forked from parflow/parflow
-
Notifications
You must be signed in to change notification settings - Fork 0
475 lines (433 loc) · 18.4 KB
/
linux.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
name: ParFlow CI Test
on: [push, pull_request]
jobs:
style-check:
runs-on: ubuntu-22.04
name: Check Style
steps:
- name: Checkout commit
uses: actions/checkout@v4
- name: Package Install
uses: awalsh128/cache-apt-pkgs-action@latest
with:
packages: curl cmake build-essential tcl-dev tk-dev
version: 1.0
execute_install_scripts: true
- name: Cache dependencies
uses: actions/cache@v4
id: cache-parflow-style-dependencies
env:
cache-name: cache-parflow-style-dependencies
cache-parflow-style-hit: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
with:
path: "~/depend"
key: cache-check-style-${{ secrets.CACHE_VERSION }}
- name: Directory Setup
run: |
mkdir -p $HOME/install
# Set necessary vars
PARFLOW_DIR="$HOME/install"
PARFLOW_DEP_DIR="$HOME/depend"
LD_LIBRARY_PATH=${PARFLOW_DEP_DIR}/lib64:${PARFLOW_DEP_DIR}/lib
# Create folders
mkdir -p ${PARFLOW_DIR} ${PARFLOW_DEP_DIR}/{include,lib}
# Verify if paths were correctly set
echo "PARFLOW_DIR=${PARFLOW_DIR}"
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}"
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"
# Vars pushed to GITHUB_ENV take effect only on the next CI steps.
echo "PARFLOW_DIR=${PARFLOW_DIR}" >> $GITHUB_ENV
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
echo "$HOME/depend/bin" >> $GITHUB_PATH
echo "$PARFLOW_DIR/bin" >> $GITHUB_PATH
- name: Build Uncrustify
env:
CACHE_HIT: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "cache-check-style-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
curl -L -o uncrustify-0.79.0.tar.gz https://github.com/uncrustify/uncrustify/archive/uncrustify-0.79.0.tar.gz
tar -xf uncrustify-0.79.0.tar.gz
cd uncrustify-uncrustify-0.79.0
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
sudo make -j 2 install
cd ../..
rm -fr uncrustify-uncrustify-0.79.0 uncrustify-0.79.0.tar.gz
fi
- name: CMake Install
env:
CACHE_HIT: ${{steps.cache-parflow-style-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "Installing"
mkdir -p $HOME/depend/{include,lib}
cd $HOME/depend
echo "cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
wget -nv --no-check-certificate https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.tar.gz
tar -xf cmake-3.25.1-linux-x86_64.tar.gz
$HOME/depend/cmake-3.25.1-linux-x86_64/bin/cmake --version
echo "$HOME/depend/cmake-3.25.1-linux-x86_64/bin" >> $GITHUB_PATH
fi
- name: ParFlow CMake Configure
run: |
cmake -Bbuild -DPARFLOW_ENABLE_PYTHON=ON -DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR
- name: ParFlow CMake Build
run: (cd build; make -j 2 install)
- name: Run Uncrustify
run: |
./bin/pfformat --check
build:
name: ${{ matrix.config.name }}
runs-on: ${{ matrix.config.os }}
strategy:
# fail-fast: true
matrix:
config:
- {
name: "Ubuntu 24.04 GCC",
os: ubuntu-24.04,
cudaos: 'ubuntu2404',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "none",
amps_layer: mpi1,
netcdf: "true"
}
- {
name: "Ubuntu 24.04 LLVM",
os: ubuntu-24.04,
