Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff

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Hi George,

Try changing OPENCV = FALSE in the configuration file.

Best,
Erney

Quoting George Magklaras <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 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

Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff

Image processing framework to integrate EM software packages.

Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff