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ezralanglois / arachnid

Image analysis software for cryo-electron microscopy
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AttributeError: 'module' object has no attribute '__TypeDict__' #9

Open jamesmkrieger opened 7 years ago

jamesmkrieger commented 7 years ago

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 commented 7 years ago

One workaround is to downgrade mpi4py

ezralanglois commented 7 years ago

So I remember how to fix this:

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

https://github.com/radiocosmology/caput/commit/b2726522f4c273e9a3d2fc648b181400fe594855

ezralanglois commented 7 years ago

mpi4py=1.3 might work

jamesmkrieger commented 7 years ago

Yes, downgrading mpi4py made it work. Thanks

On Tue, Jul 25, 2017 at 5:21 PM, Robert Langlois notifications@github.com wrote:

mpi4py=1.3 might work

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ezralanglois commented 7 years ago

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

jamesmkrieger commented 7 years ago

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 commented 7 years ago

The latest version also gives this error with mpi4py=1.3

jamesmkrieger commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

The first bug may be fixed by

python setup.py build_ext --inplace

jamesmkrieger commented 7 years ago

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

ezralanglois commented 7 years ago

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 commented 7 years ago

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

jamesmkrieger commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

My first guess is that sp-reference crashed or spider hung for some reason.

Is there a crash report?

jamesmkrieger commented 7 years ago

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 commented 7 years ago

This looks bad after the install. If I have time later tonight, I will dig into it.

On Tue, Aug 1, 2017 at 2:51 PM, James Krieger notifications@github.com wrote:

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

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jamesmkrieger commented 7 years ago

ok thanks Robert

ezralanglois commented 7 years ago

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 commented 7 years ago

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

jamesmkrieger commented 7 years ago

Ok I'll try tomorrow

On Wed, Aug 2, 2017 at 12:12 AM Robert Langlois notifications@github.com wrote:

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

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ezralanglois commented 7 years ago

Also, if you have a chance, try this branch out (https://github.com/ezralanglois/arachnid/pull/11) it may resolve the issue too.

jamesmkrieger commented 7 years ago

Ok

On Wed, Aug 2, 2017 at 12:14 AM Robert Langlois notifications@github.com wrote:

Also, if you have a chance, try this branch out (#11 https://github.com/ezralanglois/arachnid/pull/11) it may resolve the issue too.

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jamesmkrieger commented 7 years ago

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 commented 7 years ago

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

jamesmkrieger commented 7 years ago

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 commented 7 years ago

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

jamesmkrieger commented 7 years ago

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

jamesmkrieger commented 7 years ago

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 commented 7 years ago

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

jamesmkrieger commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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

The shared libraries are not loading again. Did you install it?

On Wed, Aug 2, 2017 at 10:56 AM, James Krieger notifications@github.com wrote:

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)#, compresstype=zipfile.ZIP STORED) /data/jkrieger/programs/arachnid_11_copy/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: '.ara-control.crashreport 2017_08_02_13_54_38.0' try: zf.write(filename, arcname=arcname)#, compresstype=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

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jamesmkrieger commented 7 years ago

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

ezralanglois commented 7 years ago

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 commented 7 years ago

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

ezralanglois commented 7 years ago

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 commented 7 years ago

Ok

On Thu, Aug 3, 2017 at 8:25 PM Robert Langlois notifications@github.com wrote:

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.

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