Re: [scipion-users] Installation trouble

[Grigory S. <sha...@gm...>]

Hi Tetter,

Could you try the following steps manually:

1) conda activate .scipion3env
2) cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
3) rm -f xmipp.conf
4) ./xmipp config
5) ./xmipp check_config
6) ./xmipp compileAndInstall N=4
7) ln -srfn build /home/hilvertg/tetterst/software/em/xmipp

If you have errors in step 4, please post it 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 Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...>
wrote:

> Dear all,
>
>
> I am trying to install Scipion for single particle analysis, and more
> specifically for symmetry relaxation. Unfortunately I can't seem to get the
> installation to work. I am working with Ubuntu 16.04. Please be aware that
> I am not a well-versed Ubuntu user.
>
>
> I have tried installation both via the conda version and the virtualenv
> version described on
> https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#fixing-fonts-in-a-conda-installation,
> but they both fail eventually. (I have changed the export PATH line to
> point to sr/local/cuda-9.0/bin to fit my setup.)
>
>
> Below is what happens. Any ideas?
>
>
> Thanks,
>
>
> Stephan
>
>
> hilvertg@bamf:~$ sudo apt-get install gcc g++ make libopenmpi-dev
> python3-tk libfftw3-dev libhdf5-dev libtiff-dev libjpeg-dev libsqlite3-dev
> openjdk-8-jdk
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Note, selecting 'libtiff5-dev' instead of 'libtiff-dev'
> g++ is already the newest version (4:5.3.1-1ubuntu1).
> gcc is already the newest version (4:5.3.1-1ubuntu1).
> libfftw3-dev is already the newest version (3.3.4-2ubuntu1).
> libjpeg-dev is already the newest version (8c-2ubuntu8).
> make is already the newest version (4.1-6).
> python3-tk is already the newest version (3.5.1-1).
> libopenmpi-dev is already the newest version (1.10.2-8ubuntu1).
> libsqlite3-dev is already the newest version (3.11.0-1ubuntu1.5).
> libtiff5-dev is already the newest version (4.0.6-1ubuntu0.7).
> openjdk-8-jdk is already the newest version (8u272-b10-0ubuntu1~16.04).
> libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1).
> 0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
>
> hilvertg@bamf:~$ export PATH=$PATH:/usr/local/cuda-9.0/bin
>
>
> hilvertg@bamf:~$ python -m pip install --user
> scipion-installerRequirement already satisfied: scipion-installer in
> ./.local/lib/python2.7/site-packages (1.0.9)
> Requirement already satisfied: virtualenv in
> ./.local/lib/python2.7/site-packages (from scipion-installer) (20.1.0)
> Requirement already satisfied: six<2,>=1.9.0 in
> /usr/local/lib/python2.7/dist-packages (from virtualenv->scipion-installer)
> (1.10.0)
> Requirement already satisfied: appdirs<2,>=1.4.3 in
> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer)
> (1.4.4)
> Requirement already satisfied: distlib<1,>=0.3.1 in
> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer)
> (0.3.1)
> Requirement already satisfied: importlib-resources>=1.0; python_version <
> "3.7" in ./.local/lib/python2.7/site-packages (from
> virtualenv->scipion-installer) (3.2.0)
> Requirement already satisfied: importlib-metadata<3,>=0.12; python_version
> < "3.8" in ./.local/lib/python2.7/site-packages (from
> virtualenv->scipion-installer) (2.0.0)
> Requirement already satisfied: filelock<4,>=3.0.0 in
> ./.local/lib/python2.7/site-packages (from virtualenv->scipion-installer)
> (3.0.12)
> Requirement already satisfied: pathlib2<3,>=2.3.3; python_version < "3.4"
> and sys_platform != "win32" in ./.local/lib/python2.7/site-packages (from
> virtualenv->scipion-installer) (2.3.5)
> Requirement already satisfied: typing; python_version < "3.5" in
> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0;
> python_version < "3.7"->virtualenv->scipion-installer) (3.7.4.3)
> Requirement already satisfied: contextlib2; python_version < "3" in
> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0;
> python_version < "3.7"->virtualenv->scipion-installer) (0.6.0.post1)
> Requirement already satisfied: zipp>=0.4; python_version < "3.8" in
> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0;
> python_version < "3.7"->virtualenv->scipion-installer) (1.2.0)
> Requirement already satisfied: singledispatch; python_version < "3.4" in
> ./.local/lib/python2.7/site-packages (from importlib-resources>=1.0;
