Menu
▾
▴
[scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
|
From: George M. <gma...@gm...> - 2020-05-18 15:54:39
|
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 |
