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

[Lars-Anders C. <lar...@um...>]

Thanks for the advise, the run.stdout is attached. It seems the error may be related to MPI? We have Open MPI 1.10.2 installed and it's working fine for other things, but maybe we need to change something for Scipion?

Cheers,

Lars



________________________________
From: Grigory Sharov <sha...@gm...>
Sent: 23 July 2017 20:40
Cc: sci...@li...
Subject: Re: [scipion-users] scipion 1.1 running test failure

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<tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...>

On Sun, Jul 23, 2017 at 7:17 PM, Lars-Anders Carlson <lar...@um...<mailto: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:%2B44%20%280%29%201223%20267542> <tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...> <mailto:gs...@mr...<mailto:gs...@mr...>>

On Sun, Jul 23, 2017 at 6:55 PM, Lars-Anders Carlson
<lar...@um...<mailto:lar...@um...> <mailto: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/

    ------------------------------------------------------------------------------
    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...>
    <mailto: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
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
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