Merge pull request #41 from thomas-robinson/2021.03Updates

2021.03 updates

README.md

@@ -70,6 +70,14 @@ The following components are available in the
 
 ## Building AM4
 
+###Containers
+The [container folder](container) provides example Dockerfiles and Signularity 
+definition files to use to build AM4 containers using either GCC/GFORTAN or 
+Intel oneAPI. There is a script that can be used to build the intel 
+singularity containers, and the first step of this script can be used with the
+other GFDL climate models. 
+
+### From source
 The [exec](exec) directory contains Makefiles that can be used to
 build the AM4 executable.  These Makefiles were generated using the
 [Make Makefile (mkmf)](https://github.com/NOAA-GFDL/mkmf) program.

container/Dockerfile

@@ -1,18 +1,123 @@
-FROM thomasrobinson/centos7-netcdff:4.5.3-c4.7.4-gcc-mpich-slurm
-## Dockerfile used to create AM4
+FROM intel/oneapi-hpckit:2021.2-devel-centos8 as builder
+LABEL maintainer "Tom Robinson"
 
-## Set up spack
-RUN . /opt/spack/share/spack/setup-env.sh
-## Make the AM4 directory
+#-------------------------------------------------------------
+## 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/AM4
-## Build the AM4 from github
-RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.02 \
-    && cd AM4/exec \ 
-    && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
-    && cp am4_xanadu_2021.02.x /opt/AM4 \
-    && make clean_all
-## Add the AM4 executable to the path
-ENV PATH=/opt/AM4/:${PATH}
+RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.03 \
+ && cd AM4/exec \
+ && make HDF_INCLUDE=-I/opt/hdf5/include \
+ && cp am4_xanadu_2021.03.x /opt/AM4 \
+ && make clean_all
+
+##############################################################################################################
+# Stage 2 with the minimum
+FROM intel/oneapi-runtime:centos8
+RUN ls
+COPY --from=builder /opt/netcdf-c /opt/netcdf-c
+COPY --from=builder /opt/netcdf-fortran /opt/netcdf-fortran
+COPY --from=builder /opt/hdf5 /opt/hdf5
+COPY --from=builder /opt/AM4 /opt/AM4
+ENV PATH=/opt/AM4:/opt/netcdf-fortran/bin:/opt/netcdf-c/bin:${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 AM4
-RUN chmod 777 /opt/AM4/am4_xanadu_2021.02.x
+RUN chmod 777 /opt/AM4/am4_xanadu_2021.03.x
 

container/Dockerfile.gnu

@@ -6,13 +6,13 @@ RUN . /opt/spack/share/spack/setup-env.sh
 ## Make the AM4 directory
 RUN mkdir -p /opt/AM4
 ## Build the AM4 from github
-RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.02 \
+RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.03 \
     && cd AM4/exec \ 
     && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
-    && cp am4_xanadu_2021.02.x /opt/AM4 \
+    && cp am4_xanadu_2021.03.x /opt/AM4 \
     && make clean_all
 ## Add the AM4 executable to the path
 ENV PATH=/opt/AM4/:${PATH}
 ## Add permissions to the AM4
-RUN chmod 777 /opt/AM4/am4_xanadu_2021.02.x
+RUN chmod 777 /opt/AM4/am4_xanadu_2021.03.x
 

container/Dockerfile.intel_sources

@@ -101,10 +101,10 @@ ENV LIBRARY_PATH=${LD_LIBRARY_PATH}
 
 ## Build the model
 RUN mkdir -p /opt/AM4
-RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.02 \
+RUN git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.03 \
  && cd AM4/exec \
  && make HDF_INCLUDE=-I/opt/hdf5/include \
- && cp am4_xanadu_2021.02.x /opt/AM4 \
+ && cp am4_xanadu_2021.03.x /opt/AM4 \
  && make clean_all
 
