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yufenghe22yufenghe22
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Merge branch 'cvode_7.1.1' into SoybeanParameterization
2 parents c1a154b + 657ec3d commit 77224bf

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‎.github/workflows/test-suite.yml‎

Lines changed: 88 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,9 @@ name: Test of package installation & execution
1010
jobs:
1111
build_cxx:
1212
runs-on: ${{ matrix.os }}
13+
defaults:
14+
run:
15+
shell: bash -el {0}
1316
strategy:
1417
matrix:
1518
sundials-version: [latest]
@@ -18,25 +21,50 @@ jobs:
1821
with-asan: [false, true]
1922
with-elf: [false]
2023
with-valgrind: [false, true]
24+
with-mpi: [false]
2125
include:
2226
- sundials-version: "5.7.0"
2327
os: ubuntu-latest
2428
with-coverage: false
2529
with-asan: false
2630
with-elf: false
2731
with-valgrind: false
32+
with-mpi: false
2833
- sundials-version: "6.7.0"
2934
os: ubuntu-latest
3035
with-coverage: false
3136
with-asan: false
3237
with-elf: false
3338
with-valgrind: false
39+
with-mpi: false
3440
- sundials-version: "7.1.1"
3541
os: ubuntu-latest
3642
with-coverage: false
3743
with-asan: false
3844
with-elf: false
3945
with-valgrind: false
46+
with-mpi: false
47+
- sundials-version: latest
48+
os: ubuntu-latest
49+
with-coverage: false
50+
with-asan: false
51+
with-elf: false
52+
with-valgrind: false
53+
with-mpi: true
54+
- sundials-version: "6.7.0"
55+
os: ubuntu-latest
56+
with-coverage: false
57+
with-asan: false
58+
with-elf: false
59+
with-valgrind: false
60+
with-mpi: true
61+
- sundials-version: "7.1.1"
62+
os: ubuntu-latest
63+
with-coverage: false
64+
with-asan: false
65+
with-elf: false
66+
with-valgrind: false
67+
with-mpi: true
4068
exclude:
4169
- os: windows-latest
4270
with-asan: true
@@ -71,65 +99,113 @@ jobs:
7199
- name: Set up MSVC Compiler on windows
72100
uses: ilammy/msvc-dev-cmd@v1
73101
if: matrix.os == 'windows-latest'
74-
- name: Set up miniconda test environment
102+
- name: Set up miniconda test environment (W/O MPI)
103+
if: matrix.with-mpi == false
75104
uses: conda-incubator/setup-miniconda@v3
76105
with:
77106
activate-environment: ephoto
78107
environment-file: environment.yml
79108
auto-update-conda: true
80109
channels: conda-forge
81110
channel-priority: strict
82-
# miniforge-variant: Mambaforge
83111
miniforge-version: latest
84112
use-mamba: true
85113
mamba-version: "1.5.10"
114+
conda-remove-defaults: true
115+
- name: Set up miniconda test environment (W/ MPI)
116+
if: matrix.with-mpi == true
117+
uses: conda-incubator/setup-miniconda@v3
118+
with:
119+
activate-environment: ephoto
120+
environment-file: environment_mpi.yml
121+
auto-update-conda: true
122+
channels: conda-forge
123+
channel-priority: strict
124+
miniforge-version: latest
125+
use-mamba: true
126+
mamba-version: "1.5.10"
127+
conda-remove-defaults: true
86128
- name: Set USERPROFILE
87129
if: matrix.os == 'windows-latest'
88-
shell: bash -el {0}
89130
run: |
90131
echo "USERPROFILE=${{ github.workspace }}" >> "$GITHUB_ENV"
91-
- name: Install specific version of Sundials
92-
if: matrix.sundials-version != 'latest'
93-
shell: bash -l {0}
132+
- name: Install specific version of Sundials via conda
133+
if: matrix.sundials-version != 'latest' && matrix.with-mpi == false
94134
run: |
95135
mamba install sundials==${{ matrix.sundials-version }} -y
96136
- name: Check mamba installation
97-
shell: bash -el {0}
98137
run: |
99138
mamba info
100139
mamba list
101140
- name: Install doxgen on unix systems
102141
if: matrix.os != 'windows-latest'
103-
shell: bash -l {0}
104142
run: |
105143
mamba install doxygen>=1.9.2 graphviz -y
106144
- name: Install compilers using conda on Linux/Mac
107145
if: matrix.os != 'windows-latest' && matrix.with-valgrind != true
108-
shell: bash -l {0}
109146
run: |
110147
mamba install c-compiler cxx-compiler
111148
- name: Install valgrind on unix systems (and required debug symbols)
112149
if: matrix.os != 'windows-latest' && matrix.with-valgrind == true
113-
shell: bash -l {0}
114150
run: |
115151
sudo apt-get update
116152
sudo apt-get install libc6-dbg
117153
mamba install valgrind
154+
155+
###################################
156+
# INSTALL SUNDIALS W/ MPI
157+
###################################
158+
- name: CMake flags for building Sundials W/ MPI
159+
shell: bash -l {0}
160+
if: matrix.with-mpi == true
161+
run: |
162+
CMAKE_BUILD_TYPE_TEST="RelWithDebInfo"
163+
echo "CMAKE_BUILD_TYPE_TEST=RelWithDebInfo" >> "$GITHUB_ENV"
164+
echo "CMAKE_ARGS=-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DENABLE_MPI:BOOL=ON -DEXAMPLES_ENABLE_C:BOOL=OFF -DEXAMPLES_ENABLE_CXX:BOOL=OFF" >> "$GITHUB_ENV"
165+
- name: Clone Sundials for build W/ MPI
166+
if: matrix.with-mpi == true
167+
run: |
168+
git clone https://github.com/LLNL/sundials.git
169+
- name: Check out specific version of Sundials for build W/ MPI
170+
if: matrix.sundials-version != 'latest' && matrix.with-mpi == true
171+
run: |
172+
cd sundials
173+
git checkout tags/v${{ matrix.sundials-version }} -b tagged
174+
- name: Configure Sundials W/ MPI
175+
