Menu
▾
▴
pytom-mail — PyTom mailing list for updates and other issues
You can subscribe to this list here.
| 2012 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(2) |
Jul
(7) |
Aug
(5) |
Sep
|
Oct
|
Nov
(7) |
Dec
(9) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2013 |
Jan
(11) |
Feb
(3) |
Mar
|
Apr
(3) |
May
(28) |
Jun
(19) |
Jul
(11) |
Aug
(1) |
Sep
(3) |
Oct
(4) |
Nov
(11) |
Dec
|
| 2014 |
Jan
|
Feb
(10) |
Mar
|
Apr
(1) |
May
|
Jun
|
Jul
|
Aug
|
Sep
(1) |
Oct
|
Nov
(4) |
Dec
|
| 2015 |
Jan
|
Feb
(1) |
Mar
(6) |
Apr
(4) |
May
|
Jun
(19) |
Jul
(14) |
Aug
(5) |
Sep
(11) |
Oct
(10) |
Nov
(4) |
Dec
|
| 2016 |
Jan
|
Feb
(46) |
Mar
(11) |
Apr
(2) |
May
(2) |
Jun
(5) |
Jul
|
Aug
|
Sep
(4) |
Oct
(1) |
Nov
|
Dec
|
| 2017 |
Jan
|
Feb
|
Mar
(3) |
Apr
|
May
|
Jun
|
Jul
(7) |
Aug
|
Sep
(4) |
Oct
(8) |
Nov
|
Dec
|
| 2018 |
Jan
|
Feb
|
Mar
(1) |
Apr
|
May
|
Jun
|
Jul
(7) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
| 2021 |
Jan
|
Feb
|
Mar
(4) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Dustin M. <dus...@gm...> - 2021-03-30 16:17:54
|
Hi Ricardo, I remember this now, I had written my own alignment scripts and was doing icosahedral symmetry, and I know that was working, so I will do some digging and try to send you the patch for making multisym work. Cheers, Dustin On Tue, 30 Mar 2021 at 17:26, Ricardo Righetto <ric...@gm...> wrote: > Thanks Dustin! > > I have tried it, but then I get this error: > > Traceback (most recent call last): > File > "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/bin/align.py", line > 45, in <module> > exj.fromXMLFile(jobFile) > File > "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py", > line 74, in fromXMLFile > self.fromStr(lines) > File > "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py", > line 47, in fromStr > self.fromXML(root) > File > "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/alignment/ExMaxAlignment.py", > line 275, in fromXML > self._symmetry = symmetryFactory.fromXML(symmetryXML[0]) > IndexError: list index out of range > > I see there is indeed a MultiSymmetries class that expects an XML > description of symmetries, but I could not find the specification of such a > file. > > From the example in the documentation, it seems that only Cn symmetries > are supported in this kind of job? > > <Symmetry X="0.0" Z2="0.0" NFold="1"/>*<!-- Symmetry information (C-X) > supported currently)* > http://strubi.chem.uu.nl/pytom/doc/pytom/RealSpaceExMax.html > > -- > Ricardo Diogo Righetto > > > Em ter., 30 de mar. de 2021 às 15:26, Dustin Morado < > dus...@gm...> escreveu: > >> Hi Ricardo, >> >> Did you have the symmetries wrapped in a multi-symmetry object? It should >> look something like this: >> >> <MultiSymmetries> >> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="0.0" Z2="0.0"/> >> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="180.0" Z2="90.0"/> >> </MultiSymmetries> >> >> Cheers, >> >> Dustin >> >> >> On Tue, 30 Mar 2021 at 14:06, Ricardo Righetto <ric...@gm...> >> wrote: >> >>> Hi, >>> >>> For imposing C4 symmetry in a real space alignment job, I use the >>> following tag in the job XML file: >>> >>> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" >>> Type="PointSymmetry" X="0.0" Z2="0.0"/> >>> >>> But how would I go about imposing D4 symmetry? I tried adding another >>> line to describe an additional 2-fold axis rotated by the 90 degrees, but >>> it is ignored and only the C4 is imposed... >>> >>> Thanks! >>> >>> -- >>> Ricardo Diogo Righetto >>> _______________________________________________ >>> Pytom-mail mailing list >>> Pyt...@li... >>> https://lists.sourceforge.net/lists/listinfo/pytom-mail >>> >> |
|
From: Ricardo R. <ric...@gm...> - 2021-03-30 15:26:14
|
Thanks Dustin!
