Merge pull request #5 from thomas-robinson/esm2021.02

Esm2021.02

containers/Dockerfile

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+FROM thomasrobinson/centos7-netcdff:4.5.3-c4.7.4-gcc-mpich-slurm
+## Dockerfile used to create ESM4
+
+## Set up spack
+RUN . /opt/spack/share/spack/setup-env.sh
+## Make the ESM4 directory
+RUN mkdir -p /opt/ESM4
+## Build the ESM4 from github
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.02 \
+    && cd ESM4/exec \ 
+    && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
+    && cp esm4.1.x /opt/ESM4 \
+    && make clean_all
+## Add the ESM4 executable to the path
+ENV PATH=/opt/ESM4/:${PATH}
+## Add permissions to the ESM4
+RUN chmod 777 /opt/ESM4/esm4.1.x
+

containers/Dockerfile.gnu

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+FROM thomasrobinson/centos7-netcdff:4.5.3-c4.7.4-gcc-mpich-slurm
+## Dockerfile used to create ESM4
+
+## Set up spack
+RUN . /opt/spack/share/spack/setup-env.sh
+## Make the ESM4 directory
+RUN mkdir -p /opt/ESM4
+## Build the ESM4 from github
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.02 \
+    && cd ESM4/exec \ 
+    && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
+    && cp esm4.1.x /opt/ESM4 \
+    && make clean_all
+## Add the ESM4 executable to the path
+ENV PATH=/opt/ESM4/:${PATH}
+## Add permissions to the ESM4
+RUN chmod 777 /opt/ESM4/esm4.1.x
+

