Successfully compile and run GCHP on ubuntu 18.04 with gcc 7.3.0

scripts/build_environment/GCHP/deploy_GCHP.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
-GC_VERSION=12.1.0
+GC_VERSION=b544322
 GCHP_VERSION=12.1.0
 
 # Input data directory, need to pull real data later
-mkdir -p ~/ExtData/HEMCO
+mkdir -p $HOME/ExtData/HEMCO
 
 # Create tutorial folder for demo project
 mkdir ~/tutorial
@@ -13,31 +13,32 @@ cd ~/tutorial
 # Source code
 git clone https://github.com/geoschem/geos-chem.git Code.GCHP
 cd Code.GCHP
-git checkout -b $GC_VERSION
+git checkout $GC_VERSION
 
 # GCHP subdirectory
 git clone https://github.com/geoschem/gchp.git GCHP
 cd GCHP
-git checkout -b $GCHP_VERSION
+git checkout $GCHP_VERSION
 
+# generate run directory
 cd Run
 rm ${HOME}/.geoschem/config
-echo "$HOME/ExtData
-2
-1
-$HOME/tutorial
-gchp_standard
-n" | ./createRunDir.sh
+printf "$HOME/ExtData \n 2 \n 1 \n $HOME/tutorial \n gchp_standard \n n" | ./createRunDir.sh
 
+# compile source code
 cd ~/tutorial/gchp_standard
+ln -s gchp.env  ~/gchp.ubuntu.env  # need to copy ubuntu/gchp.ubuntu.env
+make compile_clean
 
-ln -sf /home/ec2-user/ExtData/GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.c24_standard.nc  initial_GEOSChem_rst.c24_standard.nc 
 
-# read low-resolution metfields to save space
-ln -sf /home/ec2-user/ExtData/GEOS_4x5/GEOS_FP MetDir
+# modify run-time configurations
+
+# correctly link restart file
+ln -sf $HOME/ExtData/GEOSCHEM_RESTARTS/v2018-11/initial_GEOSChem_rst.c24_standard.nc  initial_GEOSChem_rst.c24_standard.nc 
 
-# only scan the first few lines, do not modify non-metfields
-sed -i -e 1,120s/025x03125.nc/4x5.nc/g ExtData.rc
+# read low-resolution metfields to save space
+ln -sf $HOME/ExtData/GEOS_4x5/GEOS_FP MetDir 
+sed -i -e 1,120s/025x03125.nc/4x5.nc/g ExtData.rc # only scan the first few lines, do not modify non-metfields
 
 # hard to see why simulation crashes with default debug level 0
 sed -i -e "s#DEBUG_LEVEL.*#DEBUG_LEVEL: 5#" CAP.rc

scripts/build_environment/GCHP/ubuntu/gchp.ubuntu.env

@@ -0,0 +1,77 @@
+#==============================================================================
+# Environment variables
+#==============================================================================
+
+# Specify compilers
+export CC=gcc
+export OMPI_CC=$CC
+
+export CXX=g++
+export OMPI_CXX=$CXX
+
+export FC=gfortran
+export F77=$FC
+export F90=$FC
+export OMPI_FC=$FC
+export COMPILER=$FC
+export ESMF_COMPILER=gfortran
+
+# MPI Communication
+export ESMF_COMM=mpich2
+export MPI_ROOT=$( dirname $( dirname $( which mpirun ) ) ) 
+
+# Base paths
+export NETCDF_HOME=/usr
+export NETCDF_FORTRAN_HOME=/usr
+
+export GC_BIN="$NETCDF_HOME/bin"
+export GC_INCLUDE="$NETCDF_HOME/include"
+export GC_LIB="$NETCDF_HOME/lib"
+
+# Add to primary path
+export PATH=${NETCDF_HOME}/bin:$PATH
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${NETCDF_HOME}/lib
+
+# If using NetCDF after the C/Fortran split (4.3+), then you will need to
+# specify the following additional environment variables
+export GC_F_BIN="$NETCDF_FORTRAN_HOME/bin"
+export GC_F_INCLUDE="$NETCDF_FORTRAN_HOME/include"
+export GC_F_LIB="$NETCDF_FORTRAN_HOME/lib"
+export PATH=${NETCDF_FORTRAN_HOME}/bin:$PATH
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${NETCDF_FORTRAN_HOME}/lib
+
+# Set ESMF optimization (g=debugging, O=optimized (capital o))
+export ESMF_BOPT=O
+
+#==============================================================================
+# Raise memory limits
+#==============================================================================
+
+ulimit -c unlimited              # coredumpsize
+ulimit -l unlimited              # memorylocked
+ulimit -u 50000                  # maxproc
+ulimit -v unlimited              # vmemoryuse
+
+#==============================================================================
+# additional fixes for MAPL
+#==============================================================================
+export GC_CODE_DIR=$HOME/tutorial/Code.GCHP
+
+# --- Fixes for Makefile ---
+# Dependencies files *.d in MAPL are messed up in that
+# 1. It directly specifies library headers like mpi.h as dependency, which should have been handled by MPI wrapper like mpicc.
+# 2. It cannot find *.mod files that are in another directory.
+# VPATH allows makefile to search additional directories, although is not a good practice.
+# This prevents the error "no rule to make target"
+export VPATH=/usr/include/x86_64-linux-gnu:$VPATH # sys/resource.h
+export VPATH=$GC_CODE_DIR/GCHP/Shared/MAPL_Base:$VPATH # mapl_*.mod
+export VPATH=$GC_CODE_DIR/GCHP/ESMF/Linux/mod:$VPATH # esmf.mod
+
+# --- Fixed for header files ("#include <xxx.h>" statement) ---
+# This prevents the error "cannot find..."
+export CPATH=$GC_CODE_DIR/GCHP/Shared/MAPL_Base:$CPATH # MAPL_Generic.h
+export CPATH=$GC_CODE_DIR/GCHP/Shared/GFDL_fms/shared/include:$CPATH # fms_platform.h
+
+# --- Fixes for module files ("USE xxx" statement) ---
+# zonal.f is looking for mapl_constantsmod.mod in its own directory. Even /usr/include/ is not included
+sudo ln -sf $GC_CODE_DIR/GCHP/Shared/MAPL_Base/mapl_constantsmod.mod $GC_CODE_DIR/GCHP/Shared/GEOS_Util/plots/

scripts/build_environment/GCHP/ubuntu/install_libraries.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+# Tested on ubuntu 18.04 LTS (ami-0ac019f4fcb7cb7e6)
+sudo apt-get update
+
+# The quickest way to install NetCDF libraries. Can compile GEOS-Chem classic.
+sudo apt-get install -y bc gcc gfortran \
+    libnetcdf-dev libnetcdff-dev netcdf-bin \
+    python-numpy mpich
+
+sudo ln -s /usr/include/mpich/* /usr/include/ # so that MAPL can find header files
+
+# GCHP directly uses `gmake` command, which is not available on ubuntu
+# https://ubuntuforums.org/showthread.php?t=1811030
+sudo ln -s /usr/bin/make /usr/bin/gmake
+
+# hemco_standalone.x and geos both links -lmpichf9 which doesn't exist.
+sudo ln -s /usr/lib/mpich/lib/libmpichfort.so /usr/lib/mpich/lib/libmpichf90.so
+sudo ln -s /usr/lib/mpich/lib/libmpichfort.a /usr/lib/mpich/lib/libmpichf90.a