I have tried it, but then I get this error:
Traceback (most recent call last):
File "/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/bin/align.py",
line 45, in <module>
exj.fromXMLFile(jobFile)
File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py",
line 74, in fromXMLFile
self.fromStr(lines)
File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/basic/structures.py",
line 47, in fromStr
self.fromXML(root)
File
"/fs/pool/pool-bmapps/hpcl8/app/soft/PYTOM/0.97/pytom/alignment/ExMaxAlignment.py",
line 275, in fromXML
self._symmetry = symmetryFactory.fromXML(symmetryXML[0])
IndexError: list index out of range
I see there is indeed a MultiSymmetries class that expects an XML
description of symmetries, but I could not find the specification of such a
file.
>From the example in the documentation, it seems that only Cn symmetries are
supported in this kind of job?
<Symmetry X="0.0" Z2="0.0" NFold="1"/>*<!-- Symmetry information (C-X)
supported currently)*
http://strubi.chem.uu.nl/pytom/doc/pytom/RealSpaceExMax.html
--
Ricardo Diogo Righetto
Em ter., 30 de mar. de 2021 às 15:26, Dustin Morado <dus...@gm...>
escreveu:
> Hi Ricardo,
>
> Did you have the symmetries wrapped in a multi-symmetry object? It should
> look something like this:
>
> <MultiSymmetries>
> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="0.0" Z2="0.0"/>
> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="180.0" Z2="90.0"/>
> </MultiSymmetries>
>
> Cheers,
>
> Dustin
>
>
> On Tue, 30 Mar 2021 at 14:06, Ricardo Righetto <ric...@gm...>
> wrote:
>
>> Hi,
>>
>> For imposing C4 symmetry in a real space alignment job, I use the
>> following tag in the job XML file:
>>
>> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0"
>> Type="PointSymmetry" X="0.0" Z2="0.0"/>
>>
>> But how would I go about imposing D4 symmetry? I tried adding another
>> line to describe an additional 2-fold axis rotated by the 90 degrees, but
>> it is ignored and only the C4 is imposed...
>>
>> Thanks!
>>
>> --
>> Ricardo Diogo Righetto
>> _______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>
|
|
From: Dustin M. <dus...@gm...> - 2021-03-30 13:26:34
|
Hi Ricardo, Did you have the symmetries wrapped in a multi-symmetry object? It should look something like this: <MultiSymmetries> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="0.0" Z2="0.0"/> <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="180.0" Z2="90.0"/> </MultiSymmetries> Cheers, Dustin On Tue, 30 Mar 2021 at 14:06, Ricardo Righetto <ric...@gm...> wrote: > Hi, > > For imposing C4 symmetry in a real space alignment job, I use the > following tag in the job XML file: > > <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" > Type="PointSymmetry" X="0.0" Z2="0.0"/> > > But how would I go about imposing D4 symmetry? I tried adding another line > to describe an additional 2-fold axis rotated by the 90 degrees, but it is > ignored and only the C4 is imposed... > > Thanks! > > -- > Ricardo Diogo Righetto > _______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > |
|
From: Ricardo R. <ric...@gm...> - 2021-03-30 12:06:07
|
Hi, For imposing C4 symmetry in a real space alignment job, I use the following tag in the job XML file: <Symmetry NFold="4" SearchAngle="0" SearchAxisX="0.0" SearchAxisZ2="0.0" Type="PointSymmetry" X="0.0" Z2="0.0"/> But how would I go about imposing D4 symmetry? I tried adding another line to describe an additional 2-fold axis rotated by the 90 degrees, but it is ignored and only the C4 is imposed... Thanks! -- Ricardo Diogo Righetto |
|
From: Junichi K. <kis...@gm...> - 2018-07-24 01:56:43
|
Hi, everyone, My trouble was solved. I had mistake on the settings of MPI. As the result, the calculation of template matching using tutorial dataset took about 1 hr. Thanks, Jun Kishikawa 2018年7月18日(水) 10:32 Junichi Kishikawa <kis...@gm...>: > Hi everyone, > > I'm a beginner for cryo-tomography and subtomogram. > I just installed PyTom 0.971 on CentOS7. > > Now, I'm trying to reconstruct using tutorial dataset. > The tomogram reconstruction was well done. > But, template matching using the reconstructed tomogram takes much long > time (>10 h) and don't finish yet. > > How long dose it take using tutorial dataset ? > My environment is CentOS7, Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz. > The job is running with 4 processes. > > Thanks. > > Jun Kishikawa > -- ------------------------------------------------------------------------------------ 岸川 淳一 （情報工学博士） 〒603-8555 京都府京都市北区上賀茂本山 京都産業大学 総合生命科学部 生命システム学科 生体膜エネルギー研究室 研究助教 TEL; 075-705-3221 FAX; 075-705-1914 e-mail; kis...@cc... URL; http://www.cc.kyoto-su.ac.jp/~yokoken/index-j.htm ------------------------------------------------------------------------------------ |
|
From: Junichi K. <kis...@gm...> - 2018-07-18 01:33:08
|
Hi everyone, I'm a beginner for cryo-tomography and subtomogram. I just installed PyTom 0.971 on CentOS7. Now, I'm trying to reconstruct using tutorial dataset. The tomogram reconstruction was well done. But, template matching using the reconstructed tomogram takes much long time (>10 h) and don't finish yet. How long dose it take using tutorial dataset ? My environment is CentOS7, Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz. The job is running with 4 processes. Thanks. Jun Kishikawa |
