tlambert03
commented
2 years ago Can you tell me what OS you're trying to install on?
Open parthnatekar opened 2 years ago
tlambert03
commented
2 years ago Can you tell me what OS you're trying to install on?
parthnatekar
commented
2 years ago Its Ubuntu 18.04
parthnatekar
commented
2 years ago Hi, any updates on this, still getting the same error!
tlambert03
commented
2 years ago I actually did do some updates in early december... but not sure if it's going to fix this. Can you try this exactly and let me know what happens?
conda create -n newenv -c conda-forge python=3.9 cudadecon
conda activate newenv
pip install llspy[pyqt,napari]
lls guiHi,
Thanks for your updates.
I was able to install and import llspy using the above. I'm closing this for now but I'll let you know if I have any trouble later on.
Thanks
parthnatekar
commented
2 years ago Hi, getting the following error now on running process or autoprocess:
llspy.exceptions.CUDAbinException: cudadecon could not be located or is not executable: <<PATH>>
output of conda list please?
parthnatekar
commented
2 years ago Here is the output. I can see CudaDecon here.
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alabaster 0.7.12 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
asttokens 2.0.5 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
babel 2.9.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
black 21.12b0 pypi_0 pypi
boost-cpp 1.74.0 h359cf19_5 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cachey 0.2.1 pypi_0 pypi
certifi 2021.10.8 pypi_0 pypi
charset-normalizer 2.0.10 pypi_0 pypi
click 8.0.3 pypi_0 pypi
cloudpickle 2.0.0 pypi_0 pypi
cudadecon 0.0.11 h32a6c52_0 conda-forge
cudatoolkit 11.6.0 habf752d_9 conda-forge
cycler 0.11.0 pypi_0 pypi
dask 2022.1.0 pypi_0 pypi
debugpy 1.5.1 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
docstring-parser 0.13 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
entrypoints 0.3 pypi_0 pypi
executing 0.8.2 pypi_0 pypi
fftw 3.3.10 nompi_h77c792f_102 conda-forge
fonttools 4.29.0 pypi_0 pypi
freetype-py 2.2.0 pypi_0 pypi
fsspec 2022.1.0 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.2 pypi_0 pypi
icu 69.1 h9c3ff4c_0 conda-forge
idna 3.3 pypi_0 pypi
imageio 2.14.1 pypi_0 pypi
imagesize 1.3.0 pypi_0 pypi
importlib-metadata 4.10.1 pypi_0 pypi
intervaltree 3.1.0 pypi_0 pypi
ipykernel 6.7.0 pypi_0 pypi
ipython 8.0.1 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 pypi_0 pypi
jinja2 3.0.3 pypi_0 pypi
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 4.4.0 pypi_0 pypi
jupyter-client 7.1.2 pypi_0 pypi
jupyter-core 4.9.1 pypi_0 pypi
kiwisolver 1.3.2 pypi_0 pypi
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libdeflate 1.8 h7f98852_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgfortran-ng 11.2.0 h69a702a_12 conda-forge
libgfortran5 11.2.0 h5c6108e_12 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libtiff 4.3.0 h6f004c6_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
llspy 0.5.0 pypi_0 pypi
llspy-slm 0.2.1 pypi_0 pypi
llvmlite 0.38.0 pypi_0 pypi
locket 0.2.1 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
magicgui 0.3.4 pypi_0 pypi
markupsafe 2.0.1 pypi_0 pypi
matplotlib 3.5.1 pypi_0 pypi
matplotlib-inline 0.1.3 pypi_0 pypi
mypy-extensions 0.4.3 pypi_0 pypi
napari 0.4.13 pypi_0 pypi
napari-console 0.0.4 pypi_0 pypi
napari-plugin-engine 0.2.0 pypi_0 pypi
napari-svg 0.1.6 pypi_0 pypi
ncurses 6.3 h9c3ff4c_0 conda-forge
nest-asyncio 1.5.4 pypi_0 pypi
npe2 0.1.1 pypi_0 pypi
numba 0.55.0 pypi_0 pypi
numpy 1.21.5 pypi_0 pypi
numpydoc 1.2 pypi_0 pypi
openssl 3.0.0 h7f98852_2 conda-forge
packaging 21.3 pypi_0 pypi
pandas 1.4.0 pypi_0 pypi
parse 1.19.0 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
partd 1.2.0 pypi_0 pypi
pathspec 0.9.0 pypi_0 pypi
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.0.0 pypi_0 pypi
pint 0.18 pypi_0 pypi
pip 21.3.1 pyhd8ed1ab_0 conda-forge
platformdirs 2.4.1 pypi_0 pypi
prompt-toolkit 3.0.24 pypi_0 pypi
psutil 5.9.0 pypi_0 pypi
psygnal 0.2.0 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pydantic 1.9.0 pypi_0 pypi
pygments 2.11.2 pypi_0 pypi
pyopengl 3.1.5 pypi_0 pypi
pyparsing 3.0.7 pypi_0 pypi
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.9.0 pypi_0 pypi
pyrsistent 0.18.1 pypi_0 pypi
python 3.9.9 h543edf9_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytomlpp 1.0.10 pypi_0 pypi
pytz 2021.3 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 22.3.0 pypi_0 pypi
qtconsole 5.2.2 pypi_0 pypi
