Python crashes when running any module but PyHum.read

[LZarri]

The script used is attached below. I have installed all modules and am running the newest PyHum, 1.3.9. Windows 7 with 64 bit Python and Anaconda package. I get the message that python has crashed (or the iPython kernel if I am using Spyder) when I run any module but PyHum.read. Any advice?

Thanks, Liam

BuscombeFixR00217.txt

[dbuscombe-usgs]

Please paste the error message

[danhamill]

Liam,

I would recommend calling your script from cmd. I do not think spyder supports parallel processing and does not behave as expected when you do.

Often times spyder will report the something other than actual error causing the program to crash. Even worse sometimes it won't report any error and the kernel will crash.

On Feb 22, 2016, at 8:29 AM, Daniel Buscombe notifications@github.com wrote:

Please paste the error message

— Reply to this email directly or view it on GitHub.

[LZarri]

Attempted to run PyHum.test from Windows Powershell and even this causes Python to crash (see image below) any suggestions?

Thanks, Liam

[LZarri]

In addition: danhamill I have tried running PyHum.test from both cmd and Powershell; both have crashed. I am trying the PyHum.test through previous versions (1.3.8, 1.3.7, ect) to see if an older version will work.

[danhamill]

I am trying to reproduce this error on my machine as well. I am using windows 10, 64 bit python. It is working on my machine, but is printing out the warning install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree lots of times…

PS C:\Users\dan> python -c "import PyHum; PyHum.dotest()" install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree Input file is C:\Users\dan\pyhum_test\test.DAT Son files are in C:\Users\dan\pyhum_test cs2cs arguments are epsg:26949 Draft: 0.3 Celerity of sound: 1450.0 m/s Port and starboard will be flipped Transducer length is 0.108 m Bed picking is auto Chunks based on distance of 100 m Data is from the 998 series Heading based on course-over-ground Checking the epsg code you have chosen for compatibility with Basemap ... ... epsg code compatible WARNING: Because files have to be read in byte by byte, this could take a very long time ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree port sonar data will be parsed into 3.0, 99 m chunks starboard sonar data will be parsed into 3.0, 99 m chunks memory-mapping failed in sliding window - trying memory intensive version low-freq. sonar data will be parsed into 3.0, 99 m chunks high-freq. sonar data will be parsed into 3.0, 99 m chunks memory-mapping failed in sliding window - trying memory intensive version Processing took 53.8397424164 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test Max. transducer power is 1000.0 W pH is 7.0 Temperature is 10.0 install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree Processing took 55.7617520289 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test Window is 31 square pixels install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree Processing took 99.2304036867 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test Window is 100 square pixels Min shift is 10 pixels Image will be sampled every 15 pixels Number of sediment classes: 4 Max scale as inverse fraction of data length: 20 Notes per octave: 4 [Default] Number of processors is 8 processing port side ... processing starboard side ... 30316 windows to process install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree 30316 windows to process install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree 30316 windows to process install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree Plotting ... Plotting ... Plotting ... Processing took 174.409865997 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test cs2cs arguments are epsg:26949 Gridding resolution: 99.0 Mode for gridding: 1 Number of nearest neighbours for gridding: 64 Threshold number of standard deviations in sidescan intensity per grid cell up to which to accept: 5 getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... drawing and printing map ... grid resolution is 0.519345 getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... drawing and printing map ... grid resolution is 0.519345 getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... drawing and printing map ... grid resolution is 0.519345 Processing took 179.663404535 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test cs2cs arguments are epsg:26949 Gridding resolution: 1.0 Mode for gridding: 1 Number of nearest neighbours for gridding: 64 Threshold number of standard deviations in texture lengthscale per grid cell up to which to accept: getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... getting point cloud ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree creating kmz file ... Processing took 413.873785254 seconds to analyse Done! Input file is C:\Users\dan\pyhum_test\test.DAT Sonar file path is C:\Users\dan\pyhum_test cs2cs arguments are epsg:26949 Beam is 20.0 deg pH is 7.0 Temperature is 10.0 Dwnward sonar freq. is 200.0 number of records for integration is 5 number of returned acoustic clusters is 3 install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree drawing and printing map ... drawing and printing map ... drawing and printing map ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree drawing and printing map ... drawing and printing map ... drawing and printing map ... install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/pykdtree drawing and printing map ... drawing and printing map ... drawing and printing map ...

