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

[Elad B. <el...@gm...>]

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...>
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...
>
> On Tue, Nov 1, 2016 at 9:12 PM, Carlos Oscar Sorzano <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
>> E-Mail: el...@gm...
>> ________________________________
>>
>>
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>> _______________________________________________
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>>
>> --
>> ------------------------------------------------------------------------
>> Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
>> Biocomputing unit                             http://biocomp.cnb.csic.es
>> National Center of Biotechnology (CSIC)
>> c/Darwin, 3
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>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>> _______________________________________________
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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: +1-615-481-4408
E-Mail: el...@gm...
________________________________