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Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
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From: Pablo C. <pc...@cn...> - 2020-05-18 17:45:10
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Hi all, not sure about this, but it might help: Scipion uses <scipion-home>/software/lib where it compiles it's libraries...among them libtiff If you remove the one it should take system one (otherwise try a link). Then all libtiff will be the system one. Just one concern about system tiff. Scipion installs a modification of libtiff --> bigtiff, i think it coems from here: http://bigtiff.org/ Is meant to be compatible with libtiff but accepts tiff files bigger than 4GB? Regarding flagging opencv=False, you will not get optical flow and one more method from xmipp. We usually recommend that if there are compilation issues and no strong interest in xmipp OF. On 18/5/20 19:30, George Magklaras wrote: > Hi Erny, > > If I set the OPENCV=FALSE, I am able to build the xmippSrc plugin , > however, when I try to perform an xmipp3 optical alignment (see > attached screenshot), I get the error: > "It seems that Xmipp Optical Alignment is not installed. OpenCV should > be installed in the system to compile it. > Please, install OpenCV in your system and, then, re-install Xmipp by > running 'scipion installb xmippSrc'." > > The idea here is that I have a system with both libtiff4 and opencv > installed as part of yum packages, however, it seems that this is not > compatible with the scipion environment. I get the same error if I try > to use the xmippBin_Centos binary plugin. My users need the optical > alignment xmipp3 functionality. Any ideas? > > GM > > On Mon, May 18, 2020 at 6:58 PM Erney Ramírez Aportela > <era...@cn... <mailto:era...@cn...>> wrote: > > Hi George, > > Try changing OPENCV = FALSE in the configuration file. > > Best, > Erney > > > Quoting George Magklaras <gma...@gm... > <mailto:gma...@gm...>>: > > > Dear all, > > > > I have installed a fresh version of 'Scipion v2.0 (2019-04-23) > Diocletian' > > from sources on a GPU enabled CentOS 7 server (CentOS Linux release > > 7.8.2003 (Core) > > My scipion.conf file looks like this: > > > > [root@gpu1 <mailto:root@gpu1> config]# cat scipion.conf > > [DIRS_GLOBAL] > > SCIPION_TESTS = data/tests > > SCIPION_SOFTWARE = software > > > > [REMOTE] > > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > > SCIPION_URL_SOFTWARE = %(SCIPION_URL)s/software > > SCIPION_URL_TESTDATA = %(SCIPION_URL)s/data/tests > > > > [BUILD] > > CC = gcc > > CXX = g++ > > LINKERFORPROGRAMS = g++ > > CCFLAGS = -std=c99 > > CXXFLAGS = > > LINKFLAGS = > > MPI_CC = mpicc > > MPI_CXX = mpiCC > > MPI_LINKERFORPROGRAMS = mpiCC > > MPI_LIB = mpi > > MPI_LIBDIR = /usr/lib64/openmpi3/lib > > MPI_INCLUDE = /usr/include/openmpi3-x86_64 > > MPI_BINDIR = /usr/lib64/openmpi3/bin > > CUDA_LIB = /lsc/nvidia/cuda/8.0-GA2/lib64 > > CUDA_BIN = /lsc/nvidia/cuda/8.0-GA2/bin/nvcc > > NVCC = nvcc --x cu -D_FORCE_INLINES -Xcompiler -fPIC > > -Wno-deprecated-gpu-targets > > NVCC_INCLUDE = /lsc/nvidia/cuda/8.0-GA2/include > > NVCC_LIBDIR = %(CUDA_LIB)s > > MATLAB_DIR = /usr/local/MATLAB/R2011a > > JAVA_HOME = > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64 > > JAVA_BINDIR = %(JAVA_HOME)s/bin > > JAVAC = %(JAVA_BINDIR)s/javac > > JAR = %(JAVA_BINDIR)s/jar > > JNI_CPPPATH = %(JAVA_HOME)s/include:%(JAVA_HOME)s/include/linux > > JAVA_MAX_MEMORY = 2 > > GTEST = False > > CUDA = True > > DEBUG = False > > MATLAB = False > > OPENCV = True > > OPENCV_VER = 2.4.13 > > REMOTE_MESA_LIB = /services/guacamole/usr/mesa/lib/ > > > > produced no warnings. After launching the GUI and using the > plugin manager > > to install the xmippSrc-3.19.04 plugin (part of the > scipion-em-xmipp), I > > hit a glitch. The way I understand it is that in essence, > despite having > > both the vanilla centOS packages for openCV and libtiff4: > > > > root@sekulicgpu1 <mailto:root@sekulicgpu1> config]# yum list > installed | grep -i opencv > > opencv.x86_64 2.4.5-3.el7 @base > > > > opencv-core.x86_64 2.4.5-3.el7 @base > > > > opencv-devel.x86_64 2.4.5-3.el7 @base > > > > opencv-python.x86_64 2.4.5-3.el7 @base > > > > [root@sekulicgpu1 <mailto:root@sekulicgpu1> config]# yum list > installed | grep -i libtiff > > compat-libtiff3.x86_64 3.9.4-12.el7 @base > > > > libtiff.x86_64 4.0.3-32.el7 @base > > > > libtiff-devel.x86_64 4.0.3-32.el7 @base > > > > libtiff-static.x86_64 4.0.3-32.el7 @base > > > > libtiff-tools.x86_64 4.0.3-32.el7 @base > > > > > > the compilation process from the plugin manager fails with this > errors > > message (plugin.log): > > ... > > > > 01353: g++ -o bin/xmipp_transform_mask > > applications/programs/transform_mask/transform_mask_main.o > > > -L/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore/lib > > -Llib -Llib -L/lsc/scipion/2.0source/scipion/software/lib > > -L/lsc/scipion/2.0source/scipion/software/lib > -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 > > -L/lsc/scipion/2.0source/scipion/software/em/xmipp/lib > > -L/lsc/fftw/3.3.8withopenmpi/lib -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 > > -lfftw3_threads -ljpeg -ltiff -lXmippCore > > 01354: g++ -o bin/xmipp_reconstruct_art_xray > > > applications/programs/reconstruct_art_xray/reconstruct_art_xray_main.o > > > -L/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore/lib > > -Llib -Llib -L/lsc/scipion/2.0source/scipion/software/lib > > -L/lsc/scipion/2.0source/scipion/software/lib > -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 > > -L/lsc/scipion/2.0source/scipion/software/em/xmipp/lib > > -L/lsc/fftw/3.3.8withopenmpi/lib -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 > > -lfftw3_threads -ljpeg -ltiff -lXmippCore > > 01355: g++ -o > applications/programs/image_align/image_align_main.o -c > > -std=c++11 -O3 -Iexternal -Ilibraries > > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src > > -I/lsc/scipion/2.0source/scipion/software/include > > applications/programs/image_align/image_a01356: lign_main.cpp > > 01357: g++ -o > > > applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.o > -c > > -std=c++11 -O3 -Iexternal -Ilibraries > > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src > > -I/lsc/scipion/2.0source/scipion/software/include > > > applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.cpp > > 01358: g++ -o bin/xmipp_validation_tilt_pairs > > > applications/programs/validation_tilt_pairs/validation_tilt_pairs_main.o > > > -L/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore/lib > > -Llib -Llib -L/lsc/scipion/2.0source/scipion/software/lib > > -L/lsc/scipion/2.0source/scipion/software/lib > -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 > > -L/lsc/scipion/2.0source/scipion/software/em/xmipp/lib > > -L/lsc/fftw/3.3.8withopenmpi/lib -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 > > -lfftw3_threads -ljpeg -ltiff -lXmippCore > > 01359: g++ -o > > > applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.o > > -c -std=c++11 -O3 -Iexternal -Ilibraries > > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore > > -I/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src > > -I/lsc/scipion/2.0source/scipion/software/include > > > applications/programs/metadata_convert_to_spider/metadata_convert_to_spider_main.cpp > > 01360: g++ -o bin/xmipp_movie_optical_alignment_cpu > > > applications/programs/movie_optical_alignment_cpu/movie_optical_alignment_cpu.o > > > -L/lsc/scipion/2.0source/scipion/software/em/xmippSrc-v3.19.04/src/xmippCore/lib > > -Llib -Llib -L/lsc/scipion/2.0source/scipion/software/lib > > -L/lsc/scipion/2.0source/scipion/software/lib > -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 > > -L/lsc/scipion/2.0source/scipion/software/em/xmipp/lib > > -L/lsc/fftw/3.3.8withopenmpi/lib -L/usr/lib64/openmpi3/lib > > -L/lsc/nvidia/cuda/8.0-GA2/lib64 -lopencv_core -lopencv_imgproc > > -lopencv_video -lopencv_calib3d -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 > > -lfftw3_threads -ljpeg -ltiff -lXmippCore > > 01361: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFIsTiled@LIBTIFF_4.0' > > 01362: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFOpen@LIBTIFF_4.0' > > 01363: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFReadEncodedStrip@LIBTIFF_4.0' > > 01364: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFSetField@LIBTIFF_4.0' > > 01365: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFWriteScanline@LIBTIFF_4.0' > > 01366: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFGetField@LIBTIFF_4.0' > > 01367: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFScanlineSize@LIBTIFF_4.0' > > 01368: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFSetWarningHandler@LIBTIFF_4.0' > > 01369: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFSetErrorHandler@LIBTIFF_4.0' > > 01370: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFReadEncodedTile@LIBTIFF_4.0' > > 01371: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFReadRGBATile@LIBTIFF_4.0' > > 01372: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFClose@LIBTIFF_4.0' > > 01373: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFRGBAImageOK@LIBTIFF_4.0' > > 01374: //usr/lib64/libopencv_highgui.so.2.4: undefined > reference to > > `TIFFReadRGBAStrip@LIBTIFF_4.0' > > 01375: collect2: error: ld returned 1 exit status > > 01376: scons: *** [bin/xmipp_movie_optical_alignment_cpu] Error 1 > > 01377: scons: building terminated because of errors. > > 01378: > > 01379: Some error found compiling > 'xmipp_movie_optical_alignment_cpu' > > program. > > 01380: You can skip this program by including 'OPENCV=False' > in the > > config file. > > 01381: > > 01382: Some error occurred during the compilation of 'xmipp'. > > 01383: > > 01384: 2020-05-18 16:47:06,240 INFO: Error executing the > operation: > > install xmippSrc-3.19.04 > > > > Can you please suggest how to resolve this? If the Centos > packaged libs are > > not suitable, which ones should I use to compile the source plugin > > properly? > > > > Best regards, > > GM > > > > NCMM - University of Oslo > > _______________________________________________ > 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 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