containers/Dockerfile.intel_sources

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+FROM intel/oneapi-hpckit:2021.2-devel-centos8 as builder
+LABEL maintainer "Tom Robinson"
+
+#-------------------------------------------------------------
+## Set up packages needed
+RUN yum update -y 
+RUN yum install -y git
+RUN yum install -y patch
+RUN yum install -y zlib
+RUN yum install -y wget
+RUN yum install -y curl 
+RUN yum install -y m4
+
+## Set compilers
+ENV FC=ifort
+ENV CC=icc
+ENV build=/opt
+ENV IO_LIBS=${build}/io_libs
+## Build zlib and szip and curl
+RUN cd $build \
+&& zlib="zlib-1.2.11" \
+&& rm -rf zlib* \
+&& wget http://www.zlib.net/zlib-1.2.11.tar.gz \
+&& tar xzf zlib-1.2.11.tar.gz \
+&& cd $zlib \
+&& ./configure --prefix=${IO_LIBS} \
+&& make \
+&& make -j 20 install
+ENV CC "icc -fPIC"
+RUN cd $build \
+&& szip="szip-2.1.1" \
+&& rm -rf szip* \
+&& wget https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz \
+&& tar xzf szip-2.1.1.tar.gz \
+&& cd $szip \
+&& ./configure FC=ifort CC=icc --prefix=${IO_LIBS} CPPDEFS="-fPIC" \
+&& make \
+&& make -j 20 install
+RUN cd $build \
+&& curl="curl-7.74.0" \
+&& rm -rf curl* \
+&& wget https://curl.haxx.se/download/${curl}.tar.gz \
+&& tar xzf ${curl}.tar.gz \
+&& cd $curl \
+&& ./configure FC=ifort CC=icc --prefix=${IO_LIBS} \
+&& make \
+&& make -j 20 install
+
+ENV LD_LIBRARY_PATH=${IO_LIBS}/lib:${LD_LIBRARY_PATH}:/opt/io_libs/lib
+
+## Set compilers
+ENV FC=ifort
+ENV CC=icc
+## Install HDF5
+RUN cd /opt \
+&& hdf5="hdf5-1.12.0"  \
+&& wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/${hdf5}/src/${hdf5}.tar.gz \
+&& tar xzf ${hdf5}.tar.gz \
+&& cd $hdf5 \
+&& hdf5_opts="FC=ifort CC=icc --prefix=/opt/hdf5 --enable-fortran --enable-hl" \
+&& ./configure $hdf5_opts \
+&& make -j 20 install \
+&& echo "HDF5 finished building"
+
+#*********************
+## Install NetCDF-C
+#*********************
+ENV LD_LIBRARY_PATH=/opt/hdf5/lib:${LD_LIBRARY_PATH}
+RUN cd /opt \
+&& version="4.7.4" \
+&& netcdfc="netcdf-c-"${version} \
+&& rm -rf netcdf \
+&& wget -O ${netcdfc}.tar.gz https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz \
+&& tar xzf ${netcdfc}.tar.gz \
+&& cd $netcdfc \
+&& ./configure --prefix=/opt/netcdf-c CPPFLAGS='-I/opt/hdf5/include -I${IO_LIBS}/include' LDFLAGS='-L/opt/hdf5/lib -L${IO_LIBS}/lib' --disable-dap \ 
+&& make \
+&& make -j 20 install \
+&& echo " NetCDF-C finished building"
+
+ENV LD_LIBRARY_PATH=/opt/netcdf-c/lib:${LD_LIBRARY_PATH}
+ENV PATH=/opt/netcdf-c/bin:${PATH}
+
+## Install netcdf fortran
+ENV LDFLAGS="-L/opt/netcdf-c/lib -lnetcdf"
+RUN cd /opt \
+&& nfversion=4.5.3 \
+&& netcdff="netcdf-fortran-${nfversion}" \
+&& rm -rf $netcdff \
+&& wget -O ${netcdff}.tar.gz https://github.com/Unidata/netcdf-fortran/archive/v${nfversion}.tar.gz \
+&& tar xzf ${netcdff}.tar.gz \
+&& cd $netcdff \
+&& ./configure CPPFLAGS="-I/opt/netcdf-c/include -I/opt/hdf5/include/" --prefix=/opt/netcdf-fortran \
+&& make \
+&& make -j20 install
+
+ENV PATH=/opt/netcdf-fortran/bin:${PATH}
+
+ENV LD_LIBRARY_PATH=/opt/netcdf-c/lib:/opt/hdf5/lib:/opt/netcdf-fortran/lib:${LD_LIBRARY_PATH}
+ENV LIBRARY_PATH=${LD_LIBRARY_PATH}
+
+## Build the model
+RUN mkdir -p /opt/ESM4
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.02 \
+ && cd ESM4/exec \
+ && make HDF_INCLUDE=-I/opt/hdf5/include \
+ && cp esm4.1.x /opt/ESM4 \
+ && make clean_all
+
+##############################################################################################################
+# Stage 2 with the minimum
+FROM intel/oneapi-runtime:centos8
+RUN ls
+COPY --from=builder /opt/netcdf-c /opt/netcdf-c
+COPY --from=builder /opt/netcdf-fortran /opt/netcdf-fortran
+COPY --from=builder /opt/hdf5 /opt/hdf5
+COPY --from=builder /opt/ESM4 /opt/ESM4
+ENV PATH=/opt/ESM4:/opt/netcdf-fortran/bin:/opt/netcdf-c/bin:${PATH}
+ENV LD_LIBRARY_PATH=/opt/netcdf-c/lib:/opt/hdf5/lib:/opt/netcdf-fortran/lib:/opt/io_libs/lib${LD_LIBRARY_PATH}
+ENV LIBRARY_PATH=${LD_LIBRARY_PATH}
+## Add permissions to the ESM4
+RUN chmod 777 /opt/ESM4/esm4.1.x
+