> python_version < "3.7"->virtualenv->scipion-installer) (3.4.0.3)
> Requirement already satisfied: configparser>=3.5; python_version < "3" in
> ./.local/lib/python2.7/site-packages (from importlib-metadata<3,>=0.12;
> python_version < "3.8"->virtualenv->scipion-installer) (4.0.2)
> Requirement already satisfied: scandir; python_version < "3.5" in
> /usr/local/lib/python2.7/dist-packages (from pathlib2<3,>=2.3.3;
> python_version < "3.4" and sys_platform !=
> "win32"->virtualenv->scipion-installer) (1.9.0)
>
>
> hilvertg@bamf:~$ python3 -m scipioninstaller ~/tetterst -venv -j 4created
> virtual environment CPython3.5.2.final.0-64 in 99ms
>   creator CPython3Posix(dest=/home/hilvertg/tetterst/.scipion3env,
> clear=False, global=False)
>   seeder FromAppData(download=False, wheel=bundle, setuptools=bundle,
> pip=bundle, via=copy, app_data_dir=/home/hilvertg/.local/share/virtualenv)
>     added seed packages: Pillow==7.1.2, SCons==4.0.1, bibtexparser==1.2.0,
> biopython==1.76, certifi==2020.6.20, chardet==3.0.4, configparser==4.0.2,
> cycler==0.10.0, future==0.18.2, idna==2.10, joblib==0.14.1,
> kiwisolver==1.1.0, littleutils==0.2.2, matplotlib==3.0.3, numpy==1.18.4,
> outdated==0.2.0, peppercorn==0.6, pip==20.2.4, plotter==1.3.17,
> psutil==5.7.0, pyparsing==2.4.7, python_dateutil==2.8.1, requests==2.23.0,
> scikit_learn==0.22.1, scipion_app==3.0.5, scipion_em==3.0.4,
> scipion_em_xmipp==20.7.1, scipion_pyworkflow==3.0.5, scipy==1.4.1,
> setuptools==50.3.2, six==1.15.0, urllib3==1.25.11, wheel==0.35.1
>   activators
> PythonActivator,FishActivator,PowerShellActivator,CShellActivator,XonshActivator,BashActivator
> DEPRECATION: Python 3.5 reached the end of its life on September 13th,
> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip
> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove
> support for this functionality.
> Requirement already satisfied: scipion-pyworkflow in
> ./.scipion3env/lib/python3.5/site-packages (3.0.5)
> Requirement already satisfied: matplotlib<=3.2.2 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (3.0.3)
> Requirement already satisfied: psutil<=5.7.0 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (5.7.0)
> Requirement already satisfied: requests<=2.23.0 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow)
> (2.23.0)
> Requirement already satisfied: numpy<=1.18.4 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow)
> (1.18.4)
> Requirement already satisfied: pillow<=7.1.2 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (7.1.2)
> Requirement already satisfied: bibtexparser<=1.2.0 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (1.2.0)
> Requirement already satisfied: configparser<=5.0.0 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-pyworkflow) (4.0.2)
> Requirement already satisfied: cycler>=0.10 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow) (0.10.0)
> Requirement already satisfied: python-dateutil>=2.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow) (2.8.1)
> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow) (2.4.7)
> Requirement already satisfied: kiwisolver>=1.0.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow) (1.1.0)
> Requirement already satisfied: certifi>=2017.4.17 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests<=2.23.0->scipion-pyworkflow) (2020.6.20)
> Requirement already satisfied: idna<3,>=2.5 in
> ./.scipion3env/lib/python3.5/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
> ./.scipion3env/lib/python3.5/site-packages (from
> requests<=2.23.0->scipion-pyworkflow) (1.25.11)
> Requirement already satisfied: chardet<4,>=3.0.2 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests<=2.23.0->scipion-pyworkflow) (3.0.4)
> Requirement already satisfied: future>=0.16.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> bibtexparser<=1.2.0->scipion-pyworkflow) (0.18.2)
> Requirement already satisfied: six in
> ./.scipion3env/lib/python3.5/site-packages (from
> cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow) (1.15.0)
> Requirement already satisfied: setuptools in
> ./.scipion3env/lib/python3.5/site-packages (from
> kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow) (50.3.2)
> DEPRECATION: Python 3.5 reached the end of its life on September 13th,
> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip
> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove
> support for this functionality.