@dbuscombe-usgs I just installed the latest version of PyHum (1.3.9) and noticed it changed by joblib install from version 0.9.4 to version 0.7.1. Is that new to this version?

Any ideas why I am getting the memory-mapping failed in sliding window - trying memory intensive version warning in the PyHum.read module?

On Mon, Feb 22, 2016 at 1:43 PM, LZarri notifications@github.com wrote:

In addition: danhamill I have tried running PyHum.test from both cmd and

Powershell; both have crashed. I am trying the PyHum.test through previous versions (1.3.8, 1.3.7, ect) to see if an older version will work.

— Reply to this email directly or view it on GitHub https://github.com/dbuscombe-usgs/PyHum/issues/16#issuecomment-187374748 .

​

On Mon, Feb 22, 2016 at 1:43 PM, LZarri notifications@github.com wrote:

In addition: danhamill I have tried running PyHum.test from both cmd and Powershell; both have crashed. I am trying the PyHum.test through previous versions (1.3.8, 1.3.7, ect) to see if an older version will work.

— Reply to this email directly or view it on GitHub https://github.com/dbuscombe-usgs/PyHum/issues/16#issuecomment-187374748 .

[LZarri]

PyScripter also crashed, but it gave me more error information: EOFError: [Errno 10054]. I am running this from my work station so there may be interference from work firewall (???) however I reckon that is unlikely given that python crashes when I run the script on my personal computer as well.

[LZarri]

PyScripter finally threw a full error message when running PyHum.dotest()

[LZarri]

The fault module name appears to be ntdll.dll

[dbuscombe-usgs]

The OS kernel issue, i.e. related to your operating system, or could be a hardware problem. Do you have issued running other python scripts? other _compiled _python scripts? Are you running a 32-bit python on a 64-bit machine (or vice-versa)?

[dbuscombe-usgs]

@danhamill I thought I had fixed memory mapping issues on Windows. Obviously not. I am in the field the rest of the week so will look into it next week. I am beginning to hate Windows - nothing ever works properly.

[LZarri]

I have ran the modules read, correct, rmshadows and map each independently. The only one that works is read. Could there perhaps be a mistake in the way my computer is interpreting the output of the PyHum.read module that causes an error in the other modules? That being said, a crash of python could indicate that it is not a problem with the code but instead with my hardware.

Dan, do you have a suggestion of another compiled python script I could run to test whether the problem is with my hardware?

I am running 64 bit python on a 64 bit machine.

Thanks, Liam

[LZarri]

@danhamill You successfully ran the script with Windows 10? Perhaps that is my problem-I am still running windows 7...I guess its time to get with the program and upgrade.

[danhamill]

I don't think windows 10 would help much to resolve the issue with python crashing. I check all the program you use for their compatibility with window 10 before updating. I had trouble getting drivers for my video card and regularly got BSOD.

Based on the errors you have reported above, I would try a fresh anaconda install. That might eliminate any firmware related issues and help isolate a hardware problem; if there are any. You could also check your system's environment variable and check for conflicting python paths.

Which version of python are you using?

I am using 2.7.11.

On Wed, Feb 24, 2016 at 4:06 PM, LZarri notifications@github.com wrote:

@danhamill https://github.com/danhamill You successfully ran the script with Windows 10? Perhaps that is my problem-I am still running windows 7...I guess its time to get with the program and upgrade.

