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Re: [scipion-users] OpenCV not found for Xmipp
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From: Lugmayr, W. <w.l...@uk...> - 2019-08-12 16:10:30
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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! [ http://ucm.es/ ] _____ Dr. David Maluenda Niubó [ mailto:dma...@cn... | dma...@cn... ] - (+34) 619 029 310 [ http://www.cnb.csic.es/ | CSIC - Centro Nacional de Biotecnología ] [ http://biocomputingunit.es/ | BioComputing Unit ] 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 < [ mailto:sci...@li... | 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 >> [ mailto:sci...@li... | sci...@li... ] >> [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] > > > _______________________________________________ > scipion-users mailing list > [ mailto:sci...@li... | sci...@li... ] > [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
