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Re: [scipion-users] get problem during the compilation of xmipp (hdf5 linking error)
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From: Jorge <jji...@cn...> - 2020-10-05 07:35:29
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Hello Tao, We've been updating the documentation these days. The following link contains detailed information and instructions about how to install Scipion3 in different Linux distributions, and may solve your hdf5 issue. https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html Please have a look and in case the problem remains, do not hesitate to contact us. We'll be pleased to help you. Have a good day! Jorge On 10/3/20 8:48 PM, 王涛 wrote: > hello everyone, > I got a problem while installing scipion3 with miniconda. > I installed conda at first,then: > > pip install --user scipion-installer python3 -m scipioninstaller > /path/where/you/want/scipion -j 4 > then program failed in compiling module 'xmipp',and log showed that there may be some errors in linking > hdf5 library,but I have hdf5 installed by conda with default channel. There is another warning about > libjpeg.so at /usr/lib64 in error logs, so I think program may not find library in .scipion3env as normal,and > I don't know which file should I configure.(maybe xmipp.conf or SConscript or SConstruct?) > (.scipion3env) [raozh@mgmt01 scipion3]$ conda list hdf5 > # packages in environment at /home/raozh/wtao/conda/miniconda/envs/.scipion3env: > # > # Name Version Build Channel > hdf5 1.10.7 hb1b8bf9_0 > Anybody got any idea about this? > Thanks for any help. > Tao Wang > Ph.D candidate, > Tsinghua University > here are logs: > (.scipion3env) [raozh@mgmt01 scipion3]$ python3 -m scipioninstaller /home/raozh/wtao/scipion3/ -j 4 > conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass --venv . > WARNING: A conda environment already exists at '/home/raozh/wtao/conda/miniconda/envs/.scipion3env' > Remove existing environment (y/[n])? > > > CondaSystemExit: Exiting. > > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (3.2.2) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (7.1.2) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (5.7.0) > Requirement already satisfied: requests<=2.23.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (2.23.0) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.18.4) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow) (1.2.0) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (1.2.0) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (3.0.4) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2020.6.20) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests<=2.23.0->scipion-pyworkflow) (1.25.10) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0) > Requirement already satisfied: scipion-app in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (3.0.4) > Requirement already satisfied: scipion-em in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (3.0.3) > Requirement already satisfied: outdated==0.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-app) (0.2.0) > Requirement already satisfied: scipion-pyworkflow in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (3.0.4) > Requirement already satisfied: biopython==1.76 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em->scipion-app) (1.76) > Requirement already satisfied: littleutils in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (0.2.2) > Requirement already satisfied: requests in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from outdated==0.2.0->scipion-app) (2.23.0) > Requirement already satisfied: configparser<=5.0.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.0.0) > Requirement already satisfied: pillow<=7.1.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (7.1.2) > Requirement already satisfied: numpy<=1.18.4 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.18.4) > Requirement already satisfied: psutil<=5.7.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (5.7.0) > Requirement already satisfied: matplotlib<=3.2.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (3.2.2) > Requirement already satisfied: bibtexparser<=1.2.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: idna<3,>=2.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2.10) > Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (1.25.10) > Requirement already satisfied: certifi>=2017.4.17 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (2020.6.20) > Requirement already satisfied: chardet<4,>=3.0.2 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from requests->outdated==0.2.0->scipion-app) (3.0.4) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7) > Requirement already satisfied: python-dateutil>=2.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1) > Requirement already satisfied: cycler>=0.10 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0) > Requirement already satisfied: kiwisolver>=1.0.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.2.0) > Requirement already satisfied: future>=0.16.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2) > Requirement already satisfied: six>=1.5 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from python-dateutil>=2.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.15.0) > Scipion v3.0.4 () devel > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window) > > > Building scipion-em-xmipp ... > /home/raozh/wtao/conda/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-xmipp==20.7rc1 > Requirement already satisfied: scipion-em-xmipp==20.7rc1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (20.7rc1) > Requirement already satisfied: scons in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (4.0.1) > Requirement already satisfied: plotter in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (1.3.17) > Requirement already satisfied: joblib in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.17.0) > Requirement already satisfied: scikit-learn==0.22.1 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.22.1) > Requirement already satisfied: peppercorn in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scipion-em-xmipp==20.7rc1) (0.6) > Requirement already satisfied: setuptools in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scons->scipion-em-xmipp==20.7rc1) (49.6.0.post20200925) > Requirement already satisfied: numpy>=1.11.