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AttributeError: 'module' object has no attribute '__TypeDict__' #9

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jamesmkrieger opened this issue Jul 25, 2017 · 41 comments · May be fixed by #11
Open

AttributeError: 'module' object has no attribute '__TypeDict__' #9

jamesmkrieger opened this issue Jul 25, 2017 · 41 comments · May be fixed by #11
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@jamesmkrieger
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This error comes up quite early on and a red cross appears next to project.

2017-07-25 16:53:46,409 WARNING Failed to load EMAN2 module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_filter.so module
2017-07-25 16:53:46,409 WARNING Failed to load _image_utility.so module - certain functions will not be available
2017-07-25 16:53:46,409 WARNING Failed to load _resample.so module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_interpolate.so module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_rotate.so module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_rotate.so module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_ctf.so module
2017-07-25 16:53:46,409 WARNING Failed to load _spider_reconstruct.so
2017-07-25 16:53:46,410 INFO Program: arachnid.pyspider.reference
2017-07-25 16:53:46,411 INFO Version: UNKNOWN
2017-07-25 16:53:46,411 INFO PID: 5608
2017-07-25 16:53:46,411 INFO Created: 1501016025
2017-07-25 16:53:46,411 WARNING Script does not support OpenMP - set OMP_NUM_THREADS in environment (otherwise developer needs to set supports_OMP in the script)
2017-07-25 16:53:46,412 WARNING Using extension from SPIDER params file: local/ctf/params.dat
2017-07-25 16:53:46,439 INFO SPIDER Version = 22.9 - /home/ezra/spider/bin/spider_linux_mp_opt64
2017-07-25 16:53:46,590 INFO Params: local/ctf/params.dat
2017-07-25 16:53:46,591 INFO Bin-factor: 1.000000
2017-07-25 16:53:46,591 INFO Pixel size: 0.700000
2017-07-25 16:53:46,591 INFO Window: 160.000000
2017-07-25 16:53:46,591 INFO Thread Count: 1
2017-07-25 16:53:46,592 ERROR ***Unexpected error occurred: AttributeError: 'module' object has no attribute 'TypeDict'

See .ara-control.crash_report for more details
2017-07-25 16:53:46,592 ERROR Unexpected error occurred
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid/arachnid/core/app/program.py", line 314, in launch_program
main_template.main(args, main_module, **param)
File "/data/jkrieger/programs/arachnid/arachnid/core/app/file_processor.py", line 230, in main
for index, filename in mpi_utility.mpi_reduce(process, files, init_process=init_process, ignored_errors=ignored_errors, **extra):
File "/data/jkrieger/programs/arachnid/arachnid/core/parallel/mpi_utility.py", line 376, in mpi_reduce
mpi_type = MPI.TypeDict[lenbuf.dtype.char] if MPI is not None else None
AttributeError: 'module' object has no attribute 'TypeDict'
2017-07-25 16:53:46,593 INFO Attempting to close SPIDER
2017-07-25 16:53:46,593 INFO Closing SPIDER
2017-07-25 16:53:46,594 INFO Workflow ended
@ezralanglois
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One workaround is to downgrade mpi4py

@ezralanglois
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So I remember how to fix this:

try:
return MPI.TypeDict[np.dtype(dtype).char]
except AttributeError:
return MPI._typedict[np.dtype(dtype).char]

radiocosmology/caput@b272652

@ezralanglois
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mpi4py=1.3 might work

@jamesmkrieger
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jamesmkrieger commented Jul 25, 2017 via email

@ezralanglois
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I just fixed some bugs in master. If you get a chance, upgrade to the lastest mpi4py and see if it works now.

@jamesmkrieger
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jamesmkrieger commented Jul 27, 2017 •
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It doesn't work with the latest mpi4py. I now have the following traceback and the controller doesn't open.

