Re: [scipion-users] scipion 1.1 running test failure

[Grigory S. <sha...@gm...>]

Not exactly. The file you should look for is
ScipionUserData/projects/TestXmippWorkflow/Runs/***_XmippProtML2D/logs/run.stdout

It would be great if you could attach this file here.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson <
lar...@um...> wrote:

> Hi Grigory,
> The subdirectory (of TestXmippWorkflow) Logs is empty. Is that where I'd
> expect the log files to be?
> Cheers,
> Lars
>
> On 2017-07-23 20:13, Grigory Sharov wrote:
>
>> Hello Lars,
>>
>> if you open the test project and find the failed protocol, the output
>> logs should give more details why it didn't work.
>>
>> Best regards,
>> Grigory
>>
>> ------------------------------------------------------------
>> --------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267542 <tel:+44%201223%20267542>
>> e-mail: gs...@mr... <mailto:gs...@mr...>
>>
>> On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
>> <lar...@um... <mailto:lar...@um...>> wrote:
>>
>>     Hi scipion team,
>>     We've just installed Scipion 1.1 and started going through the
>>     running test from Small towards Large. All the small tests were
>>     successful (although with the message "Some paths do not exist in:
>>     /usr/local/cuda-7.5/lib64" that others also reported - we ignored it
>>     for now). But the Xmipp Workflow test failed with the message below.
>>     Any idea what happened? I apologise if I'm overlooking something
>>     obvious at this point..
>>     Thanks a lot in advance,
>>     Lars
>>
>>
>>
>>     >>> ERROR running protocol scipion - ml2d
>>         FAILED with error:
>>
>>     [   FAILED ] TestXmippWorkflow.testXmippWorkflow
>>
>>     Traceback (most recent call last):
>>       File
>>     "/usr/local/bin/scipion/software/lib/python2.7/unittest/case.py",
>>     line 329, in run
>>         testMethod()
>>       File
>>     "/usr/local/bin/scipion/pyworkflow/tests/em/workflows/test_
>> workflow_xmipp.py",
>>     line 138, in testXmippWorkflow
>>         self.launchProtocol(protML2D)
>>       File "/usr/local/bin/scipion/pyworkflow/tests/tests.py", line 102,
>>     in launchProtocol
>>         raise Exception("ERROR launching protocol.")
>>     Exception: ERROR launching protocol.
>>
>>     [==========] run 1 tests (139.809 secs)
>>     [  FAILED  ] 1 tests
>>     [  PASSED  ] 0 tests
>>
>>
>>
>>
>>
>>     ---
>>     Lars-Anders Carlson
>>     Assistant Professor
>>     Dept of Medical Biochemistry and Biophysics
>>     Wallenberg Centre for Molecular Medicine
>>     Umeå University
>>     901 87 Umeå, Sweden
>>
>>     lab website including OPEN POSITIONS:
>>     http://www.carlsonlab.se/
>>
>>     ------------------------------------------------------------
>> ------------------
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>>
>>
>>
>> ------------------------------------------------------------
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>>
>>
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>>
> --
> Lars-Anders Carlson
> Assistant Professor
> Dept of Medical Biochemistry and Biophysics
> Wallenberg Centre for Molecular Medicine
> Umeå University
> 901 87 Umeå, Sweden
>
> lab website including OPEN POSITIONS:
> http://www.carlsonlab.se/
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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