Re: [Pytom-mail] transformation conversion

[Dustin M. <dus...@gm...>]

Hi Sui,

The code is here:
http://pytom.org/doc/epydoc/pytom.angles.angleFnc-pysrc.html#zxzToMat
http://pytom.org/doc/epydoc/pytom.tools.maths-pysrc.html#XRotationMatrix.__init__
http://pytom.org/doc/epydoc/pytom.tools.maths-pysrc.html#ZRotationMatrix.__init__

--
Hope that helps,
Dustin

___

Cheers,
Dustin M.


On Fri, Oct 6, 2017 at 6:04 AM, Haixin Sui <su...@ho...> wrote:

> The output of localization, pl.xml, contains "Rotation X="140.044778063"
> Paradigm="ZXZ" Z1="19.9999994182" Z2="180.000005009". It looks like
> the parameters represent a rotation transformation, that can rotate a
> subvolume extracted from the tomogram, to the orientation matches the
> reference volume.
>
>
> The rotation paramers are in the format of Euler angles, i a ZXZ
> convention (similar to that used in eman2 or not?). Would anyone please
> provide me with  the equations that pytom used to calculate rotation
> matrix, so that I can compare the  orientations in pj.xml with that known
> for my testing data?
>
>
> Thank you!
>
>
> Haixin Sui
>
>
> <http://www.wadsworth.org/resnres/bios/sui.html>www.wadsworth.org/senior-
> staff/haixin-sui
>
>
> ------------------------------
> *From:* Haixin Sui <su...@ho...>
> *Sent:* Tuesday, October 3, 2017 7:25 PM
> *To:* Dustin Morado
> *Cc:* pyt...@li...
> *Subject:* Re: [Pytom-mail] mpirun problem
>
>
> Hi Dustin
>
>
> It worked on my laptop after changed the environment setup following you
> previous email!  I will try on my workstation tomorrow.
>
>
> Thank you very much!
>
>
> Haixin
>
> ------------------------------
> *From:* Dustin Morado <dus...@gm...>
> *Sent:* Tuesday, October 3, 2017 4:56 AM
> *To:* Haixin Sui
> *Cc:* pyt...@li...
> *Subject:* Re: [Pytom-mail] mpirun problem
>
> Hi Haixin,
>
> This is a known problem with MPI and pytom dynamically linked libraries.
>
> It is mentioned in the pytom FAQ: http://pytom.org/doc/pytom/faq.html
> PyTom: Tutorial <http://pytom.org/doc/pytom/faq.html>
> pytom.org
> Answer This is due to a old swig version ( 1.3.40). Please install a newer
> version and rerun the PyTom installation. ...
>
> You need to have the LD_PRELOAD variable set in you shell:
> BASH:
> export LD_PRELOAD='/usr/local/openmpi/lib/libmpi.so'
> CSH:
> setenv LD_PRELOAD '/usr/local/openmpi/lib/libmpi.so'
>
> --
> Hope this helps,
> Dustin Morado
> John Briggs Group
> MRC LMB
>
> ___
>
> Cheers,
> Dustin M.
>
>
> On Tue, Oct 3, 2017 at 4:06 AM, Haixin Sui <su...@ho...> wrote:
>
>> I followed Dustin's advice on the job xml file and I also modified two of
>> the basic programs as he suggested. The "localization.py can now be
>> successfully executed with the job.xml without using mpirun. If not working
>> with parallel computing, the "localization.py" runs too slow to be
>> practically useful.
>>
>> However, I failed to make the "localization.py" run with openmpi! I am
>> not sure if this is a problem with the openmpi environment we have or not.
>> I tested the openmpi on both my work station and my laptop using two
>> simple testing programs provided by openmpi distribution package. The
>> test programs worked well on both. However, when I did mpirun with
>> localization.py, I got the same error message on both of the two
>> computers.The error message has been included in this email. Any ideas
>> about what went wrong?
>>
>> Thanks for your help in advance !
>>
>> Haixin Sui
>>
>> ----------------------------
>> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 localization.py
>> job_test_1.xml 2 2 2
>> PyTom v0.971
>>
>> This license affects the software package PyTom and all the herein
>> distributed source / data files.
>> Authors:
>> Thomas Hrabe
>> Yuxiang Chen
>> Friedrich Foerster
>>
>> Copyright (c) 2008-2016
>> Max-Planck-Institute for Biochemistry
>> Dept. Molecular Structural Biology
>> 82152 Martinsried, Germany
>> http://www.pytom.org
>>
>> This program is free software: you can redistribute it and/or modify