qtpy 2.0.0 pypi_0 pypi
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pypi_0 pypi
scipy 1.7.3 pypi_0 pypi
sentry-sdk 1.5.4 pypi_0 pypi
setuptools 60.5.0 py39hf3d152e_0 conda-forge
six 1.16.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
sphinx 4.4.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.37.0 h9cd32fc_0 conda-forge
stack-data 0.1.4 pypi_0 pypi
superqt 0.2.5.post1 pypi_0 pypi
tifffile 2021.11.2 pypi_0 pypi
tk 8.6.11 h27826a3_1 conda-forge
tomli 1.2.3 pypi_0 pypi
toolz 0.11.2 pypi_0 pypi
tornado 6.1 pypi_0 pypi
tqdm 4.62.3 pypi_0 pypi
traitlets 5.1.1 pypi_0 pypi
typer 0.4.0 pypi_0 pypi
typing-extensions 4.0.1 pypi_0 pypi
tzdata 2021e he74cb21_0 conda-forge
urllib3 1.26.8 pypi_0 pypi
vispy 0.9.4 pypi_0 pypi
voluptuous 0.12.2 pypi_0 pypi
watchdog 2.1.6 pypi_0 pypi
wcwidth 0.2.5 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.13.3 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
zipp 3.7.0 pypi_0 pypi
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forgeHi, any updates on this? I believe it is just a question of pointing LLSPY to the cudaDecon installation.
tlambert03
commented
2 years ago I believe it is just a question of pointing LLSPY to the cudaDecon installation.
this is what the purpose of llspy and https://github.com/tlambert03/LLSpy/pull/35 and https://github.com/tlambert03/LLSpy/pull/36 ... so this seems to suggest a different problem.
So, if you run cudadecon on the command line, it is installed right? I'm guessing there were more places that needed to be swapped over. This has actually gotten a bit harder for me to test, since my lattice and llspy rig isn't running at the moment. If you'd like to help, could you try something for me?
In your llspy installation, go in to the process function here:
and print out the value for binary (both before and after the check for "if is None") ... I want to see if something (like a configuration somewhere) is providing something other than None
parthnatekar
commented
2 years ago Hi,
Yes, I can run cudaDecon from the command line.
When I run E.autoprocess(), an error occurs at line 418 in llsdir.py
if binary is None:
binary = CUDAbin()If I print out binary above this I get None.
tlambert03
commented
2 years ago and if you print it out afterwards? (print(binary.path)) ...
parthnatekar
commented
2 years ago It fails at that line, so I can't print out anything afterward. The entire error stack is:
Traceback (most recent call last):
File "<<<PATH>>>", line 6, in <module>
E.autoprocess(otfDir = '<<<PATH>>>')
File <<<PATH>>>/newenv/lib/python3.9/site-packages/llspy/llsdir.py", line 1106, in autoprocess
return process(self, **kwargs)
File "<<<PATH>>>/newenv/lib/python3.9/site-packages/llspy/llsdir.py", line 418, in process
binary = CUDAbin()
File "<<<PATH>>>/newenv/lib/python3.9/site-packages/llspy/cudabinwrapper.py", line 215, in __init__
binPath = get_bundled_binary()
File "<<<PATH>>>/newenv/lib/python3.9/site-packages/llspy/cudabinwrapper.py", line 101, in get_bundled_binary
raise CUDAbinException(
llspy.exceptions.CUDAbinException: cudadecon could not be located or is not executable: <<<PATH>>>/newenv/bin/cudadeconok, can you do me one more favor? I'm wondering if my (pretty old) logic for determining if a given program name is executable in the current environment is not working for you.
can you edit get_bundled_binary in cudabinwrapper.py here to
A) check that it is indeed trying to find the program cudadecon (which you said does work fine when run directly). i,e, print the value of name right in the beggining of the function.
B) if it is indeed trying to find cudadecon, see if you can figure out why util.which (which is called right here and defined here) isn't working?
parthnatekar
commented
2 years ago So all I had to do was change the default value for the name argument from cudadecon to cudaDecon and it was able to find what was needed.
Seems to be working now. I'm not sure if this was something to do with how different systems handle upper case and lower case paths.
Thanks for your support, I'll keep this open for a few more days if you don't mind in case any more problems come up.
tlambert03
commented
2 years ago arg 😖 sorry that's very annoying. thanks for helping me figure that one out. you can also leave this open until I update the code here in this repo.
cheers, Talley
Hi,
I am unable to install using conda.
Not sure how to solve this glibc error. I'm creating a new Python3.6 environment so there should be no other conflicts.