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Bring Feature/ufo geovals up to date. (#798)
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Changes to preserve functionality of feature/ufo_geovals after OS change
to Hera. Plus various updates.


- [x] New feature (non-breaking change which adds functionality)


**How Has This Been Tested?**

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on the platforms these tests were conducted. -->
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**Checklist**

- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [x] I have commented my code, particularly in hard-to-understand areas
- [x] New and existing tests pass with my changes
- [x] Any dependent changes have been merged and published

---------

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31 changes: 16 additions & 15 deletions .github/workflows/gcc.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,21 +15,21 @@ env:

# The jobs are split into:
# 1. a dependency build step (setup), and
# 2. a GSI build step (build)
# 2. a GSI build step (gsi)
# The setup is run once and the environment is cached,
# so each build of GSI can reuse the cached dependencies to save time (and compute).
# so each subsequent build of GSI can reuse the cached dependencies to save time (and compute).

jobs:
setup:
runs-on: ubuntu-latest

steps:
# Checkout the GSI to get the ci/spack.yaml file
- name: checkout-gsi
- name: checkout
if: steps.cache-env.outputs.cache-hit != 'true'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
path: GSI
path: gsi

# Cache spack, compiler and dependencies
- name: cache-env
Expand All @@ -39,33 +39,34 @@ jobs:
path: |
spack
~/.spack
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}

# Install dependencies using Spack
- name: install-dependencies-with-spack
if: steps.cache-env.outputs.cache-hit != 'true'
run: |
sudo apt-get install cmake
git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
source spack/share/spack/setup-env.sh
spack env create gsi-env GSI/ci/spack.yaml
spack env create gsi-env gsi/ci/spack.yaml
spack env activate gsi-env
spack compiler find
sudo apt install cmake
spack external find
spack add mpich@3.4.2
spack concretize
spack install -v --fail-fast --dirty
spack clean -a
build:
gsi:
needs: setup
runs-on: ubuntu-latest

steps:
- name: checkout-gsi
uses: actions/checkout@v3
- name: checkout
uses: actions/checkout@v4
with:
path: GSI
path: gsi

- name: cache-env
id: cache-env
Expand All @@ -74,13 +75,13 @@ jobs:
path: |
spack
~/.spack
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}

- name: build-gsi
- name: build
run: |
source spack/share/spack/setup-env.sh
spack env activate gsi-env
cd GSI
cd gsi
mkdir -p build && cd build
cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
make -j2 VERBOSE=1
Expand Down
47 changes: 28 additions & 19 deletions .github/workflows/intel.yml
Original file line number Diff line number Diff line change
Expand Up @@ -18,21 +18,30 @@ env:

# The jobs are split into:
# 1. a dependency build step (setup), and
# 2. a GSI build step (build)
# 2. a GSI build step (gsi)
# The setup is run once and the environment is cached,
# so each build of GSI can reuse the cached dependencies to save time (and compute).
# so each subsequent build of GSI can reuse the cached dependencies to save time (and compute).

jobs:
setup:
runs-on: ubuntu-latest

steps:
# Free up disk space
- name: free-disk-spack
run: |
df -h
sudo swapoff -a
sudo rm -f /swapfile
sudo apt clean
docker rmi $(docker image ls -aq)
# Checkout the GSI to get the ci/spack.yaml file
- name: checkout-gsi
- name: checkout
if: steps.cache-env.outputs.cache-hit != 'true'
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
path: GSI
path: gsi

# Cache spack, compiler and dependencies
- name: cache-env
Expand All @@ -43,16 +52,15 @@ jobs:
spack
~/.spack
/opt/intel
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}

- name: install-intel-compilers
if: steps.cache-env.outputs.cache-hit != 'true'
run: |
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1
sudo apt-get clean
echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
Expand All @@ -62,31 +70,32 @@ jobs:
run: |
sudo mv /usr/local/ /usr_local_mv
sudo apt-get install cmake
git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
source spack/share/spack/setup-env.sh
spack env create gsi-env GSI/ci/spack.yaml
spack env create gsi-env gsi/ci/spack.yaml
spack env activate gsi-env
spack compiler find
sudo apt install cmake
spack external find
spack add intel-oneapi-mpi
spack concretize
spack install -v --fail-fast --dirty
spack clean -a
build:
gsi:
needs: setup
runs-on: ubuntu-latest

steps:
- name: checkout-gsi
uses: actions/checkout@v3
with:
path: GSI

- name: install-intel
run: |
echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
- name: checkout
uses: actions/checkout@v4
with:
path: gsi

- name: cache-env
id: cache-env
uses: actions/cache@v3
Expand All @@ -95,13 +104,13 @@ jobs:
spack
~/.spack
/opt/intel
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('GSI/ci/spack.yaml') }}
key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('gsi/ci/spack.yaml') }}

- name: build-gsi
- name: build
run: |
source spack/share/spack/setup-env.sh
spack env activate gsi-env
cd GSI
cd gsi
mkdir -p build && cd build
cmake -DCMAKE_INSTALL_PREFIX=../install -DGSI_MODE=Regional -DENKF_MODE=GFS -DBUILD_REG_TESTING=OFF ..
make -j2 VERBOSE=1
Expand Down
2 changes: 2 additions & 0 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ endif()
option(OPENMP "Enable OpenMP Threading" OFF)
option(ENABLE_MKL "Use MKL for LAPACK implementation (if available)" ON)
option(BUILD_GSDCLOUD "Build GSD Cloud Analysis Library" OFF)
option(BUILD_MGBF "Build MGBF Library" ON)
option(BUILD_GSI "Build GSI" ON)
option(BUILD_ENKF "Build EnKF" ON)
option(BUILD_REG_TESTING "Build the Regression Testing Suite" OFF)
Expand All @@ -37,6 +38,7 @@ option(BUILD_REG_TESTING "Build the Regression Testing Suite" OFF)
message(STATUS "OPENMP ................. ${OPENMP}")
message(STATUS "ENABLE_MKL ............. ${ENABLE_MKL}")
message(STATUS "BUILD_GSDCLOUD ......... ${BUILD_GSDCLOUD}")
message(STATUS "BUILD_MGBF ............. ${BUILD_MGBF}")
message(STATUS "BUILD_GSI .............. ${BUILD_GSI}")
message(STATUS "BUILD_ENKF ............. ${BUILD_ENKF}")
message(STATUS "BUILD_REG_TESTING ...... ${BUILD_REG_TESTING}")
Expand Down
1 change: 1 addition & 0 deletions INSTALL.md
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@ CMake allows for various options that can be specified on the command line via `
| `OPENMP` | Enable OpenMP Threading (`OFF`) |
| `ENABLE_MKL` | Use MKL (`ON`), If not found use LAPACK |
| `BUILD_GSDCLOUD` | Build GSD Cloud Library (`OFF`) |
| `BUILD_MGBF` | Build MGBF Library (`ON`) |
| `BUILD_GSI` | Build GSI library and executable (`ON`) |
| `BUILD_ENKF` | Build EnKF library and executable (`ON`) |
| `BUILD_REG_TESTING` | Enable Regression Testing (`ON`) |
Expand Down
157 changes: 157 additions & 0 deletions LICENSE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,157 @@
### GNU LESSER GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc.
<https://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

This version of the GNU Lesser General Public License incorporates the
terms and conditions of version 3 of the GNU General Public License,
supplemented by the additional permissions listed below.

#### 0. Additional Definitions.

As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the
GNU General Public License.

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than an Application or a Combined Work as defined below.

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