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From: Carlos O. S. <co...@cn...> - 2020-05-20 09:40:52
|
Dear Dmitry, I am not aware of such a tool, Marta may know better than myself, but I agree that it is a good suggestion if it is not already there. Kind regards, Carlos Oscar El 19/05/2020 a las 16:48, Dmitry A. Semchonok escribió: > > Dear colleagues, > > I want to compare 2 models that have some differences: the same > subunits but repositioned, missing structures, etc. > > Is there a tool in SCIPION that can: > > - Make a list of structure A (all components/residues). A list of > elements in Structure B. > > - Compare and report the missing parts in structure B compared to > structure A? Maybe also the differences in distances between the same > helices in structure B compared to structure A? > > Thank you! > > Sincerely, > > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: George M. <gma...@gm...> - 2020-05-19 15:47:28
|
Hi Wolfgang (and David) I have tried Wolfgang's suggestions and things seem to work now (thanks Wolfgang!) , I was able to compile and run the Xmipp-optical-alignment, albeit in CPU only (the Scipion form gives the option of a GPU as well, yet my CUDA version 8.0-GA2 was not able to work with the optical alignment). CUDA works with the xmipp3 correlation alignment, not with the optical one, at least not in my system. May I also ask how one is meant to specify multiple GPUs as part of the GPU id list field. Is this possible? David: My xmipp.conf looks like this: [BUILD] CC=gcc CCFLAGS= -std=c99 CUDA=True CXX=g++ CXXFLAGS= -std=c++11 CXX_CUDA=g++ DEBUG=False INCDIRFLAGS=-I../ -I/lsc/scipion/2.0source/scipion/software/include JAR=%(JAVA_BINDIR)s/jar JAVAC=%(JAVA_BINDIR)s/javac JAVA_BINDIR=%(JAVA_HOME)s/bin JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64 JNI_CPPPATH=%(JAVA_HOME)s/include:%(JAVA_HOME)s/include/linux LIBDIRFLAGS=-L/lsc/scipion/2.0source/scipion/software/lib LINKERFORPROGRAMS=g++ LINKFLAGS= MATLAB=False MATLAB_DIR= MPI_CC=mpicc MPI_CXX=mpiCC MPI_CXXFLAGS= MPI_LINKERFORPROGRAMS=mpiCC MPI_LINKFLAGS= NVCC=nvcc NVCC_CXXFLAGS=--x cu -D_FORCE_INLINES -Xcompiler -fPIC -Wno-deprecated-gpu-targets -ccbin %(CXX_CUDA)s -std=c++11 NVCC_LINKFLAGS=-L/lsc/nvidia/cuda/8.0-GA2/lib64 -L/lsc/nvidia/cuda/8.0-GA2/lib64/stubs OPENCV=True OPENCV3= OPENCVSUPPORTSCUDA= PYTHONINCFLAGS=-I/lsc/scipion/2.0source/scipion/software/include/python2.7 -I/lsc/scipion/2.0source/scipion/software/lib/python2.7/site-packages -I/lsc/scipion/2.0source/scipion/software/lib/python2.7/site-packages/numpy/core/include USE_DL=False VERIFIED=True The opencv built by the scipion install opencv step: [root@sekulicgpu1 scipion]# ./scipion install opencv -j 16 Scipion v2.0 (2019-04-23) Diocletian Building opencv ... wget -nv -c -O /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/opencv-2.4.13.tgz 2020-05-19 16:35:54 URL: http://scipion.cnb.csic.es/downloads/scipion/software/external/opencv-2.4.13.tgz [91817825/91817825] -> "/lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz.part" [1] mv -v /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz.part /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz ‘/lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz.part’ -> ‘/lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13.tgz’ cd /lsc/scipion/2.0source/scipion/software/tmp tar -xzf opencv-2.4.13.tgz cd /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13 cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX:PATH=/lsc/scipion/2.0source/scipion/software . > /lsc/scipion/2.0source/scipion/software/log/opencv_cmake.log 2>&1 cd /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13 make -j 16 > /lsc/scipion/2.0source/scipion/software/log/opencv_make.log 2>&1 cd /lsc/scipion/2.0source/scipion/software/tmp/opencv-2.4.13 make install > /lsc/scipion/2.0source/scipion/software/log/opencv_make_install.log 2>&1 Done (6 m 57 s) ************************************************************************ * * * Congratulations, Scipion was installed successfully * * * ************************************************************************ looks like this and detected CUDA correctly: root@sekulicgpu1 xmippSrc-3.19.04]# cat /lsc/scipion/2.0source/scipion/software/log/opencv_make.log | grep -i cuda [ 26%] Building NVCC (Device) object modules/core/CMakeFiles/cuda_compile.dir/__/dynamicuda/src/cuda/./cuda_compile_generated_matrix_operations.cu.o [ 48%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] [ 49%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_clahe.cu.o [ 49%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/nvidia/core/./cuda_compile_generated_NCV.cu.o Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_row_filter.3.cu.o Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_tvl1flow.cu.o Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_calib3d.cu.o Building NVCC (Device) object 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Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_canny.cu.o [ 69%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_element_operations.cu.o [ 69%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/nvidia/NPP_staging/./cuda_compile_generated_NPP_staging.cu.o [ 69%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/nvidia/./cuda_compile_generated_NCVHaarObjectDetection.cu.o [ 69%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/nvidia/./cuda_compile_generated_NCVBroxOpticalFlow.cu.o [ 69%] Building NVCC (Device) object modules/gpu/CMakeFiles/cuda_compile.dir/src/nvidia/core/./cuda_compile_generated_NCVPyramid.cu.o [ 72%] Building CXX object modules/gpu/CMakeFiles/opencv_gpu.dir/src/cudastream.cpp.o [ 73%] [ 74%] [ 74%] [ 74%] Building NVCC (Device) object modules/superres/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_btv_l1_gpu.cu.o Building NVCC (Device) object modules/nonfree/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_surf.cu.o GM On Tue, May 19, 2020 at 11:20 AM Lugmayr, Wolfgang <w.l...