Adds initial dockerfile

fischer-ncar · Sep 23, 2021 · f2cad7c · f2cad7c
1 parent 407a345
commit f2cad7c
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diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -0,0 +1,133 @@
+FROM ubuntu:20.10 as cesm
+
+ENV USER=root
+ENV CIME_MODEL=cesm
+ENV NETCDF_FORTRAN_VERSION=4.5.2
+ENV PNETCDF_VERSION=1.12.1
+ENV PATH=/build/local/bin:$PATH
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+WORKDIR /build
+
+RUN apt update && \
+      apt install -y --no-install-recommends \
+        python3 \
+        git \
+        vim \
+        build-essential \
+        gcc-9 \
+        g++-9 \
+        gfortran-9 \
+        openmpi-bin \
+        libopenmpi-dev \
+        libcurl4-openssl-dev \
+        libnetcdf-dev \
+        netcdf-bin \
+        libxml2-utils \
+        pylint \
+        cmake \
+        curl \
+        wget \
+        subversion \
+        ca-certificates \
+      pkg-config && \
+      rm -rf /var/lib/apt/lists && \
+      update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
+      update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 10 && \
+      update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 10 && \
+      update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-9 10 && \
+      curl -L -k -o netcdf-fortran.tar.gz \
+      https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${NETCDF_FORTRAN_VERSION}.tar.gz && \
+      mkdir "${PWD}/netcdf-fortran" && \
+      tar -xvf "${PWD}/netcdf-fortran.tar.gz" -C "${PWD}/netcdf-fortran" --strip-components=1 && \
+      cd "${PWD}/netcdf-fortran" && \
+      ./configure --prefix=/build/local && \
+      make && \
+      make install && \
+      curl -L -k -o pnetcdf.tar.gz \
+      https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz && \
+      mkdir "${PWD}/pnetcdf" && \
+      tar -xvf "${PWD}/pnetcdf.tar.gz" -C "${PWD}/pnetcdf" --strip-components=1 && \
+      cd "${PWD}/pnetcdf" && \
+      ./configure --prefix=/build/local --enable-shared --disable-cxx && \
+      make && \
+      make install && \
+      cd "/build/local/include" && \
+      ln -sf /usr/include/*netcdf* . && \
+      cd "/build/local/lib" && \
+      ln -sf `nc-config --libdir`/lib* .
+
+WORKDIR /root
+
+RUN git clone https://github.com/ESMCI/cime && \
+      cd cime && \
+      git clone https://github.com/ESCOMP/CMEPS components/cmeps && \
+      git clone https://github.com/ESCOMP/CDEPS components/cdeps && \
+      git clone https://github.com/ESCOMP/CESM_CPL7andDataComps components/cpl7 && \
+      git clone https://github.com/ESCOMP/CESM_share share/ && \
+      git clone https://github.com/MCSclimate/MCT libraries/mct && \
+      git clone https://github.com/NCAR/ParallelIO libraries/parallelio
+
+RUN mkdir  ~/.cime
+
+WORKDIR /root/cime/scripts
+
+COPY config_machines.xml /root/cime_config/machines/
+COPY config_compilers.xml /root/cime_config/machines/
+
+FROM condaforge/mambaforge:latest AS e3sm
+
+ENV USER=root
+ENV CIME_MODEL=e3sm
+ENV PNETCDF_VERSION=1.12.1
+
+WORKDIR /root
+
+RUN git clone https://github.com/E3SM-Project/E3SM && \
+      cd E3SM && \
+      sed -i"" "s/git@github.com:/https:\/\/github.com\//g" .gitmodules && \
