Merge pull request #8 from thomas-robinson/2021.03Update

2021.03 update container definition files

README.md

@@ -1,9 +1,9 @@
 # Earth System Model 4
 
 ## What Is Included
-* [src/]((https://github.com/NOAA-GFDL/ESM4/tree/master/src) source code for the ESM4 model (all code is in submodules)
-* [exec/]((https://github.com/NOAA-GFDL/ESM4/tree/master/exec) Makefiles to compile the code 
-* [run/]((https://github.com/NOAA-GFDL/ESM4/tree/master/run) Simple run script
+* [src]((https://github.com/NOAA-GFDL/ESM4/tree/master/src) source code for the ESM4 model (all code is in submodules)
+* [exec]((https://github.com/NOAA-GFDL/ESM4/tree/master/exec) Makefiles to compile the code 
+* [run]((https://github.com/NOAA-GFDL/ESM4/tree/master/run) Simple run script
 
 ## Cloning
 To clone the ESM4 model please use the recursive option

container/Dockerfile

@@ -6,7 +6,7 @@ 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 \
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.03 \
     && cd ESM4/exec \ 
     && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
     && cp esm4.1.x /opt/ESM4 \

container/Dockerfile.gnu

@@ -6,7 +6,7 @@ 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 \
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.03 \
     && cd ESM4/exec \ 
     && make gcc=on HDF_INCLUDE=-I/opt/hdf5/include SH=sh CLUBB=off \
     && cp esm4.1.x /opt/ESM4 \

container/Dockerfile.intel_sources

@@ -101,7 +101,7 @@ 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 \
+RUN git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.03 \
  && cd ESM4/exec \
  && make 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 \

container/Singularity.esm4

@@ -7,7 +7,7 @@ Stage: build
   # 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
+  git clone --recursive -b 2021.03 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

container/Singularity.intel_esm4

@@ -1,18 +1,19 @@
 Bootstrap: localimage
-From: intel_netcdf_ubuntu.sif
+From: intel2021.2_netcdfc4.7.4_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 
+ git clone --recursive https://github.com/NOAA-GFDL/ESM4.git -b 2021.03
      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
+     make -j 20 HDF_INCLUDE=-I/opt/hdf5/include HDF_LIBS="-L/opt/hdf5/lib -lhdf5 -lhdf5_fortran -lhdf5_hl -lhdf5hl_fortran"
      cp esm4.1.x /opt/ESM4 
-     make clean_all
  chmod 777 /opt/ESM4/esm4.1.x
 
+## Move FMS to opt
+cp -r fms /opt
 
 Bootstrap: docker
 From: intel/oneapi-runtime:ubuntu18.04
@@ -22,12 +23,13 @@ Stage: final
 /opt/hdf5
 /opt/netcdf-c
 /opt/netcdf-fortran
+/opt/fms
 /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
+LD_LIBRARY_PATH=/opt/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/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

container/Singularity.intel_netcdf

@@ -1,14 +1,20 @@
 Bootstrap: docker
-From: intel/oneapi-hpckit:devel-ubuntu18.04 
+From: intel/oneapi-hpckit:2021.2-devel-ubuntu18.04 
 Stage: build
 
 %post
 ## Set up oneAPI
   apt-get -yqq update  
   apt-get -yqq upgrade
-  apt-get -yqq install git make
+  apt-get -yqq install git
+  apt-get -yqq install make
   apt-get -yqq install wget
   apt-get -yqq install m4
+  apt-get -yqq install autoconf
+  apt-get -yqq install automake
+  apt-get -yqq install libtool
+  apt-get -yqq install autogen
+  apt-get -yqq install intltool
 # use wget to fetch the Intel repository public key
 # cd /tmp
 # wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB

container/singularity_build.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-singularity build -f intel_netcdf_ubuntu.sif Singularity.intel_netcdf
-singularity build -f esm4_2021.02_ubuntu_intel.sif Singularity.intel_esm4
+singularity build -f intel2021.2_netcdfc4.7.4_ubuntu.sif Singularity.intel_netcdf
+singularity build -f esm4_2021.03_ubuntu_intel.sif Singularity.intel_esm4