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| Auteur: Rémi Tavon | Date: March 31 2021 | ||
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| # *Geo-Deep-Learning* - Pipeline d'inférence & post-traitement | ||
| > Note: These instruction apply only to HPC. | ||
| Répertoire de travail sur HPC pour les inférences: | ||
| `/gpfs/fs3/nrcan/nrcan_geobase/work/transfer/work/deep_learning/inference/` | ||
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| ## Configuration | ||
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| ### 1. Inference with geo-deep-learning | ||
| Clone geo-deep-learning from github repo into desired local directory | ||
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| ```.sh | ||
| cd /gpfs/fs3/nrcan/nrcan_geobase/work/transfer/work/deep_learning/inference/ | ||
| git clone https://github.com/NRCan/geo-deep-learning/ | ||
| ``` | ||
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| ### 2. Post-processing with GeoSim | ||
| 2.1 GeoSim | ||
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| - Download GeoSim QGIS plugin from https://github.com/remtav/GeoSim) as .zip | ||
| - Open QGIS, then install QGIS plugin "geo-sim" from .zip | ||
| 2.2 Postprocess-gdl | ||
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| - Clone postprocess-gdl from github repo into desired local directory | ||
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| ```.sh | ||
| cd /gpfs/fs3/nrcan/nrcan_geobase/work/transfer/work/deep_learning/inference/ | ||
| git https://github.com/remtav/postprocess-gdl | ||
| ``` | ||
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| ## Execution | ||
| - Set config in `postprocess-gdl/confif_4class.yaml` | ||
| - Set path to config yaml in `postprocess-gdl/inference_pipeline_HPC.sbatch`, then run with `sbatch postprocess-gdl/inference_pipeline_HPC.sbatch` file! |
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| name: qgis_316 | ||
| channels: | ||
| - conda-forge | ||
| - pytorch | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=conda_forge | ||
| - _openmp_mutex=4.5=1_gnu | ||
| - boost-cpp=1.74.0=hc6e9bd1_2 | ||
| - brotlipy=0.7.0=py38h497a2fe_1001 | ||
| - bzip2=1.0.8=h7f98852_4 | ||
| - c-ares=1.17.1=h36c2ea0_0 | ||
| - ca-certificates=2021.1.19=h06a4308_1 | ||
| - cairo=1.16.0=h7979940_1007 | ||
| - certifi=2020.12.5=py38h06a4308_0 | ||
| - cffi=1.14.5=py38ha65f79e_0 | ||
| - cfitsio=3.470=hb418390_7 | ||
| - chardet=4.0.0=py38h578d9bd_1 | ||
| - coverage=5.5=py38h497a2fe_0 | ||
| - cpuonly=1.0=0 | ||
| - cryptography=3.4.4=py38h3e25421_0 | ||
| - curl=7.71.1=he644dc0_8 | ||
| - dbus=1.13.6=hfdff14a_1 | ||
| - exiv2=0.27.1=had08079_0 | ||
| - expat=2.2.10=h9c3ff4c_0 | ||
