From 69f1ae8a67a824a94f4015e06e2bf7d34260befb Mon Sep 17 00:00:00 2001
From: Wei Ji <23487320+weiji14@users.noreply.github.com>
Date: Mon, 2 Oct 2023 12:54:41 +1300
Subject: [PATCH] :seedling: Initial conda environment (#1)

Add conda dependency specification file and getting started instructions in the main README.md. The conda environment.yml is paired with a conda-lock.yml lockfile for full reproducibility. Main README.md contains setup instructions to install NVIDIA GPU Direct Storage and the conda virtual environment locally.
---
 README.md       |   75 +
 conda-lock.yml  | 6445 +++++++++++++++++++++++++++++++++++++++++++++++
 environment.yml |   24 +
 3 files changed, 6544 insertions(+)
 create mode 100644 conda-lock.yml
 create mode 100644 environment.yml

diff --git a/README.md b/README.md
index eb6e41a..e5f2014 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,81 @@ data pipelines. Learn more as the Pangeo community develops tutorials at
 about the challenges and ideas on scaling machine learning in the geosciences
 with the [Pangeo ML Working Group](https://pangeo.io/meeting-notes.html#working-group-meetings).
 
+
+# Getting started
+
+## Installation
+
+### NVIDIA GPU Direct Storage
+
+Follow instructions at
+https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#install-gpudirect-storage
+to install NVIDIA GPU Direct Storage (GDS).
+
+Verify that NVIDIA GDS has been installed properly following
+https://docs.nvidia.com/gpudirect-storage/troubleshooting-guide/index.html#verify-suc-install.
+E.g. if you are on Linux and have CUDA 12.2 installed, run:
+
+    /usr/local/cuda-12.2/gds/tools/gdscheck.py -p
+
+Alternatively, if you have your conda environment setup below, follow
+https://xarray.dev/blog/xarray-kvikio#appendix-ii--making-sure-gds-is-working
+and run:
+
+    mamba activate foss4g2023oceania
+    curl -s https://github.com/raw/rapidsai/kvikio/branch-23.08/python/benchmarks/single-node-io.py | python
+
+### Basic
+
+To help out with development, start by cloning this [repo-url](/../../)
+
+    git clone <repo-url>
+
+Then I recommend [using mamba](https://mamba.readthedocs.io/en/latest/installation.html)
+to install the dependencies.
+A virtual environment will also be created with Python and
+[JupyterLab](https://github.com/jupyterlab/jupyterlab) installed.
+
+    cd foss4g2023oceania
+    mamba env create --file environment.yml
+
+Activate the virtual environment first.
+
+    mamba activate foss4g2023oceania
+
+Finally, double-check that the libraries have been installed.
+
+    mamba list
+
+### Advanced
+
+This is for those who want full reproducibility of the virtual environment.
+Create a virtual environment with just Python and conda-lock installed first.
+
+    mamba create --name foss4g2023oceania python=3.10 conda-lock=2.3.0
+    mamba activate foss4g2023oceania
+
+Generate a unified [`conda-lock.yml`](https://github.com/conda/conda-lock) file
+based on the dependency specification in `environment.yml`. Use only when
+creating a new `conda-lock.yml` file or refreshing an existing one.
+
+    conda-lock lock --mamba --file environment.yml --platform linux-64 --with-cuda=11.8
+
+Installing/Updating a virtual environment from a lockile. Use this to sync your
+dependencies to the exact versions in the `conda-lock.yml` file.
+
+    conda-lock install --mamba --name foss4g2023oceania conda-lock.yml
+
+See also https://conda.github.io/conda-lock/output/#unified-lockfile for more
+usage details.
+
+
+# References
+
+## Links
+
+- https://xarray.dev/blog/xarray-kvikio
+
 ## License
 
 All code in this repository is licensed under
diff --git a/conda-lock.yml b/conda-lock.yml
new file mode 100644
index 0000000..63a13c1
--- /dev/null
+++ b/conda-lock.yml
@@ -0,0 +1,6445 @@
+# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT!
+#
+# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
+# e.g. `conda env create`, the resulting environment will not change as new package versions become
+# available, unless you explicitly update the lock file.
