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Bug #3783

closed

[Crunch] 'arv pipeline run --run-here ...' failed at end even though all jobs/tasks completed successfully

Added by Abram Connelly over 10 years ago. Updated over 10 years ago.

Status:
Resolved
Priority:
Low
Assigned To:
Brett Smith
Category:
Crunch
Target version:
-
Start date:
09/02/2014
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

When running pipeline instance qr1hi-d1hrv-9jrnsp198ztr0kn, I get the following error after issuing an 'arv pipeline run --run-here ...' command:

2014-08-31 09:13:52 +0000 -- pipeline_instance qr1hi-d1hrv-9jrnsp198ztr0kn
ChopGFF                     qr1hi-8i9sb-g4lrf35jmn7dleq d071779966740d0f4884c17c3712a6a6+8369520
CreateChoppedGFFDirList     qr1hi-8i9sb-98eoeaborr1jlrw c26af40291d10bb6f0d94edd349be41d+64
CreateTileSetFromChoppedGFF qr1hi-8i9sb-zyva8qlbfmjsnse {:done=>176, :running=>0, :failed=>0, :todo=>0}

2014-08-31 09:14:03 +0000 -- pipeline_instance qr1hi-d1hrv-9jrnsp198ztr0kn
ChopGFF                     qr1hi-8i9sb-g4lrf35jmn7dleq d071779966740d0f4884c17c3712a6a6+8369520
CreateChoppedGFFDirList     qr1hi-8i9sb-98eoeaborr1jlrw c26af40291d10bb6f0d94edd349be41d+64
CreateTileSetFromChoppedGFF qr1hi-8i9sb-zyva8qlbfmjsnse {:done=>176, :running=>0, :failed=>0, :todo=>0}

2014-08-31 09:14:13 +0000 -- pipeline_instance qr1hi-d1hrv-9jrnsp198ztr0kn
ChopGFF                     qr1hi-8i9sb-g4lrf35jmn7dleq d071779966740d0f4884c17c3712a6a6+8369520
CreateChoppedGFFDirList     qr1hi-8i9sb-98eoeaborr1jlrw c26af40291d10bb6f0d94edd349be41d+64
CreateTileSetFromChoppedGFF qr1hi-8i9sb-zyva8qlbfmjsnse {:done=>176, :running=>0, :failed=>0, :todo=>0}
arv-run-pipeline-instance 23798: names:  Personal Tile Set Pipeline (Batches at a time)
arv-run-pipeline-instance 23798: Creating collection {:owner_uuid=>"qr1hi-tpzed-rd7cyyspidta11c", :name=>"Output of CreateTileSetFromChoppedGFF of Personal Tile Set Pipeline (Batches at a time) at 2014-08-31T09:14:16Z", :portable_data_hash=>nil, :manifest_text=>""}
/usr/local/rvm/gems/ruby-2.1.1/gems/arvados-0.1.20140829123712/lib/arvados.rb:243:in `api_exec': ["#<ActiveRecord::UnknownAttributeError: unknown attribute: name>"] (Arvados::TransactionFailedError)
        from /usr/local/rvm/gems/ruby-2.1.1/gems/arvados-0.1.20140829123712/lib/arvados.rb:82:in `block (4 levels) in initialize'
        from /usr/local/rvm/gems/ruby-2.1.1/gems/arvados-cli-0.1.20140829123712/bin/arv-run-pipeline-instance:588:in `block in run'
        from /usr/local/rvm/gems/ruby-2.1.1/gems/arvados-cli-0.1.20140829123712/bin/arv-run-pipeline-instance:501:in `each'
        from /usr/local/rvm/gems/ruby-2.1.1/gems/arvados-cli-0.1.20140829123712/bin/arv-run-pipeline-instance:501:in `run'
        from /usr/local/rvm/gems/ruby-2.1.1/gems/arvados-cli-0.1.20140829123712/bin/arv-run-pipeline-instance:748:in `<top (required)>'
        from /usr/local/rvm/gems/ruby-2.1.1/bin/arv-run-pipeline-instance:23:in `load'
        from /usr/local/rvm/gems/ruby-2.1.1/bin/arv-run-pipeline-instance:23:in `<main>'
        from /usr/local/rvm/gems/ruby-2.1.1/bin/ruby_executable_hooks:15:in `eval'
        from /usr/local/rvm/gems/ruby-2.1.1/bin/ruby_executable_hooks:15:in `<main>'

The last job in the pipeline is still marked as 'running' in workbench.

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 #1

Updated by Brett Smith over 10 years ago

  • Subject changed from 'arv pipeline run --run-here ...' failed at end even though all jobs/tasks completed successfully to [Crunch] 'arv pipeline run --run-here ...' failed at end even though all jobs/tasks completed successfully
  • Category set to Crunch

At first glance, it looks like the CLI SDK in new enough to try to use name attributes rather than name links. I think that change still hasn't been deployed to qr1hi, so that could cause a crash if arv-run-pipeline-instance doesn't have code to fall back.

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 #2

Updated by Ward Vandewege over 10 years ago

  • Priority changed from Normal to Low
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 #3

Updated by Ward Vandewege over 10 years ago

  • Priority changed from Low to Normal
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 #4

Updated by Ward Vandewege over 10 years ago

  • Priority changed from Normal to Low
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 #5

Updated by Brett Smith over 10 years ago

  • Status changed from New to Resolved
  • Assigned To set to Brett Smith

Abram,

I confirmed that the problem was that lightning-dev2 had client software that was newer than the API server. As we discussed, I downgraded that software to be compatible with the current API server.

Commands that update your installed Ruby gems, like gem update, can cause this sort of out-of-sync problem. I'm not sure if you've been dealing with gems as part of your development work, but if so, please be mindful of this potential side effect.

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