| - fontconfig=2.13.1=hba837de_1004 | ||
| - freetype=2.10.4=h0708190_1 | ||
| - freexl=1.0.5=h516909a_1002 | ||
| - future=0.18.2=py38h578d9bd_3 | ||
| - gdal=3.2.1=py38hc0b2d6b_4 | ||
| - geos=3.9.0=h9c3ff4c_0 | ||
| - geotiff=1.6.0=h2b14fbe_4 | ||
| - gettext=0.19.8.1=h0b5b191_1005 | ||
| - giflib=5.2.1=h36c2ea0_2 | ||
| - glib=2.66.7=h9c3ff4c_0 | ||
| - glib-tools=2.66.7=h9c3ff4c_0 | ||
| - gsl=2.6=he838d99_2 | ||
| - gst-plugins-base=1.14.5=h0935bb2_2 | ||
| - gstreamer=1.18.3=h3560a44_0 | ||
| - hdf4=4.2.13=h10796ff_1004 | ||
| - hdf5=1.10.6=nompi_h6a2412b_1114 | ||
| - httplib2=0.19.0=pyhd8ed1ab_0 | ||
| - icu=68.1=h58526e2_0 | ||
| - idna=2.10=pyh9f0ad1d_0 | ||
| - intel-openmp=2020.2=254 | ||
| - jinja2=2.11.3=pyh44b312d_0 | ||
| - joblib=1.0.1=pyhd3eb1b0_0 | ||
| - jpeg=9d=h36c2ea0_0 | ||
| - json-c=0.13.1=hbfbb72e_1002 | ||
| - kealib=1.4.14=he4dc956_1 | ||
| - krb5=1.17.2=h926e7f8_0 | ||
| - ld_impl_linux-64=2.33.1=h53a641e_7 | ||
| - libblas=3.9.0=8_openblas | ||
| - libcblas=3.9.0=8_openblas | ||
| - libclang=11.0.1=default_ha53f305_1 | ||
| - libcurl=7.71.1=hcdd3856_8 | ||
| - libdap4=3.20.6=hd7c4107_1 | ||
| - libedit=3.1.20191231=h14c3975_1 | ||
| - libev=4.33=h516909a_1 | ||
| - libevent=2.1.10=hcdb4288_3 | ||
| - libffi=3.3=he6710b0_2 | ||
| - libgcc-ng=9.3.0=h2828fa1_18 | ||
| - libgdal=3.2.1=h0a4f56a_4 | ||
| - libgfortran-ng=9.3.0=hff62375_18 | ||
| - libgfortran5=9.3.0=hff62375_18 | ||
| - libglib=2.66.7=h1f3bc88_0 | ||
| - libgomp=9.3.0=h2828fa1_18 | ||
| - libiconv=1.16=h516909a_0 | ||
| - libkml=1.3.0=h02e6976_1012 | ||
| - liblapack=3.9.0=8_openblas | ||
| - libllvm11=11.0.1=hf817b99_0 | ||
| - libnetcdf=4.7.4=nompi_h56d31a8_107 | ||
| - libnghttp2=1.43.0=h812cca2_0 | ||
| - libopenblas=0.3.12=pthreads_h4812303_1 | ||
| - libpng=1.6.37=h21135ba_2 | ||
| - libpq=12.3=h255efa7_3 | ||
| - libprotobuf=3.14.0=h780b84a_0 | ||
| - librttopo=1.1.0=hccdd1c9_5 | ||
| - libspatialindex=1.9.3=h9c3ff4c_3 | ||
| - libspatialite=5.0.1=h04c9dda_2 | ||
| - libssh2=1.9.0=hab1572f_5 | ||
| - libstdcxx-ng=9.3.0=h6de172a_18 | ||
| - libtiff=4.2.0=hdc55705_0 | ||
| - libuuid=2.32.1=h7f98852_1000 | ||
| - libwebp=1.2.0=h3452ae3_0 | ||
| - libwebp-base=1.2.0=h7f98852_0 | ||
| - libxcb=1.13=h7f98852_1003 | ||
| - libxkbcommon=1.0.3=he3ba5ed_0 | ||
| - libxml2=2.9.10=h72842e0_3 | ||
| - libxslt=1.1.33=h15afd5d_2 | ||
| - libzip=1.7.3=h4de3113_0 | ||
| - lz4-c=1.9.3=h9c3ff4c_0 | ||
| - markupsafe=1.1.1=py38h497a2fe_3 | ||
| - mkl=2020.2=256 | ||
| - mock=4.0.3=py38h578d9bd_1 | ||
| - mysql-common=8.0.22=ha770c72_3 | ||
| - mysql-libs=8.0.22=h935591d_3 | ||
| - ncurses=6.2=he6710b0_1 | ||
| - ninja=1.10.2=py38hff7bd54_0 | ||
| - nose2=0.9.2=py_0 | ||
| - nspr=4.29=h9c3ff4c_1 | ||
