Comments (9)
Hey Rhys, can you try the following for a dockerfile?
FROM jupyter/scipy-notebook:2021-11-20
USER root
RUN apt update -y && apt upgrade -y && \
apt install -y software-properties-common && \
add-apt-repository ppa:ubuntugis/ppa && \
apt update -y && apt install -y \
gdal-bin \
geotiff-bin \
git \
libgdal-dev \
libgl1 \
libspatialindex-dev \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN pip uninstall numpy -y
# Install Conda packages
RUN conda install -c conda-forge -y \
#python=3.7 # had to be excluded because newer version of python req by Jupyterhub \
cython \
gdal \
libspatialindex \
nbgrader \
#nbtutor \
numpy \
opencv \
pip \
pygeos \
requests \
rtree \
scipy \
wheel \
zarr \
&& conda install -c phausamann sklearn-xarray -y \
&& conda clean -a -y
RUN pip3 install --upgrade pip --no-cache-dir && pip3 install --no-cache-dir \
pip-tools \
git+https://github.com/jgrss/geowombat.git
from geowombat.
I'm going to try to add ARM to my cond-forge build - I think the issue is it has specific C compiler needs.
from geowombat.
It looks like the build got close but failed to from issues with rasterio and fiona. Going to keep googling through the error message, and wanted to share below in case anything jumps out.
67.28 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O3 -Wall -fPIC -O3 -isystem /opt/conda/include -fPIC -O3 -isystem /opt/conda/include -fPIC -I/tmp/pip-build-env-tkwl4h61/overlay/lib/python3.9/site-packages/numpy/core/include -I/opt/conda/include -I/opt/conda/include/python3.9 -c rasterio/_warp.cpp -o build/temp.linux-aarch64-cpython-39/rasterio/_warp.o -Wno-unused-parameter -Wno-unused-function -std=c++11
67.28 gcc: fatal error: cannot execute ‘cc1plus’: execvp: No such file or directory
67.28 compilation terminated.
67.28 error: command '/usr/bin/gcc' failed with exit code 1
67.28 [end of output]
67.28
67.28 note: This error originates from a subprocess, and is likely not a problem with pip.
67.28 ERROR: Failed building wheel for rasterio
67.28 Building wheel for fiona (pyproject.toml): started
69.50 Building wheel for fiona (pyproject.toml): finished with status 'error'
69.50 error: subprocess-exited-with-error
69.50
69.50 × Building wheel for fiona (pyproject.toml) did not run successfully.
69.50 │ exit code: 1
69.50 ╰─> [76 lines of output]
69.50 /tmp/pip-build-env-e4ryhszq/overlay/lib/python3.9/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'cython_compile_time_env'
69.50 warnings.warn(msg)
69.50 INFO:root:running bdist_wheel
69.50 INFO:root:running build
69.50 INFO:root:running build_py
69.50 INFO:root:creating build
69.50 INFO:root:creating build/lib.linux-aarch64-cpython-39
69.50 INFO:root:creating build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/enums.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/vfs.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/path.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/crs.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/model.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/io.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/meta.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/drvsupport.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/session.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/collection.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/logutils.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/transform.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/compat.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/__init__.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_show_versions.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/errors.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/env.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/inspector.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/rfc3339.py -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:creating build/lib.linux-aarch64-cpython-39/fiona/_vendor
69.50 INFO:root:copying fiona/_vendor/__init__.py -> build/lib.linux-aarch64-cpython-39/fiona/_vendor
69.50 INFO:root:creating build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/filter.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/options.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/bounds.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/ls.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/cat.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/collect.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/dump.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/info.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/insp.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/main.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/distrib.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/__init__.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/rm.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/calc.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/helpers.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/load.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:copying fiona/fio/env.py -> build/lib.linux-aarch64-cpython-39/fiona/fio
69.50 INFO:root:creating build/lib.linux-aarch64-cpython-39/fiona/_vendor/munch
69.50 INFO:root:copying fiona/_vendor/munch/__init__.py -> build/lib.linux-aarch64-cpython-39/fiona/_vendor/munch
69.50 INFO:root:copying fiona/_vendor/munch/python3_compat.py -> build/lib.linux-aarch64-cpython-39/fiona/_vendor/munch
69.50 INFO:root:copying fiona/gdal.pxi -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_err.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/crs.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/gdal.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/ogrext2.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_geometry.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_cpl.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_csl.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/ogrext1.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_shim.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/ogrext3.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:copying fiona/_env.pxd -> build/lib.linux-aarch64-cpython-39/fiona
69.50 INFO:root:running build_ext
69.50 INFO:root:building 'fiona._geometry' extension
69.50 INFO:root:creating build/temp.linux-aarch64-cpython-39
69.50 INFO:root:creating build/temp.linux-aarch64-cpython-39/fiona
69.50 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O3 -Wall -fPIC -O3 -isystem /opt/conda/include -fPIC -O3 -isystem /opt/conda/include -fPIC -I/opt/conda/include -I/opt/conda/include/python3.9 -c fiona/_geometry.c -o build/temp.linux-aarch64-cpython-39/fiona/_geometry.o
69.50 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -shared -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib build/temp.linux-aarch64-cpython-39/fiona/_geometry.o -L/opt/conda/lib -lgdal -o build/lib.linux-aarch64-cpython-39/fiona/_geometry.cpython-39-aarch64-linux-gnu.so
69.50 INFO:root:building 'fiona.schema' extension
69.50 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O3 -Wall -fPIC -O3 -isystem /opt/conda/include -fPIC -O3 -isystem /opt/conda/include -fPIC -I/opt/conda/include -I/opt/conda/include/python3.9 -c fiona/schema.c -o build/temp.linux-aarch64-cpython-39/fiona/schema.o
69.50 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -shared -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib build/temp.linux-aarch64-cpython-39/fiona/schema.o -L/opt/conda/lib -lgdal -o build/lib.linux-aarch64-cpython-39/fiona/schema.cpython-39-aarch64-linux-gnu.so
69.50 INFO:root:building 'fiona._transform' extension
69.50 INFO:root:gcc -pthread -B /opt/conda/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O3 -Wall -fPIC -O3 -isystem /opt/conda/include -fPIC -O3 -isystem /opt/conda/include -fPIC -I/opt/conda/include -I/opt/conda/include/python3.9 -c fiona/_transform.cpp -o build/temp.linux-aarch64-cpython-39/fiona/_transform.o -std=c++11
69.50 gcc: fatal error: cannot execute ‘cc1plus’: execvp: No such file or directory
69.50 compilation terminated.