+      git submodule update --init
+
+RUN mamba install -c conda-forge \
+      libnetcdf=*=*openmpi* \
+      netcdf-fortran=*=*openmpi* \
+      cmake \
+      make \
+      wget \
+      curl \
+      subversion \
+      m4 \
+      gcc_linux-64 \
+      gxx_linux-64 \
+      gfortran_linux-64 \
+      openmpi-mpifort
+
+SHELL ["/bin/bash", "-c"]
+
+RUN curl -L -k -o pnetcdf.tar.gz \
+      https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz && \
+      mkdir "${PWD}/pnetcdf" && \
+      tar -xvf "${PWD}/pnetcdf.tar.gz" -C "${PWD}/pnetcdf" --strip-components=1 && \
+      cd "${PWD}/pnetcdf" && \
+      source /opt/conda/etc/profile.d/conda.sh && \
+      conda activate base && \
+      ./configure --prefix /opt/conda --disable-cxx --enable-shared \
+      MPICC=/opt/conda/bin/mpicc \
+      MPICXX=/opt/conda/bin/mpicxx \
+      MPIF77=/opt/conda/bin/mpif77 \
+      MPIF90=/opt/conda/bin/mpif90 && \
+      make -j4 && \
+      make install
+
+RUN find /root/E3SM -type f -iname Makefile -exec grep -nH '$(AR) $@' {} \; | \
+          cut -d":" -f1 | \
+          xargs sed -i'' 's/$(AR) $@/$(AR) rc $@/g'
+
+RUN ln -sf /opt/conda/bin/x86_64-conda-linux-gnu-ar /opt/conda/bin/ar && \
+          ln -sf /opt/conda/bin/x86_64-conda-linux-gnu-ranlib /opt/conda/bin/ranlib
+
+WORKDIR /root/E3SM/cime/scripts
+
+COPY config_machines.xml /root/.cime/
+COPY config_compilers.xml /root/.cime/
diff --git a/docker/config_compilers.xml b/docker/config_compilers.xml
@@ -0,0 +1,130 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config_compilers version="2.0">
+	<compiler MACH="docker-mamba" COMPILER="gnu-mamba">
+		<AR>/opt/conda/bin/x86_64-conda-linux-gnu-ar</AR>
+		<CFLAGS>
+			<base> -mcmodel=medium </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=invalid,zero,overflow</append>
+			<append DEBUG="FALSE"> -O </append>
+			<append COMP_NAME="csm_share"> -std=c99 </append>
+		</CFLAGS>
+		<CXXFLAGS>
+			<base> -std=c++14 </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace </append>
+			<append DEBUG="FALSE"> -O </append>
+		</CXXFLAGS>
+		<CMAKE_OPTS>
+			<append COMP_NAME="cism"> -D CISM_GNU=ON </append>
+			<append> -D CMAKE_AR=/opt/conda/bin/x86_64-conda-linux-gnu-ar </append>
+			<append> -DCMAKE_Fortran_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib </append>
+			<append> -DCMAKE_C_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib </append>
+			<append> -DCMAKE_CXX_COMPILER_RANLIB=/opt/conda/bin/x86_64-conda-linux-gnu-ranlib </append>
+		</CMAKE_OPTS>
+		<CPPDEFS>
+			<append> -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU</append>
+			<append DEBUG="TRUE"> -DYAKL_DEBUG </append>
+		</CPPDEFS>
+		<CXX_LIBS>
+			<base> -lstdc++ </base>
+		</CXX_LIBS>
+		<CXX_LINKER>FORTRAN</CXX_LINKER>
+		<FC_AUTO_R8>
+			<base> -fdefault-real-8 </base>
+		</FC_AUTO_R8>
+		<FFLAGS>
+			<base> -mcmodel=medium -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=zero,overflow</append>
+			<append DEBUG="FALSE"> -O </append>
+		</FFLAGS>
+		<FFLAGS_NOOPT>
+			<base> -O0 </base>
+		</FFLAGS_NOOPT>
+		<FIXEDFLAGS>
+			<base>  -ffixed-form </base>
+		</FIXEDFLAGS>
+		<FREEFLAGS>
+			<base> -ffree-form </base>
+		</FREEFLAGS>
