Add BUILD_TAUDEMEXT option; Build image based on ghcr.io/lreis2415/ta…

…udem_ext

CMakeLists.txt

@@ -9,6 +9,7 @@
 #         -DINSTALL_PREFIX=<path/to/install>
 #         -DLLVM_ROOT_DIR Specific the root directory of brew installed LLVM, e.g., /usr/local/opt/llvm
 #         -DSEIMS_DOC=1 means build SEIMS documentation based on doxygen
+#         -DBUILD_TAUDEMEXT=0 means do not build TauDEM_ext
 #
 #  Routine testing platforms and compilers include:
 #     1. Windows 10 with Visual Studio 2010/2013/2015, MSMPI-v8.1, GDAL-1.11.4
@@ -18,9 +19,9 @@
 #     5. macOS 10.14.5 with Clang-10.0 with Xcode, OpenMPI-4.0.1, GDAL-2.4.2 (brew installed)
 #
 #  Created and maintained by Liangjun Zhu (zlj@lreis.ac.cn)
-#  Latest updated: Apr 15, 2023
+#  Latest updated: Jun 12, 2024
 #
-#  Copyright (C) 2013-2023 Lreis, IGSNRR, CAS, and NJNU
+#  Copyright (C) 2013-2024 Lreis, IGSNRR, CAS, and NJNU
 # ----------------------------------------------------------------------------
 ### Disable in-source builds to prevent source tree corruption.
 IF(" ${CMAKE_SOURCE_DIR}" STREQUAL " ${CMAKE_BINARY_DIR}")
@@ -72,6 +73,8 @@ option(BUILD_SHARED_LIBS "Build shared libraries (DLLs)." OFF)
 option(BUILD_WITH_STATIC_CRT "Build against dynamic CRT on windows." ON)
 # Build documatation by doxygen
 option(SEIMS_DOC "Build SEIMS documentation." OFF)
+# Build TauDEM_ext or not
+option(BUILD_TAUDEMEXT "Do not build TauDEM_ext" ON)
 
 ### Detect compiler and target platform architecture.
 INCLUDE(Utils)
@@ -213,7 +216,6 @@ ENDIF()
 
 ### Add subdirectories.
 ADD_SUBDIRECTORY(./seims)
-# ADD_SUBDIRECTORY(./gui)  # TODO
 IF(SEIMS_DOC)
   ADD_SUBDIRECTORY(./doc)
 ENDIF()

docker/Dockerfile

@@ -26,7 +26,7 @@ ARG INSTALL_DIR=/seims/dist
 RUN cd /seims \
     && mkdir build \
     && cd build \
-    && cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \
+    && cmake .. -DCMAKE_BUILD_TYPE=Release -DINSTALL_PREFIX=${INSTALL_DIR} \
     && make -j 8 \
     && make install -j 8 \
     && cd ..

docker/Dockerfile.TauDEMext

@@ -0,0 +1,68 @@
+##
+#
+# Copyright 2024 Liang-Jun Zhu <zlj@lreis.ac.cn>
+#
+
+# Use the latest master branch of TauDEM_ext image based on continuumio/miniconda3 as the build and test container, which is based on debian:12.5-slim
+# https://github.com/ContinuumIO/docker-images/blob/main/miniconda3/debian/Dockerfile
+# https://github.com/lreis2415/TauDEM_ext/pkgs/container/taudem_ext
+FROM ghrc.io/lreis2415/taudem_ext:master-debian-miniconda as builder
+
+LABEL maintainer="Liang-Jun Zhu <zlj@lreis.ac.cn>"
+
+# Copy source directory
+WORKDIR /seims
+COPY CMakeLists.txt .
+COPY cmake cmake
+COPY seims seims
+
+RUN apt-get update -q && \
+    apt-get install -q -y --no-install-recommends cmake make g++ \
+    gdal-bin openmpi-bin libgdal-dev libopenmpi-dev \
+    libmongoc-1.0-0 libmongoc-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+ARG INSTALL_DIR=/seims/dist
+RUN cd /seims \
+    && mkdir build \
+    && cd build \
+    && cmake .. -DCMAKE_BUILD_TYPE=Release -DINSTALL_PREFIX=${INSTALL_DIR} -DBUILD_TAUDEMEXT=0 \
+    && make -j 8 \
+    && make install -j 8 \
+    && cd ..
+
+## Build final image
+FROM ghrc.io/lreis2415/taudem_ext:master-debian-miniconda as runner
+
+# Copy source directory
+WORKDIR /seims
+COPY seims seims
+COPY docker docker
+
+# Create new conda environment for pyseims
+# Refers to https://pythonspeed.com/articles/activate-conda-dockerfile/
+RUN conda env create -f ./seims/pyseims_env.yml
+
+# Make RUN commands use the new environment:
+SHELL ["conda", "run", "--no-capture-output", "-n", "pyseims", "/bin/bash", "-c"]
+
+RUN apt-get update -q && \
+    apt-get install -q -y --no-install-recommends \
+    gdal-bin openmpi-bin libgomp1 tini libmongoc-1.0-0 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Order layers starting with less frequently varying ones
+ARG INSTALL_DIR=/seims/dist
+COPY --from=builder ${INSTALL_DIR}/bin/ /usr/local/bin/
+COPY --from=builder ${INSTALL_DIR}/include/ /usr/local/include/
+COPY --from=builder ${INSTALL_DIR}/lib/ /usr/local/lib/
+COPY --from=builder ${INSTALL_DIR}/share/ /usr/local/share/
+
+ENV OMPI_ALLOW_RUN_AS_ROOT=1
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+COPY docker/docker-entrypoint.sh /
+WORKDIR /seims/seims
+ENTRYPOINT ["/usr/bin/tini", "--", "/docker-entrypoint.sh"]

seims/CMakeLists.txt

@@ -27,7 +27,9 @@ ADD_SUBDIRECTORY(${FIELD_PARTITION} bin/field_partition)
 ADD_SUBDIRECTORY(${GRID_LAYERING} bin/grid_layering)
 ADD_SUBDIRECTORY(${IUH} bin/iuh)
 ADD_SUBDIRECTORY(${METIS} bin/metis)
-ADD_SUBDIRECTORY(${TAUDEM} bin/taudem)
+IF(BUILD_TAUDEMEXT)
+  ADD_SUBDIRECTORY(${TAUDEM} bin/taudem)
+ENDIF()
 ADD_SUBDIRECTORY(${SEIMS_MAIN} bin/seims_project)
 
 MESSAGE(STATUS "All SEIMS related compiled done!")