├── CESM-Lab ├── 2.1 │ ├── Dockerfile │ └── Files │ │ ├── cesm_aliases.ipy │ │ ├── condarc.yml │ │ ├── config_pes.xml │ │ ├── configs │ │ ├── cam │ │ │ └── config_pes.xml │ │ ├── cice │ │ │ └── config_pes.xml │ │ ├── cism │ │ │ └── config_pes.xml │ │ ├── clm │ │ │ └── config_pes.xml │ │ └── pop │ │ │ └── config_pes.xml │ │ ├── dask_config.yml │ │ ├── env_batch.py │ │ ├── environment.yml │ │ ├── start │ │ └── tutorials │ │ └── CESM │ │ └── Quickstart.ipynb └── 2.2 │ ├── Dockerfile │ └── Files │ ├── cartopy │ └── shapefiles │ │ └── natural_earth │ │ └── physical │ │ ├── ne_110m_coastline.dbf │ │ ├── ne_110m_coastline.shp │ │ └── ne_110m_coastline.shx │ ├── cesm.py │ ├── cesm_aliases.ipy │ ├── condarc.yml │ ├── dask_config.yml │ ├── environment.yml │ ├── start │ └── tutorials │ ├── CESM │ └── QuickStart.ipynb │ ├── images │ └── logo.png │ └── index.ipynb ├── CESM-Postprocessing ├── Dockerfile └── Files │ ├── activate_this.py │ └── environment.yml ├── CESM ├── 2.1 │ ├── Dockerfile │ └── Files │ │ ├── case_setup.py │ │ ├── config_compilers.xml │ │ ├── config_inputdata.xml │ │ ├── config_machines.xml │ │ └── ea002e626aee6bc6643e8ab5f998e5e4 └── 2.2 │ ├── Dockerfile │ └── Files │ ├── case_setup.py │ ├── config_compilers.xml │ ├── config_compsets.xml │ ├── config_inputdata.xml │ ├── config_machines.xml │ ├── config_pes.xml │ ├── configs │ ├── cam │ │ └── config_pes.xml │ ├── cice │ │ └── config_pes.xml │ ├── cism │ │ └── config_pes.xml │ ├── clm │ │ └── config_pes.xml │ └── pop │ │ └── config_pes.xml │ ├── create_scam6_iop │ ├── ea002e626aee6bc6643e8ab5f998e5e4 │ ├── machines.py │ ├── micro_mg3_0.F90 │ └── scam_shell_commands ├── ESMF ├── 8.0 │ └── Dockerfile ├── API_changes │ └── Dockerfile ├── copyright_update │ └── Dockerfile ├── dev │ └── Dockerfile ├── doc │ ├── esmf-doc-base │ │ └── Dockerfile │ ├── esmf-doc │ │ └── Dockerfile │ └── esmpy-doc │ │ └── Dockerfile ├── nuopc-app-prototypes │ ├── Dockerfile │ ├── docker-entrypoint.sh │ └── meta_test.py └── test_coverage │ └── Dockerfile ├── README.md └── base └── centos8 └── Dockerfile /CESM-Lab/2.1/Dockerfile: -------------------------------------------------------------------------------- 1 | ################################## 2 | # ESCOMP/CESM-Lab/2.1 Dockerfile # 3 | ################################## 4 | 5 | # This builds on top of the CESM 2.1 container, and adds the Jupyter Lab environment 6 | FROM escomp/cesm-2.1 7 | 8 | # Set up the Conda version - using the pangeo/base-image as a foundation here: 9 | ENV CONDA_VERSION=4.8.3-4 \ 10 | CONDA_ENV=notebook \ 11 | NB_USER=user \ 12 | NB_GROUP=ncar \ 13 | NB_UID=1000 \ 14 | SHELL=/bin/bash \ 15 | LANG=C.UTF-8 \ 16 | LC_ALL=C.UTF-8 \ 17 | CONDA_DIR=/srv/conda 18 | 19 | # Additional environment setup that depends on the above: 20 | ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/${CONDA_ENV} \ 21 | DASK_ROOT_CONFIG=${CONDA_DIR}/etc \ 22 | HOME=/home/${NB_USER} \ 23 | PATH=${CONDA_DIR}/bin:${PATH} 24 | 25 | # Add the Conda init and set permissions on the directory: 26 | # (Could clean this up, and push changes back to Pangeo -- eg, /srv is hardcoded) 27 | RUN sudo /bin/bash -c "echo '. ${CONDA_DIR}/etc/profile.d/conda.sh ; conda activate ${CONDA_ENV}' > /etc/profile.d/init_conda.sh" && \ 28 | sudo chown -R ${NB_USER}:${NB_GROUP} /srv 29 | 30 | # Install miniforge: 31 | RUN URL="https://github.com/conda-forge/miniforge/releases/download/${CONDA_VERSION}/Miniforge3-${CONDA_VERSION}-Linux-x86_64.sh" && \ 32 | wget --quiet ${URL} -O miniconda.sh && \ 33 | /bin/bash miniconda.sh -u -b -p ${CONDA_DIR} && \ 34 | rm miniconda.sh && \ 35 | conda clean -afy && \ 36 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 37 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete 38 | 39 | COPY --chown=${NB_USER}:${NB_GROUP} Files/*yml /srv/ 40 | 41 | RUN mv /srv/condarc.yml ${CONDA_DIR}/.condarc && \ 42 | mv /srv/dask_config.yml ${CONDA_DIR}/etc/dask.yml 43 | 44 | RUN sudo yum install -y graphviz 45 | 46 | RUN conda env create --name ${CONDA_ENV} -f /srv/environment.yml && \ 47 | conda clean -yaf && \ 48 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 49 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \ 50 | find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete && \ 51 | find ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete 52 | 53 | RUN pip --no-cache-dir install rechunker 54 | 55 | 56 | RUN export PATH=${NB_PYTHON_PREFIX}/bin:${PATH} && \ 57 | jupyter labextension install --clean \ 58 | @jupyter-widgets/jupyterlab-manager \ 59 | @jupyterlab/geojson-extension \ 60 | dask-labextension \ 61 | @pyviz/jupyterlab_pyviz \ 62 | jupyter-leaflet && \ 63 | sudo rm -rf /tmp/* && \ 64 | rm -rf ${HOME}/.cache ${HOME}/.npm ${HOME}/.yarn && \ 65 | rm -rf ${NB_PYTHON_PREFIX}/share/jupyter/lab/staging && \ 66 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 67 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \ 68 | find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete 69 | 70 | RUN sudo yum install -y xmlstarlet 71 | 72 | COPY Files/start /srv 73 | RUN sudo chmod +x /srv/start 74 | 75 | COPY Files/cesm_aliases.ipy /etc/ipython/ 76 | RUN sudo /bin/bash -c 'echo "c.InteractiveShellApp.exec_files = [ \"/etc/ipython/cesm_aliases.ipy\" ] " >> /etc/ipython/ipython_config.py' 77 | 78 | COPY Files/tutorials /srv/tutorials 79 | 80 | COPY Files/config_pes.xml /opt/ncar/cesm2/cime_config/ 81 | COPY Files/configs/cam/config_pes.xml /opt/ncar/cesm2/components/cam/cime_config/ 82 | COPY Files/configs/cice/config_pes.xml /opt/ncar/cesm2/components/cice/cime_config/ 83 | COPY Files/configs/cism/config_pes.xml /opt/ncar/cesm2/components/cism/cime_config/ 84 | COPY Files/configs/pop/config_pes.xml /opt/ncar/cesm2/components/pop/cime_config/ 85 | COPY Files/configs/clm/config_pes.xml /opt/ncar/cesm2/components/clm/cime_config/ 86 | 87 | COPY Files/env_batch.py /opt/ncar/cesm2/cime/scripts/lib/CIME/XML/env_batch.py 88 | 89 | ENV CESMROOT=/opt/ncar/cesm2 90 | 91 | 92 | EXPOSE 8888 93 | USER user 94 | WORKDIR /home/user 95 | ENV SHELL /bin/bash 96 | ENTRYPOINT ["/srv/start"] 97 | #ENTRYPOINT ["/opt/conda/bin/jupyter", "lab", "--ip=0.0.0.0", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.password=''"] 98 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/cesm_aliases.ipy: -------------------------------------------------------------------------------- 1 | %alias xmlchange ./xmlchange %l 2 | %alias xmlquery ./xmlquery %l 3 | %alias create_newcase ${CESMROOT}/cime/scripts/create_newcase %l 4 | %alias query_config ${CESMROOT}/cime/scripts/query_config %l 5 | %alias case.setup ./case.setup %l 6 | %alias case.build ./case.build %l 7 | %alias case.submit ./case.submit %l 8 | %alias preview_run ./preview_run %l 9 | %alias pelayout ./pelayout %l 10 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/condarc.yml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - defaults 4 | channel_priority: strict 5 | show_channel_urls: true 6 | # NOTE: defaults only work for `conda create -f`, not `conda env create -f`! 7 | # https://github.com/conda/conda/issues/9580 8 | #create_default_packages: 9 | # - pangeo-notebook=0.0.2 10 | # - ipykernel 11 | #pinned_packages: 12 | # - pangeo-notebook=0.0.2 13 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/configs/cice/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -1 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | 17 | 18 | 1 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 27 | 28 | 0 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | -2 46 | -2 47 | -2 48 | -40 49 | -40 50 | -2 51 | -2 52 | -2 53 | 54 | 55 | 2 56 | 2 57 | 2 58 | 2 59 | 2 60 | 2 61 | 2 62 | 2 63 | 64 | 65 | 0 66 | -2 67 | -4 68 | 0 69 | 0 70 | -6 71 | -8 72 | -10 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | -2 83 | -2 84 | -2 85 | -2 86 | -2 87 | -2 88 | -2 89 | -2 90 | 91 | 92 | 1 93 | 1 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 101 | 102 | 0 103 | 0 104 | 0 105 | 0 106 | 0 107 | 0 108 | 0 109 | 0 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | -4 119 | -4 120 | -4 121 | -4 122 | -4 123 | -4 124 | -4 125 | -4 126 | 127 | 128 | 2 129 | 2 130 | 2 131 | 2 132 | 2 133 | 2 134 | 2 135 | 2 136 | 137 | 138 | 0 139 | 0 140 | 0 141 | 0 142 | 0 143 | 0 144 | 0 145 | 0 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | -4 155 | -4 156 | -4 157 | -4 158 | -4 159 | -4 160 | -4 161 | -4 162 | 163 | 164 | 2 165 | 2 166 | 2 167 | 2 168 | 2 169 | 2 170 | 2 171 | 2 172 | 173 | 174 | 0 175 | 0 176 | 0 177 | 0 178 | 0 179 | 0 180 | 0 181 | 0 182 | 183 | 184 | 185 | 186 | 187 | 188 | -4 189 | -4 190 | -4 191 | -4 192 | -4 193 | -4 194 | -4 195 | -4 196 | 197 | 198 | 1 199 | 1 200 | 1 201 | 1 202 | 1 203 | 1 204 | 1 205 | 1 206 | 207 | 208 | 0 209 | 0 210 | 0 211 | 0 212 | 0 213 | 0 214 | 0 215 | 0 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 30 226 | 30 227 | 30 228 | 30 229 | 30 230 | 30 231 | 30 232 | 30 233 | 234 | 235 | 2 236 | 2 237 | 2 238 | 2 239 | 2 240 | 2 241 | 2 242 | 2 243 | 244 | 245 | 0 246 | 0 247 | 0 248 | 0 249 | 0 250 | 0 251 | 0 252 | 0 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 60 262 | 60 263 | 60 264 | 60 265 | 60 266 | 60 267 | 60 268 | 60 269 | 270 | 271 | 2 272 | 2 273 | 2 274 | 2 275 | 2 276 | 2 277 | 2 278 | 2 279 | 280 | 281 | 0 282 | 0 283 | 0 284 | 0 285 | 0 286 | 0 287 | 0 288 | 0 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 60 298 | 60 299 | 60 300 | 60 301 | 60 302 | 60 303 | 60 304 | 60 305 | 306 | 307 | 2 308 | 2 309 | 2 310 | 2 311 | 2 312 | 2 313 | 2 314 | 2 315 | 316 | 317 | 0 318 | 0 319 | 0 320 | 0 321 | 0 322 | 0 323 | 0 324 | 0 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/configs/cism/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | none 8 | 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | -1 17 | 18 | 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 1 27 | 28 | 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 0 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | none 46 | 47 | 1 48 | 1 49 | 1 50 | 1 51 | 1 52 | 1 53 | 1 54 | 1 55 | 56 | 57 | 1 58 | 1 59 | 1 60 | 1 61 | 1 62 | 1 63 | 1 64 | 1 65 | 66 | 67 | 0 68 | 0 69 | 0 70 | 0 71 | 0 72 | 0 73 | 0 74 | 0 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | none 83 | 84 | -1 85 | -1 86 | -1 87 | -1 88 | -1 89 | -1 90 | -1 91 | -1 92 | 93 | 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 1 101 | 1 102 | 103 | 104 | 0 105 | 0 106 | 0 107 | 0 108 | 0 109 | 0 110 | 0 111 | 0 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | none 120 | 121 | -8 122 | -8 123 | -8 124 | -8 125 | -8 126 | -8 127 | -8 128 | -8 129 | 130 | 131 | 1 132 | 1 133 | 1 134 | 1 135 | 1 136 | 1 137 | 1 138 | 1 139 | 140 | 141 | 0 142 | 0 143 | 0 144 | 0 145 | 0 146 | 0 147 | 0 148 | 0 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | none 157 | 158 | -2 159 | -2 160 | -2 161 | -2 162 | -2 163 | -2 164 | -2 165 | -2 166 | 167 | 168 | 1 169 | 1 170 | 1 171 | 1 172 | 1 173 | 1 174 | 1 175 | 1 176 | 177 | 178 | 0 179 | 0 180 | 0 181 | 0 182 | 0 183 | 0 184 | 0 185 | 0 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/configs/clm/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | none 8 | 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | -1 17 | 18 | 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 1 27 | 28 | 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 0 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | none 46 | 47 | -1 48 | -1 49 | -1 50 | -1 51 | -1 52 | -1 53 | -1 54 | -1 55 | 56 | 57 | 1 58 | 1 59 | 1 60 | 1 61 | 1 62 | 1 63 | 1 64 | 1 65 | 66 | 67 | 0 68 | 0 69 | 0 70 | 0 71 | 0 72 | 0 73 | 0 74 | 0 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | none 83 | 84 | -1 85 | -9 86 | -9 87 | -9 88 | -9 89 | -9 90 | -9 91 | -9 92 | 93 | 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 1 101 | 1 102 | 103 | 104 | 0 105 | -1 106 | -1 107 | -1 108 | -1 109 | -1 110 | -1 111 | -1 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | none 120 | 121 | -1 122 | -4 123 | -4 124 | -4 125 | -4 126 | -4 127 | -4 128 | -4 129 | 130 | 131 | 1 132 | 1 133 | 1 134 | 1 135 | 1 136 | 1 137 | 1 138 | 1 139 | 140 | 141 | 0 142 | -1 143 | -1 144 | -1 145 | -1 146 | -1 147 | -1 148 | -1 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | none 157 | 158 | -2 159 | -2 160 | -2 161 | -2 162 | -2 163 | -2 164 | -2 165 | -2 166 | 167 | 168 | 1 169 | 1 170 | 1 171 | 1 172 | 1 173 | 1 174 | 1 175 | 1 176 | 177 | 178 | 0 179 | 0 180 | 0 181 | 0 182 | 0 183 | 0 184 | 0 185 | 0 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | none 194 | 195 | 180 196 | 180 197 | 180 198 | 180 199 | 180 200 | 180 201 | 180 202 | 180 203 | 204 | 205 | 1 206 | 1 207 | 1 208 | 1 209 | 1 210 | 1 211 | 1 212 | 1 213 | 214 | 215 | 0 216 | 0 217 | 0 218 | 0 219 | 0 220 | 0 221 | 0 222 | 0 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | none 231 | 232 | -1 233 | -40 234 | -40 235 | -40 236 | -40 237 | -40 238 | -40 239 | -40 240 | 241 | 242 | 1 243 | 1 244 | 1 245 | 1 246 | 1 247 | 1 248 | 1 249 | 1 250 | 251 | 252 | 0 253 | -1 254 | -1 255 | -1 256 | -1 257 | -1 258 | -1 259 | -1 260 | 261 | 262 | 263 | 264 | 265 | 266 | 267 | none 268 | 269 | -4 270 | -4 271 | -4 272 | -4 273 | -4 274 | -4 275 | -4 276 | -4 277 | 278 | 279 | 1 280 | 1 281 | 1 282 | 1 283 | 1 284 | 1 285 | 1 286 | 1 287 | 288 | 289 | 0 290 | 0 291 | 0 292 | 0 293 | 0 294 | 0 295 | 0 296 | 0 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | none 305 | 306 | -1 307 | -50 308 | -50 309 | -50 310 | -50 311 | -50 312 | -50 313 | -50 314 | 315 | 316 | 1 317 | 1 318 | 1 319 | 1 320 | 1 321 | 1 322 | 1 323 | 1 324 | 325 | 326 | 0 327 | -1 328 | -1 329 | -1 330 | -1 331 | -1 332 | -1 333 | -1 334 | 335 | 336 | 337 | 338 | 339 | 340 | 341 | none 342 | 343 | -8 344 | -8 345 | -8 346 | -8 347 | -8 348 | -8 349 | -8 350 | -8 351 | 352 | 353 | 1 354 | 1 355 | 1 356 | 1 357 | 1 358 | 1 359 | 1 360 | 1 361 | 362 | 363 | 0 364 | 0 365 | 0 366 | 0 367 | 0 368 | 0 369 | 0 370 | 0 371 | 372 | 373 | 374 | 375 | 376 | 377 | 378 | none 379 | 380 | -16 381 | -16 382 | -16 383 | -16 384 | -16 385 | -16 386 | -16 387 | -16 388 | 389 | 390 | 1 391 | 1 392 | 1 393 | 1 394 | 1 395 | 1 396 | 1 397 | 1 398 | 399 | 400 | 0 401 | 0 402 | 0 403 | 0 404 | 0 405 | 0 406 | 0 407 | 0 408 | 409 | 410 | 411 | 412 | 413 | 414 | 415 | none 416 | 417 | -4 418 | -4 419 | -4 420 | -4 421 | -4 422 | -4 423 | -4 424 | -4 425 | 426 | 427 | 1 428 | 1 429 | 1 430 | 1 431 | 1 432 | 1 433 | 1 434 | 1 435 | 436 | 437 | 0 438 | 0 439 | 0 440 | 0 441 | 0 442 | 0 443 | 0 444 | 0 445 | 446 | 447 | 448 | 449 | 450 | 451 | 452 | none 453 | 454 | -16 455 | -16 456 | -16 457 | -16 458 | -16 459 | -16 460 | -16 461 | -16 462 | 463 | 464 | 1 465 | 1 466 | 1 467 | 1 468 | 1 469 | 1 470 | 1 471 | 1 472 | 473 | 474 | 0 475 | 0 476 | 0 477 | 0 478 | 0 479 | 0 480 | 0 481 | 0 482 | 483 | 484 | 485 | 486 | 487 | 488 | 489 | none 490 | 491 | -32 492 | -32 493 | -32 494 | -32 495 | -32 496 | -32 497 | -32 498 | -32 499 | 500 | 501 | 1 502 | 1 503 | 1 504 | 1 505 | 1 506 | 1 507 | 1 508 | 1 509 | 510 | 511 | 0 512 | 0 513 | 0 514 | 0 515 | 0 516 | 0 517 | 0 518 | 0 519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | none 527 | 528 | 1 529 | 1 530 | 1 531 | 1 532 | 1 533 | 1 534 | 1 535 | 1 536 | 537 | 538 | 1 539 | 1 540 | 1 541 | 1 542 | 1 543 | 1 544 | 1 545 | 1 546 | 547 | 548 | 0 549 | 0 550 | 0 551 | 0 552 | 0 553 | 0 554 | 0 555 | 0 556 | 557 | 558 | 559 | 560 | 561 | 562 | 563 | none 564 | 565 | 5 566 | 5 567 | 5 568 | 5 569 | 5 570 | 5 571 | 5 572 | 5 573 | 574 | 575 | 1 576 | 1 577 | 1 578 | 1 579 | 1 580 | 1 581 | 1 582 | 1 583 | 584 | 585 | 0 586 | 0 587 | 0 588 | 0 589 | 0 590 | 0 591 | 0 592 | 0 593 | 594 | 595 | 596 | 597 | 598 | 599 | 600 | none 601 | 602 | -4 603 | -4 604 | -4 605 | -4 606 | -4 607 | -4 608 | -4 609 | -4 610 | -4 611 | 612 | 613 | 1> 614 | 1 615 | 1 616 | 1 617 | 1 618 | 1 619 | 1 620 | 1 621 | 622 | 623 | 0 624 | 0 625 | 0 626 | 0 627 | 0 628 | 0 629 | 0 630 | 0 631 | 632 | 633 | 634 | 635 | 636 | 637 | 638 | none 639 | 640 | -2 641 | -2 642 | -2 643 | -2 644 | -2 645 | -2 646 | -2 647 | -2 648 | -2 649 | 650 | 651 | 1> 652 | 1 653 | 1 654 | 1 655 | 1 656 | 1 657 | 1 658 | 1 659 | 660 | 661 | 0 662 | 0 663 | 0 664 | 0 665 | 0 666 | 0 667 | 0 668 | 0 669 | 670 | 671 | 672 | 673 | 674 | 675 | 676 | none 677 | 678 | -1 679 | -1 680 | -1 681 | -1 682 | -1 683 | -1 684 | -1 685 | -1 686 | -1 687 | 688 | 689 | 1> 690 | 1 691 | 1 692 | 1 693 | 1 694 | 1 695 | 1 696 | 1 697 | 698 | 699 | 0 700 | 0 701 | 0 702 | 0 703 | 0 704 | 0 705 | 0 706 | 0 707 | 708 | 709 | 710 | 711 | 712 | 713 | 714 | 715 | 716 | 717 | 1 718 | 719 | 720 | 1 721 | 722 | 723 | 724 | 725 | 726 | 727 | 728 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/dask_config.yml: -------------------------------------------------------------------------------- 1 | distributed: 2 | version: 2 3 | 4 | dashboard: 5 | link: /user/{JUPYTERHUB_USER}/proxy/{port}/status 6 | 7 | scheduler: 8 | idle-timeout: 3600s 9 | 10 | # uncomment to force new worker pods after 2 hrs 11 | # worker: 12 | # lifetime: 13 | # duration: "2 hours" 14 | # stagger: "10 s" 15 | # restart: true 16 | 17 | admin: 18 | tick: 19 | limit: 5s 20 | 21 | logging: 22 | distributed: warning 23 | bokeh: critical 24 | tornado: critical 25 | tornado.application: error 26 | 27 | kubernetes: 28 | name: dask-{JUPYTERHUB_USER}-{uuid} 29 | worker-template: 30 | spec: 31 | serviceAccount: daskkubernetes 32 | restartPolicy: Never 33 | containers: 34 | - name: dask-worker 35 | image: ${JUPYTER_IMAGE_SPEC} 36 | args: 37 | - dask-worker 38 | - --nthreads 39 | - '2' 40 | - --no-dashboard 41 | - --memory-limit 42 | - 7GB 43 | - --death-timeout 44 | - '60' 45 | resources: 46 | limits: 47 | cpu: "1.75" 48 | memory: 7G 49 | requests: 50 | cpu: 1 51 | memory: 7G 52 | 53 | # Specific to each hub 54 | #gateway: 55 | # address: https://staging.hub.pangeo.io/services/dask-gateway/ 56 | # proxy-address: tls://35.225.202.35:8786 57 | 58 | labextension: 59 | factory: 60 | module: dask_gateway 61 | class: GatewayCluster 62 | args: [] 63 | kwargs: {} 64 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/environment.yml: -------------------------------------------------------------------------------- 1 | name: pangeo 2 | channels: 3 | - conda-forge 4 | dependencies: 5 | - python=3.7* 6 | - pangeo-notebook=2020.08.02 7 | - pip=20 8 | - awscli 9 | - bottleneck 10 | - boto3 11 | - cartopy 12 | - ciso 13 | - dask-ml 14 | - datashader>=0.11 15 | - descartes 16 | - eofs 17 | - fastjmd95 18 | - fsspec 19 | - gcsfs 20 | - geopandas 21 | - geoviews-core 22 | - gsw 23 | - h5netcdf 24 | - h5py 25 | - holoviews 26 | - hvplot 27 | - intake 28 | - intake-esm 29 | - intake-geopandas 30 | - intake-stac 31 | - intake-xarray 32 | - ipyleaflet 33 | - ipywidgets 34 | - jupyter-panel-proxy 35 | - lz4 36 | - matplotlib-base 37 | - metpy 38 | - nb_conda_kernels 39 | - nbstripout 40 | - nc-time-axis 41 | - netcdf4 42 | - nomkl 43 | - numcodecs 44 | - numpy 45 | - pandas 46 | - panel 47 | - prefect 48 | - pyarrow 49 | - pydap 50 | - pystac 51 | - python-blosc 52 | - python-gist 53 | - rasterio 54 | - rio-cogeo 55 | - rioxarray 56 | - s3fs 57 | - sat-search 58 | - sat-stac 59 | - satpy 60 | - scikit-image 61 | - scikit-learn 62 | - scipy 63 | - sparse 64 | - tiledb-py 65 | - xarray 66 | - xarray-spatial 67 | - xcape 68 | - xesmf 69 | - xgcm 70 | - xhistogram 71 | - xlayers 72 | - xmitgcm 73 | - xpublish 74 | - xrft 75 | - zarr 76 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/start: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | 3 | # ==== ONLY EDIT WITHIN THIS BLOCK ===== 4 | 5 | export PANGEO_ENV="notebook" 6 | if ! [[ -z "${PANGEO_SCRATCH_PREFIX}" ]] && ! [[ -z "${JUPYTERHUB_USER}" ]]; then 7 | export PANGEO_SCRATCH="${PANGEO_SCRATCH_PREFIX}/${JUPYTERHUB_USER}/" 8 | fi 9 | 10 | if [[ ! -f /home/user/.tutorial_initialized ]]; then 11 | cp -rp /srv/tutorials /home/user 12 | touch /home/user/.tutorial_initialized 13 | fi 14 | 15 | # Change the CPU counts: 16 | CPUS=$(grep -c processor /proc/cpuinfo) 17 | sudo xmlstarlet ed --inplace -u "config_machines/machine[@MACH='container']/MAX_TASKS_PER_NODE" -v ${CPUS} ${CESMROOT}/cime/config/cesm/machines/config_machines.xml 18 | sudo xmlstarlet ed --inplace -u "config_machines/machine[@MACH='container']/MAX_MPITASKS_PER_NODE" -v ${CPUS} ${CESMROOT}/cime/config/cesm/machines/config_machines.xml 19 | 20 | # ==== ONLY EDIT WITHIN THIS BLOCK ===== 21 | 22 | exec "$@" 23 | -------------------------------------------------------------------------------- /CESM-Lab/2.1/Files/tutorials/CESM/Quickstart.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "

CESM2 Quick Start Guide

\n", 8 | "\n", 9 | "This is a very quick introduction to running CESM. It will guide you through the basics of creating a case, modifying simple aspects of that case, building it, running it, and visualizing the outputs. Each step will also provide links to the full CESM documentation and additional examples." 10 | ] 11 | }, 12 | { 13 | "cell_type": "markdown", 14 | "metadata": {}, 15 | "source": [ 16 | "

1. Creating a CESM case

\n", 17 | "\n", 18 | "CESM experiments start with creating a 'case' - a configuration of the model with a specific set of component models (eg, CAM for the atmosphere model, POP for the ocean model, etc), at a particular resolution, and with a set of options defined in XML files. Let's start by using the 'create_newcase' command to set up an experiment with the following details:
\n", 19 | "\n", 23 | "\n", 24 | "This is a 'simple model' - an aquaplanet configuration at 4.5-degree resolution, using CAM4 physics. This is much less computationally intensive than a fully coupled run, so it works well for this tutorial, only requiring ~0.6GB of RAM. It will also need to download some input files, totaling approximately 127MB of size.\n", 25 | "\n", 26 | "The command to create this configuration is given below, using 'tutorial_aquaplanet' as the casename. Note that given the size and nature of this run, it's not a scientifically supported configuration, but it's still useful for learning how to run the model.\n", 27 | "\n", 28 | "Run the cell to issue the command:" 29 | ] 30 | }, 31 | { 32 | "cell_type": "code", 33 | "execution_count": null, 34 | "metadata": {}, 35 | "outputs": [], 36 | "source": [ 37 | "create_newcase --case ~/aquaplanet_test_f45 --compset QPC4 --res f45_f45_mg37 --run-unsupported" 38 | ] 39 | }, 40 | { 41 | "cell_type": "markdown", 42 | "metadata": {}, 43 | "source": [ 44 | "
\n", 45 | "
\n", 46 | "Great! You've created the default version of your first case. Before we move to the next section, if you want additional information on the create_newcase command or the compsets and resolutions, you can click on each section below for details and links.
\n", 47 | "
\n", 48 | "\n", 49 | "***\n", 50 | "\n", 51 | "Additional Information:\n", 52 | "
\n", 53 | " create_newcase\n", 54 | " \n", 55 | "
\n", 56 | "The 'create_newcase' command only requires three options - the case, compset and resolution. However, it supports a large number of options for more advanced users. To see a summary, you can run the command by itself:\n", 57 | "
\n", 58 | "
\n",
 59 |     "
\n",
 60 |     "create_newcase\n",
 61 |     "usage: create_newcase [-h] [-d] [-v] [-s] --case CASENAME --compset COMPSET\n",
 62 |     "                      --res GRID [--machine MACHINE] [--compiler COMPILER]\n",
 63 |     "                      [--multi-driver] [--ninst NINST] [--mpilib MPILIB]\n",
 64 |     "                      [--project PROJECT] [--pecount PECOUNT]\n",
 65 |     "                      [--user-mods-dir USER_MODS_DIR] [--pesfile PESFILE]\n",
 66 |     "                      [--gridfile GRIDFILE] [--workflow WORKFLOW]\n",
 67 |     "                      [--srcroot SRCROOT] [--output-root OUTPUT_ROOT]\n",
 68 |     "                      [--run-unsupported] [--walltime WALLTIME] [-q QUEUE]\n",
 69 |     "                      [--handle-preexisting-dirs {a,r,u}] [-i INPUT_DIR]\n",
 70 |     "
\n", 71 | "
\n", 72 | "Additionally, you can get detailed help via 'create_newcase --help', and you can click here for the CESM documentation on the command\n", 73 | "
\n", 74 | "
\n", 75 | "
\n", 76 | "
\n", 77 | " CESM Component Sets ('compsets')\n", 78 | " Not yet filled out; maybe this is too much information here?\n", 79 | "
\n", 80 | "
\n", 81 | " CESM Resolutions / Grids\n", 82 | " Also not filled out yet...\n", 83 | "
\n", 84 | "\n", 85 | "***\n", 86 | "\n", 87 | "
" 88 | ] 89 | }, 90 | { 91 | "cell_type": "markdown", 92 | "metadata": {}, 93 | "source": [ 94 | "

2. Modifying a CESM case

\n", 95 | "\n", 96 | "Now let's make a simple modification to the case via two easy steps:\n", 97 | "\n", 98 | "1. Change to our new case directory\n", 99 | "2. In that directory, change the duration of the run (in model-time)\n", 100 | "\n", 101 | "\n", 102 | "These changes can be made via modifying the XML files that control CESM's behavior. We could do this by hand, but the preferred way of doing it is to use the 'xmlchange' command in the case directory. By default, newly configured cases are set up to run for 5 model days - since we're just experimenting, we'll change it to 3 model days instead, for even faster runs. Run the following cells to execute the two commands:\n", 103 | "
\n", 104 | "
" 105 | ] 106 | }, 107 | { 108 | "cell_type": "code", 109 | "execution_count": null, 110 | "metadata": {}, 111 | "outputs": [], 112 | "source": [ 113 | "%cd ~/aquaplanet_test_f45 " 114 | ] 115 | }, 116 | { 117 | "cell_type": "code", 118 | "execution_count": null, 119 | "metadata": {}, 120 | "outputs": [], 121 | "source": [ 122 | "xmlchange STOP_OPTION=ndays,STOP_N=3" 123 | ] 124 | }, 125 | { 126 | "cell_type": "markdown", 127 | "metadata": {}, 128 | "source": [ 129 | "Since the default STOP_OPTION is already 'ndays', it wasn't strictly necessary to include that in the command, but by being explicit we avoid any confusion later if we had changed it previously to 'nhours' or 'nyears'. \n", 130 | "\n", 131 | "***\n", 132 | "\n", 133 | "Additional information:\n", 134 | "\n", 135 | "(I haven't put anything here yet; this is just for demo to give people a sense of things. I want to keep the basic instructions light, I think!)\n", 136 | "\n", 137 | "***" 138 | ] 139 | }, 140 | { 141 | "cell_type": "markdown", 142 | "metadata": {}, 143 | "source": [ 144 | "We don't see any output by 'xmlchange', but we can use another tool, 'xmlquery', to double-check that we have the new values:" 145 | ] 146 | }, 147 | { 148 | "cell_type": "code", 149 | "execution_count": null, 150 | "metadata": {}, 151 | "outputs": [], 152 | "source": [ 153 | "xmlquery STOP_OPTION,STOP_N" 154 | ] 155 | }, 156 | { 157 | "cell_type": "markdown", 158 | "metadata": {}, 159 | "source": [ 160 | "\n", 161 | "***\n", 162 | "\n", 163 | "Just putting the other commands here for now, no write-up yet:\n", 164 | "\n" 165 | ] 166 | }, 167 | { 168 | "cell_type": "code", 169 | "execution_count": null, 170 | "metadata": {}, 171 | "outputs": [], 172 | "source": [ 173 | "case.setup" 174 | ] 175 | }, 176 | { 177 | "cell_type": "code", 178 | "execution_count": null, 179 | "metadata": {}, 180 | "outputs": [], 181 | "source": [ 182 | "case.build" 183 | ] 184 | }, 185 | { 186 | "cell_type": "code", 187 | "execution_count": null, 188 | "metadata": {}, 189 | "outputs": [], 190 | "source": [ 191 | "case.submit" 192 | ] 193 | }, 194 | { 195 | "cell_type": "markdown", 196 | "metadata": {}, 197 | "source": [ 198 | "\n", 199 | "***\n", 200 | "\n", 201 | "\n", 202 | "

TO DO:

