Arachnid requires that spider be in /home/ezra #8

jamesmkrieger · 2017-07-25T21:00:47Z

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

ezralanglois · 2017-07-25T21:01:29Z

Thanks will look into this when I get a chance.

ezralanglois · 2017-07-26T02:42:37Z

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 · 2017-07-27T19:14:13Z

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

jamesmkrieger · 2017-07-27T19:28:01Z

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 · 2017-07-27T19:31:31Z

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 · 2017-07-28T02:59:42Z

Try the following, it may fix the problem

python setup.py build_ext --inplace

jamesmkrieger · 2017-07-28T13:57:19Z

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

ezralanglois · 2017-07-28T14:04:16Z

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 ***@***.***> 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 <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAeLvPWzTcZH3dq7VonV7skfojRHB3wks5sSei_gaJpZM4OjHzr> .

jamesmkrieger · 2017-07-28T14:39:43Z

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 · 2017-07-28T14:52:04Z

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

…

On Fri, Jul 28, 2017, 7:39 AM James Krieger ***@***.***> wrote: No, that didn't work: ***@***.***:~/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 <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAeLk5mwz2cV1_j-G-AvCBdmnX5rPGDks5sSfKvgaJpZM4OjHzr> .

ezralanglois added the bug label Jul 25, 2017

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Arachnid requires that spider be in /home/ezra #8

Arachnid requires that spider be in /home/ezra #8

jamesmkrieger commented Jul 25, 2017

ezralanglois commented Jul 25, 2017

ezralanglois commented Jul 26, 2017

jamesmkrieger commented Jul 27, 2017

jamesmkrieger commented Jul 27, 2017

jamesmkrieger commented Jul 27, 2017 •

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ezralanglois commented Jul 28, 2017

jamesmkrieger commented Jul 28, 2017

ezralanglois commented Jul 28, 2017 via email

jamesmkrieger commented Jul 28, 2017

ezralanglois commented Jul 28, 2017 via email

Arachnid requires that spider be in /home/ezra #8

Arachnid requires that spider be in /home/ezra #8

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jamesmkrieger commented Jul 25, 2017

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jamesmkrieger commented Jul 27, 2017

jamesmkrieger commented Jul 27, 2017

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jamesmkrieger commented Jul 28, 2017

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