Traceback (most recent call last):
File "/data/jkrieger/programs/anaconda2/bin/ara-control", line 11, in
load_entry_point('arachnid', 'gui_scripts', 'ara-control')()
File "/data/jkrieger/programs/arachnid/arachnid/gui/control.py", line 26, in main
from ..core.gui.ProjectUI import MainWindow as ProjectUI
File "/data/jkrieger/programs/arachnid/arachnid/core/gui/ProjectUI.py", line 20, in
from ReferenceUI import Widget as ReferenceUI
File "/data/jkrieger/programs/arachnid/arachnid/core/gui/ReferenceUI.py", line 15, in
from ..image import ndimage_file
File "/data/jkrieger/programs/arachnid/arachnid/core/image/ndimage_file.py", line 51, in
from ..parallel import mpi_utility
File "/data/jkrieger/programs/arachnid/arachnid/core/parallel/mpi_utility.py", line 103
mpi_type = mpi_dtype(vals.dtype)
^
IndentationError: unexpected indent

@jamesmkrieger
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The latest version also gives this error with mpi4py=1.3

@jamesmkrieger
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jamesmkrieger commented Jul 27, 2017 •
edited
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Back-indenting line 103 to be level with the line above fixed the problem and it now opens with both mpi4py=1.3 and 2.0

@jamesmkrieger
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jamesmkrieger commented Jul 27, 2017 •
edited
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I don't get the workflow ended error and the red cross next to project although it does stall at 66%. The version before you made these changes was also stalling at that point. I left it open over the weekend and it didn't progress. Here's a printscreen showing the control window and the traceback.
screenshot from 2017-07-27 15-49-58

@ezralanglois
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This seems to have exposed several bugs. I will try to get to them tonight, if not, it will have to wait to Monday. Going out of town this Friday.

@ezralanglois
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The first bug may be fixed by

python setup.py build_ext --inplace

@jamesmkrieger
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Not sure what you mean by the first bug but it is still stalling at 66%

@ezralanglois
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According to the log in the screen shot above, _resample.so cannot be found. This means that the shared library is in a location that Python cannot find it.

One way to help Python find it is the build the shared library in place, or in the same directory as the calling Python module.

If that does not work, then try to install the local source. Do a git pull first to ensure you have the latest version of the code before you install.

@jamesmkrieger
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Building in place does not seem to help. What do you mean install the local source?

@jamesmkrieger
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jamesmkrieger commented Aug 1, 2017 •
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Actually the build in place command doesn't work. I just tried again at deleting the binaries and the build directory and running the command again and it now says

jkrieger@zeus:~/programs/arachnid$ ara-control
-bash: /data/jkrieger/programs/anaconda2/bin/ara-control: No such file or directory

@jamesmkrieger
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I tried python setup.py install and now it's not complaining about resample but it still seems to have stalled at 66%. Here's another screenshot.
screenshot from 2017-08-01 14-04-44

@ezralanglois
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ezralanglois commented Aug 1, 2017 •
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My first guess is that sp-reference crashed or spider hung for some reason.

Is there a crash report?

@jamesmkrieger
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Yes, here it is. It is still not finding .so files. I could add them to my LD_LIBRARY_PATH but I don't know where they are.

017-08-01 13:54:39,770 WARNING Failed to load EMAN2 module
2017-08-01 13:54:39,770 WARNING Failed to load _spider_filter.so module
2017-08-01 13:54:39,770 WARNING Failed to load _image_utility.so module - certain functions will not be available
2017-08-01 13:54:39,770 WARNING Failed to load _resample.so module
2017-08-01 13:54:39,771 WARNING Failed to load _spider_interpolate.so module
2017-08-01 13:54:39,771 WARNING Failed to load _spider_rotate.so module
2017-08-01 13:54:39,771 WARNING Failed to load _spider_rotate.so module
2017-08-01 13:54:39,771 WARNING Failed to load _spider_ctf.so module
2017-08-01 13:54:39,771 WARNING Failed to load _spider_reconstruct.so
2017-08-01 13:54:39,772 INFO Program: arachnid.pyspider.reference
2017-08-01 13:54:39,772 INFO Version: UNKNOWN
2017-08-01 13:54:39,773 INFO PID: 41244
2017-08-01 13:54:39,773 INFO Created: 1501610078
2017-08-01 13:54:39,773 WARNING Script does not support OpenMP - set OMP_NUM_THREADS in environment (otherwise developer needs to set supports_OMP in the script)
2017-08-01 13:54:39,774 WARNING Using extension from SPIDER params file: local/ctf/params.dat
2017-08-01 13:54:39,783 INFO SPIDER Version = 21.0 - /data/jkrieger/programs/anaconda2/bin/spider_linux_mp_opt64
2017-08-01 13:54:39,931 INFO Params: local/ctf/params.dat
2017-08-01 13:54:39,932 INFO Bin-factor: 1.000000
2017-08-01 13:54:39,932 INFO Pixel size: 0.700000
2017-08-01 13:54:39,932 INFO Window: 160.000000
2017-08-01 13:54:39,933 INFO Thread Count: 1
2017-08-01 13:54:39,934 INFO Processing: emd_8623.map
2017-08-01 13:54:39,934 INFO Finished: 0,5
2017-08-01 13:54:39,936 INFO Pixel size: 1.060000 for /data/jkrieger/programs/arachnid/data/rawmap/emd_8623.map
2017-08-01 13:54:40,253 INFO Finished: 1,5
2017-08-01 13:54:40,253 INFO Filtering with 0.023333, 2
2017-08-01 13:54:40,253 WARNING Spatial frequency 0.023333 exceeds the safe value, switching to Gaussian filter: 2
2017-08-01 13:54:40,254 INFO Filtering with Gaussian: /dev/shm/tmp_spi_file_0.dat -> 0.023333
2017-08-01 13:55:09,043 INFO Finished: 2,5
2017-08-01 13:55:09,279 INFO Interpolating Structure: 200.000000 * 1.514286 = 302.857143 | 0.700000/1.060000 | 160.000000
2017-08-01 13:55:09,813 INFO Decreasing window size from 302 -> 160
2017-08-01 13:55:10,216 INFO Finished: 3,5