 ##############################################################################################################
@@ -119,5 +119,5 @@ ENV PATH=/opt/AM4:/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 AM4
-RUN chmod 777 /opt/AM4/am4_xanadu_2021.02.x
+RUN chmod 777 /opt/AM4/am4_xanadu_2021.03.x
 

container/Singularity.gnu

@@ -10,12 +10,12 @@ Stage: build
  mkdir -p /opt/AM4
  cd /opt
 ## Build the AM4 from github
- git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.02 
+ git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.03 
      cd AM4/exec 
      make -j 20 gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off 
-     cp am4_xanadu_2021.02.x /opt/AM4 
+     cp am4_xanadu_2021.03.x /opt/AM4 
      make clean_all
- chmod 777 /opt/AM4/am4_xanadu_2021.02.x
+ chmod 777 /opt/AM4/am4_xanadu_2021.03.x
 
 ## Add the AM4 executable to the path
 %environment
@@ -24,5 +24,5 @@ ENV PATH=/opt/AM4/:${PATH}
 ## Run AM4
 %runscript
  ulimit -s unlimited
- /opt/AM4/am4_xanadu_2021.02.x
+ /opt/AM4/am4_xanadu_2021.03.x
 

container/Singularity.intel_am4

@@ -8,35 +8,33 @@ LD_LIBRARY_PATH=/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/int
 export PATH=${PATH}:/opt/netcdf-c/bin:/opt/netcdf-fortran/bin
  cd /opt
 ## Build the AM4 from github
- git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b main 
+ git clone --recursive https://github.com/NOAA-GFDL/AM4.git -b 2021.03
      cd AM4/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 am4_xanadu_2021.03.x /opt/AM4 
-     make clean_all
  chmod 777 /opt/AM4/am4_xanadu_2021.03.x
 
-
-Bootstrap: docker
-From: intel/oneapi-runtime:ubuntu18.04
-Stage: final
-
-%files from build
-/opt/hdf5
-/opt/netcdf-c
-/opt/netcdf-fortran
-/opt/AM4/am4_xanadu_2021.03.x
-/opt/AM4/exec/fms/build/libFMS/.libs/
-## Add the AM4 executable to the path
-%environment
-PATH=/opt/AM4:/opt/netcdf-c/bin:/opt/netcdf-fortran/bin:${PATH}
-LD_LIBRARY_PATH=/opt/AM4/exec/fms/build/libFMS/.libs:/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/intel/oneapi/lib:/opt/intel/oneapi/lib/intel64/:/opt/intel/oneapi/lib/intel64/lib:/opt/intel/oneapi/lib/intel64/libfabric:${LD_LIBRARY_PATH}
-export LIBRARY_PATH=/opt/AM4/exec/fms/build/libFMS/.libs:/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
+### The two stage build with intel runtime libs is currently not working.
+#Bootstrap: docker
+#From: intel/oneapi-runtime:ubuntu18.04
+#Stage: final
+#
+#%files from build
+#/opt/hdf5
+#/opt/netcdf-c
+#/opt/netcdf-fortran
+#/opt/AM4/am4_xanadu_2021.03.x
+#/opt/AM4/exec/fms/build/libFMS/.libs
+### Add the AM4 executable to the path
+#%environment
+#PATH=/opt/AM4:/opt/netcdf-c/bin:/opt/netcdf-fortran/bin:${PATH}
+#LD_LIBRARY_PATH=/opt/AM4/exec/fms/build/libFMS/.libs:/opt/netcdf-c/lib:/opt/netcdf-fortran/lib:/opt/hdf5/lib:/opt/intel/oneapi/lib:/opt/intel/oneapi/lib/intel64/:/opt/intel/oneapi/lib/intel64/lib:/opt/intel/oneapi/lib/intel64/libfabric:/opt/intel/oneapi/mkl/2021.2.0/lib/intel64:${LD_LIBRARY_PATH}
+#export LIBRARY_PATH=/opt/AM4/exec/fms/build/libFMS/.libs:/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:/opt/intel/oneapi/mkl/2021.2.0/lib/intel64
+#export KMP_STACKSIZE=512m
+#export NC_BLKSZ=1M
+#export F_UFMTENDIAN=big
 
 ## Run AM4
 %runscript
  ulimit -s unlimited
  /opt/AM4/am4_xanadu_2021.03.x
-