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Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
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From: George M. <gma...@gm...> - 2020-05-18 16:49:48
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Hi Jose, thanks for your response. Yes, I did follow the dependencies and yes, it seems that libtiff-devel has been installed from the CentOS 7 base repo: [root@gpu1 scipion]# yum list installed | grep 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 [root@gpu1 scipion]# ldconfig -p | grep tiff libtiffxx.so.5 (libc6,x86-64) => /lib64/libtiffxx.so.5 libtiffxx.so.3 (libc6,x86-64) => /lib64/libtiffxx.so.3 libtiffxx.so (libc6,x86-64) => /lib64/libtiffxx.so libtiff.so.5 (libc6,x86-64) => /lib64/libtiff.so.5 libtiff.so.3 (libc6,x86-64) => /lib64/libtiff.so.3 libtiff.so (libc6,x86-64) => /lib64/libtiff.so Best regards, GM On Mon, May 18, 2020 at 6:08 PM Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hi GM, > > Have you installed the system dependencies listed here: > https://scipion-em.github.io/docs/docs/scipion-modes/dependencies > > From your error it seems that libtiff-devel is not installed. > > Best, > Jose Miguel > > > > On Mon, May 18, 2020 at 5:54 PM George Magklaras <gma...@gm...> > wrote: > >> 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 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 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 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... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
