83.compute-iaiguf1czbby51n-su92l[46608] INFO: Waiting for SLURM node compute30 to drain
2016-04-12_21:55:45.47984 2016-04-12 21:55:45 ComputeNodeShutdownActor.d6359dd39c83.compute-iaiguf1czbby51n-su92l[46608] INFO: Shutdown cancelled: shutdown window closed.
2016-04-12_21:55:45.48136 2016-04-12 21:55:45 ComputeNodeShutdownActor.d6359dd39c83.compute-iaiguf1czbby51n-su92l[46608] INFO: finished
2016-04-12_21:55:45.94573 2016-04-12 21:55:45 pykka[46608] DEBUG: Registered ComputeNodeShutdownActor (urn:uuid:95f04d93-2173-4214-a811-216cc861cf67)
</pre>
<p>This gets repeated over and over and over and over again.</p>
<p>A snapshot of sinfo:</p>
<pre>
sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
compute* up infinite 67 drain* compute[2,11,16,28,31,34,38-39,48,50,54-55,57-58,60,65,67-68,70,78,97-99,101,104-106,109,115,119,122,124,126,129-131,133-136,138,140-144,147,149-151,153-157,162,172-179,181-183]
compute* up infinite 74 down* compute[47,158,184-255]
compute* up infinite 12 drain compute[87,89-90,94-96,110,113,120,125,127,170]
compute* up infinite 57 alloc compute[0-1,3-5,7-10,12-14,17-18,21-27,29,33,43-44,46,61,63-64,66,72-74,76-77,81-82,84-86,88,91-93,100,102-103,107-108,111-112,114,116-118,121,123]
compute* up infinite 37 idle compute[6,15,19-20,30,32,35-37,40-42,45,49,51-53,56,59,62,69,71,75,79-80,83,132,137,139,146,148,152,161,163,167,171,180]
compute* up infinite 9 down compute[128,145,159-160,164-166,168-169]
crypto up infinite 67 drain* compute[2,11,16,28,31,34,38-39,48,50,54-55,57-58,60,65,67-68,70,78,97-99,101,104-106,109,115,119,122,124,126,129-131,133-136,138,140-144,147,149-151,153-157,162,172-179,181-183]
crypto up infinite 74 down* compute[47,158,184-255]
crypto up infinite 12 drain compute[87,89-90,94-96,110,113,120,125,127,170]
crypto up infinite 57 alloc compute[0-1,3-5,7-10,12-14,17-18,21-27,29,33,43-44,46,61,63-64,66,72-74,76-77,81-82,84-86,88,91-93,100,102-103,107-108,111-112,114,116-118,121,123]
crypto up infinite 37 idle compute[6,15,19-20,30,32,35-37,40-42,45,49,51-53,56,59,62,69,71,75,79-80,83,132,137,139,146,148,152,161,163,167,171,180]
crypto up infinite 9 down compute[128,145,159-160,164-166,168-169]
</pre>
<p>I'm <del>rolling su92l back to the previous release</del> upgrading node manager to version 0.1.20160412145128 and will report back on this ticket.</p> Arvados - Bug #8952 (Resolved): [Node manager] TypeError: execv() arg 2 must contain only stringshttps://dev.arvados.org/issues/89522016-04-12T21:31:55ZWard Vandewegeward@curii.com
<p>Seen on su92l, node manager version 0.1.20160410021132-1:</p>
<pre>
2016-04-12_21:30:25.78287 2016-04-12 21:30:25 ComputeNodeMonitorActor.dd2f7ac40e26.compute-dw4958vokgatzl7-su92l[30349] ERROR: Unexpected exception
2016-04-12_21:30:25.78395 Traceback (most recent call last):
2016-04-12_21:30:25.78409 File "/usr/local/lib/python2.7/dist-packages/arvnodeman/computenode/dispatch/__init__.py", line 406, in consider_shutdown
2016-04-12_21:30:25.78422 eligible = self.shutdown_eligible()
2016-04-12_21:30:25.78432 File "/usr/local/lib/python2.7/dist-packages/arvnodeman/computenode/dispatch/slurm.py", line 76, in shutdown_eligible
2016-04-12_21:30:25.78447 state = self._get_slurm_state(self.arvados_node['hostname'])
2016-04-12_21:30:25.78457 File "/usr/local/lib/python2.7/dist-packages/arvnodeman/computenode/dispatch/slurm.py", line 27, in _get_slurm_state
2016-04-12_21:30:25.78473 return subprocess.check_output(['sinfo', '--noheader', '-o', '%t', '-n', nodename])
2016-04-12_21:30:25.78483 File "/usr/lib/python2.7/subprocess.py", line 566, in check_output
2016-04-12_21:30:25.78496 process = Popen(stdout=PIPE, *popenargs, **kwargs)
2016-04-12_21:30:25.78506 File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
2016-04-12_21:30:25.78520 errread, errwrite)
2016-04-12_21:30:25.78528 File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
2016-04-12_21:30:25.78541 raise child_exception
2016-04-12_21:30:25.78551 TypeError: execv() arg 2 must contain only strings