cudaos: 'ubuntu2404',
cc: "clang-18", cxx: "clang++-18", fc: "gfortran",
python: "false",
backend: "none",
amps_layer: mpi1,
netcdf: "true"
}
- {
name: "Ubuntu 22.04 GCC Python",
os: ubuntu-22.04,
cudaos: 'ubuntu2204',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "true",
backend: "none",
amps_layer: mpi1,
netcdf: "true"
}
- {
name: "Ubuntu 20.04 GCC Python",
os: ubuntu-20.04,
cudaos: 'ubuntu2004',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "true",
backend: "none",
amps_layer: mpi1,
netcdf: "false"
}
- {
name: "Ubuntu 22.04 GCC OMP",
os: ubuntu-22.04,
cudaos: 'ubuntu2204',
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "omp",
amps_layer: mpi1,
netcdf: "false"
}
- {
name: "Ubuntu 24.04 LLVM OASIS3-MCT Build",
os: ubuntu-24.04,
cudaos: 'ubuntu2204',
cc: "clang-18", cxx: "clang++-18", fc: "gfortran",
python: "false",
backend: "omp",
amps_layer: oas3,
netcdf: "true"
}
- {
name: "Ubuntu 22.04 GCC CUDA Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "cuda",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false"
}
- {
name: "Ubuntu 22.04 GCC Kokkos Build",
os: ubuntu-22.04,
cc: "gcc", cxx: "g++", fc: "gfortran",
python: "false",
backend: "kokkos",
cudaos: 'ubuntu2204',
amps_layer: mpi1,
netcdf: "false"
}
steps:
- uses: actions/checkout@v4
- name: Package Install
uses: awalsh128/cache-apt-pkgs-action@latest
with:
packages: gfortran hdf5-helpers tcl-dev tk-dev libcurl4 libcurl4-gnutls-dev
version: 1.0
execute_install_scripts: true
- name: HDF5 and OpenMPI Install on Ubuntu 22.04
if: matrix.config.os == 'ubuntu-20.04' || matrix.config.os == 'ubuntu-22.04'
run: |
sudo apt-get -qq update
sudo apt -qq install libhdf5-openmpi-103 libhdf5-openmpi-dev
# libhdf5-openmpi-103 has been renamed in Ubuntu 24.04.
- name: HDF5 and OpenMPI Install on Ubuntu 24.04
if: matrix.config.os == 'ubuntu-24.04'
run: |
sudo apt-get -qq update
sudo apt -qq install libhdf5-openmpi-103-1t64 libhdf5-openmpi-dev
- name: LLVM 18.X Install
if: matrix.config.cc == 'clang-18'
run: |
sudo apt -qq install clang-18 libomp-18-dev
- name: Python Package Install
if: matrix.config.python == 'true'
run: |
sudo apt-get -qq update
sudo apt -qq install python3 python3-venv
# Cache dependencies so don't have to rebuild on each test.
# Can flush caches by resetting the CACHE_VERSION secret on GitHub
# settings for the project (using date-timestamp for secret).
- name: Cache dependencies
uses: actions/cache@v4
id: cache-parflow-dependencies
env:
cache-name: cache-parflow-dependencies
cache-parflow-hit: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
with:
path: "~/depend"
key: cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ secrets.CACHE_VERSION }}
- name: Directory Setup
run: |
mkdir -p $HOME/install
# Set necessary vars
PARFLOW_DIR="$HOME/install"
PARFLOW_DEP_DIR="$HOME/depend"
LD_LIBRARY_PATH=${PARFLOW_DEP_DIR}/lib64:${PARFLOW_DEP_DIR}/lib
# Create folders
mkdir -p ${PARFLOW_DIR} ${PARFLOW_DEP_DIR}/{include,lib}
# Verify if paths were correctly set
echo "PARFLOW_DIR=${PARFLOW_DIR}"
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}"
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"