>> it under the terms of the GNU General Public License as published by
>> the Free Software Foundation, either version 3 of the License, or
>> (at your option) any later version.
>>
>> This program is distributed in the hope that it will be useful,
>> but WITHOUT ANY WARRANTY; without even the implied warranty of
>> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
>> GNU General Public License for more details.
>>
>> The complete license can be obtained from
>> http://www.gnu.org/licenses/gpl-3.0.html.
>>
>> PyTom v0.971
>>
>> This license affects the software package PyTom and all the herein
>> distributed source / data files.
>> Authors:
>> Thomas Hrabe
>> Yuxiang Chen
>> Friedrich Foerster
>>
>> Copyright (c) 2008-2016
>> Max-Planck-Institute for Biochemistry
>> Dept. Molecular Structural Biology
>> 82152 Martinsried, Germany
>> http://www.pytom.org
>>
>> This program is free software: you can redistribute it and/or modify
>> it under the terms of the GNU General Public License as published by
>> the Free Software Foundation, either version 3 of the License, or
>> (at your option) any later version.
>>
>> This program is distributed in the hope that it will be useful,
>> but WITHOUT ANY WARRANTY; without even the implied warranty of
>> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
>> GNU General Public License for more details.
>>
>> The complete license can be obtained from
>> http://www.gnu.org/licenses/gpl-3.0.html.
>>
>> *** An error occurred in MPI_Init
>> *** on a NULL communicator
>> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> ***    and potentially your MPI job)
>> [Thinkpad-HR16395:24468] Local abort before MPI_INIT completed completed
>> successfully, but am not able to aggregate error messages, and not able to
>> guarantee that all other processes were killed!
>> -------------------------------------------------------
>> Primary job  terminated normally, but 1 process returned
>> a non-zero exit code.. Per user-direction, the job has been aborted.
>> -------------------------------------------------------
>> *** An error occurred in MPI_Init
>> *** on a NULL communicator
>> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> ***    and potentially your MPI job)
>> [Thinkpad-HR16395:24469] Local abort before MPI_INIT completed completed
>> successfully, but am not able to aggregate error messages, and not able to
>> guarantee that all other processes were killed!
>> ------------------------------------------------------------
>> --------------
>> mpirun detected that one or more processes exited with non-zero status,
>> thus causing
>> the job to be terminated. The first process to do so was:
>>
>>   Process name: [[24716,1],1]
>>   Exit code:    1
>> ------------------------------------------------------------
>> --------------
>>
>>
>> Preliminary test of our openmpi shows no problem with other testing
>> programs.
>> ===============================================
>> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 hello_c
>> Hello, world, I am 0 of 2, (Open MPI v1.10.2, package: Open MPI
>> buildd@lgw01-57 Distribution, ident: 1.10.2, repo rev:
>> v1.10.1-145-g799148f, Jan 21, 2016, 126)
>> Hello, world, I am 1 of 2, (Open MPI v1.10.2, package: Open MPI
>> buildd@lgw01-57 Distribution, ident: 1.10.2, repo rev:
>> v1.10.1-145-g799148f, Jan 21, 2016, 126)
>>
>> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 ring_c
>> Process 0 sending 10 to 1, tag 201 (2 processes in ring)
>> Process 0 sent to 1
>> Process 0 decremented value: 9
>> Process 0 decremented value: 8
>> Process 0 decremented value: 7
>> Process 0 decremented value: 6
>> Process 0 decremented value: 5
>> Process 0 decremented value: 4
>> Process 0 decremented value: 3
>> Process 0 decremented value: 2
>> Process 0 decremented value: 1
>> Process 0 decremented value: 0
>> Process 0 exiting
>> Process 1 exiting
>>
>>
>> ------------------------------------------------------------
>> ------------------
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