@ezralanglois
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ezralanglois commented Aug 1, 2017 via email

@jamesmkrieger
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ok thanks Robert

@ezralanglois
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I just remembered a possible workaround for this problem. I think renaming the reference with a 01 at the end, e.g. reference.mrc becomes reference01.mrc

If I remember correctly, SPIDER has issues if there is no number at the end. I am working on another fix, but it may take some time.

@ezralanglois
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Also, you can skip the reference generation step in the workflow by setting no.

@jamesmkrieger
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jamesmkrieger commented Aug 2, 2017 via email

@ezralanglois ezralanglois linked a pull request Aug 2, 2017 that will close this issue
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@ezralanglois
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Also, if you have a chance, try this branch out (#11) it may resolve the issue too.

@jamesmkrieger
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jamesmkrieger commented Aug 2, 2017 via email

@jamesmkrieger
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I'm not sure how to rename the reference. It's being generated from an EMD query (ID 8623).

Also not sure how to get that branch.

I'll try leaving out reference generation though and see if that works.

@jamesmkrieger
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ok I found where to rename the reference to reference01.mrc so I'll try that.

@jamesmkrieger
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Not generating a reference causes it to crash with the following crash report:

2017-08-02 12:50:20,613 WARNING Failed to load EMAN2 module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_filter.so module
2017-08-02 12:50:20,614 WARNING Failed to load _image_utility.so module - certain functions will not be available
2017-08-02 12:50:20,614 WARNING Failed to load _resample.so module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_interpolate.so module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_rotate.so module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_rotate.so module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_ctf.so module
2017-08-02 12:50:20,614 WARNING Failed to load _spider_reconstruct.so
2017-08-02 12:50:20,615 INFO Program: arachnid.util.enumerate_filenames
2017-08-02 12:50:20,615 INFO Version: UNKNOWN
2017-08-02 12:50:20,615 INFO PID: 11458
2017-08-02 12:50:20,615 INFO Created: 1501692619
2017-08-02 12:50:20,615 WARNING Script does not support OpenMP - set OMP_NUM_THREADS in environment (otherwise developer needs to set supports_OMP in the script)
2017-08-02 12:50:20,617 INFO Completed
2017-08-02 12:50:20,617 INFO Running defocus
2017-08-02 12:50:20,627 ERROR Invalid option
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/gui/Monitor.py", line 208, in _run_worker
prog.check_options_validity()
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/program.py", line 443, in check_options_validity
check_options(self.main_module, self.main_template, self.dependents, self.values)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/program.py", line 877, in check_options
if hasattr(main_module, "check_options"): main_module.check_options(options, True)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/pyspider/defocus.py", line 750, in check_options
if spider_file.is_spider_image(options.input_files[0]) and options.data_ext == "":
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/spider/spider_file.py", line 84, in is_spider_image
filename = ndimage_file.readlinkabs(filename)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/image/ndimage_file.py", line 497, in readlinkabs
if not os.path.exists(link): raise IOError, "Cannot find file: %s"%(link)
IOError: Cannot find file: other/mics/mic_00000.dat
2017-08-02 12:50:20,628 INFO Workflow ended