|
From: Irene De t. <ire...@em...> - 2018-07-16 10:34:00
|
Thank you for your reply, Dustin! I will check those possibilities. Cheers, Irene > On Jul 16, 2018, at 10:08 AM, Dustin Morado <dus...@gm...> wrote: > > Hi Irene, > > Unfortunately there's not a specific script to do this, and I just do it manually. However, there are many programs > that allow you to make masks by various means, such as shapes in UCSF Chimera, thresholding and binarize masks > in IMOD, and many other mask making utilities in EMAN2 / RELION / etc. > > HTH > ___ > > Cheers, > Dustin M. > > >> On Thu, Jul 12, 2018 at 7:56 AM Irene De teresa <ire...@em...> wrote: >> Hi Dustin, >> >> Thanks a lot for your answer! >> >> I was looking for a direct solution, since I am interested in doing template matching at around 2000 points, rather than the ~10^8 voxels that the full tomogram has... >> >> Is there some script available to do something like this? >> >> Thanks! >> Irene >> >>> On Jul 11, 2018, at 4:47 PM, Dustin Morado <dus...@gm...> wrote: >>> >>> Hi Irene, >>> >>> The best way I know of how to do this is to mask the output scores volume before picking peaks. >>> You can make a mask by binary thresholding etc. We have done this to discard the false peaks we often >>> get at the air-water interface by masking out the edges of the score volume before peak picking. >>> >>> HTH >>> ___ >>> >>> Cheers, >>> Dustin M. >>> >>> >>>> On Wed, Jul 11, 2018 at 3:35 PM Irene De teresa <ire...@em...> wrote: >>>> Hello all, >>>> >>>> I am new in PyTom and I am interested in running a template matching algorithm, but only at very specific points in a tomogram. >>>> >>>> I was checking how to modify the localization job that is provided by the PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t manage to indicate the list of points at the tomogram where I want to compute the cross-correlation coefficients with respect to the reference particle. Does anyone have an idea of how could I do it? >>>> >>>> Thanks a lot in advance! >>>> Best, >>>> >>>> Irene >>>> >>>> ------------------------------------------------------------------------------ >>>> 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... >>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail |
|
From: Dustin M. <dus...@gm...> - 2018-07-16 08:08:56
|
Hi Irene, Unfortunately there's not a specific script to do this, and I just do it manually. However, there are many programs that allow you to make masks by various means, such as shapes in UCSF Chimera, thresholding and binarize masks in IMOD, and many other mask making utilities in EMAN2 / RELION / etc. HTH ___ Cheers, Dustin M. On Thu, Jul 12, 2018 at 7:56 AM Irene De teresa <ire...@em...> wrote: > Hi Dustin, > > Thanks a lot for your answer! > > I was looking for a direct solution, since I am interested in doing > template matching at around 2000 points, rather than the ~10^8 voxels that > the full tomogram has... > > Is there some script available to do something like this? > > Thanks! > Irene > > On Jul 11, 2018, at 4:47 PM, Dustin Morado <dus...@gm...> > wrote: > > Hi Irene, > > The best way I know of how to do this is to mask the output scores volume > before picking peaks. > You can make a mask by binary thresholding etc. We have done this to > discard the false peaks we often > get at the air-water interface by masking out the edges of the score > volume before peak picking. > > HTH > ___ > > Cheers, > Dustin M. > > > On Wed, Jul 11, 2018 at 3:35 PM Irene De teresa <ire...@em...> > wrote: > >> Hello all, >> >> I am new in PyTom and I am interested in running a template matching >> algorithm, but only at very specific points in a tomogram. >> >> I was checking how to modify the localization job that is provided by the >> PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t >> manage to indicate the list of points at the tomogram where I want to >> compute the cross-correlation coefficients with respect to the reference >> particle. Does anyone have an idea of how could I do it? >> >> Thanks a lot in advance! >> Best, >> >> Irene >> >> >> ------------------------------------------------------------------------------ >> 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... >> https://lists.sourceforge.net/lists/listinfo/pytom-mail >> > |
|
From: Irene De t. <ire...@em...> - 2018-07-12 06:56:27
|
Hi Dustin, Thanks a lot for your answer! I was looking for a direct solution, since I am interested in doing template matching at around 2000 points, rather than the ~10^8 voxels that the full tomogram has... Is there some script available to do something like this? Thanks! Irene > On Jul 11, 2018, at 4:47 PM, Dustin Morado <dus...@gm...> wrote: > > Hi Irene, > > The best way I know of how to do this is to mask the output scores volume before picking peaks. > You can make a mask by binary thresholding etc. We have done this to discard the false peaks we often > get at the air-water interface by masking out the edges of the score volume before peak picking. > > HTH > ___ > > Cheers, > Dustin M. > > >> On Wed, Jul 11, 2018 at 3:35 PM Irene De teresa <ire...@em...> wrote: >> Hello all, >> >> I am new in PyTom and I am interested in running a template matching algorithm, but only at very specific points in a tomogram. >> >> I was checking how to modify the localization job that is provided by the PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t manage to indicate the list of points at the tomogram where I want to compute the cross-correlation coefficients with respect to the reference particle. Does anyone have an idea of how could I do it? >> >> Thanks a lot in advance! >> Best, >> >> Irene >> >> ------------------------------------------------------------------------------ >> 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... >> https://lists.sourceforge.net/lists/listinfo/pytom-mail |