\n", 203 | "\n", 204 | "1. Add something about visualizing the results or doing statistics on the output files\n", 205 | "2. Add something about performance\n", 206 | "3. Maybe simplify / 'interactive-ize' the output from commands, especially the running?\n", 207 | "4. Investigate 'nhfil' warning above, or turn off DOUT_S?\n", 208 | "5. Emacs / Vim within Jupyter (eg, without going to bash shell in another window) - possible?\n", 209 | "6. CIME_OUTPUT_ROOT - if we put things in a subdirectory, that still points to home. Can we put bld/run in case directories easily?\n", 210 | "7. Fix env_batch.py for non-batch jobs like this (gives a 'ERROR: No result from jobs' message, currently disabled)\n" 211 | ] 212 | } 213 | ], 214 | "metadata": { 215 | "kernelspec": { 216 | "display_name": "Python [conda env:notebook] *", 217 | "language": "python", 218 | "name": "conda-env-notebook-py" 219 | }, 220 | "language_info": { 221 | "codemirror_mode": { 222 | "name": "ipython", 223 | "version": 3 224 | }, 225 | "file_extension": ".py", 226 | "mimetype": "text/x-python", 227 | "name": "python", 228 | "nbconvert_exporter": "python", 229 | "pygments_lexer": "ipython3", 230 | "version": "3.7.8" 231 | } 232 | }, 233 | "nbformat": 4, 234 | "nbformat_minor": 4 235 | } 236 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Dockerfile: -------------------------------------------------------------------------------- 1 | ################################## 2 | # ESCOMP/CESM-Lab/2.1 Dockerfile # 3 | ################################## 4 | 5 | # This builds on top of the CESM 2.1 container, and adds the Jupyter Lab environment 6 | FROM escomp/cesm-2.2 7 | 8 | # Install software needed for Pangeo 9 | RUN sudo yum install -y graphviz libnsl libspatialite libspatialite-devel xmlstarlet 10 | 11 | # Set up the Conda version - using the pangeo/base-image as a foundation here: 12 | ENV CONDA_VERSION=4.8.5-1 \ 13 | CONDA_ENV=default \ 14 | NB_USER=user \ 15 | NB_GROUP=escomp \ 16 | NB_UID=1000 \ 17 | SHELL=/bin/bash \ 18 | CONDA_DIR=/srv/conda 19 | 20 | # Additional environment setup that depends on the above: 21 | ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/${CONDA_ENV} \ 22 | DASK_ROOT_CONFIG=${CONDA_DIR}/etc \ 23 | HOME=/home/${NB_USER} \ 24 | PATH=${CONDA_DIR}/bin:${PATH} 25 | 26 | #RUN sudo yum -y upgrade 27 | 28 | # Add the Conda init and set permissions on the directory: 29 | # (Could clean this up, and push changes back to Pangeo -- eg, /srv is hardcoded) 30 | RUN sudo /bin/bash -c "echo '. ${CONDA_DIR}/etc/profile.d/conda.sh ; conda activate ${CONDA_ENV}' > /etc/profile.d/init_conda.sh" && \ 31 | sudo chown -R ${NB_USER}:${NB_GROUP} /srv 32 | 33 | # Install miniforge: 34 | RUN URL="https://github.com/conda-forge/miniforge/releases/download/${CONDA_VERSION}/Miniforge3-${CONDA_VERSION}-Linux-x86_64.sh" && \ 35 | wget --quiet ${URL} -O miniconda.sh && \ 36 | /bin/bash miniconda.sh -u -b -p ${CONDA_DIR} && \ 37 | rm miniconda.sh && \ 38 | conda clean -afy && \ 39 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 40 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete 41 | 42 | COPY --chown=${NB_USER}:${NB_GROUP} Files/*yml /srv/ 43 | 44 | RUN mv /srv/condarc.yml ${CONDA_DIR}/.condarc && \ 45 | mv /srv/dask_config.yml ${CONDA_DIR}/etc/dask.yml 46 | 47 | 48 | RUN conda env create --name ${CONDA_ENV} -f /srv/environment.yml && \ 49 | conda clean -yaf && \ 50 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 51 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \ 52 | find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete && \ 53 | find ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete 54 | 55 | RUN export PATH=${NB_PYTHON_PREFIX}/bin:${PATH} && \ 56 | jupyter labextension install --clean \ 57 | @jupyter-widgets/jupyterlab-manager \ 58 | @jupyterlab/geojson-extension \ 59 | dask-labextension \ 60 | @pyviz/jupyterlab_pyviz \ 61 | jupyter-leaflet && \ 62 | sudo rm -rf /tmp/* && \ 63 | rm -rf ${HOME}/.cache ${HOME}/.npm ${HOME}/.yarn && \ 64 | rm -rf ${NB_PYTHON_PREFIX}/share/jupyter/lab/staging && \ 65 | find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \ 66 | find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \ 67 | find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete 68 | 69 | 70 | COPY Files/start /srv 71 | RUN sudo chmod +x /srv/start 72 | 73 | COPY Files/cesm_aliases.ipy /etc/ipython/ 74 | RUN sudo /bin/bash -c 'echo "c.InteractiveShellApp.exec_files = [ \"/etc/ipython/cesm_aliases.ipy\" ] " >> /etc/ipython/ipython_config.py' 75 | 76 | ADD https://api.github.com/repos/NCAR/CESM-Lab-Tutorial/git/refs/heads/master version.json 77 | #RUN git clone https://github.com/NCAR/CESM-Lab-Tutorial.git /srv/tutorials 78 | COPY Files/tutorials /srv/tutorials 79 | COPY Files/cartopy/shapefiles /srv/conda/envs/default/lib/python3.7/site-packages/cartopy/data/shapefiles/ 80 | COPY Files/cesm.py /srv/conda/envs/default/lib/python3.7/site-packages/ 81 | 82 | 83 | EXPOSE 8888 84 | USER user 85 | WORKDIR /home/user 86 | ENV SHELL /bin/bash 87 | ENTRYPOINT ["/srv/start"] 88 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.dbf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/ESCOMP-Containers/c48f872d5b4bbdc90ca9e1159d6c276d87407e09/CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.dbf -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.shp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/ESCOMP-Containers/c48f872d5b4bbdc90ca9e1159d6c276d87407e09/CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.shp -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.shx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/ESCOMP-Containers/c48f872d5b4bbdc90ca9e1159d6c276d87407e09/CESM-Lab/2.2/Files/cartopy/shapefiles/natural_earth/physical/ne_110m_coastline.shx -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/cesm.py: -------------------------------------------------------------------------------- 1 | # CESM module for python - includes toolkit (later) and tutorial stuff 2 | import xarray as xr 3 | import numpy as np 4 | import matplotlib.pyplot as plt 5 | import cartopy.crs as ccrs 6 | from cartopy.util import add_cyclic_point 7 | 8 | import cartopy 9 | cartopy.config['pre_existing_data_dir'] = '/srv/conda/envs/default/lib/python3.7/site-packages/cartopy/data' 10 | 11 | import os 12 | import glob 13 | 14 | def QuickViewATM(case, variable): 15 | # Currently supported variables: 16 | supported_3D = ( 'TS', ) 17 | supported_4D = ( 'T', 'U', 'V', ) 18 | 19 | # Check if we're using a supported variable: 20 | supported = supported_3D + supported_4D 21 | if variable not in supported: 22 | print('Variable is not supported - must be one of: ', supported) 23 | return 24 | 25 | # Get the list of all hist files for the atmosphere: 26 | files = glob.glob('/home/user/archive/' + case + '/atm/hist/*.nc') 27 | latest = max(files , key = os.path.getctime) 28 | dataset = xr.open_dataset(latest) 29 | 30 | if variable in supported_3D: 31 | vardata = dataset[variable][0,:,:] # Fix the time later 32 | else: 33 | vardata = dataset[variable][0,25,:,:] # Fix the level later 34 | 35 | # Set figure size 36 | fig = plt.figure(figsize=(11,8.5)) 37 | ax = plt.axes(projection=ccrs.Robinson()) 38 | 39 | # Add cyclic point to data (to get rid of gap at dateline) 40 | data, lons = add_cyclic_point(vardata, coord=vardata['lon']) 41 | 42 | # Define contour levels 43 | clevs=np.arange(np.min(data),np.max(data),1) 44 | 45 | # Make a filled contour plot 46 | cs=ax.contourf(lons, vardata['lat'], data,clevs, transform = ccrs.PlateCarree(), cmap='coolwarm',extend='both') 47 | 48 | # Add coastlines 49 | ax.coastlines() 50 | 51 | # Add gridlines 52 | ax.gridlines() 53 | 54 | # Add colorbar 55 | cbar = plt.colorbar(cs,shrink=0.7,orientation='horizontal') 56 | 57 | # Add title 58 | plt.title(case + ' : ' + variable) 59 | 60 | def QuickView(case, variable, model='atmosphere'): 61 | type = model.lower() 62 | if type in { 'atmosphere', 'atm', 'cam' }: 63 | QuickViewATM(case, variable) 64 | 65 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/cesm_aliases.ipy: -------------------------------------------------------------------------------- 1 | %alias xmlchange ./xmlchange %l 2 | %alias xmlquery ./xmlquery %l 3 | %alias create_newcase ${CESMROOT}/cime/scripts/create_newcase %l 4 | %alias query_config ${CESMROOT}/cime/scripts/query_config %l 5 | %alias case.setup ./case.setup %l 6 | %alias case.build ./case.build %l 7 | %alias case.submit ./case.submit %l 8 | %alias preview_run ./preview_run %l 9 | %alias pelayout ./pelayout %l 10 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/condarc.yml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - defaults 4 | channel_priority: strict 5 | show_channel_urls: true 6 | # NOTE: defaults only work for `conda create -f`, not `conda env create -f`! 7 | # https://github.com/conda/conda/issues/9580 8 | #create_default_packages: 9 | # - pangeo-notebook=0.0.2 10 | # - ipykernel 11 | #pinned_packages: 12 | # - pangeo-notebook=0.0.2 13 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/dask_config.yml: -------------------------------------------------------------------------------- 1 | distributed: 2 | version: 2 3 | 4 | dashboard: 5 | link: /user/{JUPYTERHUB_USER}/proxy/{port}/status 6 | 7 | scheduler: 8 | idle-timeout: 3600s 9 | 10 | # uncomment to force new worker pods after 2 hrs 11 | # worker: 12 | # lifetime: 13 | # duration: "2 hours" 14 | # stagger: "10 s" 15 | # restart: true 16 | 17 | admin: 18 | tick: 19 | limit: 5s 20 | 21 | logging: 22 | distributed: warning 23 | bokeh: critical 24 | tornado: critical 25 | tornado.application: error 26 | 27 | kubernetes: 28 | name: dask-{JUPYTERHUB_USER}-{uuid} 29 | worker-template: 30 | spec: 31 | serviceAccount: daskkubernetes 32 | restartPolicy: Never 33 | containers: 34 | - name: dask-worker 35 | image: ${JUPYTER_IMAGE_SPEC} 36 | args: 37 | - dask-worker 38 | - --nthreads 39 | - '2' 40 | - --no-dashboard 41 | - --memory-limit 42 | - 7GB 43 | - --death-timeout 44 | - '60' 45 | resources: 46 | limits: 47 | cpu: "1.75" 48 | memory: 7G 49 | requests: 50 | cpu: 1 51 | memory: 7G 52 | 53 | # Specific to each hub 54 | #gateway: 55 | # address: https://staging.hub.pangeo.io/services/dask-gateway/ 56 | # proxy-address: tls://35.225.202.35:8786 57 | 58 | labextension: 59 | factory: 60 | module: dask_gateway 61 | class: GatewayCluster 62 | args: [] 63 | kwargs: {} 64 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/environment.yml: -------------------------------------------------------------------------------- 1 | name: default 2 | channels: 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - _libgcc_mutex=0.1=conda_forge 7 | - _openmp_mutex=4.5=1_gnu 8 | - abseil-cpp=20200225.2=he1b5a44_2 9 | - adal=1.2.4=pyh9f0ad1d_0 10 | - affine=2.3.0=py_0 11 | - aiofiles=0.5.0=py_0 12 | - aiohttp=3.7.1 13 | - alembic=1.4.3=pyh9f0ad1d_0 14 | - appdirs=1.4.4=pyh9f0ad1d_0 15 | - argon2-cffi=20.1.0=py37h8f50634_2 16 | - arrow-cpp=2.0.0=py37h433b4ec_0_cpu 17 | - asciitree=0.3.3=py_2 18 | - asn1crypto=1.4.0=pyh9f0ad1d_0 19 | - async-timeout=3.0.1=py_1000 20 | - async_generator=1.10=py_0 21 | - attrs=20.2.0=pyh9f0ad1d_0 22 | - aws-c-common=0.4.59=he1b5a44_0 23 | - aws-c-event-stream=0.1.6=h84e28f3_5 24 | - aws-checksums=0.1.9=he252421_2 25 | - aws-sdk-cpp=1.8.63=h9b98462_0 26 | - awscli=1.18.160=py37hc8dfbb8_0 27 | - backcall=0.2.0=pyh9f0ad1d_0 28 | - backports=1.0=py_2 29 | - backports.functools_lru_cache=1.6.1=py_0 30 | - beautifulsoup4=4.9.3=pyhb0f4dca_0 31 | - bleach=3.2.1=pyh9f0ad1d_0 32 | - blinker=1.4=py_1 33 | - blosc=1.20.1=he1b5a44_0 34 | - bokeh=2.2.2=py37hc8dfbb8_0 35 | - boost-cpp=1.74.0=h9359b55_0 36 | - boto3=1.16.0=pyh9f0ad1d_0 37 | - botocore=1.19.0=pyh9f0ad1d_0 38 | - bottleneck=1.3.2=py37h161383b_2 39 | - branca=0.3.1=py_0 40 | - brotli=1.0.9=he1b5a44_2 41 | - brotlipy=0.7.0=py37hb5d75c8_1001 42 | - brunsli=0.1=he1b5a44_0 43 | - bzip2=1.0.8=h516909a_3 44 | - c-ares=1.16.1=h516909a_3 45 | - ca-certificates=2020.6.20=hecda079_0 46 | - cachetools=4.1.1=py_0 47 | - cachey=0.2.1=pyh9f0ad1d_0 48 | - cairo=1.16.0=h488836b_1006 49 | - cartopy=0.18.0=py37h0f91b66_2 50 | - certifi=2020.6.20=py37he5f6b98_2 51 | - certipy=0.1.3=py_0 52 | - cffi=1.14.3=py37h00ebd2e_1 53 | - cfitsio=3.470=hce51eda_7 54 | - cftime=1.2.1=py37h161383b_1 55 | - chardet=3.0.4=py37he5f6b98_1008 56 | - charls=2.1.0=he1b5a44_2 57 | - ciso=0.1.0=py37h161383b_2 58 | - click=7.1.2=pyh9f0ad1d_0 59 | - click-plugins=1.1.1=py_0 60 | - cligj=0.6.0=pyh9f0ad1d_0 61 | - cloudpickle=1.6.0=py_0 62 | - colorama=0.4.3=py_0 63 | - colorcet=2.0.1=py_0 64 | - configobj=5.0.6=py_0 65 | - croniter=0.3.35=pyh9f0ad1d_0 66 | - cryptography=3.1.1=py37hff6837a_1 67 | - curl=7.71.1=he644dc0_8 68 | - cycler=0.10.0=py_2 69 | - cytoolz=0.11.0=py37h8f50634_1 70 | - dask=2.22.0=py_0 71 | - dask-core=2.22.0=py_0 72 | - dask-gateway=0.8.0=py37hc8dfbb8_0 73 | - dask-glm=0.2.0=py_1 74 | - dask-kubernetes=0.10.1=py_0 75 | - dask-labextension=2.0.2=py_0 76 | - dask-ml=1.7.0=py_0 77 | - datashader=0.11.1=pyh9f0ad1d_0 78 | - datashape=0.5.4=py_1 79 | - decorator=4.4.2=py_0 80 | - defusedxml=0.6.0=py_0 81 | - descartes=1.1.0=py_4 82 | - distributed=2.22.0=py37hc8dfbb8_0 83 | - docker-py=4.3.1=py37hc8dfbb8_1 84 | - docker-pycreds=0.4.0=py_0 85 | - docopt=0.6.2=py_1 86 | - docrep=0.2.7=py_0 87 | - docutils=0.15.2=py37_0 88 | - entrypoints=0.3=py37hc8dfbb8_1002 89 | - eofs=1.4.0=py_0 90 | - esmf=8.0.1=nompi_hbeb3ca6_1 91 | - esmpy=8.0.1=nompi_py37h59b2dc9_2 92 | - expat=2.2.9=he1b5a44_2 93 | - fastapi=0.61.1=py_0 94 | - fasteners=0.14.1=py_3 95 | - fastjmd95=0.1=pyh9f0ad1d_0 96 | - fastprogress=1.0.0=py_0 97 | - fiona=1.8.17=py37ha3d844c_0 98 | - fontconfig=2.13.1=h1056068_1002 99 | - freetype=2.10.4=he06d7ca_0 100 | - freexl=1.0.5=h516909a_1002 101 | - fsspec=0.8.4=py_0 102 | - future=0.18.2=py37hc8dfbb8_2 103 | - gcsfs=0.7.1=py_0 104 | - gdal=3.1.2=py37h518339e_3 105 | - geopandas=0.8.1=py_0 106 | - geos=3.8.1=he1b5a44_0 107 | - geotiff=1.6.0=ha04d9d0_1 108 | - geoviews-core=1.8.2=py_0 109 | - gettext=0.19.8.1=hf34092f_1004 110 | - gflags=2.2.2=he1b5a44_1004 111 | - giflib=5.2.1=h516909a_2 112 | - glib=2.66.1=he1b5a44_1 113 | - glog=0.4.0=h49b9bf7_3 114 | - google-auth=1.22.0=py_0 115 | - google-auth-oauthlib=0.4.1=py_2 116 | - graphene=1.4=py_0 117 | - graphql-core=3.1.2=py_0 118 | - graphql-relay=3.0.0=py_0 119 | - grpc-cpp=1.32.0=h7997a97_1 120 | - gsw=3.4.0=py37h161383b_1 121 | - h11=0.11.0=pyh9f0ad1d_0 122 | - h5netcdf=0.8.1=py_0 123 | - h5py=2.10.0=nompi_py37hf7afa78_105 124 | - hdf4=4.2.13=hf30be14_1003 125 | - hdf5=1.10.6=nompi_h54c07f9_1110 126 | - heapdict=1.0.1=py_0 127 | - holoviews=1.13.4=pyh9f0ad1d_0 128 | - httptools=0.1.1=py37h8f50634_1 129 | - hvplot=0.6.0=pyh9f0ad1d_0 130 | - icu=67.1=he1b5a44_0 131 | - idna=2.10=pyh9f0ad1d_0 132 | - imagecodecs=2020.5.30=py37h5f9c477_4 133 | - imageio=2.9.0=py_0 134 | - importlib-metadata=2.0.0=py_1 135 | - importlib_metadata=2.0.0=1 136 | - importlib_resources=3.0.0=py37hc8dfbb8_1 137 | - iniconfig=1.1.0=pyh9f0ad1d_0 138 | - intake=0.6.0=py_0 139 | - intake-esm=2020.8.15=py_0 140 | - intake-geopandas=0.2.3=py_0 141 | - intake-stac=0.3.0=py_0 142 | - intake-xarray=0.4.0=py_0 143 | - ipykernel=5.3.4=py37hc6149b9_1 144 | - ipyleaflet=0.13.3=pyh9f0ad1d_0 145 | - ipython=7.18.1=py37hc6149b9_1 146 | - ipython_genutils=0.2.0=py_1 147 | - ipywidgets=7.5.1=pyh9f0ad1d_1 148 | - itsdangerous=1.1.0=py_0 149 | - jedi=0.17.2=py37hc8dfbb8_1 150 | - jinja2=2.11.2=pyh9f0ad1d_0 151 | - jmespath=0.10.0=pyh9f0ad1d_0 152 | - joblib=0.17.0=py_0 153 | - jpeg=9d=h516909a_0 154 | - json-c=0.13.1=hbfbb72e_1002 155 | - json5=0.9.5=pyh9f0ad1d_0 156 | - jsonschema=3.2.0=py_2 157 | - jupyter-panel-proxy=0.1.0=py_0 158 | - jupyter-server-proxy=1.5.0=py_0 159 | - jupyter_client=6.1.7=py_0 160 | - jupyter_core=4.6.3=py37hc8dfbb8_2 161 | - jupyter_telemetry=0.0.5=py_0 162 | - jupyterhub-base=1.1.0=py37hc8dfbb8_5 163 | - jupyterhub-singleuser=1.1.0=py37hc8dfbb8_5 164 | - jupyterlab=2.2.8=py_0 165 | - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0 166 | - jupyterlab_server=1.2.0=py_0 167 | - jxrlib=1.1=h516909a_2 168 | - kealib=1.4.13=h33137a7_1 169 | - kiwisolver=1.2.0=py37h99015e2_1 170 | - krb5=1.17.1=hfafb76e_3 171 | - kubernetes_asyncio=12.0.0=pyh9f0ad1d_0 172 | - lcms2=2.11=hbd6801e_0 173 | - ld_impl_linux-64=2.35=h769bd43_9 174 | - lerc=2.2=he1b5a44_0 175 | - libaec=1.0.4=he1b5a44_1 176 | - libblas=3.8.0=17_openblas 177 | - libcblas=3.8.0=17_openblas 178 | - libcurl=7.71.1=hcdd3856_8 179 | - libdap4=3.20.6=h1d1bd15_1 180 | - libedit=3.1.20191231=he28a2e2_2 181 | - libev=4.33=h516909a_1 182 | - libevent=2.1.10=hcdb4288_3 183 | - libffi=3.2.1=he1b5a44_1007 184 | - libgcc-ng=9.3.0=h5dbcf3e_17 185 | - libgdal=3.1.2=hb2a6f5f_3 186 | - libgfortran-ng=7.5.0=hae1eefd_17 187 | - libgfortran4=7.5.0=hae1eefd_17 188 | - libglib=2.66.1=h0dae87d_1 189 | - libgomp=9.3.0=h5dbcf3e_17 190 | - libiconv=1.16=h516909a_0 191 | - libkml=1.3.0=h74f7ee3_1012 192 | - liblapack=3.8.0=17_openblas 193 | - libllvm10=10.0.1=he513fc3_3 194 | - libnetcdf=4.7.4=nompi_h84807e1_105 195 | - libnghttp2=1.41.0=h8cfc5f6_2 196 | - libopenblas=0.3.10=pthreads_hb3c22a3_5 197 | - libpng=1.6.37=hed695b0_2 198 | - libpq=12.3=h5513abc_2 199 | - libprotobuf=3.13.0.1=h8b12597_0 200 | - libsodium=1.0.18=h516909a_1 201 | - libspatialindex=1.9.3=he1b5a44_3 202 | - libspatialite=4.3.0a=h57f1b35_1039 203 | - libssh2=1.9.0=hab1572f_5 204 | - libstdcxx-ng=9.3.0=h2ae2ef3_17 205 | - libthrift=0.13.0=h5aa387f_6 206 | - libtiff=4.1.0=hc7e4089_6 207 | - libutf8proc=2.5.0=h516909a_2 208 | - libuuid=2.32.1=h14c3975_1000 209 | - libuv=1.40.0=hd18ef5c_0 210 | - libwebp-base=1.1.0=h516909a_3 211 | - libxcb=1.13=h14c3975_1002 212 | - libxml2=2.9.10=h68273f3_2 213 | - libzopfli=1.0.3=he1b5a44_0 214 | - llvmlite=0.34.0=py37h5202443_2 215 | - locket=0.2.0=py_2 216 | - lz4=3.1.0=py37h5a7ed16_1 217 | - lz4-c=1.9.2=he1b5a44_3 218 | - mako=1.1.3=pyh9f0ad1d_0 219 | - markdown=3.3.2=pyh9f0ad1d_0 220 | - markupsafe=1.1.1=py37hb5d75c8_2 221 | - marshmallow=3.8.0=py_0 222 | - marshmallow-oneofschema=2.0.1=py_0 223 | - matplotlib-base=3.3.2=py37hc9afd2a_1 224 | - mercantile=1.1.6=pyh9f0ad1d_0 225 | - metpy=0.12.2=py_0 226 | - mistune=0.8.4=py37h8f50634_1002 227 | - monotonic=1.5=py_0 228 | - more-itertools=8.5.0=py_0 229 | - msgpack-python=1.0.0=py37h99015e2_2 230 | - multidict=4.7.5=py37h8f50634_2 231 | - multipledispatch=0.6.0=py_0 232 | - munch=2.5.0=py_0 233 | - mypy_extensions=0.4.3=py37hc8dfbb8_2 234 | - natsort=7.0.1=py_0 235 | - nb_conda_kernels=2.3.0=py37hc8dfbb8_2 236 | - nbclient=0.5.1=py_0 237 | - nbconvert=6.0.7=py37hc8dfbb8_1 238 | - nbformat=5.0.8=py_0 239 | - nbgitpuller=0.9.0=py_0 240 | - nbstripout=0.3.9=pyh9f0ad1d_0 241 | - nc-time-axis=1.2.0=py_1 242 | - ncurses=6.2=he1b5a44_2 243 | - nest-asyncio=1.4.1=py_0 244 | - netcdf-fortran=4.5.3=nompi_hfef6a68_101 245 | - netcdf4=1.5.4=nompi_py37hcbfd489_103 246 | - networkx=2.5=py_0 247 | - nodejs=14.14.0=h568c755_0 248 | - nomkl=1.0=h5ca1d4c_0 249 | - notebook=6.1.4=py37hc8dfbb8_1 250 | - numba=0.51.2=py37h9fdb41a_0 251 | - numcodecs=0.7.2=py37h3340039_1 252 | - numpy=1.19.2=py37h7008fea_1 253 | - oauthlib=3.0.1=py_0 254 | - olefile=0.46=pyh9f0ad1d_1 255 | - openjpeg=2.3.1=h981e76c_3 256 | - openssl=1.1.1h=h516909a_0 257 | - orc=1.6.5=hd3605a7_0 258 | - owslib=0.20.0=py_0 259 | - packaging=20.4=pyh9f0ad1d_0 260 | - pamela=1.0.0=py_0 261 | - pandas=1.1.3=py37h9fdb41a_2 262 | - pandoc=2.11.0.2=hd18ef5c_0 263 | - pandocfilters=1.4.2=py_1 264 | - panel=0.9.7=py_0 265 | - pangeo-dask=2020.08.01=0 266 | - pangeo-notebook=2020.08.02=0 267 | - param=1.9.3=py_0 268 | - parquet-cpp=1.5.1=2 269 | - parso=0.7.1=pyh9f0ad1d_0 270 | - partd=1.1.0=py_0 271 | - pcre=8.44=he1b5a44_0 272 | - pendulum=2.1.2=py37hc8dfbb8_0 273 | - pexpect=4.8.0=pyh9f0ad1d_2 274 | - pickleshare=0.7.5=py_1003 275 | - pillow=8.0.0=py37h718be6c_0 276 | - pint=0.16.1=py_0 277 | - pip=20.2.4=py_0 278 | - pixman=0.38.0=h516909a_1003 279 | - pluggy=0.13.1=py37hc8dfbb8_3 280 | - pooch=1.2.0=py_0 281 | - poppler=0.89.0=h4190859_1 282 | - poppler-data=0.4.9=1 283 | - postgresql=12.3=h8573dbc_2 284 | - prefect=0.13.11=py_0 285 | - proj=7.1.0=h966b41f_1 286 | - prometheus_client=0.8.0=pyh9f0ad1d_0 287 | - promise=2.3=py37hc8dfbb8_2 288 | - prompt-toolkit=3.0.8=py_0 289 | - psutil=5.7.2=py37hb5d75c8_1 290 | - pthread-stubs=0.4=h14c3975_1001 291 | - ptyprocess=0.6.0=py_1001 292 | - py=1.9.0=pyh9f0ad1d_0 293 | - pyarrow=2.0.0=py37h9303983_0_cpu 294 | - pyasn1=0.4.8=py_0 295 | - pyasn1-modules=0.2.7=py_0 296 | - pybind11=2.5.0=py37h99015e2_1 297 | - pycparser=2.20=pyh9f0ad1d_2 298 | - pyct=0.4.6=py_0 299 | - pyct-core=0.4.6=py_0 300 | - pycurl=7.43.0.5=py37h21fb010_3 301 | - pydantic=1.6.1=py37h8f50634_1 302 | - pydap=3.2.2=pyh9f0ad1d_1001 303 | - pyepsg=0.4.0=py_0 304 | - pygments=2.7.1=py_0 305 | - pyjwt=1.7.1=py_0 306 | - pykdtree=1.3.1=py37h161383b_1004 307 | - pyopenssl=19.1.0=py_1 308 | - pyorbital=1.6.0=pyh9f0ad1d_0 309 | - pyparsing=2.4.7=pyh9f0ad1d_0 310 | - pyproj=2.6.1.post1=py37hb5dadc3_1 311 | - pyresample=1.16.0=py37h9fdb41a_1 312 | - pyrsistent=0.17.3=py37h8f50634_1 313 | - pyshp=2.1.2=pyh9f0ad1d_0 314 | - pysocks=1.7.1=py37he5f6b98_2 315 | - pyspectral=0.10.1=py_0 316 | - pystac=0.5.2=pyh9f0ad1d_0 317 | - pytest=6.1.1=py37hc8dfbb8_1 318 | - python=3.7.8=h6f2ec95_1_cpython 319 | - python-blosc=1.9.2=py37h9fdb41a_2 320 | - python-box=5.1.1=py_0 321 | - python-dateutil=2.7.5=py_0 322 | - python-dotenv=0.14.0=pyh9f0ad1d_0 323 | - python-editor=1.0.4=py_0 324 | - python-geotiepoints=1.2.0=py37h03ebfcd_0 325 | - python-gist=0.9.2=pyh9f0ad1d_1 326 | - python-gnupg=0.4.6=pyh9f0ad1d_0 327 | - python-json-logger=2.0.1=pyh9f0ad1d_0 328 | - python-kubernetes=12.0.0=pyh9f0ad1d_0 329 | - python-multipart=0.0.5=py_0 330 | - python-slugify=4.0.1=pyh9f0ad1d_0 331 | - python_abi=3.7=1_cp37m 332 | - pytz=2020.1=pyh9f0ad1d_0 333 | - pytzdata=2020.1=pyh9f0ad1d_0 334 | - pyviz_comms=0.7.6=pyh9f0ad1d_0 335 | - pywavelets=1.1.1=py37h161383b_3 336 | - pyyaml=5.3.1=py37hb5d75c8_1 337 | - pyzmq=19.0.2=py37hac76be4_2 338 | - rasterio=1.1.7=py37ha3d844c_0 339 | - re2=2020.10.01=he1b5a44_0 340 | - readline=8.0=he28a2e2_2 341 | - requests=2.24.0=pyh9f0ad1d_0 342 | - requests-oauthlib=1.3.0=pyh9f0ad1d_0 343 | - rio-cogeo=2.0.1=py_0 344 | - rioxarray=0.1.0=py_0 345 | - rsa=4.4.1=pyh9f0ad1d_0 346 | - rtree=0.9.4=py37h8526d28_1 347 | - ruamel.yaml=0.16.12=py37h8f50634_1 348 | - ruamel.yaml.clib=0.2.2=py37h8f50634_1 349 | - s3fs=0.4.2=py_0 350 | - s3transfer=0.3.3=py_3 351 | - sat-search=0.3.0=py_0 352 | - sat-stac=0.4.0=pyh9f0ad1d_0 353 | - satpy=0.23.0=py_0 354 | - scikit-image=0.17.2=py37h9fdb41a_3 355 | - scikit-learn=0.23.2=py37hbb8adca_1 356 | - scipy=1.5.2=py37hb14ef9d_2 357 | - send2trash=1.5.0=py_0 358 | - setuptools=49.6.0=py37he5f6b98_2 359 | - shapely=1.7.1=py37hedb1597_1 360 | - simpervisor=0.3=py_1 361 | - simplejson=3.17.2=py37h8f50634_1 362 | - six=1.15.0=pyh9f0ad1d_0 363 | - snappy=1.1.8=he1b5a44_3 364 | - snuggs=1.4.7=py_0 365 | - sortedcontainers=2.2.2=pyh9f0ad1d_0 366 | - soupsieve=2.0.1=py_1 367 | - sparse=0.11.2=py_0 368 | - sqlalchemy=1.3.20=py37h8f50634_0 369 | - sqlite=3.33.0=h4cf870e_1 370 | - starlette=0.13.6=py_0 371 | - starlette-base=0.13.6=py_0 372 | - supermercado=0.2.0=pyh9f0ad1d_0 373 | - tabulate=0.8.7=pyh9f0ad1d_0 374 | - tbb=2020.2=hc9558a2_0 375 | - tblib=1.6.0=py_0 376 | - terminado=0.9.1=py37hc8dfbb8_1 377 | - testpath=0.4.4=py_0 378 | - text-unidecode=1.3=py_0 379 | - threadpoolctl=2.1.0=pyh5ca1d4c_0 380 | - tifffile=2020.10.1=py_0 381 | - tiledb=2.0.8=h3effe38_1 382 | - tiledb-py=0.6.6=py37h6b53312_2 383 | - tk=8.6.10=hed695b0_1 384 | - toml=0.10.1=pyh9f0ad1d_0 385 | - toolz=0.11.1=py_0 386 | - tornado=6.0.4=py37h8f50634_2 387 | - tqdm=4.50.2=pyh9f0ad1d_0 388 | - traitlets=5.0.5=py_0 389 | - traittypes=0.2.1=pyh9f0ad1d_2 390 | - trollimage=1.14.0=py_0 391 | - trollsift=0.3.4=py_1 392 | - typing-extensions=3.7.4.3=0 393 | - typing_extensions=3.7.4.3=py_0 394 | - tzcode=2020a=h516909a_0 395 | - ujson=4.0.1=py37h3340039_1 396 | - unidecode=1.1.1=py_0 397 | - urllib3=1.25.11=py_0 398 | - uvicorn=0.12.2=py37hc8dfbb8_0 399 | - uvloop=0.14.0=py37h8f50634_2 400 | - watchgod=0.6=py_0 401 | - wcwidth=0.2.5=pyh9f0ad1d_2 402 | - webencodings=0.5.1=py_1 403 | - webob=1.8.6=py_0 404 | - websocket-client=0.57.0=py37hc8dfbb8_3 405 | - websockets=8.1=py37h8f50634_2 406 | - wheel=0.35.1=pyh9f0ad1d_0 407 | - widgetsnbextension=3.5.1=py37hc8dfbb8_4 408 | - xarray=0.16.1=py_0 409 | - xarray-spatial=0.1.0=pyh9f0ad1d_0 410 | - xcape=0.1.2=py37he2cc1d9_1 411 | - xerces-c=3.2.3=hfe33f54_1 412 | - xesmf=0.3.0=py_0 413 | - xgcm=0.5.1=py_0 414 | - xhistogram=0.1.1=py_0 415 | - xlayers=0.2.2=py37hf630d0d_1 416 | - xmitgcm=0.4.1=py_0 417 | - xorg-kbproto=1.0.7=h14c3975_1002 418 | - xorg-libice=1.0.10=h516909a_0 419 | - xorg-libsm=1.2.3=h84519dc_1000 420 | - xorg-libx11=1.6.12=h516909a_0 421 | - xorg-libxau=1.0.9=h14c3975_0 422 | - xorg-libxdmcp=1.1.3=h516909a_0 423 | - xorg-libxext=1.3.4=h516909a_0 424 | - xorg-libxrender=0.9.10=h516909a_1002 425 | - xorg-renderproto=0.11.1=h14c3975_1002 426 | - xorg-xextproto=7.3.0=h14c3975_1002 427 | - xorg-xproto=7.0.31=h14c3975_1007 428 | - xpublish=0.1.0=py_0 429 | - xrft=0.2.2=pyh9f0ad1d_0 430 | - xz=5.2.5=h516909a_1 431 | - yaml=0.2.5=h516909a_0 432 | - yarl=1.6.2=py37h8f50634_0 433 | - zarr=2.4.0=py_0 434 | - zeromq=4.3.3=he1b5a44_2 435 | - zfp=0.5.5=he1b5a44_4 436 | - zict=2.0.0=py_0 437 | - zipp=3.3.1=py_0 438 | - zlib=1.2.11=h516909a_1010 439 | - zstd=1.4.5=h6597ccf_2 440 | prefix: /srv/conda/envs/default 441 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/start: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | 3 | # ==== ONLY EDIT WITHIN THIS BLOCK ===== 4 | 5 | export PANGEO_ENV="default" 6 | if ! [[ -z "${PANGEO_SCRATCH_PREFIX}" ]] && ! [[ -z "${JUPYTERHUB_USER}" ]]; then 7 | export PANGEO_SCRATCH="${PANGEO_SCRATCH_PREFIX}/${JUPYTERHUB_USER}/" 8 | fi 9 | 10 | if [[ ! -f /home/user/.tutorial_initialized ]]; then 11 | cp -rp /srv/tutorials /home/user 12 | touch /home/user/.tutorial_initialized 13 | fi 14 | 15 | # Change the CPU counts: 16 | CPUS=$(grep -c processor /proc/cpuinfo) 17 | sudo xmlstarlet ed --inplace -u "config_machines/machine[@MACH='container']/MAX_TASKS_PER_NODE" -v ${CPUS} ${CESMROOT}/cime/config/cesm/machines/config_machines.xml 18 | sudo xmlstarlet ed --inplace -u "config_machines/machine[@MACH='container']/MAX_MPITASKS_PER_NODE" -v ${CPUS} ${CESMROOT}/cime/config/cesm/machines/config_machines.xml 19 | 20 | # ==== ONLY EDIT WITHIN THIS BLOCK ===== 21 | 22 | 23 | exec jupyter lab --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' 24 | 25 | #exec "$@" 26 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/tutorials/CESM/QuickStart.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "# CESM2 - Quick Start\n", 8 | "\n", 9 | "This is a very quick introduction to running CESM. It will guide you through the basics of creating a case, modifying simple aspects of that case, building it, running it, and use a function to provide a quick visualization of the output. Each step will also provide links to the full CESM documentation and additional examples.\n", 10 | "\n", 11 | "**NOTE: Each step must be followed in order, otherwise you may encounter errors**\n", 12 | "\n", 13 | "\n", 14 | "***" 15 | ] 16 | }, 17 | { 18 | "cell_type": "markdown", 19 | "metadata": {}, 20 | "source": [ 21 | "

