Cannot build Sparta on Docker image

[ipocentro87]

Hi all, I've been trying to build Sparta on a Docker image emulating a debian linux x86_64 machine. After installing the requirements, I am stuck here:

git clone https://github.com/sparcians/map.git
cd /map
./scripts/create_conda_env.sh sparta dev

Output

+ cd ./scripts/..
+ ./scripts/render_recipe_for_platform.sh rendered_recipe.AW8Aqp
conda is /root/miniconda3/bin/conda
jq is /root/miniconda3/bin/jq
yq is /root/miniconda3/bin/yq
Rendering recipe in /map/conda.recipe
Warning: 'conda-forge' already in 'channels' list, moving to the top
+ conda render -m .ci_support/linux_64_.yaml --file rendered_recipe.AW8Aqp conda.recipe
/root/miniconda3/lib/python3.12/site-packages/conda_build/environ.py:544: UserWarning: The environment variable 'SYSTEM_DEFAULTWORKINGDIRECTORY' is being passed through with value '/map'.  If you are splitting build and test phases with --no-test, please ensure that this value is also set similarly at test time.
  warnings.warn(
./scripts/render_recipe_for_platform.sh: line 97:  4051 Killed                  conda render -m "$variant_file" --file "$rendered_output" conda.recipe

Do you have an idea on how to fix this? Thanks in advance.

[klingaard]

Why was it killed? It's been known to run for a while.

Also, if this doesn't work for you there is a file called https://github.com/sparcians/map/blob/master/scripts/rendered_safe_environment.yaml you can directly try.

We've been having trouble with a safe rendering of conda. Thinking about going with something else.

[klingaard]

conda env create -f scripts/rendered_safe_environment.yaml

[ipocentro87]

Hi @klingaard , thanks for your reply. I don't know actually, this is what the prompt is giving me.

Out of curiosity, is conda used for the visualisation tools, or it is also used by the C++ framework?

[ipocentro87]

By the way I get the following error when I try to run it with a safe environment. Here's the log:

> conda env create -f scripts/rendered_safe_environment.yaml;

/root/miniconda3/lib/python3.12/argparse.py:2000: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
  action(self, namespace, argument_values, option_string)
/root/miniconda3/lib/python3.12/site-packages/conda/base/context.py:982: FutureWarning: Adding 'defaults' to the channel list implicitly is deprecated and will be removed in 25.3. 

To remove this warning, please choose a default channel explicitly via 'conda config --add channels <name>', e.g. 'conda config --add channels defaults'.
  deprecated.topic(
/root/miniconda3/lib/python3.12/site-packages/conda/base/context.py:982: FutureWarning: Adding 'defaults' to the channel list implicitly is deprecated and will be removed in 25.3. 

To remove this warning, please choose a default channel explicitly via 'conda config --add channels <name>', e.g. 'conda config --add channels defaults'.
  deprecated.topic(
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: \ Killed

The log don't show an explicit reason on why the command failed. If you have any clue on how I can debug this it would be very helpful!

[klingaard]

When it says "Killed" is that you or did it kill itself?

[klingaard]

We're trying to use conda to provide a known/working environment for sparta's C++ needs plus the visualization tools. Truth be told, the list of requirements for just sparta is small. I think it's:

1. Latest C++ compiler
2. A relatively newer boost 1.78+
3. yaml-cpp
4. sqlite3
5. zlib
6. hdf5
7. rapidjson

[klingaard]

You can find that list here: https://github.com/sparcians/map/blob/master/sparta/cmake/sparta-config.cmake

[ipocentro87]

I finally managed to build sparta through Docker. The Docker imager needed more GBs of RAM. I still have problems on podman build though, the compilation seems to hang here:

-- Found Boost: /root/miniconda3/envs/sparta/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.74.0") found components: date_time iostreams serialization timer program_options
-- Using BOOST 1.78.0
-- Using YAML CPP 0.8.0
-- Using RapidJSON CPP 1.1.0

Any feedback would be very helpful 🙏

BTW, I was wondering whether linux/aarch64 is supported. On the supported environments I only see support for arm64 on macOS, but not linux.

[klingaard]

I unfortunately don't have much experience with container builds, so I can't help you with your specific container (unless you want to share it).

Is cmake hanging? This is the expected output past RapidJSON check:

-- Using BOOST 1.78.0
-- Using YAML CPP 0.8.0
-- Using RapidJSON CPP 1.1.0
-- Using SQLite3 3.46.0
-- Using zlib 1.3.1
-- Using HDF5 1.14.3
... more stuff related to my machine

[klingaard]

I was wondering whether linux/aarch64 is supported

Well, it's not not supported. :wink: Never tried, but don't expect any issues.

[ipocentro87]

I confirm that the compilation hangs here (with cmake <...> --trace), on a linux/amd64 podman container

> mkdir release && cd release
> cmake -DCMAKE_BUILD_TYPE=Release .. --trace
...
-- Using RapidJSON CPP 1.1.0
...
/root/miniconda3/envs/sparta/share/cmake-3.30/Modules/FindPkgConfig.cmake(145):  execute_process(COMMAND ${PKG_CONFIG_EXECUTABLE} ${PKG_CONFIG_ARGN} --libs-only-l sqlite3 OUTPUT_VARIABLE _pkgconfig_invoke_result RESULT_VARIABLE _pkgconfig_failed OUTPUT_STRIP_TRAILING_WHITESPACE )

With linux/arm64, I had a problem with wxpython not being compiled for this platform. I did a custom build this way

pip install grayskull
grayskull pypi wxpython
conda-build wxpython

However I ran into another issue with package dependencies. Basically it wanted 3.12.* *_cpython but the yaml platform configuration has 3.10.* *_cpython. I tried to change this but I ended up into another packaging problem so I gave up for now.

I can share the Dockerfile to you and give you instructions on how to build it with podman if you are curious :)