|
From: Dustin M. <dus...@gm...> - 2018-07-11 14:47:59
|
Hi Irene, The best way I know of how to do this is to mask the output scores volume before picking peaks. You can make a mask by binary thresholding etc. We have done this to discard the false peaks we often get at the air-water interface by masking out the edges of the score volume before peak picking. HTH ___ Cheers, Dustin M. On Wed, Jul 11, 2018 at 3:35 PM Irene De teresa <ire...@em...> wrote: > Hello all, > > I am new in PyTom and I am interested in running a template matching > algorithm, but only at very specific points in a tomogram. > > I was checking how to modify the localization job that is provided by the > PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t manage > to indicate the list of points at the tomogram where I want to compute the > cross-correlation coefficients with respect to the reference particle. Does > anyone have an idea of how could I do it? > > Thanks a lot in advance! > Best, > > Irene > > > ------------------------------------------------------------------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > |
|
From: Irene De t. <ire...@em...> - 2018-07-11 14:35:11
|
Hello all, I am new in PyTom and I am interested in running a template matching algorithm, but only at very specific points in a tomogram. I was checking how to modify the localization job that is provided by the PyTom tutorial (pytom.org/doc/pytom/tutorial.html), but I couldn’t manage to indicate the list of points at the tomogram where I want to compute the cross-correlation coefficients with respect to the reference particle. Does anyone have an idea of how could I do it? Thanks a lot in advance! Best, Irene |
|
From: <da...@st...> - 2018-03-09 13:26:58
|
Hi all, We've recently been playing with PyTom a bit more to do some subtomogram averaging, and a couple of questions have come up: 1) When using the WienerFilterAlignment.py, what precisely is required for the CTFSquared parameter? We're not entirely sure what it is asking for, or how to go about making that volume. Is it akin to a missing wedge mask made with ctf slices, like in relion subtomo? 2) When using GFRMAlignment.py, how do you give symmetry parameters? Digging through the code, I think there should a <MultiSymmetries> tag in the job xml file, but I'm not sure how to fill this out correctly. Any help would be great! Cheers, Daven |
|
From: Haixin S. <su...@ho...> - 2017-10-06 21:54:24
|
Hi Dustin Thank you for referring me to the right code location! The following note is also helpful in order to understand the matrix definition in Pytom. ----------------- Matrix : Index convention according to http://mathworld.wolfram.com/Matrix.html. First index is Row index , Second index is Column index. ----------------- Apparently, the Euler angle rotation operation in PYTOM is opposite to that used in EMAN2 (ZXZ) or SPIDER (ZYZ). Again, thank you very much! Haixin ________________________________ From: Dustin Morado <dus...@gm...> Sent: Friday, October 6, 2017 11:25 AM To: Haixin Sui Cc: pyt...@li... Subject: Re: transformation conversion 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...<mailto: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<https://www.wadsworth.org/senior-staff/haixin-sui> ________________________________ From: Haixin Sui <su...@ho...<mailto:su...@ho...>> Sent: Tuesday, October 3, 2017 7:25 PM To: Dustin Morado Cc: pyt...@li...<mailto: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...<mailto:dus...@gm...>> Sent: Tuesday, October 3, 2017 4:56 AM To: Haixin Sui Cc: pyt...@li...<mailto: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<http://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 |
|
From: Dustin M. <dus...@gm...> - 2017-10-06 15:25:19
|
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 >> >> >> ------------------------------------------------------------ >> ------------------ >> 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... >> https://lists.sourceforge.net/lists/listinfo/pytom-mail >> >> > |
|
From: Haixin S. <su...@ho...> - 2017-10-06 05:04:35
|
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 |
|
From: Haixin S. <su...@ho...> - 2017-10-03 23:26:04
|
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 |
|
From: Dustin M. <dus...@gm...> - 2017-10-03 08:56:16
|
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 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 > > > ------------------------------------------------------------ > ------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > |
|
From: Haixin S. <su...@ho...> - 2017-10-03 03:06:26
|
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 |
|
From: Dustin M. <dus...@gm...> - 2017-10-02 09:31:17
|
Hi Haixin, Sorry for a bit of delay, but the XML label "File" in your Reference tag in your job should actually be "Filename". There are a few quirks like this where the labels in the documentation slightly differ from the ones the code expects. If you run into an error like this again, (I think there's two more if I remember correctly) just trace the error and make sure it's not looking for a different label. I also have a few other minor changes for common errors here if you run into something similar it may be of help. Mainly if you see an "isInstance" error it should be fixed here: https://sourceforge.net/p/pytom/gitrepo/ci/461b64420e74643c92d2bba409469a4cc2b10375/ Hope that helps, Dustin Morado John Briggs Group MRC LMB ___ Cheers, Dustin M. On Sun, Oct 1, 2017 at 5:42 AM, Haixin Sui <su...@ho...> wrote: > Hi Tom and all > > > The missing lxml problem has been solved. It looks like the eman2 and > pytom environment interfere with each other. After I disabled > eman2, changed PATH setting and reinstalled pytom, the lxml is now > available under pytom. However, the UI still does not work. In fact, I > have exactly the same UI issue for the newly installed pytom on my home > ubuntu laptop today. The work station in my lab is also an ubuntu 16.04. > Has anyone complied a successful Pytem on an Ubuntu system? > > > UI is not important if command lines work. However, I am not yet able > to get the command lines work. I stuck with an IOError when trying the > localization.py ("IOError: Reference XML should either have Particles or > Filename for ParticleList"). I have attached the job.xml document, and > included the screen-output in this email. The job.xml was modified from the > example in the directory "pytom-tutorial/RibosFromLysate/localization", > and I could find any problem with it. > > > Please advise what I can do to figure out the cause of the problem. > > > Thank you! > > > Haixin > > > > --------- > hsui@Thinkpad-HR16395:~/subtomo$ /home/hsui/suilab_apps/pytom/bin/pytom > /home/hsui/suilab_apps/pytom/bin/localization.py job.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. > > Traceback (most recent call last): > File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 82, in > <module> > startLocalizationJob(jobName, splitX, splitY, splitZ, > doSplitAngles=False) > File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 10, in > startLocalizationJob > job.fromXMLFile(filename) > File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 74, in > fromXMLFile > self.fromStr(lines) > File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 47, in > fromStr > self.fromXML(root) > File "/home/hsui/suilab_apps/pytom/localization/peak_job.py", line 111, > in fromXML > self.reference.fromXML(ref) > File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 587, in > fromXML > raise IOError('Reference XML should either have Particles or Filename > for ParticleList') > IOError: Reference XML should either have Particles or Filename for > ParticleList > > > > ------------------------------ > *From:* Haixin Sui <su...@ho...> > *Sent:* Friday, September 29, 2017 5:56 PM > *To:* pyt...@li... > *Subject:* [Pytom-mail] Missing lxml in pytom? > > Hi , > > I have lxml installed and it works fine in pyton environment. However, > lxml can not be found in pytom environment. > My pytom environment seems to be incorrect. Any idea what to do to fix it? > I wonder if this is related to why the UI of the pytom did not work here. > > The test results are listed in this email. > > Thanks! > > Haixin > > Python 2.7 > --------------------------------- > hsui@dalian:~/subtomo$ python > Python 2.7.12 (default, Nov 19 2016, 06:48:10) > [GCC 5.4.0 20160609] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> from lxml import etree > >>> > ----------------------------------- > > > pytom: > ----------------------------------- > hsui@dalian:~/subtomo$ pytom > PyTom v0.971 > > This license affects the software package PyTom and all the herein > distributed source / data files. > ......(removed for easy reading) > Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) > [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> from lxml import etree > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named lxml > ------------------------- > > > ------------------------------------------------------------ > ------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > |
|
From: Haixin S. <su...@ho...> - 2017-10-01 04:42:17
|
Hi Tom and all
The missing lxml problem has been solved. It looks like the eman2 and pytom environment interfere with each other. After I disabled eman2, changed PATH setting and reinstalled pytom, the lxml is now available under pytom. However, the UI still does not work. In fact, I have exactly the same UI issue for the newly installed pytom on my home ubuntu laptop today. The work station in my lab is also an ubuntu 16.04. Has anyone complied a successful Pytem on an Ubuntu system?
