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This page compiles a list of common errors that can appear when using Scipion.

Installing Scipion/Xmipp from precompiled bundles

We have checked the following Operative Systems for the installation using the precompiled bundles:

  • Centos7: works with Scipion_Centos and Xmipp_Centos

  • Ubuntu16: works with Scipion_Ubuntu and Xmipp_Debian

  • Ubuntu18: workks with Scipion_Ubuntu and Xmipp_Debian

  • OpenSUSE42.3: works with Scipion_Ubuntu and Xmipp_Debian

For OpenSUSE15 and Debian, installation from sources is needed, so far.

Fixing not found in OpenSUSE42.3

When Scipion_Ubuntu precompiled bundle is installed, maybe a “ not found” error is raised. We have observed that OpenSUSE includes and we have checked that is also valid, thus we propose to link one to the other by

sudo ln -s /usr/lib64/ /usr/lib64/

Fixing fonts in Ubuntu 18

The Scipion font is not right in Ubuntu 18. A temporary fix for this is to move all TK and TCL files in software/lib and use the system ones.

Launching Eman boxer protocol

If you see an error like ‘Cannot mix incompatible Qt library (version 0x40806) with this library (version 0x40804)’. This means the Qt installed on your computer is conflicting with the Qt distributed with EMAN2. In most cases it gets solved by removing the Qt that comes with EMAN2 from EMAN2DIR/extlib/lib.

Relion3 compilation with CUDA8.0 and g++>6

If you are getting an error telling that g++ later than 6 is not supported by nvcc8, you can set a lower g++ compiler in the $SCIPION_HOME/config/scipion.conf for instance CC=gcc-5 and CXX=g++-5. To do that you need to have gcc/g++-5 installed.

Compiling Scipion with OpenCV

If you have problems compiling Scipion with OpenCV support (CUDA version >=6.5), e.g. opencv-2.4.9 compilation fails with an error:

Error: target 'software/lib/' not built (after running 'make install > /home/user/soft/scipion/software/log/opencv_make_install.log 2>&1')

And log file (software/log/opencv_make.log) shows something like:

[ 9%] Building NVCC (Device) object modules/core/CMakeFiles/cuda_compile.dir/src/cuda/
/usr/include/string.h: In function ‘void* __mempcpy_inline(void, const void, size_t)’:
/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
return (char *) memcpy (__dest, __src, __n) + __n;
CMake Error at (message):
Error generating file


  1. Find the micro-architecture name for your GPU card, e.g. Kepler for K40 or Fermi for M2070 card

  2. cd $SCIPION_HOME/software/tmp/opencv-2.4.9

  3. Run cmake -DCUDA_GENERATION=Kepler -DWITH_CUDA:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/path/to/scipion/software . > /path/to/scipion/software/log/opencv_cmake.log 2>&1 substituting correct path and micro-architecture

  4. Modify source files in opencv-2.4.9 folder according to this and this fix

  5. Re-run scipion install, opencv now should compile cleanly ***

Scipion freezes after click on open bibtex

This likely happens because your machine doesn’t have a default program to open bibtex. Type this in your terminal to set gedit as your default program for bibtex files:

xdg-mime default gedit.desktop text/x-bibtex

Compiling Scipion in Opensuse

Scipion instalationin Opensuse sometimes involves a few drawbacks. Once in the terminal the compilation has been launched, ./scipion install, stop the installation (Crtl+C). It is neccesary to change the python version (download python 2.7.13). Copy the download file to scipion\software\tmp\ and edit next file scipion\software\install\

The line in which the python version is specified must be modified by the downloaded version 2.7.13, it means to substitute the old version 2.7.8 by 2.7.13. Finally we can go to the terminal again and relaunch the installation by doing ./scipion install.