@jamesmkrieger
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ok asking it to write the reference as reference01.mrc still causes it to stall

@jamesmkrieger
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ok I made a version #11 by copying the differences into my version of the code

@jamesmkrieger
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ok that doesn't start:

/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/skimage/filter/init.py:6: skimage_deprecation: The skimage.filter module has been renamed to skimage.filters. This placeholder module will be removed in v0.13.
warn(skimage_deprecation('The skimage.filter module has been renamed '
/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
Traceback (most recent call last):
File "/data/jkrieger/programs/anaconda2/bin/ara-control", line 11, in
load_entry_point('arachnid', 'gui_scripts', 'ara-control')()
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/gui/control.py", line 36, in main
dialog = ProjectUI(screen_shot_file)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/gui/ProjectUI.py", line 240, in init
self.loadProject()
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/gui/ProjectUI.py", line 649, in loadProject
workflow = project.workflow_settings(settings.input_files, vars(settings))
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/util/project.py", line 168, in workflow_settings
workflow = build_workflow(files, extra)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/util/project.py", line 298, in build_workflow
workflow[i] = [workflow[i]]+list(program.collect_file_dependents(workflow[i], **extra))
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/program.py", line 362, in collect_file_dependents
parser = setup_parser(main_module, main_template, **extra)[0]
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/program.py", line 747, in setup_parser
main_module.setup_options(parser, mgroup, True)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/util/prepvol.py", line 378, in setup_options
pgroup.add_option("-o", "--raw-reference-file", output="", help="Output filename template for processed volumes", gui=dict(filetype="save"), required_file=True)
File "/data/jkrieger/programs/anaconda2/lib/python2.7/optparse.py", line 1021, in add_option
self._check_conflict(option)
File "/data/jkrieger/programs/anaconda2/lib/python2.7/optparse.py", line 996, in _check_conflict
option)
optparse.OptionConflictError: option -o/--raw-reference-file/--output: conflicting option string(s): --raw-reference-file

@jamesmkrieger
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Oh I copied that line wrong and put --raw-reference-file again instead of --reference-file. Now it loaded up fine.

@jamesmkrieger
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That version then crashes and gives the following error:

jkrieger@zeus:~/programs/arachnid_copy_2017-08-02$ ara-control
/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/skimage/filter/init.py:6: skimage_deprecation: The skimage.filter module has been renamed to skimage.filters. This placeholder module will be removed in v0.13.
warn(skimage_deprecation('The skimage.filter module has been renamed '
/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: 'project_2017_08_02_12_59_49.log'
try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)
2017-08-02 13:38:48,039 INFO Program: arachnid.util.project
2017-08-02 13:38:48,040 INFO PID: 14876
2017-08-02 13:38:48,041 INFO Created: 1501695527
2017-08-02 13:38:48,082 INFO Work flow includes 7 steps
2017-08-02 13:38:48,141 INFO Running enumerate_filenames
2017-08-02 13:38:48,143 INFO Program: arachnid.util.enumerate_filenames
2017-08-02 13:38:48,144 INFO PID: 14876
2017-08-02 13:38:48,144 INFO Created: 1501695527
2017-08-02 13:38:48,147 INFO Completed
2017-08-02 13:38:48,147 INFO Running prepvol
/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: 'project_2017_08_02_13_38_48.log'
try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)
/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: '.ara-control.crash_report_2017_08_02_13_38_48.0'
try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)
2017-08-02 13:38:48,150 INFO Program: arachnid.util.prepvol
2017-08-02 13:38:48,150 INFO PID: 14876
2017-08-02 13:38:48,150 INFO Created: 1501695527
2017-08-02 13:38:48,150 INFO Multi-threading with OpenMP - enabled
2017-08-02 13:38:48,230 INFO Multi-threading with OpenMP - set thread count to 1
2017-08-02 13:38:48,231 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:38:48,232 INFO Window size: 160
2017-08-02 13:38:48,232 INFO Pixel size: 0.700000
2017-08-02 13:38:48,883 INFO Finished: 0,1 - Time left: --
2017-08-02 13:38:48,883 WARNING Errors occurred during run