1. Creating a CESM case

\n", 22 | "\n", 23 | "CESM experiments start with creating a 'case' - a configuration of the model with a specific set of component models (eg, CAM for the atmosphere model, POP for the ocean model, etc), at a particular resolution, and with a set of options defined in XML files. Let's start by using the 'create_newcase' command to set up an experiment with the following details:
\n", 24 | "\n", 28 | "\n", 29 | "This is a 'simple model' - an aquaplanet configuration at 4.5-degree resolution, using CAM4 physics. This is much less computationally intensive than a fully coupled run, so it works well for this tutorial, only requiring ~0.6GB of RAM. It will also need to download some input files, totaling approximately 127MB of size.\n", 30 | "\n", 31 | "The command to create this configuration is given below, using 'quickstart_case' as the casename. Note that given the size and nature of this run, it's not a scientifically supported configuration, but it's still useful for learning how to run the model.\n", 32 | "\n", 33 | "Run the cell to issue the command:" 34 | ] 35 | }, 36 | { 37 | "cell_type": "code", 38 | "execution_count": null, 39 | "metadata": {}, 40 | "outputs": [], 41 | "source": [ 42 | "create_newcase --case ~/quickstart_case --compset QPC4 --res f45_f45_mg37 --run-unsupported" 43 | ] 44 | }, 45 | { 46 | "cell_type": "markdown", 47 | "metadata": {}, 48 | "source": [ 49 | "

The last few lines above should look like this:\n", 50 | "\n", 51 | ">  Creating Case directory /home/user/quickstart_case
\n", 52 | "This component includes user_mods /opt/ncar/cesm2/components/cam//cime_config/usermods_dirs/aquap
\n", 53 | "Adding user mods directory /opt/ncar/cesm2/components/cam/cime_config/usermods_dirs/aquap\n", 54 | "\n", 55 | "\n", 56 | "If so, great! You've created the default version of your first case. We'll cover this in more detail in an upcoming tutorial, and additional information can also be found in CESM's online [documentation](https://escomp.github.io/CESM/release-cesm2/quickstart.html#create-a-case).\n", 57 | "

\n", 58 | "\n", 59 | "***" 60 | ] 61 | }, 62 | { 63 | "cell_type": "markdown", 64 | "metadata": {}, 65 | "source": [ 66 | "

2. Modifying a CESM case

\n", 67 | "\n", 68 | "Now let's make a simple modification to the case via two easy steps:\n", 69 | "\n", 70 | "1. Change to our new case directory\n", 71 | "2. In that directory, change the duration of the run (in model-time)\n", 72 | "\n", 73 | "\n", 74 | "These changes can be made via modifying the XML files that control CESM's behavior. We could do this by hand, but the preferred way of doing it is to use the 'xmlchange' command in the case directory. By default, newly configured cases are set up to run for 5 model days - since we're just experimenting, we'll change it to 3 model days instead, for even faster runs. Run the following cells to execute the two commands:\n", 75 | "
\n", 76 | "
" 77 | ] 78 | }, 79 | { 80 | "cell_type": "code", 81 | "execution_count": null, 82 | "metadata": {}, 83 | "outputs": [], 84 | "source": [ 85 | "cd ~/quickstart_case" 86 | ] 87 | }, 88 | { 89 | "cell_type": "code", 90 | "execution_count": null, 91 | "metadata": {}, 92 | "outputs": [], 93 | "source": [ 94 | "xmlchange STOP_OPTION=ndays,STOP_N=3" 95 | ] 96 | }, 97 | { 98 | "cell_type": "markdown", 99 | "metadata": {}, 100 | "source": [ 101 | "Since the default STOP_OPTION is already 'ndays', it wasn't strictly necessary to include that in the command, but by being explicit we avoid any confusion later if we had changed it previously to 'nhours' or 'nyears'. \n", 102 | "\n", 103 | "We don't see any output by 'xmlchange', but we can use another tool, 'xmlquery', to double-check that we have the new values:" 104 | ] 105 | }, 106 | { 107 | "cell_type": "code", 108 | "execution_count": null, 109 | "metadata": {}, 110 | "outputs": [], 111 | "source": [ 112 | "xmlquery STOP_OPTION,STOP_N" 113 | ] 114 | }, 115 | { 116 | "cell_type": "markdown", 117 | "metadata": {}, 118 | "source": [ 119 | "

Great! You've now used the 'xmlchange' utility to modify the model's behavior, setting it up to run for 3 model days. You can do a lot more with 'xmlchange', and we'll cover some of these in another tutorial later, and additional information can also be found in CESM's online [documentation](http://esmci.github.io/cime/versions/master/html/Tools_user/xmlchange.html)\n", 120 | "

\n", 121 | "\n", 122 | "***" 123 | ] 124 | }, 125 | { 126 | "cell_type": "markdown", 127 | "metadata": {}, 128 | "source": [ 129 | "

3. Setting up the case

\n", 130 | "\n", 131 | "The next step in running CESM is to 'setup' the case - this is done by running case.setup in the case directory. This command sets up some user-customizable name lists that control the model's behavior, creates the directory where the run happens, and configures additional settings used in building the model. \n", 132 | "\n", 133 | "Run the cell to issue the command:" 134 | ] 135 | }, 136 | { 137 | "cell_type": "code", 138 | "execution_count": null, 139 | "metadata": {}, 140 | "outputs": [], 141 | "source": [ 142 | "case.setup" 143 | ] 144 | }, 145 | { 146 | "cell_type": "markdown", 147 | "metadata": {}, 148 | "source": [ 149 | "

Great! You've now used the 'case.setup' command to set up your case. As the output says, you can now use the 'preview_run' command to get additional information if needed, but it's not necessary. You can also read CESM's online documentation on [case.setup](http://esmci.github.io/cime/versions/master/html/Tools_user/case.setup.html) for more information if you like.

\n", 150 | "\n", 151 | "***" 152 | ] 153 | }, 154 | { 155 | "cell_type": "markdown", 156 | "metadata": {}, 157 | "source": [ 158 | "

4. Building the case

\n", 159 | "\n", 160 | "CESM supports a wide variety of configurations, including different components, physics options and source modifications, and the executable code you get is dependent on each of these, so it requires that cases be *compiled*. The container includes all the necessary libraries and compilers, and the 'create_newcase' and 'case.setup' commands have configured everything we need, so this is a simple process on supported machines -- we just run the 'case.build' command in the cell below.\n", 161 | "\n", 162 | "Be aware that this can take a few minutes - how long depends upon the type of system you have, but estimates are ~3-6 minutes" 163 | ] 164 | }, 165 | { 166 | "cell_type": "code", 167 | "execution_count": null, 168 | "metadata": {}, 169 | "outputs": [], 170 | "source": [ 171 | "case.build" 172 | ] 173 | }, 174 | { 175 | "cell_type": "markdown", 176 | "metadata": {}, 177 | "source": [ 178 | "

\n", 179 | "Again, this will take a few minutes. You'll know this is complete when you see the line:\n", 180 | "\n", 181 | "> MODEL BUILD HAS FINISHED SUCCESSFULLY\n", 182 | "\n", 183 | "If you see that, fantastic! You've built your first CESM case! Now we can move on to the final step of performing a simulation.

\n", 184 | "\n", 185 | "***" 186 | ] 187 | }, 188 | { 189 | "cell_type": "markdown", 190 | "metadata": {}, 191 | "source": [ 192 | "

5. Running your case

\n", 193 | "\n", 194 | "Running a case is also simple - we just issue the 'case.submit' command. This will start by checking that we have all of the necessary input data for our run, and downloading whatever is missing, and then it will perform the actual simulation - which we've configured to run for 3 model days.\n", 195 | "\n", 196 | "How long the run takes, like the build, depends heavily on the type of processor you have, and how many cores it has. Expect this to take from 1-3 minutes after the data download is finished." 197 | ] 198 | }, 199 | { 200 | "cell_type": "code", 201 | "execution_count": null, 202 | "metadata": {}, 203 | "outputs": [], 204 | "source": [ 205 | "case.submit" 206 | ] 207 | }, 208 | { 209 | "cell_type": "markdown", 210 | "metadata": {}, 211 | "source": [ 212 | "

When this step finishes, the run will complete, then the 'archive' script will execute. You will see a few warning messages about 'No such variable' - these are normal, and can be ignored. The final lines should look like:\n", 213 | "\n", 214 | ">Submitted job case.run with id None
\n", 215 | "Submitted job case.st_archive with id None\n", 216 | "\n", 217 | "\n", 218 | "If you see those, congratulations! You've run your first case -- there's a *lot* of text shown above, and we'll cover it in more detail in another tutorial, and more information can also be found in the [documentation](https://escomp.github.io/CESM/versions/cesm2.2/html/quickstart.html#run-the-case).

\n", 219 | "\n", 220 | "***" 221 | ] 222 | }, 223 | { 224 | "cell_type": "markdown", 225 | "metadata": {}, 226 | "source": [ 227 | "

6. Continuing a run

\n", 228 | "\n", 229 | "We've run our case for three model days as an initial test, but now let's go back and *continue* that run for 28 more days so we have a full month of output. This is better for estimating performance, *and* will give us a monthly history output file that we can use to visualize results.\n", 230 | "\n", 231 | "To do this, we'll use the 'xmlchange' utility to tell CESM to continue the run, and to set the number of days for the new run to 28. Then we'll call 'case.submit' again. Since we're running 9.3x longer (28 days vs. 3), we should expect this to take roughly 9.3x longer. Enter the commands below, then grab a cup of coffee as the model runs!" 232 | ] 233 | }, 234 | { 235 | "cell_type": "code", 236 | "execution_count": null, 237 | "metadata": {}, 238 | "outputs": [], 239 | "source": [ 240 | "xmlchange CONTINUE_RUN=true,STOP_N=28" 241 | ] 242 | }, 243 | { 244 | "cell_type": "code", 245 | "execution_count": null, 246 | "metadata": {}, 247 | "outputs": [], 248 | "source": [ 249 | "case.submit" 250 | ] 251 | }, 252 | { 253 | "cell_type": "markdown", 254 | "metadata": {}, 255 | "source": [ 256 | "

Excellent - you'll notice that this time the output was a little less, since it didn't need to download any new input data. We're just continuing a run that we have all the input data for.

\n", 257 | "\n", 258 | "***" 259 | ] 260 | }, 261 | { 262 | "cell_type": "markdown", 263 | "metadata": {}, 264 | "source": [ 265 | "

6. Visualize the output

\n", 266 | "\n", 267 | "As a final step, let's take a quick look at visualizing our output. Visualization in Jupyter Notebooks is a huge topic, and there are countless ways of analyzing and processing CESM's output. Since this is a 'quickstart' tutorial, we're going to use an existing function provided by the 'cesm' python package. This function, 'QuickView', takes the name of a case and one of several variables -'T' (temperature) in this case- and plots the variable with a global overlay for the lowest vertical level of the model. We'll look at more advanced visualizations in other tutorial lessons." 268 | ] 269 | }, 270 | { 271 | "cell_type": "code", 272 | "execution_count": null, 273 | "metadata": {}, 274 | "outputs": [], 275 | "source": [ 276 | "from cesm import QuickView\n", 277 | "QuickView('quickstart_case', 'T')" 278 | ] 279 | }, 280 | { 281 | "cell_type": "markdown", 282 | "metadata": {}, 283 | "source": [ 284 | "And we can do a plot of 'U' just as easily:" 285 | ] 286 | }, 287 | { 288 | "cell_type": "code", 289 | "execution_count": null, 290 | "metadata": {}, 291 | "outputs": [], 292 | "source": [ 293 | "QuickView('quickstart_case', 'U')" 294 | ] 295 | }, 296 | { 297 | "cell_type": "markdown", 298 | "metadata": {}, 299 | "source": [ 300 | "

