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Manager used in scripts with no GUI... fails #1108

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pconesa opened this issue Jul 7, 2017 · 6 comments
Open

Manager used in scripts with no GUI... fails #1108

pconesa opened this issue Jul 7, 2017 · 6 comments
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@pconesa
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pconesa commented Jul 7, 2017

In machines with no GUI using the scripts (in this case the create_project.py)....we are getting errors:

Scipion release-1.1-headless-devel (2017-07-07) f9ee9af

python "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/scripts/create_project.py" "name1" "/dls/m02/data/2017/cm16766-3/processed/scipion_template_20170707_1034.json" "/dls/m02/data/2017/cm16766-3/processed/"

creating a project at /dls/m02/data/2017/cm16766-3/processed/name1

(the default location would have been /localhome/gda2/ScipionUserData/projects/name1

Creating project at: /dls/m02/data/2017/cm16766-3/processed/name1/project.sqlite

Error loading module: 'motioncorr'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/motioncorr/init.py", line 31, in 

from protocol_motioncorr import ProtMotionCorr

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/motioncorr/protocol_motioncorr.py", line 39, in 

from pyworkflow.em.packages.xmipp3.convert import writeShiftsMovieAlignment

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'bsoft'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/bsoft/init.py", line 36, in 

from protocol_particle_pick import BsoftProtParticlePicking

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/bsoft/protocol_particle_pick.py", line 30, in

from convert import readSetOfCoordinates

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/bsoft/convert.py", line 10, in 

from pyworkflow.em.packages.xmipp3.convert import rowToCoordinate, rowFromMd

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'relion'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/relion/init.py", line 34, in 

from convert import *

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/relion/convert.py", line 41, in 

from pyworkflow.em.packages.relion.constants import V1_3, V1_4, V2_0

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/relion/init.py", line 53, in 

from wizard import *

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/relion/wizard.py", line 27, in 

from pyworkflow.em.packages.xmipp3.constants import *

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'eman2'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/eman2/init.py", line 37, in 

from protocol_boxing import EmanProtBoxing

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/eman2/protocol_boxing.py", line 36, in 

from pyworkflow.em.packages.eman2.convert import loadJson

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/eman2/init.py", line 42, in 

from viewer import EmanViewer, RefineEasyViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/eman2/viewer.py", line 35, in 

from pyworkflow.em.packages.xmipp3.viewer import XmippViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'spider'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/spider/init.py", line 42, in 

from viewer import SpiderViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/spider/viewer.py", line 32, in 

from pyworkflow.em.packages.xmipp3.viewer import XmippViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'xmipp3'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 36, in 

from convert import *

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/convert.py", line 40, in 

from pyworkflow.em.packages.xmipp3.utils import iterMdRows

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

Error loading module: 'gautomatch'

Exception: libXss.so.1: cannot open shared object file: No such file or directory

Traceback (most recent call last):

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/utils/reflection.py", line 49, in getModules

m = __import__(f)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/gautomatch/init.py", line 36, in 

from viewer import GautomatchViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/gautomatch/viewer.py", line 33, in 

from pyworkflow.em.packages.xmipp3.convert import *

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/init.py", line 54, in 

from viewer_resolution_monogenic_signal import XmippMonoResViewer

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in 

import matplotlib.pyplot as plt

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 98, in 

_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/init.py", line 28, in pylab_setup

globals(),locals(),[backend_name],0)

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 11, in 

import matplotlib.backends.tkagg as tkagg

File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/backends/tkagg.py", line 2, in 

from matplotlib.backends import _tkagg

ImportError: libXss.so.1: cannot open shared object file: No such file or directory

ERROR: protocol class name 'ProtMotionCorr' not found
@pconesa pconesa added the bug label Jul 7, 2017
@delarosatrevin
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The problem is here:

from viewer_resolution_monogenic_signal import XmippMonoResViewer
File "/dls_sw/apps/scipion/release-1.1-headless-devel/scipion/pyworkflow/em/packages/xmipp3/viewer_resolution_monogenic_signal.py", line 35, in

import matplotlib.pyplot as plt

the "plt" should be imported from our own plotter module, like:

from pyworkflow.gui.plotter import plt

In there we added the following protection to work properly when there is no GUI:

try:
    import matplotlib.pyplot as plt
except:
    plt = None

The problem is that this can easily be forgotten by developers of new viewers like in this case. I don't see a more general way right now to force that.

@pconesa
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pconesa commented Jul 11, 2017 via email

@delarosatrevin
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@pconesa Has this been addressed? Can this issue be closed?

@pconesa
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pconesa commented Nov 22, 2017

Don't think so, how is to simulate a "non GUI" environment?

@delarosatrevin
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I'm not sure about how to simulate it...make rename some basic X11 libraries...but not sure how safe is this. But when I was on Diamond we manage to bypass all matplotlib includes...I'm not sure if this viewer still includes directly the matplotlib or the one in our modules (the way to be more robust to no gui environments)

@delarosatrevin
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@pconesa Has this been fixed?

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