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Re: [scipion-users] Antw: Re: Antw: Re: Antw: Re: SCIPION installation error -- xmipp: Something went wrong (SEE ERRORS ABOVE) when running:
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From: Grigory S. <sha...@gm...> - 2021-05-20 18:55:01
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I'm running out of options.. Can you try to downgrade libtiff inside scipion conda environment? (conda install libtiff=4.1.0) 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 Thu, May 20, 2021 at 7:19 PM Christian Tüting < chr...@bi...> wrote: > Hi, > > I tried yum install libtiff libtiff-devel before, but yum says, "nothing > to do". But, yum install libtiff* helped to install the missing packages > somehow. > > So the error disappers from ./xmipp_config. There are some path missing > in PATH, but alternatives are found so I guess this is fine (see output > below). > > But ./xmipp check_config still fails. > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp config > 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/user/Data/Software/miniconda/envs/scipion3/include > OpenCV not found > rm -v xmipp_test_opencv* > 'mpirun' and 'mpiexec' not found in the PATH > Alternative found at '/usr/lib64/openmpi/bin'. > Please, press [return] to use it or type a path where to locate it: > -> /usr/lib64/openmpi/bin > 'mpicc' not found in the PATH > Alternative found at '/usr/lib64/openmpi/bin'. > Please, press [return] to use it or type a path where to locate it: > -> /usr/lib64/openmpi/bin > 'mpicxx' not found in the PATH > Alternative found at '/usr/lib64/openmpi/bin'. > Please, press [return] to use it or type a path where to locate it: > -> /usr/lib64/openmpi/bin > Java detected at: /home/user/Data/Software/miniconda/envs/scipion3 > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > Alternative found at '/usr/local/cuda/bin'. > Please, press [return] to use it or type a path where to locate it: > -> /usr/local/cuda/bin > CUDA-10.1.243 detected. > CUDA-8.0 is recommended. > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > Configuration completed..... > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp > check_config > 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/user/Data/Software/miniconda/envs/scipion3/include > -I/home/user/Data/Software/miniconda/envs/scipion3/include/python3.8 > > -I/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/numpy/core/include > g++ -L/home/user/Data/Software/miniconda/envs/scipion3/lib > xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 > -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > /usr/bin/ld: warning: libwebp.so.7, needed by > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so, not > found (try using -rpath or -rpath-link) > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPPictureImportRGB' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPInitDecBufferInternal' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPPictureFree' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPIAppend' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPIDecGetRGB' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPINewDecoder' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPPictureImportRGBA' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPConfigInitInternal' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPEncode' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPValidateConfig' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPPictureInitInternal' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPFreeDecBuffer' > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > undefined reference to `WebPIDelete' > collect2: error: ld returned 1 exit status > Check the LINKERFORPROGRAMS, LINKFLAGS and LIBDIRFLAGS > Cannot compile > Possible solutiolibhdf5-dev libopencv-dev python3-dev python3-numpy > python3-scipy > python3-mpi4py > In Manjaro: sudo pacman -Syu install hdf5 python3-numpy python3-scipy > --noconfirm > Please, see > ' > https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources.html#step-2-dependencies > ' > for more information about libraries dependencies. > Remember to re-run './xmipp config' after installing libraries in order > to take into account the new system configuration. > rm xmipp_test_main* > Check failed! Something wrong with the configuration. > > > It's still looking for libwebp.so.7, but this is present: > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ls -ltr > ../../../../miniconda/envs/scipion3/lib/libwebp.so* > -rwxrwxrwx. 2 user user 598608 Feb 1 16:15 > ../../../../miniconda/envs/scipion3/lib/libwebp.so.7.1.1 > lrwxrwxrwx. 1 user user > 16 May 20 10:07 ../../../../miniconda/envs/scipion3/lib/libwebp.so.7 -> > libwebp.so.7.1.1 > lrwxrwxrwx. 1 user user > 16 May 20 10:07 ../../../../miniconda/envs/scipion3/lib/libwebp.so -> > libwebp.so.7.1.1 > > Best > > Christian > > > >>> Grigory Sharov <sha...@gm...