@lu...> wrote: > hi, > > here is an example of my build of opencv with scipion libtiff on centos7: > > ./scipion install opencv -j N > cd software > ln -s lib lib64 > cd tmp/opencv-3.4.1 > rm -rf build; mkdir build; cd build > cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX=/beegfs/cssb/software/em/scipion/2.0/software \ > -DTIFF_LIBRARY=/beegfs/cssb/software/em/scipion/2.0/software/lib/libtiff.so -DWITH_VTK=NO -DWITH_NVCUVID=NO .. > > maybe this solves some problems. > > cheers, > wolfgang > > > ------------------------------ > *From: *"David Maluenda" <dma...@cn...> > *To: *"Mailing list for Scipion users" < > sci...@li...> > *Sent: *Monday, 18 May, 2020 19:50:30 > *Subject: *Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and > libtiff > > 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 >> > > > _______________________________________________ > 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 > |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-19 14:48:40
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Dear colleagues, I want to compare 2 models that have some differences: the same subunits but repositioned, missing structures, etc. Is there a tool in SCIPION that can: - Make a list of structure A (all components/residues). A list of elements in Structure B. - Compare and report the missing parts in structure B compared to structure A? Maybe also the differences in distances between the same helices in structure B compared to structure A? Thank you! Sincerely, Dmitry |
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From: Lugmayr, W. <w.l...@lu...> - 2020-05-19 09:12:19
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hi, here is an example of my build of opencv with scipion libtiff on centos7: ./scipion install opencv -j N cd software ln -s lib lib64 cd tmp/opencv-3.4.1 rm -rf build; mkdir build; cd build cmake -DWITH_FFMPEG=OFF -DWITH_CUDA:BOOL=ON-DWITH_LIBV4L=ON-DWITH_V4L=OFF -DCMAKE_INSTALL_PREFIX=/beegfs/cssb/software/em/scipion/2.0/software \ -DTIFF_LIBRARY=/beegfs/cssb/software/em/scipion/2.0/software/lib/libtiff.so -DWITH_VTK=NO -DWITH_NVCUVID=NO .. maybe this solves some problems. cheers, wolfgang From: "David Maluenda" <dma...@cn...> To: "Mailing list for Scipion users" <sci...@li...> Sent: Monday, 18 May, 2020 19:50:30 Subject: Re: [scipion-users] Scipion 2.0, xmipp and libs openCV and libtiff 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 [ mailto:dma...@cn... | dma...@cn... ] - (+34) 619 029 310 [ http://www.cnb.csic.es/ | CSIC - Centro Nacional de Biotecnología ] [ http://biocomputingunit.es/ | BioComputing Unit ] 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 < [ mailto:gma...@gm... | 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 < [ mailto:era...@cn... | era...@cn... ] > wrote: BQ_BEGIN Hi George, Try changing OPENCV = FALSE in the configuration file. Best, Erney Quoting George Magklaras < [ mailto:gma...@gm... | 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: > > [ [ mailto:root@gpu1 | 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 | 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: > > [ mailto:root@sekulicgpu1 | 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 > > [ [ mailto:root@sekulicgpu1 | 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 [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: David M. <dma...@cn...> - 2020-05-18 17:51:35
|
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 > |
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From: Pablo C. <pc...@cn...> - 2020-05-18 17:45:10
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Hi all, not sure about this, but it might help: Scipion uses <scipion-home>/software/lib where it compiles it's libraries...among them libtiff If you remove the one it should take system one (otherwise try a link). Then all libtiff will be the system one. Just one concern about system tiff. Scipion installs a modification of libtiff --> bigtiff, i think it coems from here: http://bigtiff.org/ Is meant to be compatible with libtiff but accepts tiff files bigger than 4GB? Regarding flagging opencv=False, you will not get optical flow and one more method from xmipp. We usually recommend that if there are compilation issues and no strong interest in xmipp OF. On 18/5/20 19:30, George Magklaras 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... <mailto:era...@cn...>> wrote: > > Hi George, > > Try changing OPENCV = FALSE in the configuration file. > > Best, > Erney > > > Quoting George Magklaras <gma...@gm... > <mailto: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 <mailto: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 <mailto: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 <mailto: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... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: George M. <gma...@gm...> - 2020-05-18 17:30:52