> Requirement already satisfied: scipion-app in
> ./.scipion3env/lib/python3.5/site-packages (3.0.5)
> Requirement already satisfied: outdated==0.2.0 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (0.2.0)
> Requirement already satisfied: scipion-em in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-app) (3.0.4)
> Requirement already satisfied: littleutils in
> ./.scipion3env/lib/python3.5/site-packages (from
> outdated==0.2.0->scipion-app) (0.2.2)
> Requirement already satisfied: requests in
> ./.scipion3env/lib/python3.5/site-packages (from
> outdated==0.2.0->scipion-app) (2.23.0)
> Requirement already satisfied: scipion-pyworkflow in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app)
> (3.0.5)
> Requirement already satisfied: biopython==1.76 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em->scipion-app)
> (1.76)
> Requirement already satisfied: idna<3,>=2.5 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests->outdated==0.2.0->scipion-app) (2.10)
> Requirement already satisfied: chardet<4,>=3.0.2 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests->outdated==0.2.0->scipion-app) (3.0.4)
> Requirement already satisfied: certifi>=2017.4.17 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests->outdated==0.2.0->scipion-app) (2020.6.20)
> Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> requests->outdated==0.2.0->scipion-app) (1.25.11)
> Requirement already satisfied: matplotlib<=3.2.2 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (3.0.3)
> Requirement already satisfied: configparser<=5.0.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (4.0.2)
> Requirement already satisfied: numpy<=1.18.4 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (1.18.4)
> Requirement already satisfied: pillow<=7.1.2 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (7.1.2)
> Requirement already satisfied: bibtexparser<=1.2.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (1.2.0)
> Requirement already satisfied: psutil<=5.7.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scipion-pyworkflow->scipion-em->scipion-app) (5.7.0)
> Requirement already satisfied: cycler>=0.10 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (0.10.0)
> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.4.7)
> Requirement already satisfied: python-dateutil>=2.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (2.8.1)
> Requirement already satisfied: kiwisolver>=1.0.1 in
> ./.scipion3env/lib/python3.5/site-packages (from
> matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app) (1.1.0)
> Requirement already satisfied: future>=0.16.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> bibtexparser<=1.2.0->scipion-pyworkflow->scipion-em->scipion-app) (0.18.2)
> Requirement already satisfied: six in
> ./.scipion3env/lib/python3.5/site-packages (from
> cycler>=0.10->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app)
> (1.15.0)
> Requirement already satisfied: setuptools in
> ./.scipion3env/lib/python3.5/site-packages (from
> kiwisolver>=1.0.1->matplotlib<=3.2.2->scipion-pyworkflow->scipion-em->scipion-app)
> (50.3.2)
> Scipion v3.0.5 () 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/hilvertg/tetterst/.scipion3env/bin/python -m pip install
> scipion-em-xmipp==20.7.1
> DEPRECATION: Python 3.5 reached the end of its life on September 13th,
> 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip
> 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove
> support for this functionality.