See .ara-control.crash_report for more details
2017-08-02 13:38:48,883 INFO Running defocus
2017-08-02 13:38:48,898 INFO Program: arachnid.pyspider.defocus
2017-08-02 13:38:48,898 INFO PID: 14876
2017-08-02 13:38:48,898 INFO Created: 1501695527
2017-08-02 13:38:48,899 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:38:48,907 INFO SPIDER Version = 21.0 - /data/jkrieger/programs/anaconda2/bin/spider_linux_mp_opt64

__`O O'_/ SPIDER -- COPYRIGHT
,xXXXx HEALTH RESEARCH INC., ALBANY, NY.
xXXXx
/ /xxx\ \ VERSION: UNIX 21.00 ISSUED: 01/03/2013
/ \ DATE: 02-AUG-2017 AT 13:38:48

If SPIDER is useful, please cite:
Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A.
SPIDER and WEB: Processing and visualization of images in 3D electron
microscopy and related fields. J. Struct. Biol. 1996; 116: 190-199.

.ENTER PROJECT/DATA EXTENSION: dat

*** FILE NOT FOUND: /guam.raid.cluster.software/spider.18.15/bin/Nextresults

Results file: results.dat.000
Running: /data/jkrieger/programs/anaconda2/bin/spider_linux_mp_opt64
.OPERATION: MD
.MODE: RESULTS OFF
RESULTS FILE TERMINATED AT USERS REQUEST

.OPERATION: MD
.MODE: TERM OFF
2017-08-02 13:38:49,057 INFO Estimating defocus over 1 files
2017-08-02 13:38:49,057 INFO Writing power spectra to local/ctf/pow/pow_000000.dat
2017-08-02 13:38:49,058 INFO Writing decimated micrographs to local/mic_sm/mic_000000.dat
2017-08-02 13:38:49,058 INFO Writing defocus to local/ctf/ctf.dat
2017-08-02 13:38:49,058 INFO Bin factor: 2.000000
2017-08-02 13:38:49,058 INFO Padding: 2
2017-08-02 13:38:49,059 INFO Pixel size: 1.400000
2017-08-02 13:38:49,059 INFO Window size: 256
2017-08-02 13:38:49,059 INFO Inverting Micrograph - common for CCD
2017-08-02 13:38:49,059 INFO Interpolate micrograph with 2.000000
2017-08-02 13:38:49,164 WARNING You are processing an image that is not gain corrected!
2017-08-02 13:38:49,244 ERROR Error for other/mics/mic_00001.dat
2017-08-02 13:38:49,246 INFO Finished: 1,1 - Time left: -- - other/mics/mic_00001.dat
2017-08-02 13:38:49,246 WARNING Errors occurred during run

See .ara-control.crash_report for more details
2017-08-02 13:38:49,564 INFO Completed
2017-08-02 13:38:49,565 INFO Running autopick
2017-08-02 13:38:49,568 INFO Program: arachnid.app.autopick
2017-08-02 13:38:49,568 INFO PID: 14876
2017-08-02 13:38:49,568 INFO Created: 1501695527
2017-08-02 13:38:49,568 INFO Multi-threading with OpenMP - enabled
2017-08-02 13:38:49,568 INFO Multi-threading with OpenMP - set thread count to 1
2017-08-02 13:38:49,569 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:38:49,569 INFO Mask Multiplier: 1.000000
2017-08-02 13:38:49,569 INFO Peak limit: 2000.000000
2017-08-02 13:38:49,569 ERROR ***Unexpected error occurred: AttributeError: 'NoneType' object has no attribute 'sinc_blackman_kernel'

See .ara-control.crash_report for more details
2017-08-02 13:38:49,570 INFO Workflow ended

@jamesmkrieger
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and the crash report is as follows:

2017-08-02 13:38:49,567 WARNING Failed to load EMAN2 module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_filter.so module
2017-08-02 13:38:49,567 WARNING Failed to load _image_utility.so module - certain functions will not be available
2017-08-02 13:38:49,567 WARNING Failed to load _resample.so module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_interpolate.so module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_rotate.so module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_rotate.so module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_ctf.so module
2017-08-02 13:38:49,567 WARNING Failed to load _spider_reconstruct.so
2017-08-02 13:38:49,568 INFO Program: arachnid.app.autopick
2017-08-02 13:38:49,568 INFO Version: UNKNOWN
2017-08-02 13:38:49,568 INFO PID: 14876
2017-08-02 13:38:49,568 INFO Created: 1501695527
2017-08-02 13:38:49,568 INFO Multi-threading with OpenMP - enabled
2017-08-02 13:38:49,568 INFO Multi-threading with OpenMP - set thread count to 1
2017-08-02 13:38:49,569 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:38:49,569 INFO Mask Multiplier: 1.000000
2017-08-02 13:38:49,569 INFO Peak limit: 2000.000000
2017-08-02 13:38:49,569 ERROR ***Unexpected error occurred: AttributeError: 'NoneType' object has no attribute 'sinc_blackman_kernel'