+		<HAS_F2008_CONTIGUOUS>FALSE</HAS_F2008_CONTIGUOUS>
+		<LDFLAGS>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append> -L/opt/conda/lib -lnetcdff -lnetcdf </append>
+		</LDFLAGS>
+		<MPI_PATH>/opt/conda</MPI_PATH>
+		<MPICC>/opt/conda/bin/mpicc</MPICC>
+		<MPICXX>/opt/conda/bin/mpicxx</MPICXX>
+		<MPIFC>/opt/conda/bin/mpif90</MPIFC>
+		<NETCDF_C_PATH>/opt/conda</NETCDF_C_PATH>
+		<NETCDF_FORTRAN_PATH>/opt/conda</NETCDF_FORTRAN_PATH>
+		<PNETCDF_PATH>/opt/conda</PNETCDF_PATH>
+		<SCC>/opt/conda/bin/x86_64-conda-linux-gnu-gcc</SCC>
+		<SCXX>/opt/conda/bin/x86_64-conda-linux-gnu-g++</SCXX>
+		<SFC>/opt/conda/bin/x86_64-conda-linux-gnu-gfortran</SFC>
+		<SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
+	</compiler>
+	<compiler MACH="docker" COMPILER="gnu">
+		<CFLAGS>
+			<base> -mcmodel=medium </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=invalid,zero,overflow</append>
+			<append DEBUG="FALSE"> -O </append>
+			<append COMP_NAME="csm_share"> -std=c99 </append>
+		</CFLAGS>
+		<CXXFLAGS>
+			<base> -std=c++14 </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace </append>
+			<append DEBUG="FALSE"> -O </append>
+		</CXXFLAGS>
+		<CMAKE_OPTS>
+			<append COMP_NAME="cism"> -D CISM_GNU=ON </append>
+		</CMAKE_OPTS>
+		<CPPDEFS>
+			<append> -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU</append>
+			<append DEBUG="TRUE"> -DYAKL_DEBUG </append>
+		</CPPDEFS>
+		<CXX_LIBS>
+			<base> -lstdc++ </base>
+		</CXX_LIBS>
+		<CXX_LINKER>FORTRAN</CXX_LINKER>
+		<FC_AUTO_R8>
+			<base> -fdefault-real-8 </base>
+		</FC_AUTO_R8>
+		<FFLAGS>
+			<base> -mcmodel=medium -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none </base>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+			<append DEBUG="TRUE"> -g -Wall -fbacktrace -fcheck=bounds -ffpe-trap=zero,overflow</append>
+			<append DEBUG="FALSE"> -O </append>
+		</FFLAGS>
+		<FFLAGS_NOOPT>
+			<base> -O0 </base>
+		</FFLAGS_NOOPT>
+		<FIXEDFLAGS>
+			<base>  -ffixed-form </base>
+		</FIXEDFLAGS>
+		<FREEFLAGS>
+			<base> -ffree-form </base>
+		</FREEFLAGS>
+		<HAS_F2008_CONTIGUOUS>FALSE</HAS_F2008_CONTIGUOUS>
+		<LDFLAGS>
+			<append compile_threaded="TRUE"> -fopenmp </append>
+		</LDFLAGS>
+		<MPICC>mpicc</MPICC>
+		<MPICXX>mpicxx</MPICXX>
+		<MPIFC>mpif90</MPIFC>
+		<NETCDF_C_PATH>$ENV{NETCDF_C_PATH}</NETCDF_C_PATH>
+		<NETCDF_FORTRAN_PATH>$ENV{NETCDF_FORTRAN_PATH}</NETCDF_FORTRAN_PATH>
+		<PNETCDF_PATH>$ENV{PNETCDF_PATH}</PNETCDF_PATH>
+		<SCC>gcc</SCC>
+		<SCXX>g++</SCXX>
+		<SFC>gfortran</SFC>
+		<SLIBS>
+			<append>$SHELL{$ENV{NETCDF_FORTRAN_PATH}/bin/nf-config --flibs} -Wl,-rpath -Wl,$ENV{NETCDF_C_PATH}/lib</append>
+			<append>$SHELL{$ENV{NETCDF_C_PATH}/bin/nc-config --libs}</append>
+		</SLIBS>
+		<SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
+	</compiler>
+</config_compilers>
diff --git a/docker/config_machines.xml b/docker/config_machines.xml
@@ -0,0 +1,82 @@
+<?xml version="1.0"?>
+
+<config_machines version="2.0">
+  <machine MACH="docker">
+    <DESC>Docker</DESC>
+    <NODENAME_REGEX>none</NODENAME_REGEX>
+    <OS>LINUX</OS>
+    <PROXY/>
+    <COMPILERS>gnu</COMPILERS>
+    <MPILIBS>openmpi</MPILIBS>