# Vars pushed to GITHUB_ENV take effect only on the next CI steps.
echo "PARFLOW_DIR=${PARFLOW_DIR}" >> $GITHUB_ENV
echo "PARFLOW_DEP_DIR=${PARFLOW_DEP_DIR}" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
echo "$HOME/depend/bin" >> $GITHUB_PATH
echo "$PARFLOW_DIR/bin" >> $GITHUB_PATH
- name: Configure OpenMPI backend compiler
run: |
export OMPI_CC=${{ matrix.config.cc }}
export OMPI_CXX=${{ matrix.config.cxx }}
export OMPI_FC=${{ matrix.config.fc }}
echo "OMPI_CC=${{ matrix.config.cc }}" >> $GITHUB_ENV
echo "OMPI_CXX=${{ matrix.config.cxx }}" >> $GITHUB_ENV
echo "OMPI_FC=${{ matrix.config.fc }}" >> $GITHUB_ENV
echo " mpicc: $(mpicc --version | head -n 1)"
echo " mpicxx: $(mpicxx --version | head -n 1)"
echo "mpifort: $(mpifort --version | head -n 1)"
- name: CMake Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
echo "Installing CMake v3.25.1"
cd $HOME/depend
echo "cache-${{ matrix.config.os }}-${{ matrix.config.backend }}-${{ secrets.CACHE_VERSION }}" > $HOME/depend/cache-key
wget -nv --no-check-certificate https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.tar.gz
tar -xf cmake-3.25.1-linux-x86_64.tar.gz
$HOME/depend/cmake-3.25.1-linux-x86_64/bin/cmake --version
fi
echo "$HOME/depend/cmake-3.25.1-linux-x86_64/bin" >> $GITHUB_PATH
- name: NVidia Driver Install
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
sudo add-apt-repository -y ppa:graphics-drivers
sudo apt-get update -qq
sudo apt-get install -y nvidia-driver-440
- name: CUDA Install
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
export CUDA_VERSION_MAJOR_MINOR=11.8.0
export CUDA_SHORT=11.8
export CUDA_OS=${{ matrix.config.cudaos }}
./bin/install-cuda.sh
export CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
echo "CUDA_HOME=${CUDA_HOME}" >> $GITHUB_ENV
export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $GITHUB_ENV
export LIBRARY_PATH=${CUDA_HOME}/lib64/stubs
echo "LIBRARY_PATH=${LIBRARY_PATH}" >> $GITHUB_ENV
echo "${CUDA_HOME}/bin" >> $GITHUB_PATH
- name: UCX
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
sudo apt install -qq -y autoconf automake libtool
URL=https://github.com/openucx/ucx/releases/download/v1.13.1/ucx-1.13.1.tar.gz
mkdir ucx
cd ucx
curl -L $URL | tar --strip-components=1 -xz
./contrib/configure-release --with-cuda=$CUDA_HOME --with-java=no --with-go=no --disable-numa --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: RMM Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
git clone --branch main --single-branch --recurse-submodules https://github.com/rapidsai/rmm.git
cd rmm
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$PARFLOW_DEP_DIR/rmm
make -j
make install
fi
echo "RMM_FLAGS=-Drmm_ROOT=$PARFLOW_DEP_DIR/rmm" >> $GITHUB_ENV
- name: Kokkos Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.backend == 'kokkos'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/kokkos/kokkos/archive/refs/tags/4.2.01.tar.gz
mkdir kokkos
cd kokkos
curl -L $URL | tar --strip-components=1 -xz
mkdir build
cd build
cmake .. -DCMAKE_CXX_COMPILER=$(pwd)/../bin/nvcc_wrapper -DCMAKE_INSTALL_PREFIX=$PARFLOW_DEP_DIR -DKokkos_ENABLE_CUDA=On -DKokkos_ENABLE_CUDA_LAMBDA=On -DKokkos_ENABLE_CUDA_UVM=On -DKokkos_ARCH_VOLTA70=On
make -j 2 install
fi
echo "KOKKOS_FLAGS=-DKOKKOS_ROOT=$PARFLOW_DEP_DIR" >> $GITHUB_ENV
- name: OpenMPI Install for CUDA
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.backend == 'cuda' || matrix.config.backend == 'kokkos'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz
mkdir openmpi
cd openmpi
curl -L $URL | tar --strip-components=1 -xz
./configure --with-cuda=$CUDA_HOME --with-ucx=$PARFLOW_DEP_DIR --prefix=$PARFLOW_DEP_DIR
sudo make -j 2 install
cd ..
fi
sudo ldconfig
# Package netcdf is missing features needed by the ParFlow writers, build from source
# netcdf is True when we want to build the PF NetCDF writer. OASIS is using the Fortran interface
# which is currently not built here. This is currently incompatible with the OASIS build which uses the NetCDF packages.
- name: NetCDF Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.netcdf == 'true'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/Unidata/netcdf-c/archive/v4.9.0.tar.gz
mkdir netcdf-c
cd netcdf-c
curl -L $URL | tar --strip-components=1 -xz
CC=mpicc CPPFLAGS=-I/usr/include/hdf5/openmpi LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ./configure --prefix=$PARFLOW_DEP_DIR
make
make install
cd ..