See .ara-control.crash_report for more details
2017-08-02 13:38:49,569 ERROR Unexpected error occurred
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/program.py", line 314, in launch_program
main_template.main(args, main_module, **param)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/app/file_processor.py", line 206, in main
f = initialize(files, extra)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/app/autopick.py", line 775, in initialize
return sorted(lfcpick.initialize(files, param))
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/app/lfcpick.py", line 354, in initialize
param["ds_kernel"] = ndimage_interpolate.sincblackman(param['bin_factor'], dtype=numpy.float32)
File "/data/jkrieger/programs/arachnid_copy_2017-08-02/arachnid/core/image/ndimage_interpolate.py", line 163, in sincblackman
_resample.sinc_blackman_kernel(kernel, int(template_min), float(frequency_cutoff))
AttributeError: 'NoneType' object has no attribute 'sinc_blackman_kernel'
2017-08-02 13:38:49,570 INFO Workflow ended

@jamesmkrieger
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That was without a reference requested. With a reference requested the stdout is as follows:

jkrieger@zeus:~/programs/arachnid_11_copy$ ara-control
/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/skimage/filter/init.py:6: skimage_deprecation: The skimage.filter module has been renamed to skimage.filters. This placeholder module will be removed in v0.13.
warn(skimage_deprecation('The skimage.filter module has been renamed '
/data/jkrieger/programs/anaconda2/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/gui/ReferenceUI.py", line 137, in onDownloadFromEMDBComplete
self.openReference(os.path.abspath(local))
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/gui/ReferenceUI.py", line 190, in openReference
diameter = measure.estimate_diameter(img, header['apix'])
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/image/measure.py", line 47, in estimate_diameter
vol_sm = ndimage_interpolate.resample_fft_fast(vol, apix/cur_apix)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/image/ndimage_interpolate.py", line 144, in resample_fft_fast
_resample.resample_fft_center_3(img, fout)
AttributeError: 'NoneType' object has no attribute 'resample_fft_center_3'
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/gui/util/BackgroundTask.py", line 33, in cleanup
task.connect_obj(task._parent, 'disconnect')
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/gui/util/BackgroundTask.py", line 67, in connect_obj
getattr(sig, connect)(psig)
RuntimeError: Failed to disconnect signal taskFinished(PyObject).
2017-08-02 13:54:38,162 INFO Program: arachnid.util.project
2017-08-02 13:54:38,163 INFO PID: 15834
2017-08-02 13:54:38,164 INFO Created: 1501696477
2017-08-02 13:54:38,202 INFO Work flow includes 7 steps
2017-08-02 13:54:38,253 INFO Running enumerate_filenames
2017-08-02 13:54:38,255 INFO Program: arachnid.util.enumerate_filenames
2017-08-02 13:54:38,255 INFO PID: 15834
2017-08-02 13:54:38,255 INFO Created: 1501696477
2017-08-02 13:54:38,258 INFO Completed
2017-08-02 13:54:38,258 INFO Running prepvol
/data/jkrieger/programs/arachnid_11_copy/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: 'project_2017_08_02_13_54_38.log'
try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)
/data/jkrieger/programs/arachnid_11_copy/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: '.ara-control.crash_report_2017_08_02_13_54_38.0'
try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)
2017-08-02 13:54:38,261 INFO Program: arachnid.util.prepvol
2017-08-02 13:54:38,261 INFO PID: 15834
2017-08-02 13:54:38,261 INFO Created: 1501696477
2017-08-02 13:54:38,261 INFO Multi-threading with OpenMP - enabled
2017-08-02 13:54:38,266 INFO Multi-threading with OpenMP - set thread count to 1
2017-08-02 13:54:38,267 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:54:38,267 INFO Window size: 160
2017-08-02 13:54:38,267 INFO Pixel size: 0.700000
2017-08-02 13:54:38,849 INFO Finished: 0,1 - Time left: --
2017-08-02 13:54:38,849 WARNING Errors occurred during run