+#
+# Install this environment as "YOURENV" with:
+#     conda-lock install -n YOURENV --file conda-lock.yml
+# To update a single package to the latest version compatible with the version constraints in the source:
+#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
+# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
+#     conda-lock -f environment.yml --lockfile conda-lock.yml
+version: 1
+metadata:
+  content_hash:
+    linux-64: fe13a3f405e4bd51f9717d572b3c7654bc42420cd40117093dc7c261013272f4
+  channels:
+  - url: conda-forge
+    used_env_vars: []
+  - url: nvidia
+    used_env_vars: []
+  platforms:
+  - linux-64
+  sources:
+  - environment.yml
+package:
+- name: _libgcc_mutex
+  version: '0.1'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+  hash:
+    md5: d7c89558ba9fa0495403155b64376d81
+    sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
+  category: main
+  optional: false
+- name: ca-certificates
+  version: 2023.7.22
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda
+  hash:
+    md5: a73ecd2988327ad4c8f2c331482917f2
+    sha256: 525b7b6b5135b952ec1808de84e5eca57c7c7ff144e29ef3e96ae4040ff432c1
+  category: main
+  optional: false
+- name: cuda-version
+  version: '11.8'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/cuda-version-11.8-h70ddcb2_2.conda
+  hash:
+    md5: 601900ec9ff06f62f76a247148e52c04
+    sha256: cb8a81465d5fa1b27e14981b7e1a9be4fc90945261a7459427e7bfb42129e26c
+  category: main
+  optional: false
+- name: font-ttf-dejavu-sans-mono
+  version: '2.37'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+  hash:
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+  category: main
+  optional: false
+- name: font-ttf-inconsolata
+  version: '3.000'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
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+  optional: false
+- name: font-ttf-source-code-pro
+  version: '2.038'
+  manager: conda
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+  hash:
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+  category: main
+  optional: false
+- name: font-ttf-ubuntu
+  version: '0.83'
+  manager: conda
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
+  hash:
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+  category: main
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+  manager: conda
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+  dependencies: {}
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+  hash:
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+  hash:
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+  optional: false
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+  version: '3.10'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda
+  hash:
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+  category: main
+  optional: false
+- name: tzdata
+  version: 2023c
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda
+  hash:
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+  category: main
+  optional: false
+- name: fonts-conda-forge
+  version: '1'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    font-ttf-dejavu-sans-mono: ''
+    font-ttf-inconsolata: ''
+    font-ttf-source-code-pro: ''
+    font-ttf-ubuntu: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
+  hash:
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+    sha256: 53f23a3319466053818540bcdf2091f253cbdbab1e0e9ae7b9e509dcaa2a5e38
+  category: main
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+  manager: conda
+  platform: linux-64
+  dependencies:
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+  url: https://conda.anaconda.org/nvidia/linux-64/libcufile-dev-1.4.0.31-0.tar.bz2
+  hash:
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+  category: main
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+  version: '1'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    fonts-conda-forge: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+  hash:
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+  url: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
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+  manager: conda
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+  dependencies:
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+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/linux-64/cudatoolkit-11.8.0-h4ba93d1_12.conda
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+    libstdcxx-ng: '>=7.5.0'
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+    libstdcxx-ng: '>=12'
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+  manager: conda
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+  platform: linux-64
+  dependencies:
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+  optional: false
+- name: lerc
+  version: 4.0.0
+  manager: conda
+  platform: linux-64
+  dependencies:
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+    libstdcxx-ng: '>=12'
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+  hash:
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+    sha256: cb55f36dcd898203927133280ae1dc643368af041a48bcf7c026acb7c47b0c12
