maweigert / biobeam Goto Github PK
View Code? Open in Web Editor NEWGPU accelerated beam propagation tools for biological light tissue simulations
License: BSD 3-Clause "New" or "Revised" License
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imagejan richardxie1119 kirayuta le-xiao wenhan-zhang-327 johndan070 nacaclanga jinhuishi dalelobbiobeam's Issues
Update installation instructions or dependency information of installed packages?
Hey Martin,
I had some issues getting biobeam running on my Fedora 27. I figured out that I need to run it on Python 3, install pyopencl, intel-opencl-drivers, numpy, scipy and pillow manually.
The scipy/pillow-issue is also discussed here: amueller/mglearn#2
Is there maybe something wrong with the dependency tree? Shouldn't all this (except intel-stuff) come directly with biobeam?
Cheers,
Robert
Has anyone managed to install it on Windows?
Hi, everyone,
I am trying to install Spimagine or Biobeam on Windows, from Anaconda prompt, without any success.
Did anyone manage this?
My system is Windows 7, Anaconda 64 bit, Python 2.7, OpenCL C 2.0, graphics card Intel HD 520 (CPU, not GPU). Can it work on such configuration in principle?
Thanks!
PS: The errors are:
pip install spimagine
...
C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -DPYGPU_PACKAGE=
pyopencl -DPYGPU_PYOPENCL=1 -DPYOPENCL_USE_SHIPPED_EXT=1 -Isrc/c_wrapper/ -Ic:\u
sers\user1\appdata\local\continuum\anaconda2\include -Ic:\users\user1\appdat
a\local\continuum\anaconda2\PC /Tpbuild\temp.win-amd64-2.7\Release\pyopencl._cff
i.cpp /Fobuild\temp.win-amd64-2.7\Release\build\temp.win-amd64-2.7\Release\pyope
ncl._cffi.obj -std=gnu++11
cl : Command line warning D9002 : ignoring unknown option '-std=gnu++11'
pyopencl._cffi.cpp
C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Include\stdint.h(82) : error C2371: 'int8_t' : redefinition; different
basic types
build\temp.win-amd64-2.7\Release\pyopencl._cffi.cpp(221) : see decla
ration of 'int8_t'
c:\users\user1\appdata\local\temp\pip-install-pxw3ou\pyopencl\src\c_wrappe
r\clinfo_ext.h(10) : fatal error C1083: Cannot open include file: 'CL/cl.h': No
such file or directory
error: command 'C:\\Users\\user1\\AppData\\Local\\Programs\\Common\\Micros
oft\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status
2
and
pip install biobeam
...
C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -DPYGPU_PACKAGE=
pyopencl -DPYGPU_PYOPENCL=1 -DPYOPENCL_USE_SHIPPED_EXT=1 -Isrc/c_wrapper/ -Ic:\u
sers\user1\appdata\local\continuum\anaconda2\include -Ic:\users\user1\appdat
a\local\continuum\anaconda2\PC /Tpbuild\temp.win-amd64-2.7\Release\pyopencl._cff
i.cpp /Fobuild\temp.win-amd64-2.7\Release\build\temp.win-amd64-2.7\Release\pyope
ncl._cffi.obj -std=gnu++11
cl : Command line warning D9002 : ignoring unknown option '-std=gnu++11'
pyopencl._cffi.cpp
C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Include\stdint.h(82) : error C2371: 'int8_t' : redefinition; different
basic types
build\temp.win-amd64-2.7\Release\pyopencl._cffi.cpp(221) : see decla
ration of 'int8_t'
c:\users\user1\appdata\local\temp\pip-install-wkccr_\pyopencl\src\c_wrappe
r\clinfo_ext.h(10) : fatal error C1083: Cannot open include file: 'CL/cl.h': No
such file or directory
error: command 'C:\\Users\\user1\\AppData\\Local\\Programs\\Common\\Micros
oft\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status
2
----------------------------------------
Command "c:\users\user1\appdata\local\continuum\anaconda2\python.exe -u -c "im
port setuptools, tokenize;__file__='c:\\users\\user1\\appdata\\local\\temp\\pi
p-install-wkccr_\\pyopencl\\setup.py';f=getattr(tokenize, 'open', open)(__file__
);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'ex
ec'))" install --record c:\users\user1\appdata\local\temp\pip-record-ms6qyf\in
stall-record.txt --single-version-externally-managed --compile" failed with erro
r code 1 in c:\users\user1\appdata\local\temp\pip-install-wkccr_\pyopencl\
opencl version
Hi,
What is the required opencl version? Will it work with OpenCL 1.2?
unit of units-parameter in nanometers and not microns?
Hey Martin,
when playing with the method biobeam.focus_field_beam, we had the feeling, that the units parameters expects values in nanometers, but according to the documentation, it's microns. Can you clearify?
Thanks,
Robert
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