URL=https://github.com/Unidata/netcdf-fortran/archive/v4.5.4.tar.gz
mkdir netcdf-fortran
cd netcdf-fortran
curl -L $URL | tar --strip-components=1 -xz
CC=mpicc FC=mpifort CPPFLAGS=-I${PARFLOW_DEP_DIR}/include LDFLAGS=-L${PARFLOW_DEP_DIR}/lib ./configure --prefix=${PARFLOW_DEP_DIR}
make
make install
fi
echo "NETCDF_FLAGS=-DNETCDF_DIR=$PARFLOW_DEP_DIR -DNETCDF_Fortran_ROOT=$PARFLOW_DEP_DIR -DPARFLOW_ENABLE_HDF5=TRUE" >> $GITHUB_ENV
- name: OASIS3-MCT Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
if: matrix.config.amps_layer == 'oas3'
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
git clone --depth 1 --branch OASIS3-MCT_5.1 https://gitlab.com/cerfacs/oasis3-mct.git
cd oasis3-mct
export OASIS_ROOT=$(pwd)
cd util/make_dir
echo 'include $(GITHUB_WORKSPACE)/misc/build_scripts/build.oasis3.ubuntu22.04' > make.inc
make realclean static-libs -f TopMakefileOasis3
mv -v ${OASIS_ROOT}/install/include/* ${PARFLOW_DEP_DIR}/include/
mv -v ${OASIS_ROOT}/install/lib/* ${PARFLOW_DEP_DIR}/lib/
fi
- name: SILO Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/LLNL/Silo/archive/refs/tags/4.11.tar.gz
mkdir silo
cd silo
curl -L $URL | tar --strip-components=1 -xz
./configure --disable-silex --disable-hzip --disable-fpzip --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: HYPRE Install
env:
CACHE_HIT: ${{steps.cache-parflow-dependencies.outputs.cache-hit}}
run: |
if [[ "$CACHE_HIT" != 'true' ]]; then
URL=https://github.com/hypre-space/hypre/archive/v2.26.0.tar.gz
mkdir hypre
cd hypre
curl -L $URL | tar --strip-components=1 -xz
cd src
./configure --prefix=$PARFLOW_DEP_DIR
make -j 2 install
fi
- name: ParFlow CMake Configure
run: |
cat $HOME/depend/cache-key
export OMPI_MCA_rmaps_base_oversubscribe=1
export OMP_NUM_THREADS=1
${{ matrix.config.cc }} -v
mpicc -v
if [[ "${{ matrix.config.amps_layer }}" == "oas3" ]]; then HAVE_CLM="OFF"; else HAVE_CLM="ON"; fi
CFLAGS="-Wall -Werror -Wno-unused-result -Wno-unused-function -Wno-stringop-overread"
if [[ "${{ matrix.config.cc }}" == "gcc" ]]; then CFLAGS="${CFLAGS} -Wno-stringop-overread"; fi
export CC=mpicc CXX=mpicxx F77=mpif77 FC=mpif90 CUDAHOSTCXX=mpicxx
cmake -Bbuild \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_C_FLAGS=$CFLAGS \
-DPARFLOW_ENABLE_TIMING=TRUE \
-DPARFLOW_AMPS_LAYER=${{ matrix.config.amps_layer }} \
-DMPIEXEC_POSTFLAGS='--oversubscribe' \
-DPARFLOW_ACCELERATOR_BACKEND=${{ matrix.config.backend }} \
-DPARFLOW_AMPS_SEQUENTIAL_IO=true \
-DPARFLOW_HAVE_CLM=${HAVE_CLM} \
-DHYPRE_ROOT=$PARFLOW_DEP_DIR \
-DOAS3_ROOT=$PARFLOW_DEP_DIR \
-DSILO_ROOT=$PARFLOW_DEP_DIR \
-DPARFLOW_ENABLE_PYTHON=${{ matrix.config.python }} \
-DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR \
$NETCDF_FLAGS $KOKKOS_FLAGS $RMM_FLAGS
- name: ParFlow CMake Build
run: (cd build; make -j 2 install)
# Can't test with GPU since have no GPU hardware on testing nodes, GPU test is build only
- name: ParFlow CTest
if: matrix.config.backend != 'cuda' && matrix.config.backend != 'kokkos'
run: |
export OMPI_MCA_rmaps_base_oversubscribe=1
export OMP_NUM_THREADS=1
(cd build; ctest --output-on-failure)