> 20.05.21 19.54 Uhr >>> > Hi Christian, > > I guess xmipp script still cannot recognize libtiff that it has > installed. > I can reproduce your problem on my machine. But I have a system library > installed. > > So, the easiest solution is to install libtiff / libtiff-devel using > your > package manager (yum) > > 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 Thu, May 20, 2021 at 6:34 PM Christian Tüting < > chr...@bi...> wrote: > > > Hi, > > > > it fails with similar errors like in the automatic installation: > > > > > > (scipion3) [user@dataanalysisserver1 scipion3]$ ldd > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so > > linux-vdso.so.1 => (0x00007ffe872c3000) > > libwebp.so.7 => > > /home/user/Data/Software/miniconda/envs/scipion3/lib/./libwebp.so.7 > > (0x00007f8f7253a000) > > libzstd.so.1 => > > /home/user/Data/Software/miniconda/envs/scipion3/lib/./libzstd.so.1 > > (0x00007f8f7246e000) > > liblzma.so.5 => > > /home/user/Data/Software/miniconda/envs/scipion3/lib/./liblzma.so.5 > > (0x00007f8f723fe000) > > libjpeg.so.9 => > > /home/user/Data/Software/miniconda/envs/scipion3/lib/./libjpeg.so.9 > > (0x00007f8f721c2000) > > libz.so.1 => > > /home/user/Data/Software/miniconda/envs/scipion3/lib/./libz.so.1 > > (0x00007f8f7244d000) > > libm.so.6 => /lib64/libm.so.6 (0x00007f8f71ea4000) > > libc.so.6 => /lib64/libc.so.6 (0x00007f8f71ad6000) > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8f718ba000) > > librt.so.1 => /lib64/librt.so.1 (0x00007f8f716b2000) > > /lib64/ld-linux-x86-64.so.2 (0x00007f8f72427000) > > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp > config > > Configuring ----------------------------------------- > > gcc detected > > 'libtiff' not found in the system > > 'libtiff' dependency not found. Do you want to install it using conda? > > [YES/no] Y > > Trying to install libtiff with conda > > conda activate scipion3 ; conda install libtiff -y -c defaults > > CommandNotFoundError: Your shell has not been properly configured to > use > > 'conda activate'. > > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > > - bash > > - fish > > - tcsh > > - xonsh > > - zsh > > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > > 'conda init'. > > Collecting package metadata (current_repodata.json): ...working... > done > > Solving environment: ...working... done > > # All requested packages already installed. > > 'libtiff' installed in conda environ 'scipion3'. > > g++ -c -w -mtune=native -march=native -std=c++11 -O3 > > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I..> 'mpirun' and > 'mpiexec' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > 'mpicc' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > 'mpicxx' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > Java detected at: /home/user/Data/Software/miniconda/envs/scipion3 > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > > Alternative found at '/usr/local/cuda/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/local/cuda/bin > > CUDA-10.1.243 detected. > > CUDA-8.0 is recommended. > > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > > Configuration completed..... > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp > config > > Configuring ----------------------------------------- > > gcc detected > > 'libtiff' not found in the system > > 'libtiff' dependency not found. Do you want to install it using conda? > > [YES/no] > > Trying to install libtiff with conda > > conda activate scipion3 ; conda install libtiff -y -c defaults > > CommandNotFoundError: Your shell has not been properly configured to > use > > 'conda activate'. > > To initialize your shell, run > > $ conda init <SHELL_NAME> > > Currently supported shells are: > > - bash > > - fish > > - tcsh > > - xonsh > > - zsh > > - powershell > > See 'conda init --help' for more information and options. > > IMPORTANT: You may need to close and restart your shell after running > > 'conda init'. > > Collecting package metadata (current_repodata.json): ...working... > done > > Solving environment: ...working... done > > # All requested packages already installed. > > 'libtiff' installed in conda exmipp_test_opencv.cpp -o > xmipp_test_opencv.o > > -I../ > > -I/home/user/Data/Software/miniconda/envs/scipion3/include > > OpenCV not found > > rm -v xmipp_test_opencv* > > 'mpirun' and 'mpiexec' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > 'mpicc' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > 'mpicxx' not found in the PATH > > Alternative found at '/usr/lib64/openmpi/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/lib64/openmpi/bin > > Java detected at: /home/user/Data/Software/miniconda/envs/scipion3 > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN) > > Alternative found at '/usr/local/cuda/bin'. > > Please, press [return] to use it or type a path where to locate it: > > -> /usr/local/cuda/bin > > CUDA-10.1.243 detected. > > CUDA-8.0 is recommended. > > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'. > > Configuration completed..... > > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp > > check_config > > 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/user/Data/Software/miniconda/envs/scipion3/include > > -I/home/user/Data/Software/miniconda/envs/scipion3/include/python3.8 > > > > > > -I/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/numpy/core/include > > g++ -L/home/user/Data/Software/miniconda/envs/scipion3/lib > > xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5 > > -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread > > /usr/bin/ld: warning: libwebp.so.7, needed by > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so, not > > found (try using -rpath or -rpath-link) > > /home/user/Data/Software/miniconda/envs/scipion3/lib/lib> > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPInitDecBufferInternal' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPPictureFree' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPIAppend' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPIDecGetRGB' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPINewDecoder' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPPictureImportRGBA' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPConfigInitInternal' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPEncode' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPValidateConfig' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPPictureInitInternal' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPFreeDecBuffer' > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so: > > undefined reference to `WebPIDelete' > > collect2: error: ld returned 1 exit status > > Check the LINKERFORPROGRAMS, LINKFLAGS and LIBDIRFLAGS > > Cannot compile > > Possible solutions > > In Ubuntu: sudo apt-get -y install libsqlite3-dev libfftw3-dev > > libhdf5-dev libopencv-dev python3-dev python3-numpy python3-scipy > > python3-mpi4py > > In Manjaro: sudo pacman -Syu install hdf5 python3-numpy python3-scipy > > --noconfirm > > Please, see > > ' > > > > https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources.html#step-2-dependencies > > ' > > for more information about libraries dependencies. > > Remember to re-run './xmipp config' after installing libraries in > order > > to take into account the new system configuration. > > rm xmipp_test_main* > > Check failed! Trying to install libtiff with conda > > conda activate scipion3 ; conda install libtiff -y -c defaults > > CommandNotFoundError: Your shell has not been properly configured to > use > > 'conda activate'. > > > > Because I can run it manually without errors: > > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ conda > activate > > scipion3 ; conda install libtiff -y -c defaults > > Collecting package metadata (current_repodata.json): done > > Solving environment: done > > # All requested packages already installed. > > > > > > And also, thanks already in advance. I really appreciate your help. > > > > Best Christian > > > > > > > > >>> Grigory Sharov <sha...@gm...> 20.05.21 18.12 Uhr >>> > > Hi, > > > > Let's try manual installation: > > > > conda activate scipion3 > > > ldd /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so > -> > > > check output for errors > > > export SCIPION_HOME="/home/user/Data/Software/scipion3/" > > > cd /home/user/Data/Software/scipion3/software/em/xmippSrc-v3.20.07 > > > ./xmipp config -> check if all is correct in xmipp.conf > > > ./xmipp check_config -> check for errors > > > ./xmipp compileAndInstall N=4 && ln -srfn build > > > /home/user/Data/Software/scipion3/software/em/xmipp && cd - && touch > > > installation_finished && rm bindings_linked 2> /dev/null > > > > > > You can post output errors from these commands here. > > > > 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 Thu, May 20, 2021 at 4:49 PM Christian Tüting < > > chr...@bi...> wrote: > > > > > Hi all, > > > > > > Dmitrys collegue here. > > > > > > yes we have the library in the scipion3 env: > > > > > > > > > [user@dataanalysisserver1 lib]$ ls -d $PWD/libwebp.so.7 > > > > > > > > > /home/user/Data/Software> > [92m conda activate scipion3 ; conda > install fftw -y -c defaults[0m > > > CommandNotFoundError: Your shell has not been properly configured to > > use > > > 'conda activate'. > > > > > > When I am coping this command, it runs without any issue. > > > > > > > > > Thanks for your help. > > > > > > best > > > Christian > > > > > > > > > > > > >>> Grigory Sharov <sha...@gm...> 20.05.21 16.39 Uhr >>> > > > Hi, > > > > > > do you have libwebp.so.7 in > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/ ? > > > > > > 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 Thu, May 20, 2021 at 3:00 PM Dmitry Semchonok > <Sem...@gm...> > > > wrote: > > > > > > > Dear colleagues, > > > > > > > > We reinstalled the centos 7 on our server as well as miniconda. > > > > > > > > > > > > > > > > The core was installed correctly but during xmipp installation > some > > error > > > > appeared. Please have a look on the file attached. > > > > > > > > > > > > > > > > Could you please advice how to proceed? > > > > > > > > > > > > > > > > > > > > > > > > > > > > Thank you in advance. > > > > > > > > > > > > Sincerely, > > > > Dmitry and > Christian_______________________________________________ > > > > 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 > |
