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Re: [scipion-users] Installation trouble
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From: Tetter S. <tet...@or...> - 2020-10-29 14:20:04
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Dear Grigory,
Step 4 does indeed cause trouble:
(.scipion3env) hilvertg@bamf:~/tetterst/software/em/xmippSrc-v3.20.07$ ./xmipp config
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
What does that mean?
Thanks,
Stephan
________________________________
Von: Grigory Sharov <sha...@gm...>
Gesendet: Mittwoch, 28. Oktober 2020 10:38:04
An: Mailing list for Scipion users
Betreff: Re: [scipion-users] Installation trouble
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<tel:+44%201223%20267228>
e-mail: gs...@mr...<mailto:gs...@mr...>
On Wed, Oct 28, 2020 at 9:00 AM Tetter Stephan <tet...@or...<mailto: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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