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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 > |
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From: Grigory S. <sha...@gm...> - 2020-05-18 17:05:02
|
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 > |
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From: Erney R. A. <era...@cn...> - 2020-05-18 16:58:01
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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 |
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From: Jose M. de la R. T. <del...@gm...> - 2020-05-18 16:53:38
|
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 > |
|
From: George M. <gma...@gm...> - 2020-05-18 16:49:48
|
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 > |
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From: Jose M. de la R. T. <del...@gm...> - 2020-05-18 16:08:19
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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 > |
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From: George M. <gma...@gm...> - 2020-05-18 15:54:39
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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 |
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From: George M. <gma...@gm...> - 2020-05-18 15:45:35
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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 |
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From: Javier V. B. D. <jav...@mc...> - 2020-05-14 15:12:14
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Hi all, For sure the methods will be in Scipion. Now we have the code in Matlab and we are porting to python. The code in Matlab will be available ASAP, the python code included in Scipion will need a little bit of more time. Best, Javier ________________________________ From: Pablo Conesa <pc...@cn...> Sent: Thursday, May 14, 2020 3:40 AM To: Pablo Conesa <sci...@li...> Subject: Re: [scipion-users] map interpretability improvement Well! Clearly there are well experience Scipion developers involved in that paper. Maybe asking them would a nice way to let them know your interest. On 14/5/20 8:53, Juha Huiskonen wrote: I believe this is the reference: https://doi.org/10.1101/2020.05.11.088013 On Thu, May 14, 2020 at 9:43 AM Carlos Oscar Sorzano <co...@cn...<mailto:co...@cn...>> wrote: Hi Dmitry, in which package are these programs? I was not aware of them. Kind regards, Carlos Oscar On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: Dear colleagues, I would like to know if the LocSpiral, LocBSharpen, LocBFactor and LocOccupancy software are available for SCIPION and is there a manual / walk-through I can use? Thank you Sincerely, Dmitry _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team |
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From: Pablo C. <pc...@cn...> - 2020-05-14 08:40:15
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Well! Clearly there are well experience Scipion developers involved in that paper. Maybe asking them would a nice way to let them know your interest. On 14/5/20 8:53, Juha Huiskonen wrote: > I believe this is the reference: https://doi.org/10.1101/2020.05.11.088013 > > On Thu, May 14, 2020 at 9:43 AM Carlos Oscar Sorzano <co...@cn... > <mailto:co...@cn...>> wrote: > > Hi Dmitry, > > in which package are these programs? I was not aware of them. > > Kind regards, Carlos Oscar > > On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: >> Dear colleagues, >> >> I would like to know if the LocSpiral, LocBSharpen, LocBFactor >> and LocOccupancy software are available for SCIPION and is there >> a manual / walk-through I can use? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Carlos O. S. <co...@cn...> - 2020-05-14 08:29:38
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Thank you very much. We will have a look. At the moment, I am not aware of these programs being accessible through Scipion, but they are made by a group who is very familiar with Scipion. Let's see what Javier says about it. Kind regards, Carlos Oscar On 5/14/20 8:57 AM, 范宏成 wrote: > Dear Carlos, > Please see this paper《Local computational methods to improve the > interpretability and analysis of cryo-EM maps》. > > Sincerely, > Hongcheng Fan > > > 范宏成 > m18...@16... > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> > > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> > 定制 > On 5/14/2020 14:41，Carlos Oscar Sorzano<co...@cn...> > <mailto:co...@cn...> wrote： > > Hi Dmitry, > > in which package are these programs? I was not aware of them. > > Kind regards, Carlos Oscar > > On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: >> Dear colleagues, >> >> I would like to know if the LocSpiral, LocBSharpen, LocBFactor >> and LocOccupancy software are available for SCIPION and is there >> a manual / walk-through I can use? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> _______________________________________________ >> 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 |
