Testing script for OpenMPI

scripts/build_environment/GCHP/openmpi/README

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+Testing OpenMPI

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

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+#==============================================================================
+# 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=openmpi
+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/openmpi/install_libraries.sh

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+#!/bin/bash
+# Tested on ubuntu 18.04 LTS (ami-0ac019f4fcb7cb7e6)
+
+# =========================
+# Additional fixes for GCHP
+# =========================
+sudo apt-get update
+
+# All libraries need for GCHP. f2py and mpich are new libraries in addition to GC-classic.
+sudo apt-get install -y bc gcc gfortran \
+    libnetcdf-dev libnetcdff-dev netcdf-bin \
+    python-numpy libopenmpi-dev
+
+# Ubuntu AMI has vim and nano but no emacs
+sudo apt-get install -y emacs
+
+# Pull S3 data without installing anaconda Python
+sudo apt-get install -y awscli
+
+# clean up cache
+sudo apt-get clean
+sudo rm -rf /var/lib/apt/lists/*
+
+# =========================
+# Additional fixes for GCHP
+# =========================
+
+# 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