Congratulations - you've walked through the basic steps of using CESM : creating a case, setting it up, building it, running it, and visualizing the output. You're all set for some of the more advanced tutorials now. " 301 | ] 302 | } 303 | ], 304 | "metadata": { 305 | "kernelspec": { 306 | "display_name": "Python [conda env:default] *", 307 | "language": "python", 308 | "name": "conda-env-default-py" 309 | }, 310 | "language_info": { 311 | "codemirror_mode": { 312 | "name": "ipython", 313 | "version": 3 314 | }, 315 | "file_extension": ".py", 316 | "mimetype": "text/x-python", 317 | "name": "python", 318 | "nbconvert_exporter": "python", 319 | "pygments_lexer": "ipython3", 320 | "version": "3.7.8" 321 | } 322 | }, 323 | "nbformat": 4, 324 | "nbformat_minor": 4 325 | } 326 | -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/tutorials/images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/ESCOMP-Containers/c48f872d5b4bbdc90ca9e1159d6c276d87407e09/CESM-Lab/2.2/Files/tutorials/images/logo.png -------------------------------------------------------------------------------- /CESM-Lab/2.2/Files/tutorials/index.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "![](images/logo.png)\n", 8 | "#
CESM-Lab Tutorials
\n", 9 | "\n", 10 | "\n", 11 | "Welcome to CESM! This tutorial is intended to provide a quick introduction to using the Community Earth System Model by providing self-contained examples in Jupyter Notebooks. A list of lessons is below; you can click on any to open up a Notebook and get started.\n", 12 | "\n", 13 | "We'd love to hear from you on the [CESM Forums](https://bb.cgd.ucar.edu/cesm/), and welcome any suggestions on missing topics, new ideas, user contributions and other ways of improving this resource!\n", 14 | "\n", 15 | "\n", 16 | "\n", 17 | "1. [Quick Start](CESM/QuickStart.ipynb) (~20-40 minutes, depending on system performance)\n", 18 | "
\n", 19 | "*This lesson is a quick walkthrough of all the key steps in running CESM out-of-the-box. You'll create a new experiment, set it up, build it, run it, and using an existing visualization function, visualize the global temperature profile.*\n", 20 | "\n", 21 | "---\n", 22 | "\n", 23 | "2. CESM Tutorials \n", 24 | "\n", 25 | " Creating cases (_coming soon_)\n", 26 | "\n", 27 | " Case settings & 'xmlchange' (_coming soon_)\n", 28 | " \n", 29 | " Modifying CESM namelists (_coming soon_)\n", 30 | " \n", 31 | "---\n", 32 | " \n", 33 | "3. Component-specific Tutorials\n", 34 | "\n", 35 | " CAM (atmosphere) (_coming soon_)\n", 36 | "\n", 37 | " CLM (land) (_coming soon_)\n", 38 | "\n", 39 | "---\n", 40 | "\n", 41 | "3. Visualization\n", 42 | "\n", 43 | " Getting started with Matplotlib (_coming soon_)\n", 44 | "\n", 45 | "---\n", 46 | "\n", 47 | "4. Analysis\n", 48 | "\n", 49 | " CESM-LENS data on AWS (_coming soon_)\n", 50 | "\n", 51 | "\n", 52 | "\n", 53 | "\n" 54 | ] 55 | } 56 | ], 57 | "metadata": { 58 | "kernelspec": { 59 | "display_name": "Python [conda env:default] *", 60 | "language": "python", 61 | "name": "conda-env-default-py" 62 | }, 63 | "language_info": { 64 | "codemirror_mode": { 65 | "name": "ipython", 66 | "version": 3 67 | }, 68 | "file_extension": ".py", 69 | "mimetype": "text/x-python", 70 | "name": "python", 71 | "nbconvert_exporter": "python", 72 | "pygments_lexer": "ipython3", 73 | "version": "3.7.8" 74 | } 75 | }, 76 | "nbformat": 4, 77 | "nbformat_minor": 4 78 | } 79 | -------------------------------------------------------------------------------- /CESM-Postprocessing/Dockerfile: -------------------------------------------------------------------------------- 1 | ######################################### 2 | # ESCOMP/CESM-Postprocessing Dockerfile # 3 | ######################################### 4 | 5 | # We're using a CentOS8 base for now: 6 | FROM centos:centos8.3.2011 7 | 8 | 9 | # Set up some variables for versions of packages & environment needs: 10 | ARG SOURCE_MPI=https://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz 11 | ARG SOURCE_MINICONDA=https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh 12 | ARG SOURCE_POSTPROCESSING="-b cheyenne_update_py3 https://github.com/briandobbins/CESM_postprocessing.git" 13 | 14 | # Set up the environment variable for the postprocessing software 15 | ENV POSTPROCESS_PATH=/opt/ncar/cesm_postprocessing 16 | 17 | 18 | # Set the shell to bash - this helps with some of the conda installation quirks in Dockerfiles 19 | SHELL [ "/bin/bash", "--login", "-c" ] 20 | 21 | 22 | # We're going to install the dnf plugins, the EPEL repo and the english language pack, then 23 | # enable the PowerTools repo (for libsz.so, needed by netcdf-devel), upgrade existing 24 | # packages, install a list of prerequisites, and clean up. 25 | # Note: Some packages, like netcdf-devel, are obvious, others like tbb less so, and a few 26 | # like 'which' are just for convenience/debugging 27 | RUN dnf install -y dnf-plugins-core epel-release glibc-langpack-en &&\ 28 | dnf config-manager --set-enabled powertools &&\ 29 | dnf upgrade -y &&\ 30 | dnf install -y calc \ 31 | diffutils \ 32 | gcc \ 33 | gcc-c++ \ 34 | gcc-gfortran \ 35 | git \ 36 | file \ 37 | libnsl \ 38 | make \ 39 | ncl-devel \ 40 | netcdf-fortran-devel \ 41 | tbb \ 42 | wget \ 43 | which &&\ 44 | dnf clean all 45 | 46 | 47 | # Now let's download & install MPI, then clean it up: 48 | ENV PACKAGE_MPI=${SOURCE_MPI} 49 | RUN mkdir -p /tmp/mpi &&\ 50 | cd /tmp/mpi &&\ 51 | curl -sSL ${PACKAGE_MPI} --output mpi.tar.gz &&\ 52 | tar zxvf mpi.tar.gz -C . --strip-components=1 &&\ 53 | ./configure --prefix=/usr/local --disable-fortran --disable-cxx &&\ 54 | make -j 2 install &&\ 55 | rm -rf /tmp/mpi 56 | 57 | 58 | # Now let's download, install and init Miniconda, then clean up: 59 | ENV PACKAGE_MINICONDA=${SOURCE_MINICONDA} 60 | RUN mkdir -p /tmp/conda &&\ 61 | cd /tmp/conda &&\ 62 | curl -sSL ${PACKAGE_MINICONDA} --output Miniconda.sh &&\ 63 | sh Miniconda.sh -b -p /opt/ncar/conda &&\ 64 | /opt/ncar/conda/bin/conda init bash &&\ 65 | rm -rf /tmp/conda 66 | 67 | 68 | # Create the cesm-env2 conda environment -- this name is hardcoded in the code, 69 | # it seems, but may be worth looking into changing later, since everything here 70 | # could be put in a default python environment, and we'd avoid the complexity of 71 | # activating non-default conda environments in containers. 72 | # Also note that I've done some effort on installing things by source, which 73 | # results in a much smaller container, but needs more debugging due to odd issues. 74 | # Finally, using the environment.yml (or specific source versions) makes it easier 75 | # to ensure compatibility at different build times. 76 | COPY Files/environment.yml / 77 | RUN conda update -n base -c defaults conda &&\ 78 | conda env create -f /environment.yml &&\ 79 | echo "conda activate cesm-env2" >> /root/.bashrc &&\ 80 | rm /environment.yml &&\ 81 | conda clean --all 82 | 83 | 84 | # Install CESM Postprocessing tools: 85 | ENV POSTPROCESSING_REPO=${SOURCE_POSTPROCESSING} 86 | RUN mkdir -p /opt/ncar && \ 87 | cd /opt/ncar && \ 88 | git clone ${POSTPROCESSING_REPO} cesm_postprocessing && \ 89 | cd cesm_postprocessing && \ 90 | ln -s /opt/ncar/conda/envs/cesm-env2 . && \ 91 | ./manage_externals/checkout_externals &&\ 92 | ./create_python_env -machine container 93 | 94 | 95 | # And add the 'activate_this.py' script (used by the CESM Postprocessing scripts) 96 | # Is this deprecrated? Are we doing something unique? My Python is pretty bad; ask Jim about this 97 | COPY Files/activate_this.py /opt/ncar/cesm_postprocessing/cesm-env2/bin 98 | 99 | 100 | CMD ["/bin/bash", "-l"] 101 | -------------------------------------------------------------------------------- /CESM-Postprocessing/Files/activate_this.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """Activate virtualenv for current interpreter: 3 | 4 | Use exec(open(this_file).read(), {'__file__': this_file}). 5 | 6 | This can be used when you must use an existing Python interpreter, not the virtualenv bin/python. 7 | """ 8 | import os 9 | import site 10 | import sys 11 | 12 | try: 13 | abs_file = os.path.abspath(__file__) 14 | except NameError: 15 | raise AssertionError("You must use exec(open(this_file).read(), {'__file__': this_file}))") 16 | 17 | bin_dir = os.path.dirname(abs_file) 18 | base = bin_dir[: -len("__BIN_NAME__") - 1] # strip away the bin part from the __file__, plus the path separator 19 | 20 | # prepend bin to PATH (this file is inside the bin directory) 21 | os.environ["PATH"] = os.pathsep.join([bin_dir] + os.environ.get("PATH", "").split(os.pathsep)) 22 | os.environ["VIRTUAL_ENV"] = base # virtual env is right above bin directory 23 | 24 | # add the virtual environments libraries to the host python import mechanism 25 | prev_length = len(sys.path) 26 | for lib in "__LIB_FOLDERS__".split(os.pathsep): 27 | path = os.path.realpath(os.path.join(bin_dir, lib)) 28 | site.addsitedir(path) 29 | sys.path[:] = sys.path[prev_length:] + sys.path[0:prev_length] 30 | 31 | sys.real_prefix = sys.prefix 32 | sys.prefix = base 33 | -------------------------------------------------------------------------------- /CESM-Postprocessing/Files/environment.yml: -------------------------------------------------------------------------------- 1 | name: cesm-env2 2 | channels: 3 | - conda-forge 4 | - defaults 5 | dependencies: 6 | - _libgcc_mutex=0.1=conda_forge 7 | - _openmp_mutex=4.5=1_gnu 8 | - boost-cpp=1.72.0=h8e57a91_0 9 | - bzip2=1.0.8=h7f98852_4 10 | - c-ares=1.17.1=h7f98852_1 11 | - ca-certificates=2020.12.5=ha878542_0 12 | - cairo=1.16.0=hcf35c78_1003 13 | - certifi=2020.12.5=py38h578d9bd_1 14 | - cfitsio=3.470=h2e3daa1_7 15 | - curl=7.76.1=h979ede3_1 16 | - esmf=8.0.0=nompi_hb0fcdcb_6 17 | - expat=2.3.0=h9c3ff4c_0 18 | - fontconfig=2.13.1=hba837de_1005 19 | - freetype=2.10.4=h0708190_1 20 | - freexl=1.0.6=h7f98852_0 21 | - g2clib=1.6.0=hf3f1b0b_9 22 | - geos=3.8.1=he1b5a44_0 23 | - geotiff=1.5.1=h05acad5_10 24 | - gettext=0.19.8.1=h0b5b191_1005 25 | - giflib=5.2.1=h36c2ea0_2 26 | - glib=2.68.1=h9c3ff4c_0 27 | - glib-tools=2.68.1=h9c3ff4c_0 28 | - gsl=2.6=he838d99_2 29 | - hdf4=4.2.13=h10796ff_1005 30 | - hdf5=1.10.5=nompi_h7c3c948_1111 31 | - hdfeos2=2.20=h64bfcee_1000 32 | - hdfeos5=5.1.16=h8b6279f_6 33 | - icu=64.2=he1b5a44_1 34 | - jasper=1.900.1=h07fcdf6_1006 35 | - jpeg=9d=h36c2ea0_0 36 | - json-c=0.13.1=hbfbb72e_1002 37 | - kealib=1.4.13=hec59c27_0 38 | - krb5=1.17.2=h926e7f8_0 39 | - ld_impl_linux-64=2.35.1=hea4e1c9_2 40 | - libblas=3.9.0=8_openblas 41 | - libcblas=3.9.0=8_openblas 42 | - libcurl=7.76.1=hc4aaa36_1 43 | - libdap4=3.20.6=hd7c4107_2 44 | - libedit=3.1.20191231=he28a2e2_2 45 | - libev=4.33=h516909a_1 46 | - libffi=3.3=h58526e2_2 47 | - libgcc-ng=9.3.0=h2828fa1_19 48 | - libgdal=3.0.4=h3dfc09a_6 49 | - libgfortran-ng=7.5.0=h14aa051_19 50 | - libgfortran4=7.5.0=h14aa051_19 51 | - libglib=2.68.1=h3e27bee_0 52 | - libgomp=9.3.0=h2828fa1_19 53 | - libiconv=1.16=h516909a_0 54 | - libkml=1.3.0=hd79254b_1012 55 | - liblapack=3.9.0=8_openblas 56 | - libnetcdf=4.7.4=nompi_h9f9fd6a_101 57 | - libnghttp2=1.43.0=h812cca2_0 58 | - libopenblas=0.3.12=pthreads_hb3c22a3_1 59 | - libpng=1.6.37=h21135ba_2 60 | - libpq=12.3=h255efa7_3 61 | - libspatialite=4.3.0a=h2482549_1038 62 | - libssh2=1.9.0=ha56f1ee_6 63 | - libstdcxx-ng=9.3.0=h6de172a_19 64 | - libtiff=4.2.0=hdc55705_0 65 | - libuuid=2.32.1=h7f98852_1000 66 | - libwebp-base=1.2.0=h7f98852_2 67 | - libxcb=1.13=h7f98852_1003 68 | - libxml2=2.9.10=hee79883_0 69 | - lz4-c=1.9.2=he1b5a44_3 70 | - ncl=6.6.2=hfe5c2fd_21 71 | - ncurses=6.2=h58526e2_4 72 | - netcdf-fortran=4.5.2=nompi_h45d7149_104 73 | - numpy=1.20.2=py38h9894fe3_0 74 | - openjpeg=2.3.1=hf7af979_3 75 | - openssl=1.1.1k=h7f98852_0 76 | - pcre=8.44=he1b5a44_0 77 | - pip=21.1=pyhd8ed1ab_0 78 | - pixman=0.38.0=h516909a_1003 79 | - poppler=0.67.0=h14e79db_8 80 | - poppler-data=0.4.10=0 81 | - postgresql=12.3=hc2f5b80_3 82 | - proj=7.0.0=h966b41f_5 83 | - pthread-stubs=0.4=h36c2ea0_1001 84 | - pyngl=1.6.1=py38h174697a_2 85 | - pynio=1.5.5=py38h031d99c_12 86 | - python=3.8.8=hffdb5ce_0_cpython 87 | - python_abi=3.8=1_cp38 88 | - readline=8.1=h46c0cb4_0 89 | - setuptools=49.6.0=py38h578d9bd_3 90 | - sqlite=3.35.5=h74cdb3f_0 91 | - tiledb=1.7.7=h8efa9f0_2 92 | - tk=8.6.10=h21135ba_1 93 | - tzcode=2021a=h7f98852_1 94 | - udunits2=2.2.27.27=h975c496_1 95 | - wheel=0.36.2=pyhd3deb0d_0 96 | - xerces-c=3.2.2=h8412b87_1004 97 | - xorg-imake=1.0.7=0 98 | - xorg-kbproto=1.0.7=h7f98852_1002 99 | - xorg-libice=1.0.10=h7f98852_0 100 | - xorg-libsm=1.2.3=hd9c2040_1000 101 | - xorg-libx11=1.6.12=h516909a_0 102 | - xorg-libxau=1.0.9=h7f98852_0 103 | - xorg-libxaw=1.0.14=h7f98852_0 104 | - xorg-libxdmcp=1.1.3=h7f98852_0 105 | - xorg-libxext=1.3.4=h516909a_0 106 | - xorg-libxmu=1.1.3=h516909a_0 107 | - xorg-libxpm=3.5.13=h516909a_0 108 | - xorg-libxrender=0.9.10=h516909a_1002 109 | - xorg-libxt=1.1.5=h516909a_1003 110 | - xorg-makedepend=1.0.6=he1b5a44_1 111 | - xorg-renderproto=0.11.1=h7f98852_1002 112 | - xorg-xextproto=7.3.0=h7f98852_1002 113 | - xorg-xproto=7.0.31=h7f98852_1007 114 | - xz=5.2.5=h516909a_1 115 | - zlib=1.2.11=h516909a_1010 116 | - zstd=1.4.8=hdf46e1d_0 117 | - pip: 118 | - antlr4-python3-runtime==4.7.2 119 | - cartopy==0.18.0 120 | - cf-units==2.1.4 121 | - cftime==1.4.1 122 | - cycler==0.10.0 123 | - dreqpy==1.0.33 124 | - ilamb==2.5 125 | - jinja2==3.0.0rc2 126 | - kiwisolver==1.3.1 127 | - markupsafe==2.0.0rc2 128 | - matplotlib==3.4.1 129 | - mpi4py==3.0.3 130 | - mpmath==1.2.1 131 | - netcdf4==1.5.6 132 | - pillow==8.2.0 133 | - ply==3.11 134 | - pyparsing==3.0.0b2 135 | - pyshp==2.1.3 136 | - python-dateutil==2.8.1 137 | - scipy==1.6.3 138 | - shapely==1.8a1 139 | - six==1.15.0 140 | - sympy==1.8 141 | prefix: /opt/ncar/conda/envs/cesm-env2 142 | -------------------------------------------------------------------------------- /CESM/2.1/Dockerfile: -------------------------------------------------------------------------------- 1 | ############################## 2 | # ESCOMP/CESM/2.1 Dockerfile # 3 | ############################## 4 | 5 | # Use the ESCOMP centos8 base - this is a base install of CentOS, plus NetCDF/HDF5/PNetCDF/MPICH 6 | FROM escomp/base-centos8 7 | 8 | # Install CESM: 9 | COPY Files/ea002e626aee6bc6643e8ab5f998e5e4 /root/.subversion/auth/svn.ssl.server/ 10 | RUN mkdir -p /opt/ncar && \ 11 | cd /opt/ncar && \ 12 | git clone -b release-cesm2.1.3 https://github.com/ESCOMP/cesm.git cesm2 && \ 13 | cd cesm2 && \ 14 | ./manage_externals/checkout_externals 15 | 16 | # Set up the environment - create the group and user, the shell variables, the input data directory and sudo access: 17 | RUN groupadd ncar && \ 18 | useradd -c 'CESM User' -d /home/user -g ncar -m -s /bin/bash user && \ 19 | yum install -y ftp && \ 20 | echo 'export CESMDATAROOT=${HOME}' >> /etc/profile.d/cesm.sh && \ 21 | echo 'export CIME_MACHINE=container' >> /etc/profile.d/cesm.sh && \ 22 | echo 'export USER=$(whoami)' >> /etc/profile.d/cesm.sh && \ 23 | echo 'export PS1="[\u@cesm2.1.3 \W]\$ "' >> /etc/profile.d/cesm.sh && \ 24 | echo 'export PATH=${PATH}:/opt/ncar/cesm2/cime/scripts' >> /etc/profile.d/cesm.sh && \ 25 | echo 'user ALL=(ALL) NOPASSWD: ALL' >> /etc/sudoers.d/ncar 26 | 27 | 28 | # Add the container versions of the config_machines & config_compilers settings - later, integrate these into CIME 29 | COPY Files/config_compilers.xml /opt/ncar/cesm2/cime/config/cesm/machines/ 30 | COPY Files/config_machines.xml /opt/ncar/cesm2/cime/config/cesm/machines/ 31 | COPY Files/config_inputdata.xml /opt/ncar/cesm2/cime/config/cesm/ 32 | COPY Files/case_setup.py /opt/ncar/cesm2/cime/scripts/lib/CIME/case/case_setup.py 33 | 34 | 35 | USER user 36 | WORKDIR /home/user 37 | ENTRYPOINT ["/bin/bash", "-l"] 38 | -------------------------------------------------------------------------------- /CESM/2.1/Files/case_setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | Library for case.setup. 3 | case_setup is a member of class Case from file case.py 4 | """ 5 | 6 | from CIME.XML.standard_module_setup import * 7 | 8 | from CIME.XML.machines import Machines 9 | from CIME.BuildTools.configure import configure 10 | from CIME.utils import get_cime_root, run_and_log_case_status, get_model, get_batch_script_for_job, safe_copy 11 | from CIME.test_status import * 12 | from CIME.locked_files import unlock_file, lock_file 13 | 14 | logger = logging.getLogger(__name__) 15 | 16 | ############################################################################### 17 | def _build_usernl_files(case, model, comp): 18 | ############################################################################### 19 | """ 20 | Create user_nl_xxx files, expects cwd is caseroot 21 | """ 22 | model = model.upper() 23 | if model == "DRV": 24 | model_file = case.get_value("CONFIG_CPL_FILE") 25 | else: 26 | model_file = case.get_value("CONFIG_{}_FILE".format(model)) 27 | expect(model_file is not None, 28 | "Could not locate CONFIG_{}_FILE in config_files.xml".format(model)) 29 | model_dir = os.path.dirname(model_file) 30 | 31 | expect(os.path.isdir(model_dir), 32 | "cannot find cime_config directory {} for component {}".format(model_dir, comp)) 33 | ninst = 1 34 | multi_driver = case.get_value("MULTI_DRIVER") 35 | if multi_driver: 36 | ninst_max = case.get_value("NINST_MAX") 37 | if model not in ("DRV","CPL","ESP"): 38 | ninst_model = case.get_value("NINST_{}".format(model)) 39 | expect(ninst_model==ninst_max,"MULTI_DRIVER mode, all components must have same NINST value. NINST_{} != {}".format(model,ninst_max)) 40 | if comp == "cpl": 41 | if not os.path.exists("user_nl_cpl"): 42 | safe_copy(os.path.join(model_dir, "user_nl_cpl"), ".") 43 | else: 44 | if ninst == 1: 45 | ninst = case.get_value("NINST_{}".format(model)) 46 | nlfile = "user_nl_{}".format(comp) 47 | model_nl = os.path.join(model_dir, nlfile) 48 | if ninst > 1: 49 | for inst_counter in range(1, ninst+1): 50 | inst_nlfile = "{}_{:04d}".format(nlfile, inst_counter) 51 | if not os.path.exists(inst_nlfile): 52 | # If there is a user_nl_foo in the case directory, copy it 53 | # to user_nl_foo_INST; otherwise, copy the original 54 | # user_nl_foo from model_dir 55 | if os.path.exists(nlfile): 56 | safe_copy(nlfile, inst_nlfile) 57 | elif os.path.exists(model_nl): 58 | safe_copy(model_nl, inst_nlfile) 59 | else: 60 | # ninst = 1 61 | if not os.path.exists(nlfile): 62 | if os.path.exists(model_nl): 63 | safe_copy(model_nl, nlfile) 64 | 65 | ############################################################################### 66 | def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False): 67 | ############################################################################### 68 | os.chdir(caseroot) 69 | 70 | # Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests, or create if machine is a container: 71 | din_loc_root = case.get_value("DIN_LOC_ROOT") 72 | if case.get_value("MACH") == "container": 73 | if not os.path.isdir(din_loc_root): 74 | logger.info("Making inputdata directory: {}".format(din_loc_root)) 75 | os.mkdir(din_loc_root) 76 | 77 | testcase = case.get_value("TESTCASE") 78 | expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"), 79 | "inputdata root is not a directory or is not readable: {}".format(din_loc_root)) 80 | 81 | # Remove batch scripts 82 | if reset or clean: 83 | # clean batch script 84 | batch_script = get_batch_script_for_job(case.get_primary_job()) 85 | if os.path.exists(batch_script): 86 | os.remove(batch_script) 87 | logger.info("Successfully cleaned batch script {}".format(batch_script)) 88 | 89 | if not test_mode: 90 | # rebuild the models (even on restart) 91 | case.set_value("BUILD_COMPLETE", False) 92 | 93 | if not clean: 94 | case.load_env() 95 | 96 | models = case.get_values("COMP_CLASSES") 97 | mach = case.get_value("MACH") 98 | compiler = case.get_value("COMPILER") 99 | debug = case.get_value("DEBUG") 100 | mpilib = case.get_value("MPILIB") 101 | sysos = case.get_value("OS") 102 | expect(mach is not None, "xml variable MACH is not set") 103 | 104 | # creates the Macros.make, Depends.compiler, Depends.machine, Depends.machine.compiler 105 | # and env_mach_specific.xml if they don't already exist. 106 | if not os.path.isfile("Macros.make") or not os.path.isfile("env_mach_specific.xml"): 107 | configure(Machines(machine=mach), caseroot, ["Makefile"], compiler, mpilib, debug, sysos) 108 | 109 | # Set tasks to 1 if mpi-serial library 110 | if mpilib == "mpi-serial": 111 | case.set_value("NTASKS", 1) 112 | 113 | # Check ninst. 114 | # In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component. 115 | multi_driver = case.get_value("MULTI_DRIVER") 116 | for comp in models: 117 | ntasks = case.get_value("NTASKS_{}".format(comp)) 118 | if comp == "CPL": 119 | continue 120 | ninst = case.get_value("NINST_{}".format(comp)) 121 | if multi_driver: 122 | expect(case.get_value("NINST_LAYOUT_{}".format(comp)) == "concurrent", 123 | "If multi_driver is TRUE, NINST_LAYOUT_{} must be concurrent".format(comp)) 124 | case.set_value("NTASKS_PER_INST_{}".format(comp), ntasks) 125 | else: 126 | if ninst > ntasks: 127 | if ntasks == 1: 128 | case.set_value("NTASKS_{}".format(comp), ninst) 129 | ntasks = ninst 130 | else: 131 | expect(False, "NINST_{comp} value {ninst} greater than NTASKS_{comp} {ntasks}".format(comp=comp, ninst=ninst, ntasks=ntasks)) 132 | 133 | case.set_value("NTASKS_PER_INST_{}".format(comp), max(1,int(ntasks / ninst))) 134 | 135 | if os.path.exists(get_batch_script_for_job(case.get_primary_job())): 136 | logger.info("Machine/Decomp/Pes configuration has already been done ...skipping") 137 | 138 | case.initialize_derived_attributes() 139 | 140 | case.set_value("SMP_PRESENT", case.get_build_threaded()) 141 | 142 | else: 143 | case.check_pelayouts_require_rebuild(models) 144 | 145 | unlock_file("env_build.xml") 146 | unlock_file("env_batch.xml") 147 | 148 | case.flush() 149 | case.check_lockedfiles() 150 | 151 | case.initialize_derived_attributes() 152 | 153 | cost_per_node = case.get_value("COSTPES_PER_NODE") 154 | case.set_value("COST_PES", case.num_nodes * cost_per_node) 155 | threaded = case.get_build_threaded() 156 | case.set_value("SMP_PRESENT", threaded) 157 | if threaded and case.total_tasks * case.thread_count > cost_per_node: 158 | smt_factor = max(1.0,int(case.get_value("MAX_TASKS_PER_NODE") / cost_per_node)) 159 | case.set_value("TOTALPES", int(case.total_tasks * max(1.0,float(case.thread_count) / smt_factor))) 160 | else: 161 | case.set_value("TOTALPES", case.total_tasks*case.thread_count) 162 | 163 | 164 | # May need to select new batch settings if pelayout changed (e.g. problem is now too big for prev-selected queue) 165 | env_batch = case.get_env("batch") 166 | env_batch.set_job_defaults([(case.get_primary_job(), {})], case) 167 | 168 | # create batch files 169 | env_batch.make_all_batch_files(case) 170 | if get_model() == "e3sm" and not case.get_value("TEST"): 171 | input_batch_script = os.path.join(case.get_value("MACHDIR"), "template.case.run.sh") 172 | env_batch.make_batch_script(input_batch_script, "case.run", case, outfile=get_batch_script_for_job("case.run.sh")) 173 | 174 | # Make a copy of env_mach_pes.xml in order to be able 175 | # to check that it does not change once case.setup is invoked 176 | case.flush() 177 | logger.debug("at copy TOTALPES = {}".format(case.get_value("TOTALPES"))) 178 | lock_file("env_mach_pes.xml") 179 | lock_file("env_batch.xml") 180 | 181 | # Create user_nl files for the required number of instances 182 | if not os.path.exists("user_nl_cpl"): 183 | logger.info("Creating user_nl_xxx files for components and cpl") 184 | 185 | # loop over models 186 | for model in models: 187 | comp = case.get_value("COMP_{}".format(model)) 188 | logger.debug("Building {} usernl files".format(model)) 189 | _build_usernl_files(case, model, comp) 190 | if comp == "cism": 191 | glcroot = case.get_value("COMP_ROOT_DIR_GLC") 192 | run_cmd_no_fail("{}/cime_config/cism.template {}".format(glcroot, caseroot)) 193 | 194 | _build_usernl_files(case, "drv", "cpl") 195 | 196 | # Create needed directories for case 197 | case.create_dirs() 198 | 199 | logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building") 200 | 201 | # Some tests need namelists created here (ERP) - so do this if we are in test mode 202 | if test_mode or get_model() == "e3sm": 203 | logger.info("Generating component namelists as part of setup") 204 | case.create_namelists() 205 | 206 | # Record env information 207 | env_module = case.get_env("mach_specific") 208 | env_module.make_env_mach_specific_file("sh", case) 209 | env_module.make_env_mach_specific_file("csh", case) 210 | env_module.save_all_env_info("software_environment.txt") 211 | 212 | logger.info("You can now run './preview_run' to get more info on how your case will be run") 213 | 214 | ############################################################################### 215 | def case_setup(self, clean=False, test_mode=False, reset=False): 216 | ############################################################################### 217 | caseroot, casebaseid = self.get_value("CASEROOT"), self.get_value("CASEBASEID") 218 | phase = "setup.clean" if clean else "case.setup" 219 | functor = lambda: _case_setup_impl(self, caseroot, clean, test_mode, reset) 220 | 221 | if self.get_value("TEST") and not test_mode: 222 | test_name = casebaseid if casebaseid is not None else self.get_value("CASE") 223 | with TestStatus(test_dir=caseroot, test_name=test_name) as ts: 224 | try: 225 | run_and_log_case_status(functor, phase, caseroot=caseroot) 226 | except: 227 | ts.set_status(SETUP_PHASE, TEST_FAIL_STATUS) 228 | raise 229 | else: 230 | if clean: 231 | ts.set_status(SETUP_PHASE, TEST_PEND_STATUS) 232 | else: 233 | ts.set_status(SETUP_PHASE, TEST_PASS_STATUS) 234 | else: 235 | run_and_log_case_status(functor, phase, caseroot=caseroot) 236 | -------------------------------------------------------------------------------- /CESM/2.1/Files/config_inputdata.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 17 | 18 | 19 | wget 20 |
ftp://ftp.cgd.ucar.edu/cesm/inputdata/
21 | anonymous 22 | user@example.edu 23 | ../inputdata_checksum.dat 24 | 25 | 26 | 27 | ftp requires the python package ftplib 28 | ftp 29 |
ftp.cgd.ucar.edu/cesm/inputdata
30 | anonymous 31 | user@example.edu 32 | ../inputdata_checksum.dat 33 | 34 | 35 | 36 | svn 37 |
https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata
38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /CESM/2.1/Files/ea002e626aee6bc6643e8ab5f998e5e4: -------------------------------------------------------------------------------- 1 | K 10 2 | ascii_cert 3 | V 2416 4 | 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 5 | K 8 6 | failures 7 | V 1 8 | 8 9 | K 15 10 | svn:realmstring 11 | V 40 12 | https://svn-ccsm-models.cgd.ucar.edu:443 13 | END 14 | -------------------------------------------------------------------------------- /CESM/2.2/Dockerfile: -------------------------------------------------------------------------------- 1 | ############################## 2 | # ESCOMP/CESM/2.2 Dockerfile # 3 | ############################## 4 | 5 | # Use the ESCOMP centos8 base - this is a base install of CentOS, plus NetCDF/HDF5/PNetCDF/MPICH 6 | FROM escomp/base:centos8 7 | 8 | # Install CESM: 9 | COPY Files/ea002e626aee6bc6643e8ab5f998e5e4 /root/.subversion/auth/svn.ssl.server/ 10 | RUN sudo mkdir -p /opt/ncar && \ 11 | cd /opt/ncar && \ 12 | sudo git clone -b release-cesm2.2.0 https://github.com/ESCOMP/cesm.git cesm2 && \ 13 | cd cesm2 && \ 14 | sudo ./manage_externals/checkout_externals 15 | 16 | # Set up the environment - create the group and user, the shell variables, the input data directory and sudo access: 17 | RUN sudo echo 'export CESMDATAROOT=${HOME}' | sudo tee /etc/profile.d/escomp.sh && \ 18 | sudo echo 'export CIME_MACHINE=container' | sudo tee -a /etc/profile.d/escomp.sh && \ 19 | sudo echo 'export USER=$(whoami)' | sudo tee -a /etc/profile.d/escomp.sh && \ 20 | sudo echo 'export PS1="[\u@cesm2.2 \W]\$ "' | sudo tee -a /etc/profile.d/escomp.sh && \ 21 | sudo echo 'ulimit -s unlimited' | sudo tee -a /etc/profile.d/escomp.sh && \ 22 | sudo echo 'export PATH=${PATH}:/opt/ncar/cesm2/cime/scripts' | sudo tee -a /etc/profile.d/escomp.sh 23 | 24 | 25 | # Add the container versions of the config_machines & config_compilers settings - later, integrate these into CIME 26 | COPY Files/config_compilers.xml /opt/ncar/cesm2/cime/config/cesm/machines/ 27 | COPY Files/config_machines.xml /opt/ncar/cesm2/cime/config/cesm/machines/ 28 | COPY Files/config_inputdata.xml /opt/ncar/cesm2/cime/config/cesm/ 29 | COPY Files/case_setup.py /opt/ncar/cesm2/cime/scripts/lib/CIME/case/case_setup.py 30 | 31 | # Add the container changes to the XML files (to be included in stock CIME soon): 32 | COPY Files/config_compsets.xml /opt/ncar/cesm2/cime_config/ 33 | COPY Files/config_pes.xml /opt/ncar/cesm2/cime_config/ 34 | COPY Files/configs/cam/config_pes.xml /opt/ncar/cesm2/components/cam/cime_config/ 35 | COPY Files/configs/cice/config_pes.xml /opt/ncar/cesm2/components/cice/cime_config/ 36 | COPY Files/configs/cism/config_pes.xml /opt/ncar/cesm2/components/cism/cime_config/ 37 | COPY Files/configs/pop/config_pes.xml /opt/ncar/cesm2/components/pop/cime_config/ 38 | COPY Files/configs/clm/config_pes.xml /opt/ncar/cesm2/components/clm/cime_config/ 39 | 40 | # Fix for SCAM with GNU in DEBUG mode (ESCOMP/CAM issue #257) 41 | COPY Files/micro_mg3_0.F90 /opt/ncar/cesm2/components/cam/src/physics/pumas/micro_mg3_0.F90 42 | 43 | # Fix for issue with mpi-serial: 44 | COPY Files/scam_shell_commands /opt/ncar/cesm2/components/cam/cime_config/usermods_dirs/scam_mandatory/shell_commands 45 | 46 | # And add the fixed 'create_scam6_iop' script for SCAM: 47 | COPY Files/create_scam6_iop /opt/ncar/cesm2/components/cam/bld/scripts 48 | 49 | ENV CESMROOT=/opt/ncar/cesm2 50 | 51 | CMD ["/bin/bash", "-l"] 52 | -------------------------------------------------------------------------------- /CESM/2.2/Files/case_setup.py: -------------------------------------------------------------------------------- 1 | """ 2 | Library for case.setup. 3 | case_setup is a member of class Case from file case.py 4 | """ 5 | 6 | from CIME.XML.standard_module_setup import * 7 | 8 | from CIME.XML.machines import Machines 9 | from CIME.BuildTools.configure import configure 10 | from CIME.utils import get_cime_root, run_and_log_case_status, get_model, get_batch_script_for_job, safe_copy 11 | from CIME.test_status import * 12 | from CIME.locked_files import unlock_file, lock_file 13 | 14 | logger = logging.getLogger(__name__) 15 | 16 | ############################################################################### 17 | def _build_usernl_files(case, model, comp): 18 | ############################################################################### 19 | """ 20 | Create user_nl_xxx files, expects cwd is caseroot 21 | """ 22 | model = model.upper() 23 | if model == "DRV": 24 | model_file = case.get_value("CONFIG_CPL_FILE") 25 | else: 26 | model_file = case.get_value("CONFIG_{}_FILE".format(model)) 27 | expect(model_file is not None, 28 | "Could not locate CONFIG_{}_FILE in config_files.xml".format(model)) 29 | model_dir = os.path.dirname(model_file) 30 | 31 | expect(os.path.isdir(model_dir), 32 | "cannot find cime_config directory {} for component {}".format(model_dir, comp)) 33 | comp_interface = case.get_value("COMP_INTERFACE") 34 | multi_driver = case.get_value("MULTI_DRIVER") 35 | ninst = 1 36 | 37 | if multi_driver: 38 | ninst_max = case.get_value("NINST_MAX") 39 | if comp_interface != "nuopc" and model not in ("DRV","CPL","ESP"): 40 | ninst_model = case.get_value("NINST_{}".format(model)) 41 | expect(ninst_model==ninst_max,"MULTI_DRIVER mode, all components must have same NINST value. NINST_{} != {}".format(model,ninst_max)) 42 | if comp == "cpl": 43 | if not os.path.exists("user_nl_cpl"): 44 | safe_copy(os.path.join(model_dir, "user_nl_cpl"), ".") 45 | else: 46 | if comp_interface == "nuopc": 47 | ninst = case.get_value("NINST") 48 | elif ninst == 1: 49 | ninst = case.get_value("NINST_{}".format(model)) 50 | nlfile = "user_nl_{}".format(comp) 51 | model_nl = os.path.join(model_dir, nlfile) 52 | if ninst > 1: 53 | for inst_counter in range(1, ninst+1): 54 | inst_nlfile = "{}_{:04d}".format(nlfile, inst_counter) 55 | if not os.path.exists(inst_nlfile): 56 | # If there is a user_nl_foo in the case directory, copy it 57 | # to user_nl_foo_INST; otherwise, copy the original 58 | # user_nl_foo from model_dir 59 | if os.path.exists(nlfile): 60 | safe_copy(nlfile, inst_nlfile) 61 | elif os.path.exists(model_nl): 62 | safe_copy(model_nl, inst_nlfile) 63 | else: 64 | # ninst = 1 65 | if not os.path.exists(nlfile): 66 | if os.path.exists(model_nl): 67 | safe_copy(model_nl, nlfile) 68 | 69 | ############################################################################### 70 | def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False, keep=None): 71 | ############################################################################### 72 | os.chdir(caseroot) 73 | 74 | non_local = case.get_value("NONLOCAL") 75 | 76 | models = case.get_values("COMP_CLASSES") 77 | mach = case.get_value("MACH") 78 | compiler = case.get_value("COMPILER") 79 | debug = case.get_value("DEBUG") 80 | mpilib = case.get_value("MPILIB") 81 | sysos = case.get_value("OS") 82 | comp_interface = case.get_value("COMP_INTERFACE") 83 | extra_machines_dir = case.get_value("EXTRA_MACHDIR") 84 | expect(mach is not None, "xml variable MACH is not set") 85 | 86 | # Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests 87 | if not non_local: 88 | din_loc_root = case.get_value("DIN_LOC_ROOT") 89 | if case.get_value("MACH") == "container": 90 | if not os.path.isdir(din_loc_root): 91 | logger.info("Making inputdata directory: {}".format(din_loc_root)) 92 | os.mkdir(din_loc_root) 93 | testcase = case.get_value("TESTCASE") 94 | expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"), 95 | "inputdata root is not a directory or is not readable: {}".format(din_loc_root)) 96 | 97 | # Remove batch scripts 98 | if reset or clean: 99 | # clean setup-generated files 100 | batch_script = get_batch_script_for_job(case.get_primary_job()) 101 | files_to_clean = [batch_script, "env_mach_specific.xml", "Macros.make", "Macros.cmake"] 102 | for file_to_clean in files_to_clean: 103 | if os.path.exists(file_to_clean) and not (keep and file_to_clean in keep): 104 | os.remove(file_to_clean) 105 | logger.info("Successfully cleaned {}".format(file_to_clean)) 106 | 107 | if not test_mode: 108 | # rebuild the models (even on restart) 109 | case.set_value("BUILD_COMPLETE", False) 110 | 111 | # Cannot leave case in bad state (missing env_mach_specific.xml) 112 | if clean and not os.path.isfile("env_mach_specific.xml"): 113 | case.flush() 114 | configure(Machines(machine=mach, extra_machines_dir=extra_machines_dir), 115 | caseroot, ["Makefile"], compiler, mpilib, debug, comp_interface, sysos, noenv=True, 116 | extra_machines_dir=extra_machines_dir) 117 | case.read_xml() 118 | 119 | if not clean: 120 | if not non_local: 121 | case.load_env() 122 | 123 | # creates the Macros.make, Depends.compiler, Depends.machine, Depends.machine.compiler 124 | # and env_mach_specific.xml if they don't already exist. 125 | if not os.path.isfile("Macros.make") or not os.path.isfile("env_mach_specific.xml"): 126 | reread = not os.path.isfile("env_mach_specific.xml") 127 | if reread: 128 | case.flush() 129 | configure(Machines(machine=mach, extra_machines_dir=extra_machines_dir), 130 | caseroot, ["Makefile"], compiler, mpilib, debug, comp_interface, sysos, noenv=True, 131 | extra_machines_dir=extra_machines_dir) 132 | if reread: 133 | case.read_xml() 134 | 135 | # Also write out Cmake macro file 136 | if not os.path.isfile("Macros.cmake"): 137 | configure(Machines(machine=mach, extra_machines_dir=extra_machines_dir), 138 | caseroot, ["CMake"], compiler, mpilib, debug, comp_interface, sysos, noenv=True, 139 | extra_machines_dir=extra_machines_dir) 140 | 141 | # Set tasks to 1 if mpi-serial library 142 | if mpilib == "mpi-serial": 143 | case.set_value("NTASKS", 1) 144 | 145 | # Check ninst. 146 | # In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component. 147 | comp_interface = case.get_value("COMP_INTERFACE") 148 | if comp_interface == "nuopc": 149 | ninst = case.get_value("NINST") 150 | 151 | multi_driver = case.get_value("MULTI_DRIVER") 152 | 153 | for comp in models: 154 | ntasks = case.get_value("NTASKS_{}".format(comp)) 155 | if comp == "CPL": 156 | continue 157 | if comp_interface != "nuopc": 158 | ninst = case.get_value("NINST_{}".format(comp)) 159 | if multi_driver: 160 | if comp_interface != "nuopc": 161 | expect(case.get_value("NINST_LAYOUT_{}".format(comp)) == "concurrent", 162 | "If multi_driver is TRUE, NINST_LAYOUT_{} must be concurrent".format(comp)) 163 | case.set_value("NTASKS_PER_INST_{}".format(comp), ntasks) 164 | else: 165 | if ninst > ntasks: 166 | if ntasks == 1: 167 | case.set_value("NTASKS_{}".format(comp), ninst) 168 | ntasks = ninst 169 | else: 170 | expect(False, "NINST_{comp} value {ninst} greater than NTASKS_{comp} {ntasks}".format(comp=comp, ninst=ninst, ntasks=ntasks)) 171 | 172 | case.set_value("NTASKS_PER_INST_{}".format(comp), max(1,int(ntasks / ninst))) 173 | 174 | if os.path.exists(get_batch_script_for_job(case.get_primary_job())): 175 | logger.info("Machine/Decomp/Pes configuration has already been done ...skipping") 176 | 177 | case.initialize_derived_attributes() 178 | 179 | case.set_value("SMP_PRESENT", case.get_build_threaded()) 180 | 181 | else: 182 | case.check_pelayouts_require_rebuild(models) 183 | 184 | unlock_file("env_build.xml") 185 | unlock_file("env_batch.xml") 186 | 187 | case.flush() 188 | case.check_lockedfiles() 189 | 190 | case.initialize_derived_attributes() 191 | 192 | cost_per_node = case.get_value("COSTPES_PER_NODE") 193 | case.set_value("COST_PES", case.num_nodes * cost_per_node) 194 | threaded = case.get_build_threaded() 195 | case.set_value("SMP_PRESENT", threaded) 196 | if threaded and case.total_tasks * case.thread_count > cost_per_node: 197 | smt_factor = max(1.0,int(case.get_value("MAX_TASKS_PER_NODE") / cost_per_node)) 198 | case.set_value("TOTALPES", int(case.total_tasks * max(1.0,float(case.thread_count) / smt_factor))) 199 | else: 200 | case.set_value("TOTALPES", case.total_tasks*case.thread_count) 201 | 202 | # May need to select new batch settings if pelayout changed (e.g. problem is now too big for prev-selected queue) 203 | env_batch = case.get_env("batch") 204 | env_batch.set_job_defaults([(case.get_primary_job(), {})], case) 205 | 206 | # create batch files 207 | env_batch.make_all_batch_files(case) 208 | if get_model() == "e3sm" and not case.get_value("TEST"): 209 | input_batch_script = os.path.join(case.get_value("MACHDIR"), "template.case.run.sh") 210 | env_batch.make_batch_script(input_batch_script, "case.run", case, outfile=get_batch_script_for_job("case.run.sh")) 211 | 212 | # Make a copy of env_mach_pes.xml in order to be able 213 | # to check that it does not change once case.setup is invoked 214 | case.flush() 215 | logger.debug("at copy TOTALPES = {}".format(case.get_value("TOTALPES"))) 216 | lock_file("env_mach_pes.xml") 217 | lock_file("env_batch.xml") 218 | 219 | # Create user_nl files for the required number of instances 220 | if not os.path.exists("user_nl_cpl"): 221 | logger.info("Creating user_nl_xxx files for components and cpl") 222 | 223 | # loop over models 224 | for model in models: 225 | comp = case.get_value("COMP_{}".format(model)) 226 | logger.debug("Building {} usernl files".format(model)) 227 | _build_usernl_files(case, model, comp) 228 | if comp == "cism": 229 | glcroot = case.get_value("COMP_ROOT_DIR_GLC") 230 | run_cmd_no_fail("{}/cime_config/cism.template {}".format(glcroot, caseroot)) 231 | 232 | _build_usernl_files(case, "drv", "cpl") 233 | 234 | # Create needed directories for case 235 | case.create_dirs() 236 | 237 | logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building") 238 | 239 | # Some tests need namelists created here (ERP) - so do this if we are in test mode 240 | if (test_mode or get_model() == "e3sm") and not non_local: 241 | logger.info("Generating component namelists as part of setup") 242 | case.create_namelists() 243 | 244 | # Record env information 245 | env_module = case.get_env("mach_specific") 246 | env_module.make_env_mach_specific_file("sh", case) 247 | env_module.make_env_mach_specific_file("csh", case) 248 | if not non_local: 249 | env_module.save_all_env_info("software_environment.txt") 250 | 251 | logger.info("You can now run './preview_run' to get more info on how your case will be run") 252 | 253 | ############################################################################### 254 | def case_setup(self, clean=False, test_mode=False, reset=False, keep=None): 255 | ############################################################################### 256 | caseroot, casebaseid = self.get_value("CASEROOT"), self.get_value("CASEBASEID") 257 | phase = "setup.clean" if clean else "case.setup" 258 | functor = lambda: _case_setup_impl(self, caseroot, clean=clean, test_mode=test_mode, reset=reset, keep=keep) 259 | 260 | if self.get_value("TEST") and not test_mode: 261 | test_name = casebaseid if casebaseid is not None else self.get_value("CASE") 262 | with TestStatus(test_dir=caseroot, test_name=test_name) as ts: 263 | try: 264 | run_and_log_case_status(functor, phase, caseroot=caseroot) 265 | except BaseException: # Want to catch KeyboardInterrupt too 266 | ts.set_status(SETUP_PHASE, TEST_FAIL_STATUS) 267 | raise 268 | else: 269 | if clean: 270 | ts.set_status(SETUP_PHASE, TEST_PEND_STATUS) 271 | else: 272 | ts.set_status(SETUP_PHASE, TEST_PASS_STATUS) 273 | else: 274 | run_and_log_case_status(functor, phase, caseroot=caseroot) 275 | -------------------------------------------------------------------------------- /CESM/2.2/Files/config_compsets.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | ========================================= 7 | compset naming convention 8 | ========================================= 9 | The compset longname below has the specified order 10 | atm, lnd, ice, ocn, river, glc wave cesm-options 11 | 12 | The notation for the compset longname is 13 | TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_ESP%phys][_BGC%phys] 14 | Where for the specific compsets below the following is supported 15 | TIME = Time period (e.g. 2000, HIST, RCP8...) 16 | ATM = [CAM40, CAM50, CAM60] 17 | LND = [CLM45, CLM50, SLND] 18 | ICE = [CICE, DICE, SICE] 19 | OCN = [DOCN, ,AQUAP, SOCN] 20 | ROF = [RTM, MOSART, SROF] 21 | GLC = [CISM1, CISM2, SGLC] 22 | WAV = [WW3, DWAV, XWAV, SWAV] 23 | ESP = [SESP] 24 | BGC = optional BGC scenario 25 | 26 | The OPTIONAL %phys attributes specify submodes of the given system 27 | For example DOCN%DOM is the data ocean model for DOCN 28 | ALL the possible %phys choices for each component are listed. 29 | ALL data models must have a %phys option that corresponds to the data model mode 30 | 31 | Each compset node is associated with the following elements 32 | - lname 33 | - alias 34 | - support (optional description of the support level for this compset) 35 | Each compset node can also have the following attributes 36 | - grid (optional regular expression match for grid to work with the compset) 37 | 38 | 39 | 40 | 41 | 42 | B1850 43 | 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD 44 | 45 | 46 | 47 | 48 | B1850C4_Tutorial 49 | B1850_CAM40_CLM50%SP_CICE_POP2%ECO_MOSART_CISM2%NOEVOLVE_SWAV_BGC%BDRD 50 | 51 | 52 | 53 | 54 | BW1850 55 | 1850_CAM60%WCTS_CLM50%BGC-CROP_CICE_POP2%ECO%NDEP_MOSART_CISM2%NOEVOLVE_WW3 56 | 57 | 58 | BWma1850 59 | 1850_CAM60%WCCM_CLM50%BGC-CROP_CICE_POP2%ECO%NDEP_MOSART_CISM2%NOEVOLVE_WW3 60 | 61 | 62 | 63 | BHIST 64 | HIST_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO_MOSART_CISM2%NOEVOLVE_WW3_BGC%BDRD 65 | 66 | 67 | 68 | 69 | 70 | B1850G 71 | 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO_MOSART_CISM2%EVOLVE_WW3_BGC%BDRD 72 | 73 | 74 | 77 | 78 | B1850G1 79 | 1850_CAM60_CLM50%BGC-CROP_CICE_POP2%ECO_MOSART_CISM1%EVOLVE_WW3_BGC%BDRD 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | ETEST 95 | 2000_CAM60_CLM50%SP_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST 96 | 97 | 98 | 99 | E1850TEST 100 | 1850_CAM60_CLM50%SP_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST 101 | 102 | 103 | 104 | 105 | 107 | B1850MOM 108 | 1850_CAM60_CLM50%BGC-CROP_CICE_MOM6_MOSART_CISM2%NOEVOLVE_SWAV_BGC%BDRD 109 | 110 | 111 | 113 | 114 | 115 | J1850G 116 | 1850_DATM%CRUv7_CLM50%BGC-CROP_CICE_POP2_MOSART_CISM2%EVOLVE_SWAV 117 | 118 | 119 | 120 | 121 | 122 | 0001-01-01 123 | 0001-01-01 124 | 1850-01-01 125 | 1955-01-01 126 | 2005-01-01 127 | 2013-01-01 128 | 129 | 130 | 131 | 132 | 133 | -------------------------------------------------------------------------------- /CESM/2.2/Files/config_inputdata.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 17 | 18 | 19 | wget 20 |
ftp://cesm-inputdata-lowres1.cgd.ucar.edu/cesm/low-res/
21 | anonymous 22 | user@example.edu 23 | ../inputdata_checksum.dat 24 | 25 | 26 | 27 | wget 28 |
ftp://ftp.cgd.ucar.edu/cesm/inputdata/
29 | anonymous 30 | user@example.edu 31 | ../inputdata_checksum.dat 32 | 33 | 34 | 35 | ftp requires the python package ftplib 36 | ftp 37 |
ftp.cgd.ucar.edu/cesm/inputdata
38 | anonymous 39 | user@example.edu 40 | ../inputdata_checksum.dat 41 | 42 | 43 | 44 | svn 45 |
https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata
46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /CESM/2.2/Files/configs/cam/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -1 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | 17 | 18 | 1 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 27 | 28 | 0 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | -2 46 | -2 47 | -2 48 | -40 49 | -40 50 | -2 51 | -2 52 | -2 53 | 54 | 55 | 2 56 | 2 57 | 2 58 | 2 59 | 2 60 | 2 61 | 2 62 | 2 63 | 64 | 65 | 0 66 | -2 67 | -4 68 | 0 69 | 0 70 | -6 71 | -8 72 | -10 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | -2 83 | -2 84 | -2 85 | -2 86 | -2 87 | -2 88 | -2 89 | -2 90 | 91 | 92 | 1 93 | 1 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 101 | 102 | 0 103 | 0 104 | 0 105 | 0 106 | 0 107 | 0 108 | 0 109 | 0 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | -4 119 | -4 120 | -4 121 | -4 122 | -4 123 | -4 124 | -4 125 | -4 126 | 127 | 128 | 2 129 | 2 130 | 2 131 | 2 132 | 2 133 | 2 134 | 2 135 | 2 136 | 137 | 138 | 0 139 | 0 140 | 0 141 | 0 142 | 0 143 | 0 144 | 0 145 | 0 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | -4 155 | -4 156 | -4 157 | -4 158 | -4 159 | -4 160 | -4 161 | -4 162 | 163 | 164 | 2 165 | 2 166 | 2 167 | 2 168 | 2 169 | 2 170 | 2 171 | 2 172 | 173 | 174 | 0 175 | 0 176 | 0 177 | 0 178 | 0 179 | 0 180 | 0 181 | 0 182 | 183 | 184 | 185 | 186 | 187 | 188 | -4 189 | -4 190 | -4 191 | -4 192 | -4 193 | -4 194 | -4 195 | -4 196 | 197 | 198 | 1 199 | 1 200 | 1 201 | 1 202 | 1 203 | 1 204 | 1 205 | 1 206 | 207 | 208 | 0 209 | 0 210 | 0 211 | 0 212 | 0 213 | 0 214 | 0 215 | 0 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 30 226 | 30 227 | 30 228 | 30 229 | 30 230 | 30 231 | 30 232 | 30 233 | 234 | 235 | 2 236 | 2 237 | 2 238 | 2 239 | 2 240 | 2 241 | 2 242 | 2 243 | 244 | 245 | 0 246 | 0 247 | 0 248 | 0 249 | 0 250 | 0 251 | 0 252 | 0 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 60 262 | 60 263 | 60 264 | 60 265 | 60 266 | 60 267 | 60 268 | 60 269 | 270 | 271 | 2 272 | 2 273 | 2 274 | 2 275 | 2 276 | 2 277 | 2 278 | 2 279 | 280 | 281 | 0 282 | 0 283 | 0 284 | 0 285 | 0 286 | 0 287 | 0 288 | 0 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 60 298 | 60 299 | 60 300 | 60 301 | 60 302 | 60 303 | 60 304 | 60 305 | 306 | 307 | 2 308 | 2 309 | 2 310 | 2 311 | 2 312 | 2 313 | 2 314 | 2 315 | 316 | 317 | 0 318 | 0 319 | 0 320 | 0 321 | 0 322 | 0 323 | 0 324 | 0 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | -------------------------------------------------------------------------------- /CESM/2.2/Files/configs/cice/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -1 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | 17 | 18 | 1 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 27 | 28 | 0 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | -2 46 | -2 47 | -2 48 | -40 49 | -40 50 | -2 51 | -2 52 | -2 53 | 54 | 55 | 2 56 | 2 57 | 2 58 | 2 59 | 2 60 | 2 61 | 2 62 | 2 63 | 64 | 65 | 0 66 | -2 67 | -4 68 | 0 69 | 0 70 | -6 71 | -8 72 | -10 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | -2 83 | -2 84 | -2 85 | -2 86 | -2 87 | -2 88 | -2 89 | -2 90 | 91 | 92 | 1 93 | 1 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 101 | 102 | 0 103 | 0 104 | 0 105 | 0 106 | 0 107 | 0 108 | 0 109 | 0 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | -4 119 | -4 120 | -4 121 | -4 122 | -4 123 | -4 124 | -4 125 | -4 126 | 127 | 128 | 2 129 | 2 130 | 2 131 | 2 132 | 2 133 | 2 134 | 2 135 | 2 136 | 137 | 138 | 0 139 | 0 140 | 0 141 | 0 142 | 0 143 | 0 144 | 0 145 | 0 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | -4 155 | -4 156 | -4 157 | -4 158 | -4 159 | -4 160 | -4 161 | -4 162 | 163 | 164 | 2 165 | 2 166 | 2 167 | 2 168 | 2 169 | 2 170 | 2 171 | 2 172 | 173 | 174 | 0 175 | 0 176 | 0 177 | 0 178 | 0 179 | 0 180 | 0 181 | 0 182 | 183 | 184 | 185 | 186 | 187 | 188 | -4 189 | -4 190 | -4 191 | -4 192 | -4 193 | -4 194 | -4 195 | -4 196 | 197 | 198 | 1 199 | 1 200 | 1 201 | 1 202 | 1 203 | 1 204 | 1 205 | 1 206 | 207 | 208 | 0 209 | 0 210 | 0 211 | 0 212 | 0 213 | 0 214 | 0 215 | 0 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 30 226 | 30 227 | 30 228 | 30 229 | 30 230 | 30 231 | 30 232 | 30 233 | 234 | 235 | 2 236 | 2 237 | 2 238 | 2 239 | 2 240 | 2 241 | 2 242 | 2 243 | 244 | 245 | 0 246 | 0 247 | 0 248 | 0 249 | 0 250 | 0 251 | 0 252 | 0 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 60 262 | 60 263 | 60 264 | 60 265 | 60 266 | 60 267 | 60 268 | 60 269 | 270 | 271 | 2 272 | 2 273 | 2 274 | 2 275 | 2 276 | 2 277 | 2 278 | 2 279 | 280 | 281 | 0 282 | 0 283 | 0 284 | 0 285 | 0 286 | 0 287 | 0 288 | 0 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 60 298 | 60 299 | 60 300 | 60 301 | 60 302 | 60 303 | 60 304 | 60 305 | 306 | 307 | 2 308 | 2 309 | 2 310 | 2 311 | 2 312 | 2 313 | 2 314 | 2 315 | 316 | 317 | 0 318 | 0 319 | 0 320 | 0 321 | 0 322 | 0 323 | 0 324 | 0 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | -------------------------------------------------------------------------------- /CESM/2.2/Files/configs/cism/config_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | none 8 | 9 | -1 10 | -1 11 | -1 12 | -1 13 | -1 14 | -1 15 | -1 16 | -1 17 | 18 | 19 | 1 20 | 1 21 | 1 22 | 1 23 | 1 24 | 1 25 | 1 26 | 1 27 | 28 | 29 | 0 30 | 0 31 | 0 32 | 0 33 | 0 34 | 0 35 | 0 36 | 0 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | none 46 | 47 | 1 48 | 1 49 | 1 50 | 1 51 | 1 52 | 1 53 | 1 54 | 1 55 | 56 | 57 | 1 58 | 1 59 | 1 60 | 1 61 | 1 62 | 1 63 | 1 64 | 1 65 | 66 | 67 | 0 68 | 0 69 | 0 70 | 0 71 | 0 72 | 0 73 | 0 74 | 0 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | none 83 | 84 | -1 85 | -1 86 | -1 87 | -1 88 | -1 89 | -1 90 | -1 91 | -1 92 | 93 | 94 | 1 95 | 1 96 | 1 97 | 1 98 | 1 99 | 1 100 | 1 101 | 1 102 | 103 | 104 | 0 105 | 0 106 | 0 107 | 0 108 | 0 109 | 0 110 | 0 111 | 0 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | none 120 | 121 | -8 122 | -8 123 | -8 124 | -8 125 | -8 126 | -8 127 | -8 128 | -8 129 | 130 | 131 | 1 132 | 1 133 | 1 134 | 1 135 | 1 136 | 1 137 | 1 138 | 1 139 | 140 | 141 | 0 142 | 0 143 | 0 144 | 0 145 | 0 146 | 0 147 | 0 148 | 0 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | none 157 | 158 | -2 159 | -2 160 | -2 161 | -2 162 | -2 163 | -2 164 | -2 165 | -2 166 | 167 | 168 | 1 169 | 1 170 | 1 171 | 1 172 | 1 173 | 1 174 | 1 175 | 1 176 | 177 | 178 | 0 179 | 0 180 | 0 181 | 0 182 | 0 183 | 0 184 | 0 185 | 0 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | -------------------------------------------------------------------------------- /CESM/2.2/Files/create_scam6_iop: -------------------------------------------------------------------------------- 1 | #!/bin/csh -fv 2 | 3 | #********************************************************************** 4 | # Run SCAM with a single IOP 5 | # This script will build and run one IOP 6 | # If a user wishes to run more than one IOP, use create_scam6_iop_multi 7 | # 8 | # Usage: 9 | # ./create_scam6_iop # where IOP name is from list below 10 | # - or - 11 | # ./create_scam6_iop # IOP is specified in the script below 12 | #********************************************************************** 13 | 14 | #------------------ 15 | # User sets options in this section 16 | #------------------ 17 | 18 | ### Full path of cesm source code and case (output) directories (see examples) 19 | 20 | # set CESMDIR=/project/amp/$USER/collections/cam5_4_175 21 | # set CASEDIR=/project/amp/$USER/cases 22 | set CESMDIR=/opt/ncar/cesm2 23 | set CASEDIR=${HOME} 24 | 25 | ### Case Name 26 | 27 | #set CASETITLE=scam_test 28 | set CASETITLE=scam_case 29 | 30 | ### Set location of user source mods (if any) 31 | setenv this_dir `pwd` 32 | setenv usrsrc ${this_dir}/mods/$CASETITLE 33 | 34 | ### Standard Run Settings 35 | set RES=T42_T42 36 | set COMPSET=FSCAM 37 | set COMPILER=gnu 38 | 39 | ### Set Desired IOP 40 | ### $1 means read from command line. Or put one of the names in: 41 | ### arm95 arm97 atex bomex cgilsS11 cgilsS12 cgilsS6 dycomsRF01 dycomsRF02 gateIII mpace rico sparticus togaII twp06 42 | 43 | if ($#argv == 0) then 44 | set IOP = arm97 45 | else 46 | set IOP = $1 47 | endif 48 | 49 | #------------------ 50 | # User should not need to set any options in this section 51 | #------------------ 52 | 53 | cd $CASEDIR 54 | 55 | set IOPNAME = scam_$IOP 56 | 57 | ## location of IOP data in CESM Tag 58 | set MODSDIR = $CESMDIR/components/cam/cime_config/usermods_dirs 59 | 60 | #Create full casename 61 | set CASENAME=${CASETITLE}.${COMPSET}.${IOP} 62 | 63 | #------------------ 64 | # create case 65 | #------------------ 66 | 67 | $CESMDIR/cime/scripts/create_newcase --compset $COMPSET --res $RES --compiler $COMPILER --case $CASEDIR/$CASENAME --user-mods-dir ${MODSDIR}/${IOPNAME} --run-unsupported 68 | 69 | cd $CASEDIR/$CASENAME 70 | 71 | ### Set build and run directories to be under case directory. 72 | 73 | set RUNDIR=${CASEDIR}/${CASENAME}/run 74 | ./xmlchange RUNDIR=$RUNDIR 75 | 76 | ./xmlchange EXEROOT=${CASEDIR}/${CASENAME}/bld 77 | 78 | #------------------ 79 | # XMLCHANGE OPTIONS HERE 80 | #------------------ 81 | 82 | ### Append to CAM configure options 83 | # ./xmlchange --append CAM_CONFIG_OPTS=' ' 84 | 85 | ### DEBUG 86 | #./xmlchange DEBUG='TRUE' 87 | 88 | #------------------ 89 | # Setup Case 90 | #------------------ 91 | 92 | ./case.setup 93 | # ./case.setup -d -v #-d -v for verbose and debug file 94 | 95 | #------------------ 96 | # source mods: copy them into case directory 97 | #------------------ 98 | 99 | /bin/cp ${usrsrc}/* SourceMods/src.cam/ 100 | 101 | #------------------ 102 | # Build 103 | #------------------ 104 | 105 | ./case.build 106 | # ./case.build -d -v #-d -v for verbose and debug file 107 | 108 | ### make timing dir kludge [REMOVE WHEN FIXED] 109 | mkdir -p $RUNDIR/timing/checkpoints 110 | 111 | #------------------ 112 | # Add all user specific cam namelist changes here 113 | # 114 | # Users should add all user specific namelist changes below in the form of 115 | # namelist_var = new_namelist_value 116 | # Namelist settings which appear in usermods_dir and here will use the values 117 | # specified below 118 | # Other namelist settings from usermods_dirs will be unchanged 119 | # Output can also be specified here (e.g. fincl1) 120 | #------------------ 121 | 122 | cat >> user_nl_cam << EOF 123 | use_topo_file = .true. 124 | mfilt = 2500 125 | nhtfrq = 1 126 | fincl1= 'CDNUMC', 'AQSNOW','ANSNOW','FREQSL','LS_FLXPRC' 127 | EOF 128 | 129 | #------------------ 130 | # Choose type of job submission (batch or interactive) 131 | #------------------ 132 | 133 | ### Submit to Queue (If you have one) 134 | ./case.submit 135 | 136 | ### OR you can run interactively instead of going through the queue 137 | #cd $RUNDIR 138 | #../bld/cesm.exe 139 | 140 | 141 | 142 | -------------------------------------------------------------------------------- /CESM/2.2/Files/ea002e626aee6bc6643e8ab5f998e5e4: -------------------------------------------------------------------------------- 1 | K 10 2 | ascii_cert 3 | V 2416 4 | 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 5 | K 8 6 | failures 7 | V 1 8 | 8 9 | K 15 10 | svn:realmstring 11 | V 40 12 | https://svn-ccsm-models.cgd.ucar.edu:443 13 | END 14 | -------------------------------------------------------------------------------- /CESM/2.2/Files/machines.py: -------------------------------------------------------------------------------- 1 | """ 2 | Interface to the config_machines.xml file. This class inherits from GenericXML.py 3 | """ 4 | from CIME.XML.standard_module_setup import * 5 | from CIME.XML.generic_xml import GenericXML 6 | from CIME.XML.files import Files 7 | from CIME.utils import convert_to_unknown_type, get_cime_config, get_all_cime_models 8 | 9 | import socket 10 | 11 | logger = logging.getLogger(__name__) 12 | 13 | class Machines(GenericXML): 14 | 15 | def __init__(self, infile=None, files=None, machine=None, extra_machines_dir=None): 16 | """ 17 | initialize an object 18 | if a filename is provided it will be used, 19 | otherwise if a files object is provided it will be used 20 | otherwise create a files object from default values 21 | 22 | If extra_machines_dir is provided, it should be a string giving a path to an 23 | additional directory that will be searched for a config_machines.xml file; if 24 | found, the contents of this file will be appended to the standard 25 | config_machines.xml. An empty string is treated the same as None. 26 | """ 27 | 28 | self.machine_node = None 29 | self.machine = None 30 | self.machines_dir = None 31 | self.custom_settings = {} 32 | schema = None 33 | supported_models = [] 34 | if files is None: 35 | files = Files() 36 | if infile is None: 37 | infile = files.get_value("MACHINES_SPEC_FILE") 38 | schema = files.get_schema("MACHINES_SPEC_FILE") 39 | logger.debug("Verifying using schema {}".format(schema)) 40 | 41 | self.machines_dir = os.path.dirname(infile) 42 | 43 | GenericXML.__init__(self, infile, schema) 44 | 45 | # Append the contents of $HOME/.cime/config_machines.xml if it exists. 46 | # 47 | # Also append the contents of a config_machines.xml file in the directory given by 48 | # extra_machines_dir, if present. 49 | # 50 | # This could cause problems if node matches are repeated when only one is expected. 