| - nss=3.62=hb5efdd6_0 | ||
| - numpy=1.20.1=py38h18fd61f_0 | ||
| - openjpeg=2.4.0=hf7af979_0 | ||
| - openssl=1.1.1k=h27cfd23_0 | ||
| - owslib=0.23.0=pyhd8ed1ab_0 | ||
| - pcre=8.44=he1b5a44_0 | ||
| - pip=21.0.1=py38h06a4308_0 | ||
| - pixman=0.40.0=h36c2ea0_0 | ||
| - plotly=4.14.3=pyh44b312d_0 | ||
| - poppler=0.89.0=h2de54a5_5 | ||
| - poppler-data=0.4.10=0 | ||
| - postgresql=12.3=hc2f5b80_3 | ||
| - proj=7.2.0=h277dcde_2 | ||
| - psycopg2=2.8.6=py38h2b97feb_1 | ||
| - pthread-stubs=0.4=h36c2ea0_1001 | ||
| - pycparser=2.20=pyh9f0ad1d_2 | ||
| - pygments=2.8.0=pyhd8ed1ab_0 | ||
| - pyopenssl=20.0.1=pyhd8ed1ab_0 | ||
| - pyparsing=2.4.7=pyh9f0ad1d_0 | ||
| - pyproj=3.0.0.post1=py38h8df5ac0_0 | ||
| - pyqt=5.12.3=py38h578d9bd_7 | ||
| - pyqt-impl=5.12.3=py38h7400c14_7 | ||
| - pyqt5-sip=4.19.18=py38h709712a_7 | ||
| - pyqtchart=5.12=py38h7400c14_7 | ||
| - pyqtwebengine=5.12.1=py38h7400c14_7 | ||
| - pyqtwebkit=5.212=py38hd669dca_1 | ||
| - pysocks=1.7.1=py38h578d9bd_3 | ||
| - python=3.8.8=hdb3f193_4 | ||
| - python-dateutil=2.8.1=py_0 | ||
| - python_abi=3.8=1_cp38 | ||
| - pytorch=1.4.0=py3.8_cpu_0 | ||
| - pytz=2021.1=pyhd8ed1ab_0 | ||
| - pyyaml=5.4.1=py38h497a2fe_0 | ||
| - qca=2.2.1=h73816c6_3 | ||
| - qgis=3.16.4=py38hf2201f9_0 | ||
| - qjson=0.9.0=h73816c6_1006 | ||
| - qscintilla2=2.11.2=py38h63a9b5b_4 | ||
| - qt=5.12.9=h9d6b050_2 | ||
| - qtkeychain=0.12.0=h2264404_0 | ||
| - qtlocation=5.12.9=he1b5a44_0 | ||
| - qtserialport=5.9.8=h73816c6_1 | ||
| - qtwebkit=5.212=h8f65c2e_1 | ||
| - qwt=6.1.6=h7ec6b3e_0 | ||
| - qwtpolar=1.1.1=h73816c6_7 | ||
| - readline=8.1=h27cfd23_0 | ||
| - requests=2.25.1=pyhd3deb0d_0 | ||
| - retrying=1.3.3=py_2 | ||
| - ruamel_yaml=0.15.87=py38h7b6447c_1 | ||
| - setuptools=52.0.0=py38h06a4308_0 | ||
| - six=1.15.0=pyh9f0ad1d_0 | ||
| - sqlite=3.34.0=h74cdb3f_0 | ||
| - tiledb=2.2.4=hb9a9e87_1 | ||
| - tk=8.6.10=hbc83047_0 | ||
| - tzcode=2021a=h7f98852_0 | ||
| - urllib3=1.26.3=pyhd8ed1ab_0 | ||
| - wheel=0.36.2=pyhd3eb1b0_0 | ||
| - xerces-c=3.2.3=h9d8b166_2 | ||
| - xorg-kbproto=1.0.7=h7f98852_1002 | ||
| - xorg-libice=1.0.10=h516909a_0 | ||
| - xorg-libsm=1.2.3=h84519dc_1000 | ||
| - xorg-libx11=1.6.12=h516909a_0 | ||
| - xorg-libxau=1.0.9=h7f98852_0 | ||
| - xorg-libxdmcp=1.1.3=h7f98852_0 | ||
| - xorg-libxext=1.3.4=h516909a_0 | ||
| - xorg-libxrender=0.9.10=h516909a_1002 | ||
| - xorg-renderproto=0.11.1=h14c3975_1002 | ||
| - xorg-xextproto=7.3.0=h7f98852_1002 | ||
| - xorg-xproto=7.0.31=h7f98852_1007 | ||
| - xz=5.2.5=h7b6447c_0 | ||
| - yaml=0.2.5=h516909a_0 | ||
| - zlib=1.2.11=h7b6447c_3 | ||
| - zstd=1.4.8=ha95c52a_1 | ||
| prefix: /home/remi/miniconda3/envs/qgis_316 |
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