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From: Juha H. <juh...@he...> - 2020-05-14 07:14:20
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I believe this is the reference: https://doi.org/10.1101/2020.05.11.088013 On Thu, May 14, 2020 at 9:43 AM Carlos Oscar Sorzano <co...@cn...> wrote: > Hi Dmitry, > > in which package are these programs? I was not aware of them. > > Kind regards, Carlos Oscar > On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: > > Dear colleagues, > > I would like to know if the LocSpiral, LocBSharpen, LocBFactor and > LocOccupancy software are available for SCIPION and is there a manual / > walk-through I can use? > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: 范宏成 <187...@16...> - 2020-05-14 06:57:53
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Dear Carlos, Please see this paper《Local computational methods to improve the interpretability and analysis of cryo-EM maps》. Sincerely, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 5/14/2020 14:41，Carlos Oscar Sorzano<co...@cn...> wrote： Hi Dmitry, in which package are these programs? I was not aware of them. Kind regards, Carlos Oscar On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: Dear colleagues, I would like to know if the LocSpiral, LocBSharpen, LocBFactor and LocOccupancy software are available for SCIPION and is there a manual / walk-through I can use? Thank you Sincerely, Dmitry _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: 范宏成 <187...@16...> - 2020-05-14 06:55:47
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Dear Carlos, Please see this paper《Local computational methods to improve the interpretability and analysis of cryo-EM maps》. Sincerely, Hongcheng Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 5/14/2020 14:41，Carlos Oscar Sorzano<co...@cn...> wrote： Hi Dmitry, in which package are these programs? I was not aware of them. Kind regards, Carlos Oscar On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: Dear colleagues, I would like to know if the LocSpiral, LocBSharpen, LocBFactor and LocOccupancy software are available for SCIPION and is there a manual / walk-through I can use? Thank you Sincerely, Dmitry _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2020-05-14 06:42:11
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Hi Dmitry, in which package are these programs? I was not aware of them. Kind regards, Carlos Oscar On 5/14/20 7:49 AM, Dmitry A. Semchonok wrote: > Dear colleagues, > > I would like to know if the LocSpiral, LocBSharpen, LocBFactor and > LocOccupancy software are available for SCIPION and is there a manual > / walk-through I can use? > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-14 05:49:08
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Dear colleagues, I would like to know if the LocSpiral, LocBSharpen, LocBFactor and LocOccupancy software are available for SCIPION and is there a manual / walk-through I can use? Thank you Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2020-05-06 08:02:27
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Thanks Dmitry for the feedback. We might think about making these easier for the future, either to use images in presentation/publication or to share with collaborators. Best, Jose Miguel On Wed, May 6, 2020 at 9:59 AM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > Thank you all for your suggestions! > > My problem indeed was connected with the memory since the dataset was > ~8000 particles. > > > > The solution was found. > > If you need to get an stk file out of your particles (the number doesn't > matter much), you can use *relion-export particles* protocol in SCIPION. > > There you have several options. You can make 1 mrc stack file that Fiji > (ImageJ) can easily read. > > > > I hope this helps. > > > > Sincerely, > > Dmitry > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Jose Miguel de la Rosa Trevin <del...@gm...> > *Sent: *Tuesday, May 5, 2020 6:13 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] java error opening the extraction particle > file with built-in ImageJ > > > > Hi Dmitry, > > > > Depending on how many particles do you have and their dimensions, ImageJ > can have some memory issues if the dataset is too big to be read into RAM > memory. > > > > Hope this helps, > > Best, > > Jose Miguel > > > > > > > > > > On Tue, May 5, 2020 at 5:33 PM Dmitry A. Semchonok <sem...@gm...> > wrote: > > Dear Grigory, > > > > Yes (please see the attachment), so > > > > Relion particles extraction protocol (analyze)à then see the particles > gallery (open with imageJ) à then the program crashes with the java error. > > > > > > Thank you! > > > > Sincerely, > > Dmitry > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Grigory Sharov <sha...@gm...> > *Sent: *Tuesday, May 5, 2020 1:41 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] java error opening the extraction particle > file with built-in ImageJ > > > > Hi, > > > > Could you be more specific? What is relion extraction file? Sqlite? Mrcs? > Star ? What error? > > > > > > > > On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <sem...@gm...> > wrote: > > Dear colleagues, > > > > While opening the relion-extraction file with ImageJ, I’m getting the java > error. > > Are there any options to open this extracted particle file directly from > the folder with ImageJ? > > I want to do stk from the extracted particles. > > > > Sincerely, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > _______________________________________________ > 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 > |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-06 07:59:43