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.18.4) > Requirement already satisfied: scipy>=0.17.0 in /home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages (from scikit-learn==0.22.1->scipion-em-xmipp==20.7rc1) (1.5.2) > Done (0.78 seconds) > Building xmippSrc-3.20.07rc ... > Skipping command: wget -nv -c -O /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07rc.tgz > mv -v /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz.part /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.20.07rc.tgz > All targets exist. > cd /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null > Configuring ----------------------------------------- > gcc detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include > OpenCV not found > rm -v xmipp_test_opencv* > > 'mpirun' and 'mpiexec' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicc' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > > 'mpicxx' not found in the PATH > Using '/usr/lib64/openmpi/bin'. > Java detected at: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64 > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > Using '/usr/local/cuda/bin'. > CUDA-10.1.168 detected. > CUDA-8.0 is recommended. > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > g++ 4.8.5 detected > g++ -c -w -mtune=native -march=native -std=c++11 -O3 xmipp_test_main.cpp -o xmipp_test_main.o -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include/python3.8 -I/home/raozh/wtao/c > onda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/numpy/core/include g++ -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_test_main* > Checking MPI configuration ... > /usr/lib64/openmpi/bin/mpicxx -c -w -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include -mtune=native -march=native -std=c++11 -O3 xmipp_mpi_test_main.cpp -o xmipp_mpi_test_main.o > /usr/lib64/openmpi/bin/mpicxx -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib xmipp_mpi_test_main.o -o xmipp_mpi_test_main -lfftw3 -lfftw3_threads -lhdf5 -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > rm xmipp_mpi_test_main* > /usr/lib64/openmpi/bin/mpirun -np 2 echo ' > This sentence should be printed 2 times if mpi runs fine.' > > This sentence should be printed 2 times if mpi runs fine. > > This sentence should be printed 2 times if mpi runs fine. > Checking Java configuration... > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/bin/javac Xmipp.java > rm Xmipp.java Xmipp.class > g++ -c -w -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include -I/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.161-2.b14.el7.x86_64/include/linux -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_jni_test.cpp -o xmipp_jn > i_test.o rm xmipp_jni_test* > Checking CUDA configuration ... > /usr/local/cuda-10.1/bin/nvcc -c -w --x cu -D_FORCE_INLINES -Xcompiler -fPIC -ccbin g++ -std=c++11 --expt-extended-lambda -gencode=arch=compute_30,code=compute_30 -gencode=arch=compute_35,code=compute_35 -gencode=arch=compute_50,code=compute_50 -gencod > e=arch=compute_60,code=compute_60 -gencode=arch=compute_61,code=compute_61 -I../ -I/home/raozh/wtao/conda/miniconda/envs/.scipion3env/include xmipp_cuda_test.cpp -o xmipp_cuda_test.o /usr/local/cuda-10.1/bin/nvcc -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > g++ -L/usr/local/cuda-10.1/targets/x86_64-linux/lib -L/usr/local/cuda-10.1/targets/x86_64-linux/lib/stubs xmipp_cuda_test.o -o xmipp_cuda_test -lcudart -lcublas -lcufft -lcurand -lcusparse -lnvToolsExt > rm xmipp_cuda_test* > Setting VERIFIED=True > Building Dependencies ------------------------------------- > make all > mkdir -p build/ > nvcc --cudart static -shared -link -Wno-deprecated-gpu-targets -o build/libcuFFTAdvisor.so obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTran > sform.o obj/sizeOptimizer.o obj/main.omkdir -p build/ > nvcc -o build/cuFFTAdvisor obj/benchmarkResult.o obj/inputParser.o obj/transform.o obj/advisor.o obj/validator.o obj/cudaAsserts.o obj/transformGenerator.o obj/benchmarker.o obj/generalTransform.o obj/sizeOptimizer.o obj/main.o -lcufft -Wno-deprecated-g > pu-targets cp src/cuFFTAdvisor/build/libcuFFTAdvisor.so src/xmipp/lib/ > Compiling ------------------------------------------- > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmippCore.so' is up to date. > scons: `lib/xmippCore.so' is up to date. > scons: done building targets. > scons -j4 > scons: Reading SConscript files ... > scons: done reading SConscript files. > scons: Building targets ... > scons: `lib/libXmipp.so' is up to date. > scons: `lib/_swig_frm.so' is up to date. > scons: `lib/libXmippCuda.a' is up to date. > scons: `lib/libXmippInterfaceCuda.so' is up to date. > scons: `lib/libXmippParallelCuda.so' is up to date. > scons: `lib/libXmippParallel.so' is up to date. > g++ -o bin/xmipp_volume_from_pdb applications/programs/volume_from_pdb/volume_from_pdb_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhd > f5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_idr_xray_tomo applications/programs/idr_xray_tomo/idr_xray_tomo_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib -lXmipp -lhdf5 -lh > df5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_image_separate_objects applications/programs/image_separate_objects/image_separate_objects_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCoreg++ -o bin/xmipp_pdb_reduce_pseudoatoms applications/programs/pdb_reduce_pseudoatoms/pdb_reduce_pseudoatoms_main.o -L/home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib -Llib -Llib -L/home/raozh/wtao/conda/miniconda/envs/.scipion > 3env/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore/usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_volume_from_pdb] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_idr_xray_tomo] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_image_separate_objects] Error 1 > /usr/bin/ld: warning: libjpeg.so.62, needed by /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/libtiff.so, may conflict with libjpeg.so.9 > lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' > lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' > /home/raozh/wtao/scipion3/software/em/xmippSrc-v3.20.07rc/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' > collect2: error: ld returned 1 exit status > scons: *** [bin/xmipp_pdb_reduce_pseudoatoms] Error 1 > scons: building terminated because of errors. > > Some error occurred during the compilation of 'xmipp' ('bin/xmipp_pdb_reduce_pseudoatoms'). > > Traceback (most recent call last): > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 449, in <module> > main() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 292, in main > installPluginMethods() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 231, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin > environment.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute > self._executeTargets(targetList) > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets > tgt.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 220, in execute > command.execute() > File "/home/raozh/wtao/conda/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 160, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scip > ion3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null')Error at main: target '/home/raozh/wtao/scipion3/software/em/xmipp/bin/xmipp_reconstruct_significant' not built (after running 'cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp compileAndInstall N=4 && ln -srf build /home/raozh/wtao/scipi > on3/software/em/xmipp && cd - && touch installation_finished && rm bindings_linked 2> /dev/null') > Something went wrong running: > eval "$(/home/raozh/wtao/conda/miniconda/condabin/conda shell.bash hook)" && > conda create -n .scipion3env python=3 && > conda activate .scipion3env && > cd /home/raozh/wtao/scipion3 && > mkdir -p software/lib && > mkdir -p software/bindings && > mkdir -p software/em && > export SCIPION_HOME=/home/raozh/wtao/scipion3 && > pip install scipion-pyworkflow && > pip install scipion-app && > python -m scipion installp -p scipion-em-xmipp -j 4 > Installation cancelled. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