See .ara-control.crash_report for more details
2017-08-02 13:54:38,850 INFO Running defocus
2017-08-02 13:54:38,862 INFO Workflow ended

and the crash report says:

2017-08-02 13:54:38,259 WARNING Failed to load EMAN2 module
2017-08-02 13:54:38,259 WARNING Failed to load _spider_filter.so module
2017-08-02 13:54:38,259 WARNING Failed to load _image_utility.so module - certain functions will not be available
2017-08-02 13:54:38,260 WARNING Failed to load _resample.so module
2017-08-02 13:54:38,260 WARNING Failed to load _spider_interpolate.so module
2017-08-02 13:54:38,260 WARNING Failed to load _spider_rotate.so module
2017-08-02 13:54:38,260 WARNING Failed to load _spider_rotate.so module
2017-08-02 13:54:38,260 WARNING Failed to load _spider_ctf.so module
2017-08-02 13:54:38,260 WARNING Failed to load _spider_reconstruct.so
2017-08-02 13:54:38,261 INFO Program: arachnid.util.prepvol
2017-08-02 13:54:38,261 INFO Version: UNKNOWN
2017-08-02 13:54:38,261 INFO PID: 15834
2017-08-02 13:54:38,261 INFO Created: 1501696477
2017-08-02 13:54:38,261 INFO Multi-threading with OpenMP - enabled
2017-08-02 13:54:38,266 INFO Multi-threading with OpenMP - set thread count to 1
2017-08-02 13:54:38,267 INFO Skipping 0 files - restarting from the beginning - configuration file changed
2017-08-02 13:54:38,267 INFO Window size: 160
2017-08-02 13:54:38,267 INFO Pixel size: 0.700000
2017-08-02 13:54:38,847 ERROR Unexpected error in process - report this problem to the developer
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/parallel/process_tasks.py", line 75, in process_mp
f = process(val, **extra)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/util/prepvol.py", line 214, in process
vol = ndimage_interpolate.resample_fft_fast(vol, apix/cur_apix)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/image/ndimage_interpolate.py", line 144, in resample_fft_fast
_resample.resample_fft_center_3(img, fout)
AttributeError: 'NoneType' object has no attribute 'resample_fft_center_3'
2017-08-02 13:54:38,849 INFO Finished: 0,1 - Time left: --
2017-08-02 13:54:38,849 WARNING Errors occurred during run

See .ara-control.crash_report for more details
2017-08-02 13:54:38,850 INFO Running defocus
2017-08-02 13:54:38,861 ERROR Invalid option
Traceback (most recent call last):
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/gui/Monitor.py", line 208, in _run_worker
prog.check_options_validity()
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/app/program.py", line 443, in check_options_validity
check_options(self.main_module, self.main_template, self.dependents, self.values)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/app/program.py", line 877, in check_options
if hasattr(main_module, "check_options"): main_module.check_options(options, True)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/pyspider/defocus.py", line 750, in check_options
if spider_file.is_spider_image(options.input_files[0]) and options.data_ext == "":
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/spider/spider_file.py", line 84, in is_spider_image
filename = ndimage_file.readlinkabs(filename)
File "/data/jkrieger/programs/arachnid_11_copy/arachnid/core/image/ndimage_file.py", line 497, in readlinkabs
if not os.path.exists(link): raise IOError, "Cannot find file: %s"%(link)
IOError: Cannot find file: other/mics/mic_00000.dat
2017-08-02 13:54:38,862 INFO Workflow ended

@ezralanglois
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ezralanglois commented Aug 2, 2017 via email

@jamesmkrieger
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I seem to get that problem regardless of whether I build, develop or install. This time I did develop I think.

@ezralanglois
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You should not get it on install. At least I don't see this on my box. You can locate them witch which ara-control and then delete all the ara-* ones and install again.

@jamesmkrieger
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I just made a new copy and did install and I still get those lines in the crash report.

@ezralanglois
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I think you need to uninstalled it from anaconda first.
You can run the following command
conda clean -a --dry-run
To see what will be removed, then if you are OK with it, then run:
conda clean -a

That should removed the installed version of arachnid, then try to reinstall.

@jamesmkrieger
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jamesmkrieger commented Aug 4, 2017 via email

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Replace sp-reference with ara-prepvol in the workflow ezralanglois/arachnid
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@ezralanglois @jamesmkrieger