UI is not important if command lines work. However, I am not yet able to get the command lines work. I stuck with an IOError when trying the localization.py ("IOError: Reference XML should either have Particles or Filename for ParticleList"). I have attached the job.xml document, and included the screen-output in this email. The job.xml was modified from the example in the directory "pytom-tutorial/RibosFromLysate/localization", and I could find any problem with it.
Please advise what I can do to figure out the cause of the problem.
Thank you!
Haixin
---------
hsui@Thinkpad-HR16395:~/subtomo$ /home/hsui/suilab_apps/pytom/bin/pytom /home/hsui/suilab_apps/pytom/bin/localization.py job.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.
Traceback (most recent call last):
File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 82, in <module>
startLocalizationJob(jobName, splitX, splitY, splitZ, doSplitAngles=False)
File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 10, in startLocalizationJob
job.fromXMLFile(filename)
File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 74, in fromXMLFile
self.fromStr(lines)
File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 47, in fromStr
self.fromXML(root)
File "/home/hsui/suilab_apps/pytom/localization/peak_job.py", line 111, in fromXML
self.reference.fromXML(ref)
File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 587, in fromXML
raise IOError('Reference XML should either have Particles or Filename for ParticleList')
IOError: Reference XML should either have Particles or Filename for ParticleList
________________________________
From: Haixin Sui <su...@ho...>
Sent: Friday, September 29, 2017 5:56 PM
To: pyt...@li...
Subject: [Pytom-mail] Missing lxml in pytom?
Hi ,
I have lxml installed and it works fine in pyton environment. However, lxml can not be found in pytom environment.
My pytom environment seems to be incorrect. Any idea what to do to fix it? I wonder if this is related to why the UI of the pytom did not work here.
The test results are listed in this email.
Thanks!
Haixin
Python 2.7
---------------------------------
hsui@dalian:~/subtomo$ python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from lxml import etree
>>>
-----------------------------------
pytom:
-----------------------------------
hsui@dalian:~/subtomo$ pytom
PyTom v0.971
This license affects the software package PyTom and all the herein distributed source / data files.
......(removed for easy reading)
Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from lxml import etree
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named lxml
-------------------------
|
|
From: Haixin S. <su...@ho...> - 2017-09-29 21:56:37
|
Hi , I have lxml installed and it works fine in pyton environment. However, lxml can not be found in pytom environment. My pytom environment seems to be incorrect. Any idea what to do to fix it? I wonder if this is related to why the UI of the pytom did not work here. The test results are listed in this email. Thanks! Haixin Python 2.7 --------------------------------- hsui@dalian:~/subtomo$ python Python 2.7.12 (default, Nov 19 2016, 06:48:10) [GCC 5.4.0 20160609] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from lxml import etree >>> ----------------------------------- pytom: ----------------------------------- hsui@dalian:~/subtomo$ pytom PyTom v0.971 This license affects the software package PyTom and all the herein distributed source / data files. ......(removed for easy reading) Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from lxml import etree Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named lxml ------------------------- |
|
From: Haixin S. <su...@ho...> - 2017-09-29 17:40:23
|
Hi Dustin You are right and I have just fixed it. Thank you very much! Haixin ________________________________ From: Dustin Morado <dus...@gm...> Sent: Friday, September 29, 2017 12:22 PM To: Haixin Sui Cc: Thomas Hrabe; pyt...@li... Subject: Re: [Pytom-mail] "cat: Command not found." Hi Haixin, ipytom and pytom are actually just CSH scripts to setup your environment and then start (i)pytom. If you use bash or another shell, then perhaps csh is not setup on your computer and the PATH environment variable does not include /usr/bin which is where cat lives. HTH, Dustin Morado John Briggs Group MRC LMB ___ Cheers, Dustin M. On Fri, Sep 29, 2017 at 4:24 PM, Haixin Sui <su...@ho...<mailto:su...@ho...>> wrote: Hi I reinstalled pytom. When I start ipytom, the following message showed up "cat: Command not found". Is it an error? What does this error indicate? --------------------- /usr/local/pytom/pytomc$ ipytom cat: Command not found. Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) Type "copyright", "credits" or "license" for more information. IPython 5.4.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. -------------------- Haixin ------------------------------------------------------------------------------ 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 |
