Re: [scipion-users] errors running xmipp3 - ctf_correct_wiener2d & xmipp3 - reconstruct significant

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

Thanks!

For the ctf program it looks like you have problems with OpenMPI: error
while loading shared libraries: libmpi.so.1: cannot open shared object
file: No such file or directory
I suggest to check if all MPI variables in scipion.config file point to
correct paths (see https://github.com/I2PC/scipion/wiki/Scipion-
Configuration) and run *scipion config* to make sure it doesn't show any
errors

For reconstruct protocol, the error is :

[1;31mXMIPP_ERROR 2:  Incorrect argument received [0m
[1;31m [1;31mAlpha values are too large: reduce the error such that the
error times the symmetry number is smaller than 1 [0m [0m
[1;31mFile:
software/em/xmipp/libraries/reconstruction/reconstruct_significant.cpp
line: 737 [0m
..
Initial significance        : 0.2
Final significance          : 0.2
*..*

Why did you use such values? You could start with default ones: 80% and
99.5%



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 Mon, Nov 7, 2016 at 1:51 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear Grigory,
>
> Please find the required files in the attachment.
>
>
> Sincerely,
> Dmitry
>
> 2016-11-07 13:33 GMT+01:00 Grigory Sharov <sha...@gm...>:
>
>> Hello Dmitry,
>>
>> this is not enough to see the source of error. Could you attach log files
>> (run.stdout) in both cases?
>>
>> 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 Mon, Nov 7, 2016 at 1:22 PM, Dmitry Semchonok <sem...@gm...>
>> wrote:
>>
>>> Dear colleagues,
>>>
>>> I have a problem with running
>>>
>>> xmipp3 - ctf_correct_wiener2d
>>> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>:
>>>
>>> xmipp3 - reconstruct significant
>>> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>:
>>>
>>>
>>> I faced the following errors:
>>>
>>> xmipp3 - ctf_correct_wiener2d
>>> <https://github.com/I2PC/scipion/wiki/XmippProtCTFCorrectWiener2D>:
>>> Protocol failed: Command 'srun  `which xmipp_mpi_ctf_correct_wiener2d`
>>> -i Runs/001129_XmippProtCTFCorrectWiener2D/input_particles.xmd  -o
>>> Runs/001129_XmippProtCTFCorrectWiener2D/corrected_ctf_particles.stk
>>> --save_metadata_stack Runs/001129_XmippProtCTFCorrec
>>> tWiener2D/corrected_ctf_particles.xmd  --pad 2  --wc -1.0
>>> --sampling_rate 2.24' returned non-zero exit status 127
>>>
>>>
>>> xmipp3 - reconstruct significant
>>> <https://github.com/I2PC/scipion/wiki/XmippProtReconstructSignificant>
>>> Protocol failed: Command 'srun  `which xmipp_mpi_reconstruct_significant`
>>> -i Runs/001892_XmippProtReconstructSignificant/extra/input_classes.xmd
>>> --sym c1 --angularSampling 5.000000 --minTilt 0.000000 --maxTilt 90.000000
>>> --maxShift -1.000000 --dontReconstruct --angDistance 10.000000 --useImed
>>> --odir Runs/001892_XmippProtReconstructSignificant/tmp/iter001 --alpha0
>>> 0.200000 --alphaF 0.200000 --numberOfVolumes 1' returned non-zero exit
>>> status 127
>>>
>>>
>>>
>>>
>>> Any suggestions?
>>>
>>> Thank you.
>>>
>>> Sincerely,
>>> Dmitry
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> 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...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>
>