[scipion-users] scipion3 installation in Centos7

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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] scipion3 installation in Centos7

Image processing framework to integrate EM software packages.

[scipion-users] scipion3 installation in Centos7