— Reply to this email directly or view it on GitHub https://github.com/dbuscombe-usgs/PyHum/issues/16#issuecomment-188503145 .

[LZarri]

I am also using Python 2.7.11

I tried a fresh install of anaconda on my work computer, personal computer, and friends windows 10 computer. All of these platforms exhibit a python crash and the Event Viewer indicates that the problem is with the ntdll.dll

[LZarri]

@danhamill Do you use the anaconda distribution?

[cambodine]

Adding my two cents: the last version of PyHum I successfully used was 1.3.3 from Anaconda 2.2 (I believe). I uninstalled anaconda and updated to newest version 2.5. I'm using Windows 7 64-bit.

Using Anaconda Cloud api site https://api.anaconda.org
Current conda install:

             platform : win-64
        conda version : 3.19.3
  conda-build version : 1.19.0
       python version : 2.7.11.final.0
     requests version : 2.9.1
     root environment : C:\Users\cameron.bodine\AppData\Local\Continuum\Anaconda
2  (writable)
  default environment : C:\Users\cameron.bodine\AppData\Local\Continuum\Anaconda
2
     envs directories : C:\Users\cameron.bodine\AppData\Local\Continuum\Anaconda
2\envs
        package cache : C:\Users\cameron.bodine\AppData\Local\Continuum\Anaconda
2\pkgs
         channel URLs : https://repo.continuum.io/pkgs/free/win-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/win-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : None
    is foreign system : False

I have the following packages installed:

