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Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff
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From: David M. <dma...@cn...> - 2020-05-18 17:51:35
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Hi George, We have experimented some issues when installing xmipp-optical-alignment in CentOs, but some time we achieved it. Let's try! First, if you have installed some libraries after the first try installing xmipp, you can try with making a new xmipp.config (it is done by discovering paths). The xmipp.conf can be found at scipion/software/em/xmippSrc-v3.19.04/xmipp.conf, please move it (or remove it if not edited) and try again with the installation. If not we can keep trying. Regards, <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Mon, May 18, 2020 at 7:30 PM George Magklaras <gma...@gm...> wrote: > Hi Erny, > > If I set the OPENCV=FALSE, I am able to build the xmippSrc plugin , > however, when I try to perform an xmipp3 optical alignment (see attached > screenshot), I get the error: > "It seems that Xmipp Optical Alignment is not installed. OpenCV should be > installed in the system to compile it. > Please, install OpenCV in your system and, then, re-install Xmipp by > running 'scipion installb xmippSrc'." > > The idea here is that I have a system with both libtiff4 and opencv > installed as part of yum packages, however, it seems that this is not > compatible with the scipion environment. I get the same error if I try to > use the xmippBin_Centos binary plugin. My users need the optical alignment > xmipp3 functionality. Any ideas? > > GM > > On Mon, May 18, 2020 at 6:58 PM Erney Ramírez Aportela < > era...@cn...> wrote: > >> 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 >> >> _______________________________________________ >> 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 > |