51 | local_infile = os.path.join(os.environ.get("HOME"),".cime","config_machines.xml") 52 | logger.debug("Infile: {}".format(local_infile)) 53 | if os.path.exists(local_infile): 54 | GenericXML.read(self, local_infile, schema) 55 | if extra_machines_dir: 56 | local_infile = os.path.join(extra_machines_dir, "config_machines.xml") 57 | logger.debug("Infile: {}".format(local_infile)) 58 | if os.path.exists(local_infile): 59 | GenericXML.read(self, local_infile, schema) 60 | 61 | if machine is None: 62 | if "CIME_MACHINE" in os.environ: 63 | machine = os.environ["CIME_MACHINE"] 64 | else: 65 | cime_config = get_cime_config() 66 | if cime_config.has_option("main", "machine"): 67 | machine = cime_config.get("main", "machine") 68 | if machine is None: 69 | machine = self.probe_machine_name() 70 | if machine is None: 71 | for potential_model in get_all_cime_models(): 72 | local_infile = os.path.join(get_cime_root(), "config",potential_model,"machines","config_machines.xml") 73 | if local_infile != infile: 74 | GenericXML.read(self, local_infile, schema) 75 | if self.probe_machine_name() is not None: 76 | supported_models.append(potential_model) 77 | GenericXML.change_file(self, infile, schema) 78 | 79 | expect(machine is not None, "Could not initialize machine object from {} or {}. This machine is not available for the target CIME_MODEL. The supported CIME_MODELS that can be used are: {}".format(infile, local_infile, supported_models)) 80 | self.set_machine(machine) 81 | 82 | def get_child(self, name=None, attributes=None, root=None, err_msg=None): 83 | if root is None: 84 | root = self.machine_node 85 | return super(Machines, self).get_child(name, attributes, root, err_msg) 86 | 87 | def get_machines_dir(self): 88 | """ 89 | Return the directory of the machines file 90 | """ 91 | return self.machines_dir 92 | 93 | def get_machine_name(self): 94 | """ 95 | Return the name of the machine 96 | """ 97 | return self.machine 98 | 99 | def get_node_names(self): 100 | """ 101 | Return the names of all the child nodes for the target machine 102 | """ 103 | nodes = self.get_children(root=self.machine_node) 104 | node_names = [] 105 | for node in nodes: 106 | node_names.append(self.name(node)) 107 | return node_names 108 | 109 | def get_first_child_nodes(self, nodename): 110 | """ 111 | Return the names of all the child nodes for the target machine 112 | """ 113 | nodes = self.get_children(nodename, root=self.machine_node) 114 | return nodes 115 | 116 | def list_available_machines(self): 117 | """ 118 | Return a list of machines defined for a given CIME_MODEL 119 | """ 120 | machines = [] 121 | nodes = self.get_children("machine") 122 | for node in nodes: 123 | mach = self.get(node, "MACH") 124 | machines.append(mach) 125 | return machines 126 | 127 | def probe_machine_name(self, warn=True): 128 | """ 129 | Find a matching regular expression for hostname 130 | in the NODENAME_REGEX field in the file. First match wins. 131 | """ 132 | 133 | names_not_found = [] 134 | 135 | nametomatch = socket.getfqdn() 136 | machine = self._probe_machine_name_one_guess(nametomatch) 137 | 138 | if machine is None: 139 | names_not_found.append(nametomatch) 140 | 141 | nametomatch = socket.gethostname() 142 | machine = self._probe_machine_name_one_guess(nametomatch) 143 | 144 | if "CIME_MACHINE" in os.environ: 145 | machine = os.environ["CIME_MACHINE"] 146 | 147 | if machine is None: 148 | names_not_found.append(nametomatch) 149 | 150 | names_not_found_quoted = ["'" + name + "'" for name in names_not_found] 151 | names_not_found_str = ' or '.join(names_not_found_quoted) 152 | if warn: 153 | logger.warning("Could not find machine match for {}".format(names_not_found_str)) 154 | 155 | return machine 156 | 157 | def _probe_machine_name_one_guess(self, nametomatch): 158 | """ 159 | Find a matching regular expression for nametomatch in the NODENAME_REGEX 160 | field in the file. First match wins. Returns None if no match is found. 161 | """ 162 | 163 | machine = None 164 | nodes = self.get_children("machine") 165 | 166 | for node in nodes: 167 | machtocheck = self.get(node, "MACH") 168 | logger.debug("machine is " + machtocheck) 169 | regex_str_node = self.get_optional_child("NODENAME_REGEX", root=node) 170 | regex_str = machtocheck if regex_str_node is None else self.text(regex_str_node) 171 | 172 | if regex_str is not None: 173 | logger.debug("machine regex string is " + regex_str) 174 | regex = re.compile(regex_str) 175 | if regex.match(nametomatch): 176 | logger.debug("Found machine: {} matches {}".format(machtocheck, nametomatch)) 177 | machine = machtocheck 178 | break 179 | 180 | return machine 181 | 182 | def set_machine(self, machine): 183 | """ 184 | Sets the machine block in the Machines object 185 | 186 | >>> machobj = Machines(machine="melvin") 187 | >>> machobj.get_machine_name() 188 | 'melvin' 189 | >>> machobj.set_machine("trump") # doctest: +IGNORE_EXCEPTION_DETAIL 190 | Traceback (most recent call last): 191 | ... 192 | CIMEError: ERROR: No machine trump found 193 | """ 194 | if machine == "Query": 195 | self.machine = machine 196 | elif self.machine != machine or self.machine_node is None: 197 | self.machine_node = super(Machines,self).get_child("machine", {"MACH" : machine}, err_msg="No machine {} found".format(machine)) 198 | self.machine = machine 199 | 200 | return machine 201 | 202 | #pylint: disable=arguments-differ 203 | def get_value(self, name, attributes=None, resolved=True, subgroup=None): 204 | """ 205 | Get Value of fields in the config_machines.xml file 206 | """ 207 | expect(self.machine_node is not None, "Machine object has no machine defined") 208 | expect(subgroup is None, "This class does not support subgroups") 209 | value = None 210 | 211 | if name in self.custom_settings: 212 | return self.custom_settings[name] 213 | 214 | # COMPILER and MPILIB are special, if called without arguments they get the default value from the 215 | # COMPILERS and MPILIBS lists in the file. 216 | if name == "COMPILER": 217 | value = self.get_default_compiler() 218 | elif name == "MPILIB": 219 | value = self.get_default_MPIlib(attributes) 220 | else: 221 | node = self.get_optional_child(name, root=self.machine_node, attributes=attributes) 222 | if node is not None: 223 | value = self.text(node) 224 | 225 | if resolved: 226 | if value is not None: 227 | value = self.get_resolved_value(value) 228 | elif name in os.environ: 229 | value = os.environ[name] 230 | 231 | value = convert_to_unknown_type(value) 232 | 233 | return value 234 | 235 | def get_field_from_list(self, listname, reqval=None, attributes=None): 236 | """ 237 | Some of the fields have lists of valid values in the xml, parse these 238 | lists and return the first value if reqval is not provided and reqval 239 | if it is a valid setting for the machine 240 | """ 241 | expect(self.machine_node is not None, "Machine object has no machine defined") 242 | supported_values = self.get_value(listname, attributes=attributes) 243 | # if no match with attributes, try without 244 | if supported_values is None: 245 | supported_values = self.get_value(listname, attributes=None) 246 | 247 | expect(supported_values is not None, 248 | "No list found for " + listname + " on machine " + self.machine) 249 | supported_values = supported_values.split(",") #pylint: disable=no-member 250 | 251 | if reqval is None or reqval == "UNSET": 252 | return supported_values[0] 253 | 254 | for val in supported_values: 255 | if val == reqval: 256 | return reqval 257 | return None 258 | 259 | def get_default_compiler(self): 260 | """ 261 | Get the compiler to use from the list of COMPILERS 262 | """ 263 | cime_config = get_cime_config() 264 | if cime_config.has_option('main','COMPILER'): 265 | value = cime_config.get('main', 'COMPILER') 266 | expect(self.is_valid_compiler(value), "User-selected compiler {} is not supported on machine {}".format(value, self.machine)) 267 | else: 268 | value = self.get_field_from_list("COMPILERS") 269 | return value 270 | 271 | def get_default_MPIlib(self, attributes=None): 272 | """ 273 | Get the MPILIB to use from the list of MPILIBS 274 | """ 275 | return self.get_field_from_list("MPILIBS", attributes=attributes) 276 | 277 | def is_valid_compiler(self,compiler): 278 | """ 279 | Check the compiler is valid for the current machine 280 | 281 | >>> machobj = Machines(machine="cori-knl") 282 | >>> machobj.get_default_compiler() 283 | 'intel' 284 | >>> machobj.is_valid_compiler("gnu") 285 | True 286 | >>> machobj.is_valid_compiler("nag") 287 | False 288 | """ 289 | return self.get_field_from_list("COMPILERS", reqval=compiler) is not None 290 | 291 | def is_valid_MPIlib(self, mpilib, attributes=None): 292 | """ 293 | Check the MPILIB is valid for the current machine 294 | 295 | >>> machobj = Machines(machine="cori-knl") 296 | >>> machobj.is_valid_MPIlib("mpi-serial") 297 | True 298 | >>> machobj.is_valid_MPIlib("fake-mpi") 299 | False 300 | """ 301 | return mpilib == "mpi-serial" or \ 302 | self.get_field_from_list("MPILIBS", reqval=mpilib, attributes=attributes) is not None 303 | 304 | def has_batch_system(self): 305 | """ 306 | Return if this machine has a batch system 307 | 308 | >>> machobj = Machines(machine="cori-knl") 309 | >>> machobj.has_batch_system() 310 | True 311 | >>> machobj.set_machine("melvin") 312 | 'melvin' 313 | >>> machobj.has_batch_system() 314 | False 315 | """ 316 | result = False 317 | batch_system = self.get_optional_child("BATCH_SYSTEM", root=self.machine_node) 318 | if batch_system is not None: 319 | result = (self.text(batch_system) is not None and self.text(batch_system) != "none") 320 | logger.debug("Machine {} has batch: {}".format(self.machine, result)) 321 | return result 322 | 323 | def get_suffix(self, suffix_type): 324 | node = self.get_optional_child("default_run_suffix") 325 | if node is not None: 326 | suffix_node = self.get_optional_child(suffix_type, root=node) 327 | if suffix_node is not None: 328 | return self.text(suffix_node) 329 | 330 | return None 331 | 332 | def set_value(self, vid, value, subgroup=None, ignore_type=True): 333 | # A temporary cache only 334 | self.custom_settings[vid] = value 335 | 336 | def print_values(self): 337 | # write out machines 338 | machines = self.get_children("machine") 339 | logger.info("Machines") 340 | for machine in machines: 341 | name = self.get(machine, "MACH") 342 | desc = self.get_child("DESC", root=machine) 343 | os_ = self.get_child("OS", root=machine) 344 | compilers = self.get_child("COMPILERS", root=machine) 345 | max_tasks_per_node = self.get_child("MAX_TASKS_PER_NODE", root=machine) 346 | max_mpitasks_per_node = self.get_child("MAX_MPITASKS_PER_NODE", root=machine) 347 | 348 | print( " {} : {} ".format(name , self.text(desc))) 349 | print( " os ", self.text(os_)) 350 | print( " compilers ",self.text(compilers)) 351 | if max_mpitasks_per_node is not None: 352 | print(" pes/node ",self.text(max_mpitasks_per_node)) 353 | if max_tasks_per_node is not None: 354 | print(" max_tasks/node ",self.text(max_tasks_per_node)) 355 | 356 | def return_values(self): 357 | """ return a dictionary of machine info 358 | This routine is used by external tools in https://github.com/NCAR/CESM_xml2html 359 | """ 360 | machines = self.get_children("machine") 361 | mach_dict = dict() 362 | logger.debug("Machines return values") 363 | for machine in machines: 364 | name = self.get(machine, "MACH") 365 | desc = self.get_child("DESC", root=machine) 366 | mach_dict[(name,"description")] = self.text(desc) 367 | os_ = self.get_child("OS", root=machine) 368 | mach_dict[(name,"os")] = self.text(os_) 369 | compilers = self.get_child("COMPILERS", root=machine) 370 | mach_dict[(name,"compilers")] = self.text(compilers) 371 | max_tasks_per_node = self.get_child("MAX_TASKS_PER_NODE", root=machine) 372 | mach_dict[(name,"max_tasks_per_node")] = self.text(max_tasks_per_node) 373 | max_mpitasks_per_node = self.get_child("MAX_MPITASKS_PER_NODE", root=machine) 374 | mach_dict[(name,"max_mpitasks_per_node")] = self.text(max_mpitasks_per_node) 375 | 376 | return mach_dict 377 | -------------------------------------------------------------------------------- /CESM/2.2/Files/scam_shell_commands: -------------------------------------------------------------------------------- 1 | # Do not change options below 2 | # these are necessary for scam runs. 3 | #======================================== 4 | # 5 | # SCAM works in SPMD mode with a single task, but the default is to run serially. 6 | # Changed for container 7 | #./xmlchange MPILIB=mpi-serial 8 | ./xmlchange NTASKS=1 9 | 10 | # SCAM doesn't have restart functionality yet. 11 | ./xmlchange REST_OPTION=never 12 | 13 | # Note that clm cannot use initial conditions with SCAM -so will only use specified phenology 14 | # Only change if CLM_FORCE_COLDSTART exists. 15 | if [ `./xmlquery --value CLM_FORCE_COLDSTART |& grep -c 'ERROR'` -eq 0 ]; then 16 | ./xmlchange CLM_FORCE_COLDSTART='on' 17 | fi 18 | -------------------------------------------------------------------------------- /ESMF/8.0/Dockerfile: -------------------------------------------------------------------------------- 1 | ############################## 2 | # ESMF/8 Dockerfile # 3 | ############################## 4 | 5 | # Use the ESCOMP centos8 base - this is a base install of CentOS, plus NetCDF/HDF5/PNetCDF/MPICH 6 | FROM escomp/base:centos8 7 | 8 | ENV ESMF_SLUG="ESMF_8_0_1" 9 | 10 | RUN mkdir -p /tmp/sources && \ 11 | cd /tmp/sources && \ 12 | wget -q https://github.com/esmf-org/esmf/archive/${ESMF_SLUG}.tar.gz && \ 13 | tar zxf ${ESMF_SLUG}.tar.gz && \ 14 | cd esmf-${ESMF_SLUG} && \ 15 | export ESMF_DIR=/tmp/sources/esmf-${ESMF_SLUG} && \ 16 | export ESMF_COMM=mpich3 && \ 17 | export ESMF_BOPT="g" && \ 18 | export ESMF_NETCDF="nc-config" && \ 19 | export ESMF_INSTALL_PREFIX=/usr/local && \ 20 | export ESMF_INSTALL_BINDIR=${ESMF_INSTALL_PREFIX}/bin && \ 21 | export ESMF_INSTALL_DOCDIR=${ESMF_INSTALL_PREFIX}/doc && \ 22 | export ESMF_INSTALL_HEADERDIR=${ESMF_INSTALL_PREFIX}/include && \ 23 | export ESMF_INSTALL_LIBDIR=${ESMF_INSTALL_PREFIX}/lib && \ 24 | export ESMF_INSTALL_MODDIR=${ESMF_INSTALL_PREFIX}/mod && \ 25 | export ESMF_TESTEXHAUSTIVE="OFF" && \ 26 | make info && \ 27 | make -j $(nproc) && \ 28 | # make check && \ 29 | make install 30 | 31 | # Build ESMPy ================================================================= 32 | 33 | RUN export ESMF_DIR=/tmp/sources/esmf-${ESMF_SLUG} && \ 34 | export ESMFMKFILE=/usr/local/lib/esmf.mk && \ 35 | cd ${ESMF_DIR}/src/addon/ESMPy && \ 36 | pip3 install numpy nose && \ 37 | python setup.py build --ESMFMKFILE=${ESMFMKFILE} && \ 38 | # python setup.py test && \ 39 | python setup.py install && \ 40 | cd && \ 41 | python -c "import ESMF" 42 | 43 | RUN rm -rf /tmp/sources 44 | -------------------------------------------------------------------------------- /ESMF/API_changes/Dockerfile: -------------------------------------------------------------------------------- 1 | ARG DOCKER_NAMESPACE="" 2 | 3 | FROM ${DOCKER_NAMESPACE}/esmf-doc-base 4 | 5 | ARG TAG1="" 6 | RUN echo "TAG1=$TAG1" 7 | 8 | ENV TAG1=$TAG1 9 | 10 | ARG TAG2="" 11 | RUN echo "TAG2=$TAG2" 12 | 13 | ENV TAG2=$TAG2 14 | 15 | ENV ESMF_ARTIFACTS=/artifacts 16 | RUN mkdir -p ${ESMF_ARTIFACTS} 17 | 18 | WORKDIR ${HOME}/sandbox/esmf 19 | RUN git clone https://github.com/esmf-org/esmf.git src-git 20 | 21 | ENV ESMF_DIR=${HOME}/sandbox/esmf/src-git 22 | RUN echo "ESMF_DIR=$ESMF_DIR" 23 | 24 | RUN git clone https://github.com/esmf-org/esmf-test-scripts.git scripts-git 25 | RUN scripts-git/API_change_script/harvestAPIs 26 | 27 | RUN cp -rv APIs*.out ${ESMF_ARTIFACTS}/ 28 | RUN cp -rv diff*.out ${ESMF_ARTIFACTS}/ 29 | 30 | RUN zip -r ${ESMF_ARTIFACTS}/api_change-artifacts.zip ${ESMF_ARTIFACTS} 31 | -------------------------------------------------------------------------------- /ESMF/copyright_update/Dockerfile: -------------------------------------------------------------------------------- 1 | ############################################# 2 | # Documentation build dependencies for ESMF # 3 | ############################################# 4 | 5 | FROM ubuntu:18.04 6 | 7 | ENV _DEBIAN_FRONTEND=$DEBIAN_FRONTEND 8 | # Avoid having to interact with terminal when installing time-related packages 9 | ENV DEBIAN_FRONTEND=noninteractive 10 | RUN ln -fs /usr/share/zoneinfo/America/Denver /etc/localtime 11 | RUN apt-get -y update && apt-get -y install texlive-full latex2html perl csh \ 12 | git build-essential zip gfortran 13 | ENV DEBIAN_FRONTEND=$_DEBIAN_FRONTEND 14 | ENV _DEBIAN_FRONTEND="" 15 | 16 | ######################################## 17 | # clone ESMF and run copyright update # 18 | ######################################## 19 | ARG DOCKER_NAMESPACE="" 20 | 21 | ARG ESMF_BRANCH="" 22 | RUN echo "ESMF_BRANCH=$ESMF_BRANCH" 23 | 24 | # Clone ESMF 25 | WORKDIR ${HOME}/sandbox/esmf 26 | RUN git clone --branch ${ESMF_BRANCH} --depth 1 https://github.com/esmf-org/esmf.git esmf 27 | RUN cd esmf 28 | RUN git checkout copyright_update 29 | RUN cd .. 30 | 31 | 32 | RUN git clone https://github.com/esmf-org/esmf-test-scripts.git 33 | RUN cp -r esmf-test-scripts/copyright_update/replace_string . 34 | RUN chmod +x replace_string 35 | 36 | RUN find esmf > outfiles 37 | RUN grep -v "eps" outfiles > no_eps_files 38 | RUN grep -v "vsd" no_eps_files > no_vsd_files 39 | RUN grep -v "cdd" no_vsd_files > no_cdd_files 40 | RUN grep -v "vtk" no_cdd_files > final_files 41 | 42 | RUN ./replace_string -nb -nq -s s/2002\-2020/2002\-2021/g -F final_files 43 | 44 | RUN cd esmf 45 | RUN git add . 46 | RUN git commit -a -m " Copyright update pushed at `date` " 47 | RUN git push -u origin copyright_update 48 | -------------------------------------------------------------------------------- /ESMF/dev/Dockerfile: -------------------------------------------------------------------------------- 1 | ARG DOCKER_NAMESPACE="" 2 | 3 | FROM ${DOCKER_NAMESPACE}/centos8 4 | 5 | ARG ESMF_BRANCH="" 6 | 7 | # Build ESMF ================================================================== 8 | 9 | ENV ESMF_DIR=/tmp/sources/esmf 10 | ENV ESMPY_DIR=${ESMF_DIR}/src/addon/ESMPy 11 | ENV ESMFMKFILE=/usr/local/lib/esmf.mk 12 | 13 | ENV ESMF_COMM=mpich3 14 | ENV ESMF_BOPT="g" 15 | ENV ESMF_NETCDF="nc-config" 16 | ENV ESMF_INSTALL_PREFIX=/usr/local 17 | ENV ESMF_INSTALL_BINDIR=${ESMF_INSTALL_PREFIX}/bin 18 | ENV ESMF_INSTALL_DOCDIR=${ESMF_INSTALL_PREFIX}/doc 19 | ENV ESMF_INSTALL_HEADERDIR=${ESMF_INSTALL_PREFIX}/include 20 | ENV ESMF_INSTALL_LIBDIR=${ESMF_INSTALL_PREFIX}/lib 21 | ENV ESMF_INSTALL_MODDIR=${ESMF_INSTALL_PREFIX}/mod 22 | ENV ESMF_TESTEXHAUSTIVE="ON" 23 | 24 | RUN mkdir -p /tmp/sources && \ 25 | mkdir -p /tmp/artifacts && \ 26 | cd /tmp/sources && \ 27 | git clone --branch ${ESMF_BRANCH} --depth 1 https://github.com/esmf-org/esmf.git && \ 28 | cd esmf && \ 29 | make info 2>&1 | tee /tmp/artifacts/esmf-make-info.out && \ 30 | make -j $(nproc) 2>&1 | tee /tmp/artifacts/esmf-make.out && \ 31 | make install 2>&1 | tee /tmp/artifacts/esmf-make-install.out 32 | 33 | # Build ESMPy ================================================================= 34 | 35 | RUN cd ${ESMPY_DIR} && \ 36 | pip3 install numpy nose && \ 37 | python setup.py build --ESMFMKFILE=${ESMFMKFILE} && \ 38 | python setup.py install && \ 39 | cd && \ 40 | python -c "import ESMF" 41 | 42 | RUN cd /tmp && zip -rv artifacts.zip artifacts 43 | 44 | WORKDIR ${ESMF_DIR} 45 | -------------------------------------------------------------------------------- /ESMF/doc/esmf-doc-base/Dockerfile: -------------------------------------------------------------------------------- 1 | ############################################# 2 | # Documentation build dependencies for ESMF # 3 | ############################################# 4 | 5 | FROM ubuntu:18.04 6 | 7 | ENV _DEBIAN_FRONTEND=$DEBIAN_FRONTEND 8 | # Avoid having to interact with terminal when installing time-related packages 9 | ENV DEBIAN_FRONTEND=noninteractive 10 | RUN ln -fs /usr/share/zoneinfo/America/Denver /etc/localtime 11 | RUN apt-get -y update && apt-get -y install texlive-full latex2html perl csh \ 12 | git build-essential zip gfortran 13 | ENV DEBIAN_FRONTEND=$_DEBIAN_FRONTEND 14 | ENV _DEBIAN_FRONTEND="" 15 | -------------------------------------------------------------------------------- /ESMF/doc/esmf-doc/Dockerfile: -------------------------------------------------------------------------------- 1 | ######################################## 2 | # Build and collect ESMF documentation # 3 | ######################################## 4 | ARG DOCKER_NAMESPACE="" 5 | 6 | FROM ${DOCKER_NAMESPACE}/esmf-doc-base 7 | 8 | ARG ESMF_BRANCH="" 9 | RUN echo "ESMF_BRANCH=$ESMF_BRANCH" 10 | 11 | # Where documentation artifacts will be stored in the container 12 | ENV ESMF_ARTIFACTS=/artifacts 13 | RUN mkdir -p ${ESMF_ARTIFACTS} 14 | 15 | # Clone ESMF 16 | WORKDIR ${HOME}/sandbox/esmf 17 | RUN git clone --branch ${ESMF_BRANCH} --depth 1 https://github.com/esmf-org/esmf.git src-git 18 | 19 | ENV ESMF_DIR=${HOME}/sandbox/esmf/src-git 20 | 21 | # Make the NUOPC documentation 22 | WORKDIR ${ESMF_DIR}/src/addon/NUOPC/doc 23 | RUN make localdoc 2>&1 | tee ${ESMF_ARTIFACTS}/nuopc-make-doc.out 24 | 25 | # Make the ESMF documentation 26 | WORKDIR ${ESMF_DIR} 27 | RUN make doc 2>&1 | tee ${ESMF_ARTIFACTS}/esmf-make-doc.out 28 | 29 | # Make the ESMF dev guide documentation 30 | WORKDIR ${ESMF_DIR}/src/doc/dev_guide 31 | RUN make 2>&1 | tee ${ESMF_ARTIFACTS}/dev_guide-make-doc.out 32 | 33 | # Collect and compress the documentation artifacts 34 | WORKDIR ${ESMF_DIR} 35 | RUN cp -rv doc ${ESMF_ARTIFACTS}/doc-esmf 36 | RUN mkdir ${ESMF_ARTIFACTS}/doc-nuopc 37 | RUN cp -rv src/addon/NUOPC/doc/*.pdf src/addon/NUOPC/doc/NUOPC_refdoc src/addon/NUOPC/doc/NUOPC_howtodoc ${ESMF_ARTIFACTS}/doc-nuopc 38 | RUN mkdir ${ESMF_ARTIFACTS}/doc-dev_guide 39 | RUN cp -rv src/doc/dev_guide ${ESMF_ARTIFACTS}/doc-dev_guide 40 | 41 | RUN zip -r ${ESMF_ARTIFACTS}/doc-artifacts.zip ${ESMF_ARTIFACTS} 42 | -------------------------------------------------------------------------------- /ESMF/doc/esmpy-doc/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:focal 2 | 3 | ENV _DEBIAN_FRONTEND=$DEBIAN_FRONTEND 4 | # Avoid having to interact with terminal when installing time-related packages 5 | ENV DEBIAN_FRONTEND=noninteractive 6 | RUN apt-get --yes update && apt-get --yes install latexmk texlive-fonts-recommended \ 7 | texlive-latex-recommended texlive-latex-extra build-essential gfortran git \ 8 | python3-pip 9 | ENV DEBIAN_FRONTEND=$_DEBIAN_FRONTEND 10 | ENV _DEBIAN_FRONTEND="" 11 | 12 | ARG ESMF_BRANCH="" 13 | RUN echo "ESMF_BRANCH=$ESMF_BRANCH" 14 | 15 | ENV ARTIFACTS=/artifacts/doc-esmpy 16 | RUN mkdir -p ${ARTIFACTS} 17 | 18 | WORKDIR /opt/ 19 | RUN git clone --branch ${ESMF_BRANCH} --depth 1 https://github.com/esmf-org/esmf.git 20 | 21 | ENV ESMF_DIR=/opt/esmf 22 | ENV ESMF_INSTALL_PREFIX=/usr/local 23 | ENV ESMF_INSTALL_BINDIR=${ESMF_INSTALL_PREFIX}/bin 24 | ENV ESMF_INSTALL_DOCDIR=${ESMF_INSTALL_PREFIX}/doc 25 | ENV ESMF_INSTALL_HEADERDIR=${ESMF_INSTALL_PREFIX}/include 26 | ENV ESMF_INSTALL_LIBDIR=${ESMF_INSTALL_PREFIX}/lib 27 | ENV ESMF_INSTALL_MODDIR=${ESMF_INSTALL_PREFIX}/mod 28 | 29 | WORKDIR ${ESMF_DIR} 30 | RUN make 2>&1 | tee esmf-make.out 31 | RUN make install 2>&1 | tee esmf-make-install.out 32 | 33 | ENV ESMFMKFILE=${ESMF_INSTALL_LIBDIR}/esmf.mk 34 | RUN pip3 install sphinx sphinxcontrib-packages sphinxcontrib-bibtex==1.0.0 numpy nose 35 | 36 | WORKDIR ${ESMF_DIR}/src/addon/ESMPy 37 | RUN pip install . 38 | WORKDIR doc 39 | RUN make html latexpdf 2>&1 | tee ${ARTIFACTS}/esmpy-make-doc.out 40 | 41 | RUN cp -r esmpy_doc ${ARTIFACTS} && \ 42 | cd /artifacts && \ 43 | zip -r doc-esmpy.zip doc-esmpy 44 | -------------------------------------------------------------------------------- /ESMF/nuopc-app-prototypes/Dockerfile: -------------------------------------------------------------------------------- 1 | ARG DOCKER_NAMESPACE="esmf" 2 | ARG ESMF_BRANCH="develop" 3 | 4 | FROM ${DOCKER_NAMESPACE}/esmf:${ESMF_BRANCH} 5 | 6 | RUN git clone --depth 1 https://github.com/esmf-org/nuopc-app-prototypes.git 7 | WORKDIR nuopc-app-prototypes 8 | RUN git checkout ${ESMF_BRANCH} || echo "WARNING: ESMF_BRANCH does not exist. Checking out develop" && git checkout develop 9 | RUN ln -s /usr/bin/make /usr/bin/gmake || echo "INFO: gmake symlink already exists" 10 | 11 | ENV ESMF_ARTIFACTS=/opt/artifacts 12 | RUN mkdir -p ${ESMF_ARTIFACTS} 13 | 14 | RUN pip3 install --user unittest-xml-reporting 15 | ADD ./meta_test.py /opt/meta_test.py 16 | ADD ./docker-entrypoint.sh /opt/docker-entrypoint.sh 17 | 18 | RUN mkdir -p /outgoing 19 | -------------------------------------------------------------------------------- /ESMF/nuopc-app-prototypes/docker-entrypoint.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | set -Eeuxo pipefail 3 | 4 | case "${1}" in 5 | 6 | testProtos) 7 | # Catch || to true require to allow scripts to continue? Seems like a hack 8 | # and it is, but is required given testing. 9 | ./testProtos.sh 2>&1 | tee "${ESMF_ARTIFACTS}"/testProtos.out || true 10 | ;; 11 | 12 | meta_test) 13 | python /opt/meta_test.py -v 2>&1 | tee "${ESMF_ARTIFACTS}"/meta_test.out 14 | ;; 15 | 16 | prep_artifacts) 17 | cd "${ESMF_ARTIFACTS}"/.. && zip -rv artifacts.zip artifacts 18 | ;; 19 | 20 | *) 21 | echo "ERROR: Command not found"; exit 1 22 | ;; 23 | 24 | esac 25 | -------------------------------------------------------------------------------- /ESMF/nuopc-app-prototypes/meta_test.py: -------------------------------------------------------------------------------- 1 | import os 2 | import re 3 | import unittest 4 | from collections import OrderedDict 5 | 6 | import xmlrunner 7 | 8 | 9 | class TestsContainer(unittest.TestCase): 10 | longMessage = True 11 | expected = 48 12 | ran = 0 13 | logs = os.getcwd() 14 | 15 | def setUp(self): 16 | print(self._testMethodName) 17 | print('\n') 18 | 19 | def test_all_tests_ran(self): 20 | self.assertEqual(self.expected, self.ran) 21 | 22 | def test_logs_have_no_errors(self): 23 | def the_pred(de): 24 | if de.name.endswith('.ESMF_LogFile'): 25 | return True 26 | else: 27 | return False 28 | 29 | to_find = ['ERROR'] 30 | problems = [] 31 | for de in walk_files(self.logs, the_pred): 32 | with open(de.path, 'r') as f: 33 | lines = f.readlines() 34 | for line_number, line in enumerate(lines, start=1): 35 | line = line.strip() 36 | for tf in to_find: 37 | if tf in line: 38 | problems.append((de, line, line_number)) 39 | 40 | msg = ['\n'] 41 | for tup in problems: 42 | de, line, line_number = tup 43 | msg.append(de.name + ':' + str(line_number) + ': ' + line) 44 | msg = '\n'.join(msg) 45 | 46 | self.assertEqual(len(problems), 0, msg=msg) 47 | 48 | 49 | def make_test_function(description, pass_fail): 50 | def test(self): 51 | self.assertEqual(pass_fail, "PASS", description) 52 | return test 53 | 54 | 55 | def walk_files(path, pred): 56 | for de in os.scandir(path): 57 | if de.is_dir(): 58 | for de2 in walk_files(de.path, pred): 59 | yield de2 60 | else: 61 | if pred(de): 62 | yield de 63 | 64 | 65 | def make_testsmap_nuopc_protos(outfile): 66 | testsmap = OrderedDict() 67 | ran = 0 68 | with open(outfile, 'r') as f: 69 | parse = False 70 | for line in f: 71 | line = line.strip() 72 | if '== TEST SUMMARY STOP ==' in line: 73 | break 74 | elif '== TEST SUMMARY START ==' in line: 75 | parse = True 76 | elif parse: 77 | result = re.search('(?P.*): (?P.*)$', line) 78 | if result['name'] in testsmap: 79 | result_name = result['name'] + '_' + str(ran) 80 | else: 81 | result_name = result['name'] 82 | testsmap[result_name] = result['pass_fail'] 83 | ran += 1 84 | testsmap['ran'] = ran 85 | return testsmap 86 | 87 | 88 | if __name__ == '__main__': 89 | xmlout = os.path.join(os.environ['ESMF_ARTIFACTS'], 'meta_test') 90 | outfile = os.path.join(os.environ['ESMF_ARTIFACTS'], 'testProtos.out') 91 | 92 | testsmap = make_testsmap_nuopc_protos(outfile) 93 | 94 | ran = testsmap.pop('ran') 95 | TestsContainer.ran = ran 96 | 97 | for name, pass_fail in testsmap.items(): 98 | test_func = make_test_function(name, pass_fail) 99 | setattr(TestsContainer, 'test_{0}'.format(name), test_func) 100 | 101 | unittest.main(testRunner=xmlrunner.XMLTestRunner(output=xmlout)) 102 | -------------------------------------------------------------------------------- /ESMF/test_coverage/Dockerfile: -------------------------------------------------------------------------------- 1 | ARG DOCKER_NAMESPACE="" 2 | 3 | FROM ${DOCKER_NAMESPACE}/esmf-doc-base 4 | 5 | ARG ESMF_BRANCH="" 6 | RUN echo "ESMF_BRANCH=$ESMF_BRANCH" 7 | 8 | ENV ESMF_ARTIFACTS=/artifacts 9 | RUN mkdir -p ${ESMF_ARTIFACTS} 10 | 11 | WORKDIR ${HOME}/sandbox/esmf 12 | RUN git clone --branch ${ESMF_BRANCH} --depth 1 https://github.com/esmf-org/esmf.git src-git 13 | 14 | ENV ESMF_DIR=${HOME}/sandbox/esmf/src-git 15 | 16 | RUN mkdir store 17 | 18 | ENV LOGDIR=${HOME}/sandbox/esmf/store 19 | 20 | RUN export ESMF_DIR=${HOME}/sandbox/esmf/src-git 21 | RUN export LOGDIR=${HOME}/sandbox/esmf/store 22 | 23 | RUN echo "ESMF_DIR=$ESMF_DIR" 24 | RUN echo "LOGDIR=$LOGDIR" 25 | 26 | RUN git clone https://github.com/esmf-org/esmf-test-scripts.git scripts-git 27 | RUN chmod +x scripts-git/test_coverage_script/test_coverage 28 | 29 | WORKDIR ${ESMF_DIR} 30 | RUN bash ../scripts-git/test_coverage_script/test_coverage 31 | 32 | WORKDIR ${HOME}/sandbox/esmf 33 | RUN cp -rv store/* ${ESMF_ARTIFACTS}/ 34 | 35 | RUN zip -r ${ESMF_ARTIFACTS}/test_coverage-artifacts.zip ${ESMF_ARTIFACTS} 36 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | Containerized versions of ESCOMP software (eg, CESM) 3 | 4 | (This is currently in development; documentation and versions are likely to change rapidly.) 5 | 6 | 7 | 8 | # Quick Start for CESM: 9 | 10 | You need to mount a directory in to the container to save any files / inputdata - this is done via the '-v' option to 'docker'. For example, to run an interactive bash shell with a local 'cesm' directory (/Users/me/cesm) mounted into home, do: 11 | 12 | docker run -it -v /Users/me/cesm:/home/user escomp/cesm-2.1 13 | 14 | 15 | NOTE: For systems with many cores, you might also need to use an option like --dev-shm=512M, since each MPI process will require some space in /dev/shm 16 | 17 | (Unlike a CESM configuration on an HPC system, with dedicated directories for inputdata and scratch, this containerized version stores everything in the /home/user directory, so mounting a local directory ensures you'll not have to download input data multiple times, or lose run data.) 18 | 19 | This will give you a bash prompt like this: 20 | 21 | [user@cesm2.1.3 ~]$ 22 | 23 | From here, you can follow the standard CESM documentation on creating / building / submitting cases - in this case, the submission runs in the foreground. An example set of commands to build a 2-degree F2000climo (scientifically unsupported, just used as an example) case, with a case name / directory of 'test1' follows:

24 | 25 | create_newcase --case test1 --compset F2000climo --res f19_g17 --run-unsupported
26 | cd test1
27 | ./xmlchange NTASKS=4
28 | ./case.setup
29 | ./case.build
30 | ./case.submit
31 | 32 | 33 | This will require ~7-10GB of RAM for 1-4 tasks - if you haven't configured your Docker environment to allow that, you'll need to change that under Docker's settings. 34 | 35 | (These will change soon; this is just a is-it-working example.) 36 | -------------------------------------------------------------------------------- /base/centos8/Dockerfile: -------------------------------------------------------------------------------- 1 | ################################################################################################################ 2 | # escomp/base-centos8 Dockerfile # 3 | #--------------------------------------------------------------------------------------------------------------# 4 | # A base CentOS8 install + MPI, HDF5, NetCDF and PNetCDF, as well as other core packages for escomp containers # 5 | ################################################################################################################ 6 | 7 | # Use latest CentOS8: 8 | FROM centos:8 9 | 10 | # First, we upate the default packages and install some other necessary ones - while this may give 11 | # some people updated versions of packages vs. others, these differences should not be numerically 12 | # important or affect run-time behavior (eg, a newer Bash version, or perl-XML-LibXML version). 13 | 14 | RUN yum -y update && \ 15 | yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm && \ 16 | yum -y install vim emacs-nox git subversion which sudo csh make m4 cmake wget file byacc curl-devel zlib-devel && \ 17 | yum -y install perl-XML-LibXML gcc-gfortran gcc-c++ dnf-plugins-core python3 perl-core && \ 18 | yum -y install ftp xmlstarlet diffutils && \ 19 | yum -y install git-lfs latexmk texlive-amscls texlive-anyfontsize texlive-cmap texlive-fancyhdr texlive-fncychap \ 20 | texlive-dvisvgm texlive-metafont texlive-ec texlive-titlesec texlive-babel-english texlive-tabulary \ 21 | texlive-framed texlive-wrapfig texlive-parskip texlive-upquote texlive-capt-of texlive-needspace \ 22 | texlive-times texlive-makeindex texlive-helvetic texlive-courier texlive-gsftopk texlive-dvips texlive-mfware texlive-dvisvgm && \ 23 | pip3 install rst2pdf sphinx sphinxcontrib-programoutput && \ 24 | pip3 install git+https://github.com/esmci/sphinx_rtd_theme.git@version-dropdown-with-fixes && \ 25 | dnf --enablerepo=powertools install -y blas-devel lapack-devel && \ 26 | ln -s /usr/bin/python3 /usr/bin/python && \ 27 | echo '/usr/local/lib' > /etc/ld.so.conf.d/local.conf && \ 28 | ldconfig && \ 29 | yum clean all 30 | 31 | 32 | # Second, let's install MPI - we're doing this by hand because the default packages install into non-standard locations, and 33 | # we want our image as simple as possible. We're also going to use MPICH, though any of the MPICH ABI-compatible libraries 34 | # will work. This is for future compatibility with offloading to cloud. 35 | 36 | RUN mkdir /tmp/sources && \ 37 | cd /tmp/sources && \ 38 | wget -q http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz && \ 39 | tar zxf mpich-3.3.2.tar.gz && \ 40 | cd mpich-3.3.2 && \ 41 | ./configure --prefix=/usr/local && \ 42 | make -j 2 install && \ 43 | rm -rf /tmp/sources 44 | 45 | 46 | # Next, let's install HDF5, NetCDF and PNetCDF - we'll do this by hand, since the packaged versions have 47 | # lots of extra dependencies (at least, as of CentOS 7) and this also lets us control their location (eg, put in /usr/local). 48 | # NOTE: We do want to change where we store the versions / download links, so it's easier to change, but that'll happen later. 49 | RUN mkdir /tmp/sources && \ 50 | cd /tmp/sources && \ 51 | wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.gz && \ 52 | tar zxf hdf5-1.12.0.tar.gz && \ 53 | cd hdf5-1.12.0 && \ 54 | ./configure --prefix=/usr/local && \ 55 | make -j 2 install && \ 56 | cd /tmp/sources && \ 57 | wget -q ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.4.tar.gz && \ 58 | tar zxf netcdf-c-4.7.4.tar.gz && \ 59 | cd netcdf-c-4.7.4 && \ 60 | ./configure --prefix=/usr/local && \ 61 | make -j 2 install && \ 62 | ldconfig && \ 63 | cd /tmp/sources && \ 64 | wget -q ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.5.3.tar.gz && \ 65 | tar zxf netcdf-fortran-4.5.3.tar.gz && \ 66 | cd netcdf-fortran-4.5.3 && \ 67 | ./configure --prefix=/usr/local && \ 68 | make -j 2 install && \ 69 | ldconfig && \ 70 | cd /tmp/sources && \ 71 | wget -q https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz && \ 72 | tar zxf pnetcdf-1.12.1.tar.gz && \ 73 | cd pnetcdf-1.12.1 && \ 74 | ./configure --prefix=/usr/local && \ 75 | make -j 2 install && \ 76 | ldconfig && \ 77 | rm -rf /tmp/sources 78 | 79 | RUN groupadd escomp && \ 80 | useradd -c 'ESCOMP User' -d /home/user -g escomp -m -s /bin/bash user && \ 81 | echo 'export USER=$(whoami)' >> /etc/profile.d/escomp.sh && \ 82 | echo 'export PS1="[\u@escomp \W]\$ "' >> /etc/profile.d/escomp.sh && \ 83 | echo 'user ALL=(ALL) NOPASSWD: ALL' >> /etc/sudoers.d/escomp 84 | 85 | ENV SHELL=/bin/bash \ 86 | LANG=C.UTF-8 \ 87 | LC_ALL=C.UTF-8 88 | 89 | USER user 90 | WORKDIR /home/user 91 | CMD ["/bin/bash", "-l"] 92 | #ENTRYPOINT ["/bin/bash", "-l"] 93 | --------------------------------------------------------------------------------