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Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
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From: Grigory S. <sha...@gm...> - 2020-05-18 17:05:02
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Hi GM, do you by chance/mistake have conda activated in you .bashrc? Then you could run "conda remove libtiff" or deactivate conda. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, May 18, 2020 at 5:50 PM George Magklaras <gma...@gm...> wrote: > 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 >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