[Anaconda2] C:\Users\cameron.bodine>conda list
# packages in environment at C:\Users\cameron.bodine\AppData\Local\Continuum\Ana
conda2:
#
alabaster                 0.7.7                    py27_0    <unknown>
anaconda                  2.5.0               np110py27_0    <unknown>
anaconda-client           1.2.2                    py27_0    <unknown>
argcomplete               1.0.0                    py27_1    <unknown>
astropy                   1.1.1               np110py27_0    <unknown>
babel                     2.2.0                    py27_0    <unknown>
backports-abc             0.4                       <pip>
backports.ssl-match-hostname 3.4.0.2                   <pip>
backports_abc             0.4                      py27_0    <unknown>
basemap                   1.0.7               np110py27_0    defaults
beautifulsoup4            4.4.1                    py27_0    <unknown>
bitarray                  0.8.1                    py27_1    <unknown>
blaze                     0.9.0                     <pip>
blaze-core                0.9.0                    py27_0    <unknown>
bokeh                     0.11.0                   py27_0    <unknown>
boto                      2.39.0                   py27_0    <unknown>
bottleneck                1.0.0               np110py27_0    <unknown>
bzip2                     1.0.6                     vc9_2  [vc9]  <unknown>
cdecimal                  2.3                      py27_1    <unknown>
cffi                      1.2.1                    py27_0    <unknown>
clyent                    1.2.0                    py27_0    <unknown>
colorama                  0.3.6                    py27_0    <unknown>
comtypes                  1.1.2                    py27_0    <unknown>
conda                     3.19.3                   py27_0    defaults
conda-build               1.19.0                   py27_0    <unknown>
conda-env                 2.4.5                    py27_0    defaults
configobj                 5.0.6                    py27_0    <unknown>
console_shortcut          0.1.1                    py27_1    <unknown>
cryptography              1.0.2                    py27_0    <unknown>
curl                      7.45.0                    vc9_1  [vc9]  <unknown>
cycler                    0.10.0                   py27_0    defaults
cython                    0.23.4                   py27_0    <unknown>
cytoolz                   0.7.5                    py27_0    <unknown>
dask                      0.8.0                     <pip>
datashape                 0.5.0                    py27_0    <unknown>
decorator                 4.0.6                    py27_0    <unknown>
docutils                  0.12                     py27_1    <unknown>
enum34                    1.1.2                    py27_0    <unknown>
et-xmlfile                1.0.1                     <pip>
et_xmlfile                1.0.1                    py27_0    <unknown>
fastcache                 1.0.2                    py27_0    <unknown>
flask                     0.10.1                   py27_1    <unknown>
freetype                  2.5.5                     vc9_0  [vc9]  <unknown>
funcsigs                  0.4                      py27_0    <unknown>
futures                   3.0.3                    py27_0    <unknown>
gevent                    1.0.2                    py27_0    <unknown>
gevent-websocket          0.9.5                    py27_0    <unknown>
greenlet                  0.4.9                    py27_0    <unknown>
grin                      1.2.1                    py27_2    <unknown>
h5py                      2.5.0               np110py27_4    <unknown>
hdf5                      1.8.15.1                  vc9_4  [vc9]  <unknown>
idna                      2.0                      py27_0    <unknown>
ipaddress                 1.0.14                   py27_0    <unknown>
ipykernel                 4.2.2                    py27_0    <unknown>
ipython                   4.0.3                    py27_0    <unknown>
ipython-genutils          0.1.0                     <pip>
ipython-notebook          4.0.4                    py27_3    <unknown>
ipython-qtconsole         4.0.1                    py27_4    <unknown>
ipython_genutils          0.1.0                    py27_0    <unknown>
ipywidgets                4.1.1                    py27_0    <unknown>
itsdangerous              0.24                     py27_0    <unknown>
jdcal                     1.2                      py27_0    <unknown>
jedi                      0.9.0                    py27_0    <unknown>
jinja2                    2.8                      py27_0    <unknown>
joblib                    0.7.1                     <pip>
jpeg                      8d                        vc9_0  [vc9]  <unknown>
jsonschema                2.4.0                    py27_0    <unknown>
jupyter                   1.0.0                    py27_1    <unknown>
jupyter-client            4.1.1                     <pip>
jupyter-console           4.1.0                     <pip>
jupyter-core              4.0.6                     <pip>
jupyter_client            4.1.1                    py27_0    <unknown>
jupyter_console           4.1.0                    py27_0    <unknown>
jupyter_core              4.0.6                    py27_0    <unknown>
launcher                  1.0.0                         4    <unknown>
libpng                    1.6.17                    vc9_1  [vc9]  <unknown>
libsodium                 1.0.3                         0    <unknown>
libtiff                   4.0.6                     vc9_1  [vc9]  <unknown>
llvmlite                  0.8.0                    py27_0    <unknown>
lxml                      3.5.0                    py27_0    <unknown>
markupsafe                0.23                     py27_0    <unknown>
matplotlib                1.5.1               np110py27_0    <unknown>
menuinst                  1.3.2                    py27_0    defaults
mistune                   0.7.1                    py27_0    <unknown>