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:Wingdings; panose-1:5 0 0 0 0 0 0 0 0 0;} @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><div><p class=MsoNormal><span lang=EN-GB>Dear colleagues, <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Thank you all for your suggestions! <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>My problem indeed was connected with the memory since the dataset was ~8000 particles.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>The solution was found.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>If you need to get an stk file out of your particles (the number doesn't matter much), you can use <b>relion-export particles</b> protocol in SCIPION. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>There you have several options. You can make 1 mrc stack file that Fiji (ImageJ) can easily read.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>I hope this helps.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:del...@gm...">Jose Miguel de la Rosa Trevin</a><br><b>Sent: </b>Tuesday, May 5, 2020 6:13 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] java error opening the extraction particle file with built-in ImageJ</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Dmitry, </p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Depending on how many particles do you have and their dimensions, ImageJ can have some memory issues if the dataset is too big to be read into RAM memory.</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Hope this helps,</p></div><div><p class=MsoNormal>Best,</p></div><div><p class=MsoNormal>Jose Miguel</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Tue, May 5, 2020 at 5:33 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear Grigory,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Yes (please see the attachment), so</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Relion particles extraction protocol (analyze)<span style='font-family:Wingdings'>à</span> then see the particles gallery (open with imageJ) <span style='font-family:Wingdings'>à</span> then the program crashes with the java error.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you!</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:sha...@gm..." target="_blank">Grigory Sharov</a><br><b>Sent: </b>Tuesday, May 5, 2020 1:41 PM<br><b>To: </b><a href="mailto:sci...@li..." target="_blank">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] java error opening the extraction particle file with built-in ImageJ</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi,</p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Could you be more specific? What is relion extraction file? Sqlite? Mrcs? Star ? What error? </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <<a href="mailto:sem...@gm..." target="_blank">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear colleagues,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>While opening the relion-extraction file with ImageJ, I’m getting the java error.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Are there any options to open this extracted particle file directly from the folder with ImageJ?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I want to do stk from the extracted particles.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Jose M. de la R. T. <del...@gm...> - 2020-05-05 16:13:31
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Hi Dmitry, Depending on how many particles do you have and their dimensions, ImageJ can have some memory issues if the dataset is too big to be read into RAM memory. Hope this helps, Best, Jose Miguel On Tue, May 5, 2020 at 5:33 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear Grigory, > > > > Yes (please see the attachment), so > > > > Relion particles extraction protocol (analyze)à then see the particles > gallery (open with imageJ) à then the program crashes with the java error. > > > > > > Thank you! > > > > Sincerely, > > Dmitry > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Grigory Sharov <sha...@gm...> > *Sent: *Tuesday, May 5, 2020 1:41 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] java error opening the extraction particle > file with built-in ImageJ > > > > Hi, > > > > Could you be more specific? What is relion extraction file? Sqlite? Mrcs? > Star ? What error? > > > > > > > > On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <sem...@gm...> > wrote: > > Dear colleagues, > > > > While opening the relion-extraction file with ImageJ, I’m getting the java > error. > > Are there any options to open this extracted particle file directly from > the folder with ImageJ? > > I want to do stk from the extracted particles. > > > > Sincerely, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > _______________________________________________ > 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 > |
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