Requirement already satisfied

Conditions 1. you had Scipion already installed (from source) 2. later on you installed numpy again (e.g. with pandas) 3. you want to reinstall Scipion (from source)


Building numpy ...
python /home/user/Scipion/software/lib/python2.7/site-packages/pip install numpy==1.14.1
Requirement already satisfied: numpy==1.14.1 in /home/user/.local/lib/python2.7/site-packages
Error: target '/home/user/Scipion/software/lib/python2.7/site-packages/numpy' not built (after running 'python /home/user/Scipion/software/lib/python2.7/site-packages/pip install numpy==1.14.1')


Numpy version conflict?


uninstall Scipion’s version of numpy

scipion run pip uninstall numpy
rm -rf software/lib/python2.7/site-packages/numpy

run install again

scipion install -j 8

ImportError: cannot import name HTTPSHandler


Building pip ...
python scripts/ -I --no-setuptools
Traceback (most recent call last):
  File "scripts/", line 19177, in <module>
  File "scripts/", line 194, in main
  File "scripts/", line 82, in bootstrap
    import pip
  File "/tmp/tmpXJbtSy/", line 16, in <module>
    # *
  File "/tmp/tmpXJbtSy/", line 9, in <module>
  File "/tmp/tmpXJbtSy/", line 30, in <module>
  File "/tmp/tmpXJbtSy/", line 39, in <module>
  File "/tmp/tmpXJbtSy/", line 14, in <module>
  File "/tmp/tmpXJbtSy/", line 31, in <module>
ImportError: cannot import name HTTPSHandler
Error: target 'scipion/software/lib/python2.7/site-packages/pip' not built (after running 'python scripts/ -I --no-setuptools')


Missing libssl-dev


sudo apt-get install libssl-dev
rm -rf software/bin/python* software/lib/python2.7/
./scipion install

Launching XMIPP3 CL2D protocol

Error: - No such file or directory

If executing Xmipp3-cl2d protocol fails with an error:

.../Scipion/Projects/release-1.2.1/scipion/software/em/xmipp/bin/xmipp_mpi_classify_CL2D: error while loading shared libraries: cannot open shared object file: No such file or directory
Protocol failed: Command 'mpirun -np 4 -bynode  `which xmipp_mpi_classify_CL2D` -i
Runs/002697_XmippProtCL2D/tmp/input_particles.xmd --odir Runs/002697_XmippProtCL2D/extra --oroot level --nref 8
--iter 10  --distance correlation --classicalMultiref --nref0 2' returned non-zero exit status 127

This means that the library installed on your computer cannot open.


Create a symbolic link to this library at the location of the library (/usr/lib/ in Ubunut16 or /usr/lib/x86_64-linux-gnu in Ubuntu18).


Assuming that ls /usr/lib/ find a file:

ln -s /usr/lib/ /usr/lib/

We have experimented something similar with

ln -s /usr/lib/ /usr/lib/


This has been reported on an UBUNTU-18 machine using binaries, but may happen at compile time using sources. It was happening when launching scipion. The error reported looked like this:

Traceback (most recent call last):
  File "/home/xxx/bin/scipion/pyworkflow/apps/", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/home/xxx/bin/scipion/pyworkflow/gui/", line 27, in <module>
    from gui import *
  File "/home/xxx/bin/scipion/pyworkflow/gui/", line 34, in <module>
    from import Message, Color, Icon
  File "/home/xxx/bin/scipion/pyworkflow/utils/", line 30, in <module>
    from utils import *
  File "/home/xxx/bin/scipion/pyworkflow/utils/", line 32, in <module>
    import numpy as np
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/", line 153, in <module>
    from . import add_newdocs
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/lib/", line 18, in <module>
    from .polynomial import *
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/lib/", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/linalg/", line 50, in <module>
    from .linalg import *
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/linalg/", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: cannot open shared object file: No such file or directory

Cause: Missing

Fix :

The missing library can be installed using: sudo apt-get install libgfortran3

bigtiff in Claudio

We have updated the tiff library to handle BIGtiff data and it will be available from Scipion version 2.0.0. If you are running Claudio (v1.2.1) there are some steps you can follow to enable Scipion to work with bigtiff data. Please, take into account that this hasn’t been extensively tested but all our tests where successful. Our recommendation would be to wait for v2.0 release (Spring 2019 aprox.).


