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

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

Hi Lars,

yes, it is MPI-related. I suggest to verify that all MPI-related vars in
scipion.conf file point to correct path where your 1.10.2 is installed (see
here <https://github.com/I2PC/scipion/wiki/Scipion-Configuration>). After
that you can check whether mpi works by simply running in command line:

scipion run mpirun -np 4 hostname



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 9:48 PM, Lars-Anders Carlson <
lar...@um...> wrote:

> 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 <+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
>>> 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...
>> 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...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>