if: matrix.with-mpi == true
176+
run: |
177+
cd sundials
178+
mkdir build
179+
cd build
180+
cmake .. ${{ env.CMAKE_ARGS }}
181+
- name: Build Sundials W/ MPI in parallel (CONDA, UNIX)
182+
if: matrix.with-mpi == true && matrix.os != 'windows-latest'
183+
run: |
184+
cd sundials/build
185+
cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }} -- -j 4
186+
- name: Build Sundials W/ MPI in serial (CONDA, WINDOWS)
187+
if: matrix.with-mpi == true && matrix.os == 'windows-latest'
188+
run: |
189+
cd sundials/build
190+
cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }}
191+
- name: Install Sundials W/ MPI
192+
if: matrix.with-mpi == true
193+
run: |
194+
cd sundials/build
195+
cmake --install . --prefix /home/runner/miniconda3/envs/ephoto
118196
119197
###################################
120198
# PIP INSTALL THINGS
121199
###################################
122200
- name: Install packages not current on conda-forge (gcovr)
123201
if: matrix.with-coverage == true
124-
shell: bash -l {0}
125202
run: |
126203
pip install gcovr
127204
128205
###################################
129206
# SET CONFIG FLAGS
130207
###################################
131208
- name: Global config flags
132-
shell: bash -l {0}
133209
run: |
134210
CMAKE_BUILD_TYPE_TEST="Debug"
135211
echo "CMAKE_BUILD_TYPE_TEST=Debug" >> "$GITHUB_ENV"
@@ -138,29 +214,24 @@ jobs:
138214
echo "TEST_FLAGS=-C ${CMAKE_BUILD_TYPE_TEST} --output-on-failure -VV" >> "$GITHUB_ENV"
139215
- name: Coverage config flags
140216
if: matrix.with-coverage == true && matrix.os != 'windows-latest'
141-
shell: bash -l {0}
142217
run: |
143218
echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_COVERAGE=ON" >> "$GITHUB_ENV"
144219
- name: ASAN config flags
145220
if: matrix.with-asan == true
146-
shell: bash -l {0}
147221
run: |
148222
echo "CMAKE_ARGS=${{ env.CMAKE_ARGS }} -DWITH_ASAN=ON" >> "$GITHUB_ENV"
149223
echo "ASAN_OPTIONS=detect_odr_violation=0:detect_container_overflow=0" >> $GITHUB_ENV
150224
echo "TEST_FLAGS=${{ env.TEST_FLAGS }} -E valgrind*" >> "$GITHUB_ENV"
151225
- name: ASAN dynamic library
152226
if: matrix.with-asan == true && matrix.os == 'macos-latest'
153-
shell: bash -l {0}
154227
run: |
155228
echo "DYLD_INSERT_LIBRARIES=$(clang -print-file-name=libclang_rt.asan_osx_dynamic.dylib)" >> "$GITHUB_ENV"
156229
- name: ELF config flags
157230
if: matrix.with-elf == true
158-
shell: bash -l {0}
159231
run: |
160232
echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_ELF=ON" >> "$GITHUB_ENV"
161233
- name: Valgrind off config flags
162234
if: matrix.with-valgrind == true
163-
shell: bash -l {0}
164235
run: |
165236
echo "CMAKE_ARGS_TEST=${{ env.CMAKE_ARGS_TEST }} -DTEST_VALGRIND=ON" >> "$GITHUB_ENV"
166237
@@ -169,7 +240,6 @@ jobs:
169240
###################################
170241
- name: Conda library paths on Windows
171242
if: matrix.os == 'windows-latest'
172-
shell: bash -l {0}
173243
run: |
174244
# This isn't necessary, but it speeds up the build
175245
LIB_DIRECTORY="${CONDA_PREFIX}/Library/lib"
@@ -183,7 +253,6 @@ jobs:
183253
# Configure
184254
###################################
185255
- name: Configure (CONDA)
186-
shell: bash -l {0}
187256
run: |
188257
mkdir build
189258
cd build
@@ -195,13 +264,11 @@ jobs:
195264
###################################
196265
- name: Build C++ & C in parallel (CONDA, UNIX)
197266
if: matrix.os != 'windows-latest'
198-
shell: bash -l {0}
199267
run: |
200268
cd build
201269
cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }} -- -j 4
202270
- name: Build C++ & C in serial (CONDA, WINDOWS)
203271
if: matrix.os == 'windows-latest'
204-
shell: bash -l {0}
205272
run: |
206273
cd build
207274
cmake --build . --config ${{ env.CMAKE_BUILD_TYPE_TEST }}
@@ -211,7 +278,6 @@ jobs:
211278
###################################
212279
- name: Test C++
213280
if: matrix.with-coverage != true
214-
shell: bash -l {0}
215281
run: |
216282
mamba list
217283
echo "PATH=$PATH"
@@ -220,34 +286,29 @@ jobs:
220286
ctest ${{ env.TEST_FLAGS }}
221287
- name: Test C++ (COVERAGE)
222288
if: matrix.with-coverage && matrix.os != 'windows-latest'
223-
shell: bash -l {0}
224289
run: |
225290
mamba list
226291
echo "PATH=$PATH"
227292
cd build
228293
make coverage
229294
- name: Preserve coverage information
230295
if: matrix.with-coverage && matrix.os != 'windows-latest'
231-
shell: bash -l {0}
232296
run: |
233297
cp -r build/coverage coverage
234298
235299
###################################
236300
# Build Python
237301
###################################
238302
# - name: Set CMAKE_ARGS for Python build
239-
# shell: bash -l {0}
240303
# run: |
241304
# echo "OLD_CMAKE_ARGS=${{ env.CMAKE_ARGS }}" >> "$GITHUB_ENV"
242305
# echo "CMAKE_ARGS=${{ env.CMAKE_ARGS }} -DBUILD_PYTHON=ON" >> "$GITHUB_ENV"
243306
# - name: Build Python (CONDA)
244-
# shell: bash -l {0}
245307
# run: |
246308
# cd build
247309
# which cmake
248310
# cmake .. ${{ env.CMAKE_ARGS }} ${{ env.CMAKE_ARGS_TEST }}
249311
# - name: Unset CMAKE_ARGS for Python build
250-
# shell: bash -l {0}
251312
# run: |
252313
# echo "CMAKE_ARGS=${{ env.OLD_CMAKE_ARGS }}" >> "$GITHUB_ENV"
253314

@@ -256,7 +317,6 @@ jobs:
256317
###################################
257318
# - name: Test Python Interfaces (CONDA)
258319
# if: matrix.with-elf == false && matrix.with-valgrind == false
259-
# shell: bash -l {0}
260320
# run: |
261321
# pytest -sv tests/python
262322

@@ -265,7 +325,6 @@ jobs:
265325
###################################
266326
- name: Build docs
267327
if: matrix.os != 'windows-latest'
268-
shell: bash -l {0}
269328
run: |
270329
python scripts/devtasks.py docs --rebuild
271330

‎CMakeLists.txt‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
2424

2525
cmake_minimum_required(VERSION 3.5)
2626

27-
project(ePhotosynthesisProject LANGUAGES CXX)
27+
project(ePhotosynthesisProject LANGUAGES C CXX)
2828

2929
set(PACKAGE_NAME "ePhotosynthesis")
3030
set(PACKAGE_STRING "ePhotosynthesis 1.0.0")
@@ -175,9 +175,12 @@ add_library(EPhotosynthesis SHARED ${SOURCES})
175175
add_executable(ePhoto bin/ePhotosynthesis.cpp)
176176

177177
find_package(Boost 1.36.0 REQUIRED COMPONENTS regex)
178-
find_package(SUNDIALS REQUIRED)
179-
if(NOT SUNDIALS_LIBRARIES)
180-
message(FATAL_ERROR "Failed to find sundials libraries")
178+
# Find MPI
179+
find_package(MPI COMPONENTS C CXX)
180+
181+
find_package(SUNDIALS REQUIRED CONFIG COMPONENTS kinsol cvode)
182+
if (NOT SUNDIALS_LIBRARIES)
183+
set(SUNDIALS_LIBRARIES SUNDIALS::kinsol SUNDIALS::cvode)
181184
endif()
182185
message(STATUS "SUNDIALS_LIBRARIES = ${SUNDIALS_LIBRARIES}")
183186
message(STATUS "SUNDIALS_INCLUDE_DIRS = ${SUNDIALS_INCLUDE_DIRS}")

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