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Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
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From: Jose M. de la R. T. <del...@gm...> - 2020-05-18 16:53:38
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I saw a minor issue in your configuration...the CUDA_BIN should point to the bin folder, not to nvcc binary. Nonetheless, this seems unrelated to your xmipp compilation issue. Maybe the xmipp developers can provide some hints. Best, Jose Miguel On Mon, May 18, 2020 at 6:50 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 > |
