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

[Jose M. de la R. T. <del...@gm...>]

Hi Lars,

As Grigory mentioned, you should look at which protocol failed and then
look into its log file.
After launching the logs....you can run the following command (assuming
that you are running
scipion script from the installation folder):

./scipion last &

This should open the last project (the failed one) and then you can check
which protocol
failed...and look its log in
ScipionUserData/TestProjectName/Runs/0000xxx_FailledProtocol/logs/

Hope this helps,
Jose Miguel


On Sun, Jul 23, 2017 at 8:40 PM, Grigory Sharov <sha...@gm...>
wrote:

> 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_w
>>> orkflow_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/
>>>
>>>     ------------------------------------------------------------
>>> ------------------
>>>     Check out the vibrant tech community on one of the world's most
>>>     engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>     _______________________________________________
>>>     scipion-users mailing list
>>>     sci...@li...
>>>     <mailto:sci...@li...>
>>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>     <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
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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
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>