mkl                       11.3.1                        0    <unknown>
mkl-service               1.1.2                    py27_0    <unknown>
msvc_runtime              1.0.1                     vc9_0  [vc9]  defaults
multipledispatch          0.4.8                    py27_0    <unknown>
nbconvert                 4.1.0                    py27_0    <unknown>
nbformat                  4.0.1                    py27_0    <unknown>
networkx                  1.11                     py27_0    <unknown>
nltk                      3.1                      py27_0    <unknown>
node-webkit               0.10.1                        0    <unknown>
nose                      1.3.7                    py27_0    <unknown>
notebook                  4.1.0                    py27_0    <unknown>
numba                     0.23.1              np110py27_0    <unknown>
numexpr                   2.4.6               np110py27_1    <unknown>
numpy                     1.10.4                   py27_0    <unknown>
odo                       0.4.0                    py27_0    <unknown>
openpyxl                  2.3.2                    py27_0    <unknown>
pandas                    0.17.1              np110py27_0    <unknown>
path.py                   8.1.2                    py27_1    <unknown>
patsy                     0.4.0               np110py27_0    <unknown>
pep8                      1.7.0                    py27_0    <unknown>
pickleshare               0.5                      py27_0    <unknown>
pil                       1.1.7                    py27_0    defaults
pillow                    3.1.1                    py27_0    defaults
pip                       8.0.3                    py27_0    defaults
ply                       3.8                      py27_0    <unknown>
psutil                    3.4.2                    py27_0    <unknown>
py                        1.4.31                   py27_0    <unknown>
pyasn1                    0.1.9                    py27_0    <unknown>
pycosat                   0.6.1                    py27_0    defaults
pycparser                 2.14                     py27_0    <unknown>
pycrypto                  2.6.1                    py27_3    defaults
pyflakes                  1.0.0                    py27_0    <unknown>
pygments                  2.1                      py27_0    <unknown>
pyhum                     1.3.9                     <pip>
pyopenssl                 0.15.1                   py27_1    <unknown>
pyparsing                 2.0.3                    py27_0    <unknown>
pyproj                    1.9.5                     <pip>
pyqt                      4.11.4                   py27_5    defaults
pyreadline                2.1                      py27_0    <unknown>
pyresample                1.1.6                     <pip>
pytables                  3.2.2               np110py27_1    <unknown>
pytest                    2.8.5                    py27_0    <unknown>
python                    2.7.11                        2    <unknown>
python-dateutil           2.4.2                    py27_0    <unknown>
pytz                      2015.7                   py27_0    <unknown>
pywin32                   219                      py27_2    <unknown>
pyyaml                    3.11                     py27_2    defaults
pyzmq                     15.2.0                   py27_0    <unknown>
qt                        4.8.7                     vc9_6  [vc9]  defaults
qtconsole                 4.1.1                    py27_0    <unknown>
requests                  2.9.1                    py27_0    defaults
rope                      0.9.4                    py27_1    <unknown>
scikit-image              0.11.3              np110py27_0    <unknown>
scikit-learn              0.17                np110py27_2    <unknown>
scipy                     0.17.0              np110py27_0    <unknown>
setuptools                20.1.1                   py27_0    defaults
simplegeneric             0.8.1                    py27_0    <unknown>
simplekml                 1.2.8                     <pip>
singledispatch            3.4.0.3                  py27_0    <unknown>
sip                       4.16.9                   py27_2    <unknown>
six                       1.10.0                   py27_0    <unknown>
snowballstemmer           1.2.1                    py27_0    <unknown>
sockjs-tornado            1.0.1                    py27_0    <unknown>
sphinx                    1.3.5                    py27_0    <unknown>
sphinx-rtd-theme          0.1.9                     <pip>
sphinx_rtd_theme          0.1.9                    py27_0    <unknown>
spyder                    2.3.8                    py27_0    <unknown>
spyder-app                2.3.8                    py27_0    <unknown>
sqlalchemy                1.0.11                   py27_0    <unknown>
ssl_match_hostname        3.4.0.2                  py27_0    <unknown>
statsmodels               0.6.1               np110py27_0    <unknown>
sympy                     0.7.6.1                  py27_0    <unknown>
tables                    3.2.2                     <pip>
tk                        8.5.18                    vc9_0  [vc9]  <unknown>
toolz                     0.7.4                    py27_0    <unknown>
tornado                   4.3                      py27_0    <unknown>
traitlets                 4.1.0                    py27_0    <unknown>
unicodecsv                0.14.1                   py27_0    <unknown>
werkzeug                  0.11.3                   py27_0    <unknown>
wheel                     0.29.0                   py27_0    defaults
xlrd                      0.9.4                    py27_0    <unknown>
xlsxwriter                0.8.4                    py27_0    <unknown>
xlwings                   0.6.4                    py27_1    <unknown>
xlwt                      1.0.0                    py27_0    <unknown>
zlib                      1.2.8                     vc9_2  [vc9]  <unknown>

