Installation Errors, glibc incompatibility

[parthnatekar]

Hi,

I am unable to install using conda.

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions
The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.27=0
  - feature:|@/linux-64::__glibc==2.27=0

Your installed version is: 2.27

Not sure how to solve this glibc error. I'm creating a new Python3.6 environment so there should be no other conflicts.

[tlambert03]

Can you tell me what OS you're trying to install on?

[parthnatekar]

Its Ubuntu 18.04

[parthnatekar]

Hi, any updates on this, still getting the same error!

[tlambert03]

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 gui

[parthnatekar]

Hi,

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]

Hi, getting the following error now on running process or autoprocess:

llspy.exceptions.CUDAbinException: cudadecon could not be located or is not executable: <<PATH>>

[tlambert03]

output of conda list please?

[parthnatekar]

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-forge

[parthnatekar]

Hi, any updates on this? I believe it is just a question of pointing LLSPY to the cudaDecon installation.

[tlambert03]

I believe it is just a question of pointing LLSPY to the cudaDecon installation.

this is what the purpose of llspy and #35 and #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:

LLSpy/llspy/llsdir.py

Lines 1139 to 1146 in 39b344e

	def process(self, filepattern, otf, indir=None, binary=None, **opts):
	if binary is None:
	binary = CUDAbin()
	if indir is None:
	indir = str(self.path)
	output = binary.process(indir, filepattern, otf, **opts)
	return output

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]

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.