|
From: Dustin M. <dus...@gm...> - 2017-09-29 16:22:39
|
Hi Haixin, ipytom and pytom are actually just CSH scripts to setup your environment and then start (i)pytom. If you use bash or another shell, then perhaps csh is not setup on your computer and the PATH environment variable does not include /usr/bin which is where cat lives. HTH, Dustin Morado John Briggs Group MRC LMB ___ Cheers, Dustin M. On Fri, Sep 29, 2017 at 4:24 PM, Haixin Sui <su...@ho...> wrote: > Hi > > I reinstalled pytom. When I start ipytom, the following message showed up > "cat: Command not found". Is it an error? What does this error indicate? > > --------------------- > /usr/local/pytom/pytomc$ ipytom > cat: Command not found. > Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) > Type "copyright", "credits" or "license" for more information. > > IPython 5.4.1 -- An enhanced Interactive Python. > ? -> Introduction and overview of IPython's features. > %quickref -> Quick reference. > help -> Python's own help system. > object? -> Details about 'object', use 'object??' for extra details. > -------------------- > > > Haixin > > > ------------------------------------------------------------ > ------------------ > 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... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > |
|
From: Haixin S. <su...@ho...> - 2017-09-29 15:24:41
|
Hi I reinstalled pytom. When I start ipytom, the following message showed up "cat: Command not found". Is it an error? What does this error indicate? --------------------- /usr/local/pytom/pytomc$ ipytom cat: Command not found. Python 2.7.13 | packaged by conda-forge | (default, May 2 2017, 12:48:11) Type "copyright", "credits" or "license" for more information. IPython 5.4.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. -------------------- Haixin |
|
From: Kenny C. <kec...@gm...> - 2017-07-27 18:23:06
|
Dear Thomas, Thank you for your advice! I will try command line. Sincerely yours, Kenny 2017-07-26 11:46 GMT-04:00 Thomas Hrabe <th...@gm...>: > Hi Kenny, Haixin, > > Thank you for the trace. > > The user interface is old and written at times where I must admit had > little experience with web technologies. > It needs a major overhaul - anyone interested :D …? > > I suggest to use the command line tools to create an alignment job instead. > > Please try > > pytom/bin/alignJob.py > > Please let us know if it works. > > Cheers, > Thomas > > Am 24.07.2017 um 16:48 schrieb Haixin Sui <su...@ho...>: > > Hi Tom, > > Thank you very much for your response. > > I tried to repeat Kenny's test. The full stack trace and the screenshots, > before and after the error message showed up, have been been included in > the end of this email. > > What we did was to generate a new Alignment job with the GI. This is the > first job we have tested, i.e. no previous reconstruction or localization > was carried out with pytom. We assumed we could start with running an > Alignment job. > > After I input the parameters and files. When clicked on the green button > "create Job", a window popped up showing" InvildStateError: XMLHttpRequest > state must not be LOADING or DONE." > It is where we stopped. > > Please help to identify the possible reasons of the error message. > > Thank you > > Haixin > > > The full stack trace list: > ================== > vb@dalian:/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test$ pytom > /usr/local/pytom/frontend/pytomServer.py -h "dalian" & > [1] 26708 > vb@dalian:/DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test$ cat: Command > not found. > ------------------------------------------------------------ > ---------------------------- > Starting Pytom Webserver on hostname dalian and port 8080 > Paste the following line into your browser to start > http://dalian:8080 > Starting browser: firefox > > ------------------------------------------------------------ > ---------------------------- > firefox http://dalian:8080/index.html > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET / HTTP/1.1" 200 - > /usr/local/pytom/frontend/html// > /usr/local/pytom/frontend/html/javascript/javascript/functions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/functions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/functions.js > /usr/local/pytom/frontend/html/javascript/javascript/ > reconstructionFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/reconstructionFunctions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/ > reconstructionFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/mcoEXMXFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/mcoEXMXFunctions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/mcoEXMXFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/ > localizationFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/localizationFunctions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/ > localizationFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/alignmentFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/alignmentFunctions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/alignmentFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/mcoACFunctions.