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[scipion-users] get problem during the compilation of xmipp (hdf5 linking error)
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From: 王涛 <wt...@ma...> - 2020-10-03 18:48:56
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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. |
