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Re: [scipion-users] scipion3 installation in Centos7
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From: Grigory S. <sha...@gm...> - 2021-11-24 12:43:51
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Hi, looking at (base) [fanhc@localhost scipion]$ ./scipion3 installp -p scipion-em-xmipp -j 12 | tee -a install.log I'm 99% sure you have eman activated. Eman installer does a horrible thing by modifying bashrc by default so that it's always activated. You should not install scipion into eman environment 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 Wed, Nov 24, 2021 at 12:40 PM Alberto Garcia Mena < alb...@cn...> wrote: > Hello 范宏成, > > Please be sure you have activate conda enviroment. > > Follow the steps described here > <https://scipion-em.github.io/docs/scipion3_instalation/docs/scipion-modes/install-from-sources.html> > : > > *sudo yum install gcc gcc-c++ openmpi-devel > export PATH=$PATH:/usr/lib64/openmpi/bin/:/usr/local/cuda/bin > conda activate > pip install --user scipion-installer > python3 -m scipioninstaller /path/where/you/want/scipion -j 4 > * > > and for the xmipp plugin, follow this steps Installing Xmipp on Centos 7 > <https://github.com/I2PC/xmipp/wiki/Installing-Xmipp-on-CentOS-7-9.2009> > > Thanks > > > On 24/11/21 12:56, 范宏成 wrote: > > Hi all, > I recently intalled the scipion3 in my workstation(Cenos7) I faced the > followting problems. How to fix it? Thank you! > Hongcheng Fan > > (base) [fanhc@localhost scipion]$ ./scipion3 installp -p scipion-em-xmipp > -j 12 | tee -a install.log > Collecting scipion-em-xmipp==21.9.0 > Using cached scipion_em_xmipp-21.9.0-py3-none-any.whl > Collecting scons > Using cached SCons-4.3.0-py3-none-any.whl (4.2 MB) > Collecting plotter > Using cached plotter-1.3.19-py3-none-any.whl (11 kB) > Collecting scikit-learn==0.22.1 > Using cached scikit_learn-0.22.1-cp38-cp38-manylinux1_x86_64.whl (7.0 MB) > Collecting joblib > Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB) > Collecting peppercorn > Using cached peppercorn-0.6-py3-none-any.whl (4.8 kB) > Collecting PyWavelets > Using cached > PyWavelets-1.2.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (6.3 > MB) > Collecting scipy>=0.17.0 > Using cached > scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 > MB) > Requirement already satisfied: numpy>=1.11.0 in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from > scikit-learn==0.22.1->scipion-em-xmipp==21.9.0) (1.18.4) > Requirement already satisfied: setuptools in > /data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages (from > scons->scipion-em-xmipp==21.9.0) (58.0.4) > Installing collected packages: scipy, joblib, scons, scikit-learn, > PyWavelets, plotter, peppercorn, scipion-em-xmipp > Successfully installed PyWavelets-1.2.0 joblib-1.1.0 peppercorn-0.6 > plotter-1.3.19 scikit-learn-0.22.1 scipion-em-xmipp-21.9.0 scipy-1.7.2 > scons-4.3.0 > Configuring ----------------------------------------- > gcc detected > g++ found in /bin/g++ > g++ found in /bin/g++ > 'libfftw3' not found in the system > Trying to install fftw with conda > conda activate scipion3 ; conda install fftw -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 (repodata.json): ...working... done > Solving environment: ...working... > The environment is inconsistent, please check the package plan carefully > The following packages are causing the inconsistency: > > - defaults/linux-64::libstdcxx-ng==9.3.0=hd4cf53a_17 > - defaults/linux-64::libgcc-ng==9.3.0=h5101ec6_17 > - defaults/linux-64::libffi==3.3=he6710b0_2 > - defaults/linux-64::ncurses==6.3=h7f8727e_2 > - defaults/linux-64::openssl==1.1.1l=h7f8727e_0 > - defaults/linux-64::xz==5.2.5=h7b6447c_0 > - defaults/linux-64::zlib==1.2.11=h7b6447c_3 > - defaults/linux-64::readline==8.1=h27cfd23_0 > - defaults/linux-64::tk==8.6.11=h1ccaba5_0 > - defaults/linux-64::sqlite==3.36.0=hc218d9a_0 > - defaults/linux-64::python==3.8.12=h12debd9_0 > - defaults/linux-64::certifi==2021.10.8=py38h06a4308_0 > - defaults/noarch::wheel==0.37.0=pyhd3eb1b0_1 > - defaults/linux-64::setuptools==58.0.4=py38h06a4308_0 > - defaults/linux-64::pip==21.2.4=py38h06a4308_0 > done > /bin/sh: line 1: 25730 Segmentation fault (core dumped) conda install > fftw -y -c defaults > CUDA-8.0.44 detected. > CUDA-10.2 is recommended. > Checking for compatible GCC to be used with your CUDA > No valid compiler found. Skipping CUDA compilation. > To manually set the compiler, export CXX_CUDA=/path/to/requested_compiler' > and run again 'xmipp config'. > 'mpirun' detected. > 'mpicc' detected. > 'mpicxx' detected. > Java detected at: > /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.292.b10-1.el7_9.x86_64 > Matlab detected at /opt/Matlab_R2017b/bin > > Do you want to build tests [yes/NO] False > Configuration completed..... > Checking configuration ------------------------------ > Checking compiler configuration ... > Detected /bin/g++ in version 4.8.5. > Version 6.0 or higher is required. > Traceback (most recent call last): > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/data1/fanhc/miniconda3/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > Error at main: target > '/data3/fanhc/scipion/software/em/xmipp/bin/xmipp_reconstruct_significant' > not built (after running 'cd . && ./xmipp config noAsk && ./xmipp > check_config && ./xmipp compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null') > > Scipion v3.0.9 - Eugenius > Building scipion-em-xmipp ... > /data1/fanhc/miniconda3/envs/scipion3/bin/python -m pip install > scipion-em-xmipp==21.9.0 > Done (12.35 seconds) > > >>> WARNING: Image library not found! > > Please install Xmipp to get full functionality. > (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin > manager window) > > > Building xmippSrc-3.21.09.0 ... > Skipping command: wget -nv -c -O > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.21.09.0.tgz > mv -v /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz.part > /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0.tgz > All targets exist. > Skipping command: tar -xf xmippSrc-v3.21.09.0.tgz > All targets exist. > cd /data3/fanhc/scipion/software/em/xmippSrc-v3.21.09.0 > cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp > compileAndInstall N=12 && ln -srfn build > /data3/fanhc/scipion/software/em/xmipp && cd - && touch > installation_finished && rm bindings_linked 2> /dev/null > (base) [fanhc@localhost scipion]$ ls > config install.log scipion3 software > (base) [fanhc@localhost scipion]$ gedit install.log > > (gedit:25963): GLib-GIO-CRITICAL **: 04:18:19.895: g_dbus_proxy_new_sync: > assertion 'G_IS_DBUS_CONNECTION (connection)' failed > > (gedit:25963): dconf-WARNING **: 04:18:19.912: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:19.934: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.127: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > (gedit:25963): dconf-WARNING **: 04:18:20.128: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > > ** (gedit:25963): WARNING **: 04:18:26.209: Set document metadata failed: > Setting attribute metadata::gedit-position not supported > > (gedit:25963): dconf-WARNING **: 04:18:26.220: failed to commit changes to > dconf: Error spawning command line “dbus-launch > --autolaunch=38a60bf1cf8d4bf0bd8a51b1789aad9a --binary-syntax > --close-stderr”: Child process exited with code 1 > (base) [fanhc@localhost scipion]$ > > > > > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