containers/README.md

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+# ESM4 containers
+This is a very basic *0.1* version of a README for these containers.  Please feel free to
+add to it or open a GitHub issue if there is something missing.
+
+## Building with Docker
+The Dockerfiles are set up to build an ESM4 run using Docker.  There are two Dockerfiles, 
+one to build with intel oneAPI 2021.2 and one to build with GCC 10.2.0
+
+## Building with Singularity
+The Singularity definition files are included to build using intel oneAPI 2021.2 compilers.
+You can build using the singularity_build.sh script
+```bash
+./singularity_build.sh
+```
+
+## Running using singularity
+The containers are all using mpich-compatible MPI, so if you run using singularity bind 
+or hybrid methods, make sure you are using some flavor of mpich and not openmpi.
+
+## Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is
+provided on an 'as is' basis and the user assumes responsibility for
+its use.  DOC has relinquished control of the information and no
+longer has responsibility to protect the integrity, confidentiality,
+or availability of the information.  Any claims against the Department
+of Commerce stemming from the use of its GitHub project will be
+governed by all applicable Federal law.  Any reference to specific
+commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply
+their endorsement, recommendation or favoring by the Department of
+Commerce.  The Department of Commerce seal and logo, or the seal and
+logo of a DOC bureau, shall not be used in any manner to imply
+endorsement of any commercial product or activity by DOC or the United
+States Government.
+
+This project code is made available through GitHub but is managed by
+NOAA-GFDL at https://gitlab.gfdl.noaa.gov.
+

containers/Singularity.esm4

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+Bootstrap: docker
+From: thomasrobinson/centos7-netcdff:4.5.3-c4.7.4-gcc-mpich
+
+Stage: build
+
+%post
+  # Install all the required software
+  . /opt/spack/share/spack/setup-env.sh
+  # Install ESM4
+  git clone --recursive -b 2021.02 https://github.com/NOAA-GFDL/ESM4.git && cd ESM4/exec
+  make gcc=on OPENMP=on SH=sh CLUBB=off
+  mkdir -p /opt/ESM4
+  cp esm4.1.x /opt/ESM4
+
+%environment
+  export PATH=/opt/ESM4:$PATH
+
+%runscript
+  ulimit -s unlimited
+  /opt/ESM4/esm4.1.x
+

containers/Singularity.intel_esm4

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+Bootstrap: localimage
+From: intel_netcdf_ubuntu.sif
+Stage: build
+## Singularity def file used to create ESM4
+
+%post
+ cd /opt
+## Build the ESM4 from github
+ git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.02 
+     cd ESM4/exec 
+     make -j 20 HDF_INCLUDE=-I/opt/hdf5/include HDF_LIBS="-L/opt/hdf5/lib -lhdf5 -lhdf5_fortran -lhdf5_hl -lhdf5hl_fortran" SH=sh
+     cp esm4.1.x /opt/ESM4 
+     make clean_all
+ chmod 777 /opt/ESM4/esm4.1.x
+
+
+Bootstrap: docker
+From: intel/oneapi-runtime:ubuntu18.04
+Stage: final
+
+%files from build
+/opt/hdf5
+/opt/netcdf-c
+/opt/netcdf-fortran
+/opt/ESM4/esm4.1.x
+## Add the ESM4 executable to the path
+%environment
+PATH=/opt/ESM4:/opt/netcdf-c/bin:/opt/netcdf-fortran/bin:${PATH}
+LD_LIBRARY_PATH=/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/intel/oneapi/lib:/opt/intel/oneapi/lib/intel64/:/opt/intel/oneapi/lib/intel64/lib:/opt/intel/oneapi/lib/intel64/libfabric:${LD_LIBRARY_PATH}
+export LIBRARY_PATH=/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/intel/oneapi/lib:/opt/intel/oneapi/lib/intel64/:/opt/intel/oneapi/lib/intel64/lib:/opt/intel/oneapi/lib/intel64/libfabric
+export KMP_STACKSIZE=512m
+export NC_BLKSZ=1M
+export F_UFMTENDIAN=big
+
+## Run ESM4
+%runscript
+ ulimit -s unlimited
+ /opt/ESM4/esm4.1.x
+