+  category: main
+  optional: false
+- name: libabseil
+  version: '20230802.1'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20230802.1-cxx17_h59595ed_0.conda
+  hash:
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+    sha256: 8729021a93e67bb93b4e73ef0a132499db516accfea11561b667635bcd0507e7
+  category: main
+  optional: false
+- name: libaec
+  version: 1.1.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.1-h59595ed_0.conda
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+    sha256: 16fc7b40024adece716ba7227e5c123a2deccc13f946a10d9a3270493908d11c
+  category: main
+  optional: false
+- name: jupyterlab_server
+  version: 2.25.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    babel: '>=2.10'
+    importlib-metadata: '>=4.8.3'
+    jinja2: '>=3.0.3'
+    json5: '>=0.9.0'
+    jsonschema: '>=4.18'
+    jupyter_server: '>=1.21,<3'
+    packaging: '>=21.3'
+    python: '>=3.8'
+    requests: '>=2.31'
+  url: https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: a52834fa7e3d12abc5efdf06b2097a05
+    sha256: 608a878d08e0f4f51dd9a61eaead7c0e22d07f48aad06e3e2f6d6f1d0a929746
+  category: main
+  optional: false
+- name: lightning
+  version: 2.0.9.post0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    arrow: <3.0,>=1.2.0
+    backoff: <4.0,>=2.2.1
+    beautifulsoup4: <6.0,>=4.8.0
+    click: <10.0
+    croniter: <1.5.0,>=1.3.0
+    dateutils: <2.0
+    deepdiff: <8.0,>=5.7.0
+    fastapi: <2.0,>=0.92.0
+    fsspec: <2025.0,>=2022.5.0
+    inquirer: <5.0,>=2.10.0
+    jinja2: <5.0
+    lightning-cloud: '>=0.5.38'
+    lightning-utilities: <2.0,>=0.7.0
+    numpy: <3.0,>=1.17.2
+    packaging: ''
+    psutil: <7.0
+    pydantic: <2.2.0,>=1.7.4
+    python: '>=3.8'
+    python-multipart: <2.0,>=0.0.5
+    pytorch: <4.0,>=1.11.0
+    pytorch-lightning: ''
+    pyyaml: <8.0
+    requests: <4.0
+    rich: <15.0,>=12.3.0
+    starlette: ''
+    starsessions: <2.0,>=1.2.1
+    torchmetrics: <3.0,>=0.7.0
+    tqdm: <6.0,>=4.57.0
+    traitlets: <7.0,>=5.3.0
+    typing-extensions: <6.0,>=4.0.0
+    urllib3: <4.0
+    uvicorn: <2.0
+    websocket-client: <3.0
+    websockets: <13.0
+  url: https://conda.anaconda.org/conda-forge/noarch/lightning-2.0.9.post0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 176e3200b742c487e3e42717081d502b
+    sha256: 168206b0c49063854a93b7546883c0327d4e6b4e147b6d2aa889db8c335a28bb
+  category: main
+  optional: false
+- name: notebook-shim
+  version: 0.2.3
+  manager: conda
+  platform: linux-64
+  dependencies:
+    jupyter_server: '>=1.8,<3'
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda
+  hash:
+    md5: 67e0fe74c156267d9159e9133df7fd37
+    sha256: f028d7ad1f2175cde307db08b60d07e371b9d6f035cfae6c81ea94b4c408c538
+  category: main
+  optional: false
+- name: xbatcher
+  version: 0.3.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    dask: ''
+    numpy: ''
+    python: '>=3.8'
+    xarray: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/xbatcher-0.3.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 14aa97411b796937db2ba62ec5c95472
+    sha256: e181b350dcd091addfab9636e32c2c2a5631f5345fefeda6ce0c5f5272f946e5
+  category: main
+  optional: false
+- name: jupyterlab
+  version: 4.0.6
+  manager: conda
+  platform: linux-64
+  dependencies:
+    async-lru: '>=1.0.0'
+    importlib_metadata: '>=4.8.3'
+    importlib_resources: '>=1.4'
+    ipykernel: ''
+    jinja2: '>=3.0.3'
+    jupyter-lsp: '>=2.0.0'
+    jupyter_core: ''
+    jupyter_server: '>=2.4.0,<3'
+    jupyterlab_server: '>=2.19.0,<3'
+    notebook-shim: '>=0.2'
+    packaging: ''
+    python: '>=3.8'
+    tomli: ''
+    tornado: '>=6.2.0'
+    traitlets: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.6-pyhd8ed1ab_0.conda
+  hash:
+    md5: 80bb1cc3b540790cb5afecd73c2d4d1f
+    sha256: 5eb157e0ec794c0d4b100e9b11efefcc8d8b50b6c298539df31ab79ff9fbe446
+  category: main
+  optional: false
+- name: cupy-xarray
+  version: 0+untagged.43.gd7394ef
+  manager: pip
+  platform: linux-64
+  dependencies:
+    cupy: '*'
+    xarray: '>=0.19.0'
+  url: git+https://github.com/dcherian/cupy-xarray.git@d7394ef7bdc941df7e418918ef2aabb7fea5839e
+  hash:
+    sha256: d7394ef7bdc941df7e418918ef2aabb7fea5839e
+  category: main
+  source:
+    type: url
+    url: git+https://github.com/dcherian/cupy-xarray.git@d7394ef7bdc941df7e418918ef2aabb7fea5839e
+  optional: false
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..f378bfe
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,24 @@
+name: foss4g2023oceania
+channels:
+  - conda-forge
+  - nvidia
+  - nodefaults
+dependencies:
+  - conda-lock~=2.3.0
+  - cupy~=12.2.0
+  - gcsfs~=2023.9.2
+  - gsutil~=5.26
+  - jupyterlab~=4.0.6
+  - rapidsai::kvikio~=23.06.00
+  - lightning~=2.0.9.post0
+  - pip~=23.2.1
+  - pynvml~=11.5.0
+  - python~=3.10
+  - torchdata~=0.6.1
+  - xarray~=2023.9.0
+  - xbatcher~=0.3.0
+  - zarr~=2.16.1
+  - zen3geo~=0.6.2
+  - pip:
+      # https://github.com/xarray-contrib/cupy-xarray/pull/10
+      - git+https://github.com/dcherian/cupy-xarray.git@d7394ef7bdc941df7e418918ef2aabb7fea5839e