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[Pytom-mail] transformation conversion
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From: Haixin S. <su...@ho...> - 2017-10-06 05:04:35
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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<https://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...<mailto: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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Pytom-mail mailing list Pyt...@li...<mailto:Pyt...@li...> https://lists.sourceforge.net/lists/listinfo/pytom-mail |
