Troubleshooting

Pablo Conesa edited this page Oct 30, 2018 · 25 revisions




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

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.


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/libopencv_core.so' 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/cuda_compile_generated_gpu_mat.cu.o
/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 cuda_compile_generated_gpu_mat.cu.o.cmake:264 (message):
Error generating file
/home/mag/opencv/build_opencv_master/modules/core/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_gpu_mat.cu.o

Then:

  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\script.py

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.


Endless list of CUDA related errors

Conditions

  • CUDA set to True (in config\scipion.conf)
  • Multiple CUDA versions are installed

Example

 /usr/local/cuda/include/crt/common_functions.h:64:0: warning: "__CUDACC_VER__" redefined #define __CUDACC_VER__ "__CUDACC_VER__ is no longer supported. Use __CUDACC_VER_MAJOR__, __CUDACC_VER_MINOR__, and __CUDACC_VER_BUILD__ instead." ^ <command-line>:0:0: note: this is the location of the previous definition
 /usr/local/cuda/include/device_atomic_functions.h(107): warning: missing return statement at end of non-void function "atomicAdd"

Cause

Version conflict while linking

Fix

make sure that all paths to *CUDA* and *NVCC* in config\scipion.conf are absolute


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)

Example

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')

Cause

Numpy version conflict?

Fix

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

Example

Building pip ...
python scripts/get-pip.py -I --no-setuptools
Traceback (most recent call last):
  File "scripts/get-pip.py", line 19177, in <module>
    main()
  File "scripts/get-pip.py", line 194, in main
    bootstrap(tmpdir=tmpdir)
  File "scripts/get-pip.py", line 82, in bootstrap
    import pip
  File "/tmp/tmpXJbtSy/pip.zip/pip/__init__.py", line 16, in <module>
    # *
  File "/tmp/tmpXJbtSy/pip.zip/pip/vcs/subversion.py", line 9, in <module>
  File "/tmp/tmpXJbtSy/pip.zip/pip/index.py", line 30, in <module>
  File "/tmp/tmpXJbtSy/pip.zip/pip/wheel.py", line 39, in <module>
  File "/tmp/tmpXJbtSy/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module>
  File "/tmp/tmpXJbtSy/pip.zip/pip/_vendor/distlib/compat.py", 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/get-pip.py -I --no-setuptools')

Cause

Missing libssl-dev

Fix

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

Launching XMIPP3 CL2D protocol

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: libmpi.so.1: 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 libmpi.so.1 library installed on your computer cannot open.

** Fix **

Create a symbolic link to this library at the location of the libmpi.so library.

Example:

ln -s /usr/lib/libmpi.so /usr/lib/libmpi.so.1

ImportError: libgfortran.so.3

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/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/home/xxx/bin/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/home/xxx/bin/scipion/pyworkflow/gui/gui.py", line 34, in <module>
    from pyworkflow.utils.properties import Message, Color, Icon
  File "/home/xxx/bin/scipion/pyworkflow/utils/__init__.py", line 30, in <module>
    from utils import *
  File "/home/xxx/bin/scipion/pyworkflow/utils/utils.py", line 32, in <module>
    import numpy as np
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/__init__.py", line 153, in <module>
    from . import add_newdocs
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 50, in <module>
    from .linalg import *
  File "/home/xxx/bin/scipion/software/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory

Cause: Missing libgfortran.so.3

Fix :

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

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