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Re: [scipion-users] OpenCV not found for Xmipp
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From: Carlos O. S. S. <co...@cn...> - 2019-08-13 02:33:16
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Thanks a lot. El 12/08/2019 a las 18:10, Lugmayr, Wolfgang escribió: > hi, > > i fixed now the problem with opencv and got a running gpu-based xmipp > from source (set opencv version in config and put cuda-8.0 into path): > ./scipion install opencv -j 1 > cd software > ln -s lib lib64 > cd tmp/opencv-3.4.1 > rm -rf build; mkdir build; cd build > cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX=/beegfs/cssb/software/em/scipion/2.0/software \ > -DTIFF_LIBRARY=/beegfs/cssb/software/em/scipion/2.0/software/lib/libtiff.so -DWITH_VTK=NO -DWITH_NVCUVID=NO .. > make > make install > cheers, > wolfgang > > ------------------------------------------------------------------------ > *From: *"Lugmayr, Wolfgang" <w.l...@uk...> > *To: *"Mailing list for Scipion users" > <sci...@li...> > *Sent: *Thursday, 13 June, 2019 11:22:33 > *Subject: *Re: [scipion-users] OpenCV not found for Xmipp > > hi david, > > sorry it took a while to try your tip. > > now i have a python problem: > cmake -DWITH_FFMPEG=OFF > -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF > -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software > . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log > 2>&1 > Error: target > '/beegfs/cssb/software/em/scipion/2.0/software/tmp/opencv-2.4.13/Makefile' > not built (after running 'cmake -DWITH_FFMPEG=OFF > -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF > -DCMAKE_INSTALL_PREFIX:PATH=/beegfs/cssb/software/em/scipion/2.0/software > . > /beegfs/cssb/software/em/scipion/2.0/software/log/opencv_cmake.log > 2>&1') > > the lines in the log are: > -- Could NOT find PythonLibs: Found unsuitable version "2.7.5", but > required is exact version "2.7.15" (found /lib64/libpython2.7.so) > : > -- Python: > -- Interpreter: > /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 (ver 2.7.15) > -- Libraries: /lib64/libpython2.7.so (ver 2.7.5) > -- numpy: > /beegfs/cssb/software/em/scipion/2.0/software/lib/python2.7/site-packages/numpy/core/include > (ver 1.14.1) > -- packages path: lib/python2.7/site-packages > > so if i do in a new login terminal: > $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 > libpython2.7.so.1.0 => /lib64/libpython2.7.so.1.0 (0x00002b49812b3000) > > i also made an environment module to set the LD_LIBRARY_PATH to the > right location and then: > $ ldd /beegfs/cssb/software/em/scipion/2.0/software/bin/python2 > libpython2.7.so.1.0 => > /beegfs/cssb/software/em/scipion/2.0/software/lib/libpython2.7.so.1.0 > (0x00002afad38b5000) > > but the scipion install seems to ignore these LD_LIBRARY_PATH > > cheers, > wolfgang > > > > > ------------------------------------------------------------------------ > *From: *"David Maluenda" <dma...@cn...> > *To: *"Mailing list for Scipion users" > <sci...@li...> > *Sent: *Wednesday, 29 May, 2019 10:40:48 > *Subject: *Re: [scipion-users] OpenCV not found for Xmipp > > Hi David, Wolfgang and Scipion users, > > Regarding the first question of why the openCV code of Xmipp is not > compailing when OpenCV is in a alternate location, Xmipp needs the > headers files of OpenCV to compile that part of the code, thus you > must have installed the devel version of the OpenCV package and, also, > the include folder of the openCV must be seeable during the > compilation time. > > Regarding the libtiff versions fight, yes Scipion has libtiff5, then > if other libtiff is used to compile the system's openCV, it will fail. > > Both issues might be fixed by installing OpenCV inside Scipion via > > $ cd $SCIPION_HOME > $ ./scipion install opencv -j N > > where N is the number of processors (take into account that this > installation takes a while, thus the bigger N is better). > > NOTE: Regarding the OpenCV inside Scipion, we have using the > OpenCV-v2.4.13 by default and we have checked that it works fine for > Centos7 and Ubuntu16. However, for Ubuntu 18, we have observed that > the OpenCV-v3.4.1 should be used. Therefore, if you use Ubuntu18, you > should edit the$SCIPION_HOME/config/scipion.conf in such a way that > OPENCV_VER=3.4.1 and then install opencv using the command above (this > only works if Scipion is installed from sources, not from binaries). > > > Finally, just to note that OpenCV is used by Xmipp only for two non > critical protocols (Optical Alignment and Enric -former Volume > Homogenizer-). Therefore, if you don't need this two protocols and it > still not working even with the hints pointed out above, the OpenCV > code in Xmipp can be ignored by editing > $SCIPION_HOME/config/scipion.conf in such a way that OPENCV=False and, > then, trying to compile Xmipp again. > > > I hope tht it will help and my appologies for the late reply. > > > Thanks for reporting! > > > *_____ > Dr. David Maluenda Niubó* > dma...@cn... <mailto:dma...@cn...> - (+34) 619 029 310 > CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> > BioComputing Unit <http://biocomputingunit.es/> > > This email message and any documents attached to it may contain > confidential or legally protected material and are intended solely for > the use of the individual or organization to whom they are addressed. > We remind you that if you are not the intended recipient of this email > message or the person responsible for processing it, then you are not > authorized to read, save, modify, send, copy or disclose any of its > contents. If you have received this email message by mistake, we > kindly ask you to inform the sender of this and to eliminate both the > message and any attachments it carries from your account. Thank you > for your collaboration. > > > > On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via > scipion-users <sci...@li... > <mailto:sci...@li...>> wrote: > > No. I've been attempting to compile Xmipp from source, but that > is even harder. > > David Hoover > HPC @ NIH > > On 5/27/2019 11:28 AM, Pablo Conesa wrote: > > Hi David! Have we ever replied to you with a solution? > > > > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users > wrote: > >> Hi, > >> > >> I recently installed Scipion 2.0 and all the plugins, and > attempted to run the tutorials. We have OpenCV installed in an > alternate location, and I make it available by setting $PATH and > $LD_LIBRARY_PATH. I keep getting complaints that it is not > installed, and that I should fix this and reinstall Xmipp. > >> > >> How does Xmipp know where OpenCV is? Can I set a configuration > somewhere stating where it is located? > >> > >> David Hoover > >> HPC @ NIH > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > <mailto:sci...@li...> > >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://i2pc.es/coss National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