+    <SAVE_TIMING_DIR>/data/cime_testing/scratch/$CASE/timings</SAVE_TIMING_DIR>
+    <CIME_OUTPUT_ROOT>/data/cime_testing/scratch</CIME_OUTPUT_ROOT>
+    <DIN_LOC_ROOT>/data/cime_testing/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>/data/cime_testing/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
+    <DOUT_S_ROOT>/data/cime_testing/scratch/$CASE/archive</DOUT_S_ROOT>
+    <BASELINE_ROOT>/data/cime_testing/baselines</BASELINE_ROOT>
+    <CCSM_CPRNC>/data/cime_testing/tools/cprnc</CCSM_CPRNC>
+    <GMAKE>make</GMAKE>
+    <GMAKE_J>8</GMAKE_J>
+    <TESTS>e3sm_developer</TESTS>
+    <BATCH_SYSTEM>none</BATCH_SYSTEM>
+    <SUPPORTED_BY>jasonb5</SUPPORTED_BY>
+    <MAX_TASKS_PER_NODE>20</MAX_TASKS_PER_NODE>
+    <MAX_MPITASKS_PER_NODE>20</MAX_MPITASKS_PER_NODE>
+    <mpirun mpilib="openmpi">
+      <executable>mpiexec</executable>
+      <arguments>
+        <arg name="ntasks"> -n {{ total_tasks }} </arg>
+	<arg name="oversubscribe"> --oversubscribe </arg>
+      </arguments>
+    </mpirun>
+    <module_system type="none"/>
+    <RUNDIR>/data/cime_testing/scratch/$CASE/run</RUNDIR>
+    <EXEROOT>/data/cime_testing/scratch/$CASE/bld</EXEROOT>
+    <environment_variables>
+      <env name="OMPI_ALLOW_RUN_AS_ROOT">1</env>
+      <env name="OMPI_ALLOW_RUN_AS_ROOT_CONFIRM">1</env>
+      <env name="NETCDF_C_PATH">/build/local</env>
+      <env name="NETCDF_FORTRAN_PATH">/build/local</env>
+      <env name="PNETCDF_PATH">/build/local</env>
+    </environment_variables>
+  </machine>
+  <machine MACH="docker-mamba">
+    <DESC>Docker</DESC>
+    <NODENAME_REGEX>none</NODENAME_REGEX>
+    <OS>LINUX</OS>
+    <PROXY/>
+    <COMPILERS>gnu-mamba</COMPILERS>
+    <MPILIBS>openmpi</MPILIBS>
+    <SAVE_TIMING_DIR>/data/cime_testing/scratch/$CASE/timings</SAVE_TIMING_DIR>
+    <CIME_OUTPUT_ROOT>/data/cime_testing/scratch</CIME_OUTPUT_ROOT>
+    <DIN_LOC_ROOT>/data/cime_testing/inputdata</DIN_LOC_ROOT>
+    <DIN_LOC_ROOT_CLMFORC>/data/cime_testing/inputdata-clmforc</DIN_LOC_ROOT_CLMFORC>
+    <DOUT_S_ROOT>/data/cime_testing/scratch/$CASE/archive</DOUT_S_ROOT>
+    <BASELINE_ROOT>/data/cime_testing/baselines</BASELINE_ROOT>
+    <CCSM_CPRNC>/data/cime_testing/tools/cprnc</CCSM_CPRNC>
+    <GMAKE>make</GMAKE>
+    <GMAKE_J>8</GMAKE_J>
+    <TESTS>e3sm_developer</TESTS>
+    <BATCH_SYSTEM>none</BATCH_SYSTEM>
+    <SUPPORTED_BY>jasonb5</SUPPORTED_BY>
+    <MAX_TASKS_PER_NODE>20</MAX_TASKS_PER_NODE>
+    <MAX_MPITASKS_PER_NODE>20</MAX_MPITASKS_PER_NODE>
+    <mpirun mpilib="openmpi">
+      <executable>mpiexec</executable>
+      <arguments>
+        <arg name="ntasks"> -n {{ total_tasks }} </arg>
+	<arg name="oversubscribe"> --oversubscribe </arg>
+      </arguments>
+    </mpirun>
+    <module_system type="none"/>
+    <RUNDIR>/data/cime_testing/scratch/$CASE/run</RUNDIR>
+    <EXEROOT>/data/cime_testing/scratch/$CASE/bld</EXEROOT>
+    <environment_variables>
+      <env name="OMPI_ALLOW_RUN_AS_ROOT">1</env>
+      <env name="OMPI_ALLOW_RUN_AS_ROOT_CONFIRM">1</env>
+      <env name="NETCDF_C_PATH">/build/local</env>
+      <env name="NETCDF_FORTRAN_PATH">/build/local</env>
+      <env name="PNETCDF_PATH">/build/local</env>
+    </environment_variables>
+  </machine>
+</config_machines>