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ezralanglois / arachnid

Image analysis software for cryo-electron microscopy
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Arachnid requires that spider be in /home/ezra #8

Open jamesmkrieger opened 7 years ago

jamesmkrieger commented 7 years ago

Otherwise it said it could not find the spider binary even though it was specified on the GUI.

ezralanglois commented 7 years ago

Thanks will look into this when I get a chance.

ezralanglois commented 7 years ago

If you can provide an exception stack trace or crash report, that would be a big help. I don't remember the code well enough to fix this quickly at the moment.

jamesmkrieger commented 7 years ago

I'm failing to reproduce this bug now. The controller won't go back to the previous steps.

jamesmkrieger commented 7 years ago

It is now running spider as /data/jkrieger/programs/anaconda2/bin/spider_linux_mp_opt64 but there is something else not found in the traceback.

/data/jkrieger/programs/arachnid_skype_day/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: '.ara-control.crash_report_2017_07_27_15_24_43.0' try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED) /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_skype_day/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: 'project_2017_07_27_15_24_43.log' try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED) /data/jkrieger/programs/arachnid_skype_day/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: 'project_2017_07_27_15_25_55.log' try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED) /data/jkrieger/programs/arachnid_skype_day/arachnid/core/app/tracing.py:448: UserWarning: Duplicate name: '.ara-control.crash_report_2017_07_27_15_25_55.0' try: zf.write(filename, arcname=arcname)#, compress_type=zipfile.ZIP_STORED)

__`O O'/ SPIDER -- COPYRIGHT ,xXXXx_ HEALTH RESEARCH INC., ALBANY, NY. xXXXx__ / /xxx\ \ VERSION: UNIX 21.00 ISSUED: 01/03/2013 / \ DATE: 27-JUL-2017 AT 15:25:55

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

jamesmkrieger commented 7 years ago

The files related to this are copied here. I'm not sure if this is the same issue or not though.

jkrieger@zeus:/data/jkrieger/programs/arachnid_skype_day$ cat .ara-control.crash_report.0 2017-07-27 15:25:56,079 WARNING Failed to load EMAN2 module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_filter.so module 2017-07-27 15:25:56,079 WARNING Failed to load _image_utility.so module - certain functions will not be available 2017-07-27 15:25:56,079 WARNING Failed to load _resample.so module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_interpolate.so module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_rotate.so module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_rotate.so module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_ctf.so module 2017-07-27 15:25:56,079 WARNING Failed to load _spider_reconstruct.so 2017-07-27 15:25:56,080 INFO Program: arachnid.app.autopick 2017-07-27 15:25:56,080 INFO Version: UNKNOWN 2017-07-27 15:25:56,080 INFO PID: 5878 2017-07-27 15:25:56,080 INFO Created: 1501183554 2017-07-27 15:25:56,080 INFO Multi-threading with OpenMP - enabled 2017-07-27 15:25:56,082 INFO Multi-threading with OpenMP - set thread count to 1 2017-07-27 15:25:56,082 INFO Skipping 0 files - restarting from the beginning - configuration file changed 2017-07-27 15:25:56,082 INFO Mask Multiplier: 1.000000 2017-07-27 15:25:56,082 INFO Peak limit: 2000.000000 2017-07-27 15:25:56,082 ERROR ***Unexpected error occurred: AttributeError: 'NoneType' object has no attribute 'sinc_blackman_kernel'

See .ara-control.crash_report for more details 2017-07-27 15:25:56,082 ERROR Unexpected error occurred Traceback (most recent call last): File "/data/jkrieger/programs/arachnid_skype_day/arachnid/core/app/program.py", line 314, in launch_program main_template.main(args, main_module, **param) File "/data/jkrieger/programs/arachnid_skype_day/arachnid/core/app/file_processor.py", line 206, in main f = initialize(files, extra) File "/data/jkrieger/programs/arachnid_skype_day/arachnid/app/autopick.py", line 775, in initialize return sorted(lfcpick.initialize(files, param)) File "/data/jkrieger/programs/arachnid_skype_day/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_skype_day/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' 2017-07-27 15:25:56,083 INFO Workflow ended jkrieger@zeus:/data/jkrieger/programs/arachnid_skype_day$ cat project.log 2017-07-27 15:25:56,080 INFO Program: arachnid.app.autopick 2017-07-27 15:25:56,080 INFO PID: 5878 2017-07-27 15:25:56,080 INFO Created: 1501183554 2017-07-27 15:25:56,080 INFO Multi-threading with OpenMP - enabled 2017-07-27 15:25:56,082 INFO Multi-threading with OpenMP - set thread count to 1 2017-07-27 15:25:56,082 INFO Skipping 0 files - restarting from the beginning - configuration file changed 2017-07-27 15:25:56,082 INFO Mask Multiplier: 1.000000 2017-07-27 15:25:56,082 INFO Peak limit: 2000.000000 2017-07-27 15:25:56,082 ERROR ***Unexpected error occurred: AttributeError: 'NoneType' object has no attribute 'sinc_blackman_kernel'

See .ara-control.crash_report for more details 2017-07-27 15:25:56,083 INFO Workflow ended jkrieger@zeus:/data/jkrieger/programs/arachnid_skype_day$ cat control.log 2017-07-27 15:25:53,301 WARNING Assuming image is MRC format - format is not correct (Likely this image came from Yifan's GPU alignment)

ezralanglois commented 7 years ago

Try the following, it may fix the problem

python setup.py build_ext --inplace

jamesmkrieger commented 7 years ago

That doesn't make any binaries in my path. Where did it put them?

ezralanglois commented 7 years ago

It should place the binaries in the same folder as the source files. This allows Python to find them easier.

If that does not work, then you may just need to run the install command. If you do that then you have to remember to run it after each change.

On Fri, Jul 28, 2017 at 6:57 AM, James Krieger notifications@github.com wrote:

That doesn't make any binaries in my path. Where did it put them?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ezralanglois/arachnid/issues/8#issuecomment-318658786, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAeLvPWzTcZH3dq7VonV7skfojRHB3wks5sSei_gaJpZM4OjHzr .

jamesmkrieger commented 7 years ago

No, that didn't work:

jkrieger@zeus:~/programs/arachnid_copy$ sudo find / -iname ara-control /data/jkrieger/programs/anaconda2/pkgs/arachnid-dev-0.2.0-py27_1/bin/ara-control /data/jkrieger/bin/EMAN2.2/bin/ara-control

ezralanglois commented 7 years ago

Sorry, I should have said shared libs, the .so files

On Fri, Jul 28, 2017, 7:39 AM James Krieger notifications@github.com wrote:

No, that didn't work:

jkrieger@zeus:~/programs/arachnid_copy$ sudo find / -iname ara-control

/data/jkrieger/programs/anaconda2/pkgs/arachnid-dev-0.2.0-py27_1/bin/ara-control /data/jkrieger/bin/EMAN2.2/bin/ara-control

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/ezralanglois/arachnid/issues/8#issuecomment-318669723, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAeLk5mwz2cV1_j-G-AvCBdmnX5rPGDks5sSfKvgaJpZM4OjHzr .