Comments (9)
mmann1123
commented on June 19, 2024
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.
mmann1123
commented on June 19, 2024
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.
Rhys-L
commented on June 19, 2024
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.
mmann1123
commented on June 19, 2024
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.
Rhys-L
commented on June 19, 2024
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.
mmann1123
commented on June 19, 2024
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.
Rhys-L
commented on June 19, 2024
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.
mmann1123
commented on June 19, 2024
I'll let you know how the conda-forge build goes. Till then use apporto.
from geowombat.
mmann1123
commented on June 19, 2024
@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)
- Ml no data HOT 2
- gw.open bug?? HOT 5
- Apply example
- Apply on bands error HOT 1
- Apply HOT 2
- Expand pinned python version HOT 1
- 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 6
- Slow extract HOT 2
- mosaic bounds HOT 4
- fit_predict
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from geowombat.