Tuesday, May 03, 2016

installing and using pynlo

Looking around for supercontinuum generation literature, came across PyNLO's documentation. Tried to install and use it. Was a bit of a struggle at first, but finally it all came together.


  1. Anaconda3 version 4.0 installation on Windows XP failed - reported that it failed to change path variable etc, but more importantly, the exes were not running - "this is not a valid Windows executable".
  2. On Ubuntu 14.04, tried a direct pip install. Some dependency issues. Thought upgrading to 16.04 would help - ran out of hard disk space - 13 GB. Formatted and installed Lubuntu instead. With many hiccups on the way - like while doing a manual partitioning, we must not touch the swap space - because that is where the installer stores the installation files!
  3. With Anaconda3 and pynlo, errors like Missing parenthesis in call to print - so had to install Anaconda2 instead.
  4. Trying installation with pip install pynlo - installation of the required pyfftw failed with the error  fftw3.h: No such file or directory - it needed libfftw2-dev as mentioned in the comments at this post
  5. After pynlo installed also, running the example script gave errors IOError: [Errno 2] No such file or directory: .../pynlo/media/fibers/nist_fibers.txt and on copy-pasting general_fibers.txt to nist_fibers.txt, an assertion error - pynlo/interactions/FourWaveMixing/SSFM.py, line 662, in conditional_fftshift assert chksum == np.sum(abs(x)) AssertionError
  1. Currently pynlo needs Python 2.7 to run, won't run on Python3. So, install Anaconda2 and not Anaconda3. 
  2. On Windows, this page says that Windows XP is supported only for Anaconda versions 2.2 and below, so downloaded 2.2 instead of the latest.  
  3. Installing libfftw2-dev on Linux with apt-get install libfftw2-dev solved the pyfftw install issues. Similarly, on Windows, the way to install it is given at https://pypi.python.org/pypi/pyFFTW#downloads - ie. download the fftw dlls and put them in the same folder as the pyfftw wheel folder before install. The pyfftw whl file was installed as pip install wheelfile.whl without any issues. 
  4. Using the latest git code solved all the pynlo issues, using
    pip install git+https://github.com/pyNLO/PyNLO.git like this post
  5. Git for windows was installed from https://git-scm.com/download/win
  6. On Windows XP, everything was 32 bit, and the example took 55 seconds to run. On 64-bit Lubuntu, it ran in almost the same time. Lubuntu's desktop CPU meter indicates that it was using only one core of my dual-core Athlon, ie. 50% cpu.   

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