If you are determined to move forward follow this steps:

  1. open a terminal and cd to the scipion folder

  2. backup your old libtiff files:

mkdir software/lib/old_tiff
mv software/lib/libtiff* software/lib/old_tiff/
  1. modify scipion to use libtiff 4.0.10 (bigtiff lib)

sed -i -e s/tiff-3.9.4/tiff-4.0.10/ install/

  1. Tell scipion to install bigtiff

./scipion install tiff --no-xmipp

Install Xmipp3 in Diocletian

Because we haven’t installed xmipp yet, you’ll see a message saying something like this in the terminal:

Scipion v2.0 (2019-03-12) Diocletian (release-2.0.0-fixes 50b9908)

>>>>> python  /home/yaiza/Desktop/scipion/pyworkflow/apps/

>>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
   > Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp in Scipion manager window)

or this one when importing something:

Error: AttributeError
Description: 'NoneType' object has no attribute 'isImage'
  File "/home/me/scipion/pyworkflow/protocol/", line 1817, in validate
    childErrors = self._validate()

  File "/home/me/scipion/pyworkflow/em/protocol/protocol_import/", line 372, in validate
    errors += self.validateImages()

  File "/home/me/scipion/pyworkflow/em/protocol/protocol_import/", line 354, in validateImages

  File "/home/me/scipion/pyworkflow/em/convert/", line 436, in isImageFile
    return xmippLib.FileName(imgFn).isImage()
  • Open Plugin Manager

Scipion project manager
  • Select Xmipp to install it by clicking on the empty checkbox on the left.

plugin manager
  • Add the number of processors you’d like to use (the more, the merrier!). Then click on the install button on the operations tab

plugin manager install xmipp
  • Now we can check the progress on the Output log tab (or go make some coffee, Xmipp installation will take a bit!). You might have to refresh the logs by clicking on the refresh symbol on the right. Please note that messages might not appear in order if we are using more than 1 processor.

install xmipp logs
  • When the operation gets a green check, it’s done!

install xmipp logs

Note: if xmipp installation fails, you might have to uninstall it with the plugin manager:

uninstall xmipp

And manually remove leftover elements:

rm -rf software/em/xmipp*
  • Now when we close and re-launch Scipion, we should get no messages.


 Scipion v2.0 (2019-03-12) Diocletian (release-2.0.0-fixes 50b9908)

 >>>>> python  /home/yaiza/Desktop/scipion/pyworkflow/apps/

scikit-learn installation fails

If you are getting error while scipion tries to install scikit-learn python package, something like:

00086:   Building scikit-learn ...
00087:   /home/fanhc/Programs/scipion/software/bin/python /home/fanhc/Programs/scipion/software/lib/python2.7/site-packages/pip install scikit-learn==0.17
00088:   Collecting scikit-learn==0.17
00089:     Using cached
00090:   Building wheels for collected packages: scikit-learn
00091:     Building wheel for scikit-learn ( started
00092:     Building wheel for scikit-learn ( finished with status 'error'
00093:     Running clean for scikit-learn
00094:   Failed to build scikit-learn
00095:   Installing collected packages: scikit-learn
00096:     Running install for scikit-learn: started
00097:       Running install for scikit-learn: finished with status 'error'

Try to run:

scipion python -m pip install scikit-learn==0.17.1

sh_alignment installation fails

Some program in Xmipp use the sh_alignent library. If you get some of the errors below try the following:

  • swig: Command not found: Install swig in your computer, ie. sudo apt-get install swig (yum in Centos distros and zypper in OpenSUSE).

Deep consensus fail due to index out of run.

We have find a bug reporting the following error:

133   consensusNpixels = consensusRadius* boxSize
135   # Add the rest of coordinates
136   Ncurrent = N0
137   for n in range(1, len(coords_files)):
138     for coord in coords[n]:  <----------------------- BUG
    coord = array([2379,  102])
    coords = [array([[3543,  222],
   [3757,  133],
   [3063, 3935],
   [ 712, 3944]]), array([[1136,  280],
   [2388, 2416],
  ... 120],
   [1788,  624],
   [2608, 3204]]), array([[ 663, 3811],
   [ 287, 3688],
  ... 162],
   [3048,  159],
   [2379,  102]])]
    n = 3
139       if Ncurrent > 0:
140         dist = np.sum((coord - allCoords[0:Ncurrent])**2, axis=1)
141         imin = np.argmin(dist)
142         if sqrt(dist[imin]) < consensusNpixels:

This bug should be fixed for versions after v19.04. However, to fix it in prior versions, please download the bug-fixed file to your Xmipp installation.

wget -O $(scipionBIN run printenv | grep XMIPP_HOME | sed 's/.*=//')/bin/xmipp_coordinates_consensus

Please, ensure it has executable permissions

chmod a+x $(scipionBIN run printenv | grep XMIPP_HOME= | sed 's/.*=//')/bin/xmipp_coordinates_consensus