When running the test pyhum script, I recieve the following output/error:

`[Anaconda2] C:\Users\cameron.bodine>python -c "import PyHum; PyHum.test.dotest()
"
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
Directory not copied. Error: [Error 183] Cannot create a file when that file alr
eady exists: 'C:\\Users\\cameron.bodine\\pyhum_test'
Input file is C:\Users\cameron.bodine\pyhum_test\test.DAT
Son files are in C:\Users\cameron.bodine\pyhum_test
cs2cs arguments are epsg:26949
Draft: 0.3
Celerity of sound: 1450.0 m/s
Port and starboard will be flipped
Transducer length is 0.108 m
Bed picking is auto
Chunks based on distance of 100 m
Data is from the 998 series
Heading based on course-over-ground
Checking the epsg code you have chosen for compatibility with Basemap ...
... epsg code compatible
WARNING: Because files have to be read in byte by byte,
this could take a very long time ...
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
install pykdtree for faster kd-tree operations: https://github.com/storpipfugl/p
ykdtree
port sonar data will be parsed into 3.0, 99 m chunks
starboard sonar data will be parsed into 3.0, 99 m chunks
memory-mapping failed in sliding window - trying memory intensive version
low-freq. sonar data will be parsed into 3.0, 99 m chunks
high-freq. sonar data will be parsed into 3.0, 99 m chunks
memory-mapping failed in sliding window - trying memory intensive version
Processing took  88.5734137794 seconds to analyse
Done!
Input file is C:\Users\cameron.bodine\pyhum_test\test.DAT
Sonar file path is C:\Users\cameron.bodine\pyhum_test
Max. transducer power is 1000.0 W
pH is 7.0
Temperature is 10.0

[Anaconda2] C:\Users\cameron.bodine>`

Which results in the same "python.exe has stopped working" as listed in an earlier comment. I have attempted the scripts from the Anaconda Prompt as well as the Windows Command Prompt. I updated my system variables to match the updated version of Anaconda and as a precaution, removed the variables for my Python installation with ArcGIS. Any thoughts?

[dbuscombe-usgs]

Thanks for the detailed info - I will try to get on a Windows machine in the next few days and troubleshoot. At this stage, I'm not sure what I did to cause such errors

[LZarri]

Here is an error code that was thrown after the Python window crashed during PyHum.read after listing temp = 10.0

Working on debugging using pdb to find what line the error is occuring on. In the meantime, I will attempt to run PyHum on Linux Ubuntu.

[LZarri]

I believe the problem is caused by the installation of Anaconda 2.5. I uninstalled Anaconda and reinstalled Python with the appropriate packages and this has resolved the error. @cambodine have you tried this?

[cambodine]

I will try it. @LZarri which version of Anaconda ended up working for you? My current installation is 2.5.

[LZarri]

I completely uninstall Anaconda and then reinstalled only Python 2.7.11 from the source page. I manually installed most of the necessary python libraries using pip, but had to download SciPy and Basemap from the Unofficial Windows Binaries for Python webpage because for some reason pip could not pull them without having the .whl file.

I am going to check today if Anaconda 2.4 is compatible with PyHum.

[danhamill]

@LZarri @cambodine On my windows 7 machine, PyHum runs on anaconda 2.1.0

On Tue, Mar 8, 2016 at 9:56 AM, LZarri notifications@github.com wrote:

I completely uninstall Anaconda and then reinstalled only Python 2.7.11 from the source page. I manually installed most of the necessary python libraries using pip, but had to download SciPy and Basemap from the Unofficial Windows Binaries for Python http://www.lfd.uci.edu/%7Egohlke/pythonlibs/ webpage because for some reason pip could not pull them without having the .whl file.

I am going to check today if Anaconda 2.4 is compatible with PyHum.

— Reply to this email directly or view it on GitHub https://github.com/dbuscombe-usgs/PyHum/issues/16#issuecomment-193866240 .

[LZarri]

PyHum also runs on Anaconda 2.4.1 it must be Anaconda 2.5 that is causing the problem.