</pre> Arvados - Bug #8872 (Resolved): [Node Manager] On node creation, node search fails, and unhandled...https://dev.arvados.org/issues/88722016-04-03T19:22:42ZWard Vandewegeward@curii.comArvados - Bug #7870 (Resolved): [Crunch] crunch-dispatch fails to mark a job failed when its retr...https://dev.arvados.org/issues/78702015-11-26T18:45:38ZWard Vandewegeward@curii.com
<p>See <a class="external" href="https://workbench.c97qk.arvadosapi.com/pipeline_instances/c97qk-d1hrv-stxx1wltwlzssp5">https://workbench.c97qk.arvadosapi.com/pipeline_instances/c97qk-d1hrv-stxx1wltwlzssp5</a></p>
<p>Node manager log:</p>
<pre>
2015-11-26_18:44:34.74860 2015-11-26 18:44:34 arvnodeman.arvados_nodes[64971] DEBUG: ArvadosNodeListMonitorActor (at 140615574139536) sending poll
2015-11-26_18:44:34.75008 2015-11-26 18:44:34 arvnodeman.jobqueue[64971] DEBUG: JobQueueMonitorActor (at 140615574836752) sending poll
2015-11-26_18:44:34.75613 2015-11-26 18:44:34 arvnodeman.cloud_nodes[64971] DEBUG: CloudNodeListMonitorActor (at 140615594757200) sending poll
2015-11-26_18:44:36.31902 2015-11-26 18:44:36 arvnodeman.arvados_nodes[64971] DEBUG: ArvadosNodeListMonitorActor (at 140615574139536) got response with 233 items
2015-11-26_18:44:37.12386 2015-11-26 18:44:37 arvnodeman.jobqueue[64971] DEBUG: Sending server wishlist: (empty)
2015-11-26_18:44:37.12394 2015-11-26 18:44:37 arvnodeman.jobqueue[64971] DEBUG: JobQueueMonitorActor (at 140615574836752) got response with 0 items
2015-11-26_18:44:37.12487 2015-11-26 18:44:37 arvnodeman.daemon[64971] DEBUG: Standard_D4: idle nodes 0, wishlist size 0
2015-11-26_18:44:37.12501 2015-11-26 18:44:37 arvnodeman.daemon[64971] DEBUG: Standard_D3: idle nodes 0, wishlist size 0
2015-11-26_18:44:37.12517 2015-11-26 18:44:37 arvnodeman.daemon[64971] DEBUG: Standard_D2: idle nodes 0, wishlist size 0
2015-11-26_18:44:37.12535 2015-11-26 18:44:37 arvnodeman.daemon[64971] DEBUG: Standard_D1: idle nodes 0, wishlist size 0
2015-11-26_18:44:44.12915 2015-11-26 18:44:44 arvnodeman.cloud_nodes[64971] DEBUG: CloudNodeListMonitorActor (at 140615594757200) got response with 0 items
</pre> Arvados - Bug #5989 (Resolved): [API] API server repositories permissions list doesn't list repos...https://dev.arvados.org/issues/59892015-05-10T02:00:45ZWard Vandewegeward@curii.com
<p>bug 1: it does not create the 'auto' subdirectory if it does not exist yet:</p>
<pre>
Error: No such file or directory @ rb_sysopen - /usr/local/arvados/gitolite-tmp/gitolite-admin/conf/auto/XXXXX-s0uqq-asdfasdfadsfaafds.conf20150510-28428-1xbndn3.tmp
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/tempfile.rb:146:in `initialize'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/tempfile.rb:146:in `open'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/tempfile.rb:146:in `block in initialize'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/tmpdir.rb:142:in `create'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/tempfile.rb:136:in `initialize'
/usr/local/arvados/update-gitolite.rb:62:in `new'
/usr/local/arvados/update-gitolite.rb:62:in `replace_file'
/usr/local/arvados/update-gitolite.rb:95:in `ensure_in_git'
/usr/local/arvados/update-gitolite.rb:103:in `ensure_in_git'
/usr/local/arvados/update-gitolite.rb:186:in `ensure_config'
/usr/local/arvados/update-gitolite.rb:242:in `block in <main>'
/usr/local/arvados/update-gitolite.rb:240:in `each'
/usr/local/arvados/update-gitolite.rb:240:in `<main>'
</pre>
<p>bug 2: it does not create any defined repositories on disk unless there is at least <strong>one</strong> ssh key associated with a user in the system. This is problematic because the 'arvados' repo is not created on disk.</p> Arvados - Bug #5834 (Resolved): [API] Be careful about memory usage when responding to collection...https://dev.arvados.org/issues/58342015-04-28T15:32:21ZWard Vandewegeward@curii.com
<p>API server logs:</p>
<pre>
#<NoMemoryError: failed to allocate memory>
/data/www/qr1hi.arvadosapi.com/releases/20150423194138/app/controllers/application_controller.rb:189:in `dump'
/data/www/qr1hi.arvadosapi.com/releases/20150423194138/app/controllers/application_controller.rb:189:in `send_json'
