Make stack easily usable in Windows

[slarson]

Make the docker container run on Windows.

[slarson]

Been working on this over here: https://github.com/slarson/OpenWorm/blob/windows/INSTALL-WINDOWS.md

[slarson]

Currently seeing this error:

Python >>  Initialised C302NRNSimulation of length 100 ms and dt = 0.005 ms...
Python muscle signal generator class: C302NRNSimulation loaded!
Configuration was loaded
 CL_PLATFORM_VERSION [0]:       OpenCL 2.1 LINUX
 CL_PLATFORM_VERSION [1]:       OpenCL 1.2
Unfortunately OpenCL couldn't find device GPU
OpenCL try to init existing device
Sib_c302  >>>
Sib_c302  >>> ************************************************************************
Sib_c302  >>> *
Sib_c302  >>> *  Generating images for neuronal activity...
Sib_c302  >>> *
Sib_c302  >>> ************************************************************************
pyNeuroML >>> Reloading data specified in LEMS file: simulations/C2_FW_2018-02-10_17-42-33/LEMS_c302.xml, base_dir: simulations/C2_FW_2018-02-10_17-42-33
Traceback (most recent call last):
  File "sibernetic_c302.py", line 357, in <module>
    main()
  File "sibernetic_c302.py", line 111, in main
    run(a=args)
  File "sibernetic_c302.py", line 319, in run
    verbose=True)
  File "/usr/local/lib/python2.7/dist-packages/pyNeuroML-0.3.2-py2.7.egg/pyneuroml/pynml.py", line 781, in reload_saved_data
    'file %s' % file_name))
OSError: Could not find simulation output file /home/ow/sibernetic/NeuroML2/results/c302_C2_FW.dat
[debug] pName = "main_sim"
[debug] PyPath = ":/home/ow/CElegansNeuroML/CElegans/pythonScripts/c302:/home/ow/sibernetic:/usr/lib/python2.7/:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload"
Python muscle signal generator class: MuscleSimulation loaded!
Killing SignalSimulator!
Python >>  MuscleSimulation does NOT save results
Simulation has reached end of file
Traceback (most recent call last):
  File "master_openworm.py", line 201, in <module>
    outstr = check_output(command, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 574, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command 'ffmpeg -i /home/ow/shared/output/C2_FW_2018-02-10_17-42-33/C2_FW_2018-02-10_17-42-33.mp4 -vf blackdetect=d=0:pic_th=0.70:pix_th=0.10 -an -f null - 2>&1 | grep blackdetect' returned non-zero exit status 1

@lungd Any ideas? I'm trying to understand why the path to the c302_C2_FW.dat would be any different in this setup versus the linux case... @balicea are you seeing something different?

[clausagerskov]

I just followed your guide for the windows branch and get the same error, of course as well as OpenGL not recognizing my GPU

[slarson]

@clausagerskov OK at least that is a match. I'm looking into it right now.

As for the GPU, right now OpenCL is not going to work with the GPU; that is a known issue we would like to improve (see here: #262 )

[slarson]

@lungd OK I'm pretty sure that Sibernetic is just crashing, therefore it isn't generating output, therefore it isn't being found:

ow@576343d398e7:~/sibernetic$ ./Release/Sibernetic -f worm -no_g device=CPU
[debug] pName = "main_sim"
[debug] PyPath = ":/home/ow/CElegansNeuroML/CElegans/pythonScripts/c302:/home/ow/sibernetic:/usr/lib/python2.7/:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload"
Python muscle signal generator class: MuscleSimulation loaded!
Configuration was loaded
 CL_PLATFORM_VERSION [0]:       OpenCL 2.1 LINUX
 CL_PLATFORM_VERSION [1]:       OpenCL 1.2
Segmentation fault

Now the question is what to do about it. I love debugging seg faults...

[clausagerskov]

yea i also had some segmentation fault when trying to compile a 64 bit exe for windows.

[slarson]

@skhayrulin @a-palyanov Any idea what we might do here? We are running Sibernetic inside a linux container but on Windows and seeing this. Same linux container on mac / linux runs fine. I've tried rebuilding Sibernetic via make clean; make all but it seems to compile fine and makes no difference to the seg fault :(

[slarson]

@lungd do you know of a low-level opencl test that could be easily installed in the container to check out how opencl is seeing the system?

[pgleeson]

I've retested the recently added build.cmd and run.cmd in the development branch (https://github.com/openworm/OpenWorm/tree/development) and these work fine for running the simulation & generating the movie. Can some others test?

[clausagerskov]

Works for me on Windows 10 pro! (Using Linux docker containers)

[pgleeson]

Thanks for testing @clausagerskov