Re: [scipion-users] RCT in the initial vol tutorial

[Carlos O. S. <co...@cn...>]

Dear Elad,

in version 1.0.1, mpi is not fully working. You may try to use only 
threads, or no parallelization at all (thread=1, mpi=1)

Kind regards, Carlos Oscar


On 11/28/16 19:56, Elad Binshtein wrote:
> Hi All,
>
> I still try to run the xmipp RCT wiyh no luck.
>
> I have this error with the mpi4py in the terminal:
>
> Running runJobMPISlave:  1
> Traceback (most recent call last):
>   File 
> "/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/apps/pw_protocol_mpirun.py", 
> line 57, in <module>
>     runJobMPISlave(comm)
>   File 
> "/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/utils/mpi.py", 
> line 107, in runJobMPISlave
>     done, command = req_recv.test()
>   File "Request.pyx", line 237, in mpi4py.MPI.Request.test 
> (src/mpi4py.MPI.c:52898)
>   File "pickled.pxi", line 401, in mpi4py.MPI.PyMPI_test 
> (src/mpi4py.MPI.c:31080)
> mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated
>
> our IT try to fix it together with SBgrid and it not working. Do 
> anyone have this error?
>
> Thanks,
>
>
> On Tue, Nov 1, 2016 at 3:41 PM, Grigory Sharov 
> <sha...@gm... <mailto:sha...@gm...>> wrote:
>
>     Hi,
>
>     the thing is that protocol runs with mpi=2 and 1 thread (by
>     default in the protocol, thread number is not taken from GUI) and
>     prints all output to console and not to run.stdout.
>
>     Elad, in principle it should still run (however slowly), you could
>     check the output in the console where you launched scipion (if it
>     was done interactively) or the output log file from the job
>     submission system on your cluster (if you run it on cluster).
>
>     Best regards,
>     Grigory
>
>     --------------------------------------------------------------------------------
>     Grigory Sharov, Ph.D.
>     Institute of Genetics and Molecular and Cellular Biology
>     Integrated Structural Biology Department (CBI)
>     1, rue Laurent Fries
>     67404 Illkirch, France
>     tel. 03 69 48 51 00
>     e-mail: sh...@ig... <mailto:sh...@ig...>
>
>     On Tue, Nov 1, 2016 at 9:12 PM, Carlos Oscar Sorzano
>     <co...@cn... <mailto:co...@cn...>> wrote:
>
>         Dear Elad,
>
>         can you send the log so that we can better see what may be
>         happening? If you attach a screenshot of the project, we may
>         try to figure out the workflow you have followed.
>
>         Kind regards, Carlos Oscar
>
>
>         On 11/01/16 17:05, Elad Binshtein wrote:
>>         Hi,
>>         I'm try to go through the  initial vol tutorial and in the
>>         lass step EMAN and ransac is work good I can not run the
>>         xmipp RCT protocol (no error on the run log just stuck on
>>         step 1/8)
>>         any suggestion?
>>
>>         Thanks
>>
>>         -- 
>>         ________________________________
>>         Elad Binshtein, Ph.D.
>>         Cryo EM specialist - staff scientist
>>         Center for Structure Biology (CSB)
>>         Vanderbilt University
>>         Nashville, TN
>>         Mobile: +1-615-481-4408 <tel:%2B1-615-481-4408>
>>         E-Mail: el...@gm... <mailto:el...@gm...>
>>         ________________________________
>>
>>
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>
>         -- 
>         ------------------------------------------------------------------------
>         Carlos Oscar Sánchez Sorzano                  e-mail:co...@cn... <mailto:co...@cn...>
>         Biocomputing unithttp://biocomp.cnb.csic.es
>         National Center of Biotechnology (CSIC)
>         c/Darwin, 3
>         Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
>         28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
>         ------------------------------------------------------------------------
>
>         ------------------------------------------------------------------------------
>         Developer Access Program for Intel Xeon Phi Processors Access
>         to Intel Xeon Phi processor-based developer platforms. With
>         one year of Intel Parallel Studio XE. Training and support
>         from Colfax. Order your platform today.
>         http://sdm.link/xeonphi
>         _______________________________________________ scipion-users
>         mailing list sci...@li...
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> -- 
> ________________________________ Elad Binshtein, Ph.D.
> Cryo EM specialist - staff scientist Center for Structure Biology 
> (CSB) MCN Room 1207 Vanderbilt University Nashville, TN Office: 
> +1-615-322-4671 Mobile: +1-615-481-4408E-Mail: el...@gm... 
> <mailto:el...@gm...> ________________________________
-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
------------------------------------------------------------------------