/data/www/qr1hi.arvadosapi.com/releases/20150423194138/app/controllers/application_controller.rb:458:in `render_list'
/data/www/qr1hi.arvadosapi.com/releases/20150423194138/app/controllers/application_controller.rb:76:in `index'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/implicit_render.rb:4:in `send_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/base.rb:167:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rendering.rb:10:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/callbacks.rb:18:in `block in process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:579:in `_run__2616472115270357727__process_action__4453107480639721567__callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `__run_callback'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:385:in `_run_process_action_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:81:in `run_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/callbacks.rb:17:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rescue.rb:29:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/instrumentation.rb:30:in `block in process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications.rb:123:in `block in instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications.rb:123:in `instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/instrumentation.rb:29:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/params_wrapper.rb:207:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/railties/controller_runtime.rb:18:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/base.rb:121:in `process'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/rendering.rb:45:in `process'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal.rb:203:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rack_delegation.rb:14:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal.rb:246:in `block in action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:73:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:73:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:36:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:68:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:56:in `each'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:56:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:608:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/strategy.rb:177:in `call!'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/strategy.rb:157:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/builder.rb:48:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/best_standards_support.rb:17:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/etag.rb:23:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/conditionalget.rb:25:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/head.rb:14:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/params_parser.rb:21:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/flash.rb:242:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:210:in `context'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:205:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/cookies.rb:341:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/query_cache.rb:64:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/connection_adapters/abstract/connection_pool.rb:479:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/callbacks.rb:28:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `_run__1960694728971137051__call__1126081408567888176__callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `__run_callback'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:385:in `_run_call_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:81:in `run_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/callbacks.rb:27:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/debug_exceptions.rb:16:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/show_exceptions.rb:56:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:32:in `call_app'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:16:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/tagged_logging.rb:22:in `tagged'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:16:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/request_id.rb:22:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/methodoverride.rb:21:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/runtime.rb:17:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/cache/strategy/local_cache.rb:72:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/lock.rb:15:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:136:in `forward'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:245:in `fetch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:185:in `lookup'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:66:in `call!'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:51:in `call'
/data/www/qr1hi.arvadosapi.com/releases/20150423194138/app/middlewares/arvados_api_token.rb:59:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/remote_ip.rb:31:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/engine.rb:484:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/application.rb:231:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/railtie/configurable.rb:30:in `method_missing'
/usr/lib/ruby/vendor_ruby/phusion_passenger/rack/thread_handler_extension.rb:74:in `process_request'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:141:in `accept_and_process_next_request'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:109:in `main_loop'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler.rb:455:in `block (3 levels) in start_threads'
Error 1430180085+f49f1f8f: 422
Rendered text template (0.0ms)
Completed 422 Unprocessable Entity in 9907.9ms (Views: 0.5ms | ActiveRecord: 5932.8ms)
</pre> Arvados - Bug #5742 (Resolved): [Workbench] the user setup page creates broken shell usernameshttps://dev.arvados.org/issues/57422015-04-15T19:39:14ZWard Vandewegeward@curii.com
<p>The shell username links get created as user/user instead of user, because that's what is now needed for git.</p> Arvados - Support #5251 (Resolved): [Support] Fix bugs and write tests (first half)https://dev.arvados.org/issues/52512015-02-18T18:44:40ZWard Vandewegeward@curii.comArvados - Feature #5072 (Resolved): [Documentation] (recurring) Refresh user documentationhttps://dev.arvados.org/issues/50722015-01-23T19:27:13ZWard Vandewegeward@curii.comArvados - Feature #4027 (Resolved): [Crunch] Accept SDK version as a runtime constraint. Install ...https://dev.arvados.org/issues/40272014-09-29T19:54:38ZWard Vandewegeward@curii.com
<p>During jobs.create and jobs.update, <code>runtime_constraints['arvados_sdk_version']</code> provided by the client should be resolved to a commit hash and stored in <code>arvados_sdk_hash</code>.</p>
<p>Example:</p>
In jobs.create request:
<ul>
<li><pre>
"runtime_constraints":{
"arvados_sdk_version":"master"
}
</pre></li>
</ul>
In jobs.show response:
<ul>
<li><pre>
"arvados_sdk_hash":"7b2d04380952ac79453bd0771679e40c81281f5c"
"runtime_constraints":{
"arvados_sdk_version":"master"
}
</pre></li>
</ul>
During the "install source" phase of crunch-job (i.e., at least once per container before any task runs there), crunch-job should do something like this:
<ul>
<li><pre>
cd {path-to-arvados-tree}
git reset --hard {arvados_sdk_hash}
cd sdk
./install.sh
</pre></li>
</ul>
<p>The <code>sdk/install.sh</code> program should install Python, Ruby, and Perl client libraries to the system package directories where they can be imported by Crunch tasks.</p> Arvados - Bug #4012 (Resolved): [Crunch] crunch-job bandaid: use eval/retry to wrap api calls tha...https://dev.arvados.org/issues/40122014-09-26T18:47:25ZWard Vandewegeward@curii.comArvados - Feature #2886 (Resolved): Recurring: support beta usershttps://dev.arvados.org/issues/28862014-05-27T14:53:31ZWard Vandewegeward@curii.comArvados - Feature #2881 (Resolved): [OPS] Basic node manager that can start/stop compute nodes ba...https://dev.arvados.org/issues/28812014-05-27T14:26:51ZWard Vandewegeward@curii.com