69.50 error: command '/usr/bin/gcc' failed with exit code 1
69.50 [end of output]
69.50
69.50 note: This error originates from a subprocess, and is likely not a problem with pip.
69.50 ERROR: Failed building wheel for fiona
69.50 Successfully built geowombat
69.50 Failed to build rasterio fiona
69.50 ERROR: Could not build wheels for rasterio, fiona, which is required to install pyproject.toml-based projects
------
Dockerfile:41
--------------------
40 |
41 | >>> RUN pip3 install --upgrade pip --no-cache-dir && pip3 install --no-cache-dir \
42 | >>> pip-tools \
43 | >>> git+https://github.com/jgrss/geowombat.git
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c pip3 install --upgrade pip --no-cache-dir && pip3 install --no-cache-dir pip-tools git+https://github.com/jgrss/geowombat.git" did not complete successfully: exit code: 1
from geowombat.
For dockerfile try the simple version:
FROM jupyter/scipy-notebook
USER root
RUN mamba install -c conda-forge -y geowombat
CMD ["/bin/bash"]
from geowombat.
Got another error with that, I think because it is failing to find a version of the package. I'm currently looking into how we can use Docker compose and base image of linux with an intermediate image of a C compiler. Also reading up on this: https://learning.oreilly.com/library/view/learn-docker-in/9781617297052/OEBPS/Text/16.xhtml#heading_id_8, and open to any other docker reading/watching recommendations.
Error message:
> [2/2] RUN mamba install -c conda-forge -y geowombat:
8.332
8.332 __ __ __ __
8.332 / \ / \ / \ / \
8.332 / \/ \/ \/ \
8.332 ███████████████/ /██/ /██/ /██/ /████████████████████████
8.332 / / \ / \ / \ / \ \____
8.332 / / \_/ \_/ \_/ \ o \__,
8.332 / _/ \_____/ `
8.332 |/
8.332 ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
8.332 ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
8.332 ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
8.332 ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
8.332 ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
8.332 ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
8.332
8.332 mamba (0.18.1) supported by @QuantStack
8.332
8.332 GitHub: https://github.com/mamba-org/mamba
8.332 Twitter: https://twitter.com/QuantStack
8.332
8.332 █████████████████████████████████████████████████████████████
8.332
8.332
8.332 Looking for: ['geowombat']
8.332
8.332
8.332 Pinned packages:
8.332 - python 3.9.*
8.332 - python 3.9.7
8.332
8.332
8.332 Encountered problems while solving:
8.332 - nothing provides requested geowombat
8.332
8.332 conda-forge/linux-aarch6
8.332 conda-forge/noarch
------
Dockerfile:5
--------------------
3 | USER root
4 |
5 | >>> RUN mamba install -c conda-forge -y geowombat
6 |
7 | CMD ["/bin/bash"]
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c mamba install -c conda-forge -y geowombat" did not complete successfully: exit code: 1
from geowombat.
That is very strange. Geowombat is definitely available through conda-forge, and I was able to run that docker file. How are you building it? Could u be limiting Internet access somehow???
from geowombat.
I cloned the repo and I'm inside the top level directory and running the following command:
docker image build -t geowombat:arm .
Are there any different flags I should use here? I don't think it's a connectivity issue from inside the image or from my home internet.
from geowombat.
I'll let you know how the conda-forge build goes. Till then use apporto.
from geowombat.
@Rhys-L @jgrss I just pushed the osx arm build to the conda feedstock. Hopefully within a few hours it should be good to go!
from geowombat.
Related Issues (20)
- Feedstock Issues HOT 1
- Failed to Install Geowombat on pip and conda HOT 12
- Requirement differences between package & conda-forge HOT 6
- Coordinating efforts on potential new geospatial Xarray accessor HOT 2
- Regression capability in geowombat HOT 3
- Apply interpolation HOT 4
- Stac import HOT 2
- series.apply big tiff / bad block
- EVI equation is wrong HOT 2
- Support for pyproj 3.4.1? HOT 8
- Slow extract HOT 2
- mosaic bounds HOT 4
- fit_predict
- Stack & Mosaic Advice? HOT 6
- writing with Bigtiff HOT 2
- [] in open trigger stacking
- polygon_to_array returns shorter y dimension than source rasters HOT 26
- band names HOT 1
- Unable to import geowombat HOT 1
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from geowombat.