> Requirement already satisfied: scipion-em-xmipp==20.7.1 in
> ./.scipion3env/lib/python3.5/site-packages (20.7.1)
> Requirement already satisfied: joblib in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1)
> (0.14.1)
> Requirement already satisfied: peppercorn in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1)
> (0.6)
> Requirement already satisfied: plotter in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1)
> (1.3.17)
> Requirement already satisfied: scons in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1)
> (4.0.1)
> Requirement already satisfied: scikit-learn==0.22.1 in
> ./.scipion3env/lib/python3.5/site-packages (from scipion-em-xmipp==20.7.1)
> (0.22.1)
> Requirement already satisfied: setuptools in
> ./.scipion3env/lib/python3.5/site-packages (from
> scons->scipion-em-xmipp==20.7.1) (50.3.2)
> Requirement already satisfied: scipy>=0.17.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.4.1)
> Requirement already satisfied: numpy>=1.11.0 in
> ./.scipion3env/lib/python3.5/site-packages (from
> scikit-learn==0.22.1->scipion-em-xmipp==20.7.1) (1.18.4)
> Done (0.36 seconds)
> Building xmippSrc-3.20.07 ...
>   Skipping command: wget -nv -c -O
> /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part
> http://scipion.cnb.csic.es/downloads/scipion/software/em/xmippSrc-v3.20.07.tgz
> mv -v /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz.part
> /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07.tgz
>   All targets exist.
>   Skipping command: tar -xf xmippSrc-v3.20.07.tgz
>   All targets exist.
> cd /home/hilvertg/tetterst/software/em/xmippSrc-v3.20.07
> cd . && ./xmipp config noAsk && ./xmipp check_config && ./xmipp
> compileAndInstall N=4 && ln -srfn build
> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch
> installation_finished && rm bindings_linked 2> /dev/null
> Traceback (most recent call last):
>   File "./xmipp", line 1753, in <module>
>     XMIPP_SCRIPT_VERSION = getScriptVersion()
>   File "./xmipp", line 1718, in getScriptVersion
>     return lastCommit[0].strip()
> IndexError: list index out of range
> Traceback (most recent call last):
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py",
> line 453, in <module>
>     main()
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/__main__.py",
> line 296, in main
>     installPluginMethods()
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/install_plugin.py",
> line 231, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/plugin_funcs.py",
> line 166, in installBin
>     environment.execute()
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py",
> line 748, in execute
>     self._executeTargets(targetList)
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py",
> line 690, in _executeTargets
>     tgt.execute()
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py",
> line 220, in execute
>     command.execute()
>   File
> "/home/hilvertg/tetterst/.scipion3env/lib/python3.5/site-packages/scipion/install/funcs.py",
> line 161, in execute
>     "running '%s')" % (t, cmd))
> AssertionError: target
> '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant'
> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
> check_config && ./xmipp compileAndInstall N=4 && ln -srfn build
> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch
> installation_finished && rm bindings_linked 2> /dev/null')
> Error at main: target
> '/home/hilvertg/tetterst/software/em/xmipp/bin/xmipp_reconstruct_significant'
> not built (after running 'cd . && ./xmipp config noAsk && ./xmipp
> check_config && ./xmipp compileAndInstall N=4 && ln -srfn build
> /home/hilvertg/tetterst/software/em/xmipp && cd - && touch
> installation_finished && rm bindings_linked 2> /dev/null')
>
> Something went wrong running:
>  cd /home/hilvertg/tetterst &&
> /usr/bin/python3 -m virtualenv --python=python3 .scipion3env &&
> . /home/hilvertg/tetterst/.scipion3env/bin/activate &&
> cd /home/hilvertg/tetterst &&
> mkdir -p software/lib &&
> mkdir -p software/bindings &&
> mkdir -p software/em &&
> export SCIPION_HOME=/home/hilvertg/tetterst &&
> pip install scipion-pyworkflow &&
> pip install scipion-app &&
> python -m scipion installp -p scipion-em-xmipp -j 4
> Installation cancelled.
>
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