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/mcoACFunctions.js > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/javascript/javascript/mcoACFunctions.js > /usr/local/pytom/frontend/html/javascript/javascript/cookies.js > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /javascript/cookies.js HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/javascript/javascript/cookies.js > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /images/pytom_logo.png HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > /usr/local/pytom/frontend/html/css/css/pytomMainCSS.css > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /css/pytomMainCSS.css HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/css/css/pytomMainCSS.css > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /images/pytom_logo.png HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/images/images/pytom_logo.png > /usr/local/pytom/frontend/html/css/css/cssMainMenu.css > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /css/cssMainMenu.css HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/css/css/cssMainMenu.css > /usr/local/pytom/frontend/html/../serverpages/apiDocumentationURL.py > 127.0.0.1 - - [24/Jul/2017 09:40:27] "GET /apiDocumentationURL.py > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/apiDocumentationURL.py > /usr/local/pytom/frontend/html/pages/pages/newAlignmentJob.html > 127.0.0.1 - - [24/Jul/2017 09:40:34] "GET /pages/newAlignmentJob.html > HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/pages/pages/newAlignmentJob.html > /usr/local/pytom/frontend/html/../serverpages/loadParticleList.py > 127.0.0.1 - - [24/Jul/2017 09:41:27] "GET /loadParticleList.py?DIR=/ > DvbWork1/rv1265rec/KM_20161216_rec/Pytom_test/KM_NS_A_sybvol HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/../serverpages/loadParticleList.py > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:44:24] "GET /imageSlice.py?File=/DvbWork1/ > rv1265rec/KM_20161216_rec/Pytom_test/Reference/Reference.mrc HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Reference/Reference.png > 127.0.0.1 - - [24/Jul/2017 09:44:24] "GET /DvbWork1/rv1265rec/KM_ > 20161216_rec/Pytom_test/Reference/Reference.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Reference/Reference.png > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:44:57] "GET /imageSlice.py?File=/DvbWork1/ > rv1265rec/KM_20161216_rec/Pytom_test/Mask/Mask.mrc HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Mask/Mask.png > 127.0.0.1 - - [24/Jul/2017 09:44:57] "GET /DvbWork1/rv1265rec/KM_ > 20161216_rec/Pytom_test/Mask/Mask.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Mask/Mask.png > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > 127.0.0.1 - - [24/Jul/2017 09:46:58] "GET /imageSlice.py?File=/DvbWork1/ > rv1265rec/KM_20161216_rec/Pytom_test/Mask/rmask125_r70G2.mrc HTTP/1.1" > 200 - > /usr/local/pytom/frontend/html/../serverpages/imageSlice.py > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Mask/rmask125_r70G2.png > 127.0.0.1 - - [24/Jul/2017 09:46:58] "GET /DvbWork1/rv1265rec/KM_ > 20161216_rec/Pytom_test/Mask/rmask125_r70G2.png HTTP/1.1" 200 - > /usr/local/pytom/frontend/html/images/DvbWork1/rv1265rec/KM_20161216_rec/ > Pytom_test/Mask/rmask125_r70G2.png > > ------------ > The above has completed listing of the full stack trace. > > Before we clicked the "Create Job", the screen-shot is following. (does it > look right?) > > <pastedImage.png> > > After I clicked on the green "Create Job", the screen-shot is following. > When it happened, no additional information was triggers in the stack > trace window. > > > <pastedImage.png> > > ------------------------------ > *From:* Thomas Hrabe <th...@gm...> > *Sent:* Monday, July 24, 2017 8:52 AM > *To:* Kenny Chen > *Cc:* pyt...@li... > *Subject:* Re: [Pytom-mail] Error message when creating job file > > Hi Kenny, > > Thank you for the error report. > Could you please send the full stack trace to identify your problem in > more detail? > > Thanks, > Thomas > > > On Jul 20, 2017, at 11:24 PM, Kenny Chen <kec...@gm...> wrote: > > > > Hi, > > > > I get an error message "InvalidStateError: XMLHttpRequest state must not > be LOADING or DONE." when I create the alignment job xml file from the web > server front end. > > > > I am using firefox. > > > > > > > > Thank you for your help! > > > > > > Kenny > > ------------------------------------------------------------ > ------------------ > > 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... > > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http:// > sdm.link/slashdot > _______________________________________________ > Pytom-mail mailing list > Pyt...@li... > https://lists.sourceforge.net/lists/listinfo/pytom-mail > > > |
6 messages has been excluded from this view by a project administrator.
