Merge pull request #40 from fetch4/docs7_setup

Document build process for GISS-GC

doc/GISS-GC-DOC/build_on_linux_laptop.md

@@ -0,0 +1,390 @@
+## Building GISS-GC on a laptop with a Linux operating system
+
+#### Step 1: Basic setup
+
+> [!INFO] Do this the first time only.
+
+Choose the location where GISS-GC will exist (e.g., `~/software/GISS-GC`) and use it to define the `${GISS_HOME}` environment variable:
+```sh
+export GISS_HOME=${HOME}/software/GISS-GC
+```
+
+Checkout the GISS-GC repository into the `${GISS_HOME}` location and set up its submodules:
+```sh
+git clone [email protected]:fetch4/GISS-GC.git ${GISS_HOME}
+cd ${GISS_HOME}
+git checkout develop
+git submodule init
+git submodule update
+```
+
+In the directory, create a script `setup.sh` for defining modules to be loaded and various paths required for the GISS-GC build. Copy and paste the following code block into the script, noting that a few entries will require modification:
+```sh
+#!/bin/bash
+
+# ============================================================================ #
+# Activate the Python and Spack environments used by GISS-GC.                  #
+# ============================================================================ #
+
+# Environment variables for GISS modelE
+export SOFTWARE=${HOME}/software          # NOTE: Edit if you're using a different location for software
+export GISS_HOME=${SOFTWARE}/GISS-GC      # NOTE: This should be consistent with the location you cloned GISS-GC to
+export ModelE_Support=${HOME}/run/giss-gc # NOTE: Edit if you're using a different run directory location
+mkdir -p ${ModelE_Support}/exec
+mkdir -p ${ModelE_Support}/huge_space
+mkdir -p ${ModelE_Support}/prod_decks
+mkdir -p ${ModelE_Support}/prod_input_files
+mkdir -p ${ModelE_Support}/prod_runs
+# Misc. environment variables
+export F_UFMTENDIAN=big
+export KMP_STACKSIZE=100000000
+export OMP_NUM_THREADS=36
+
+# Spack environment # NOTE: Edit MPI_ROOT to match the path to your Spack-installed MPI distribution
+spack env activate -p giss-gc
+export MPI_ROOT=${SOFTWARE}/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/openmpi-4.1.6-s3fu5gvaasgjy4jecnb6rvemx7oofexx
+
+# Environment variables for passing NetCDF-C paths to GEOS-Chem
+export NETCDF_HOME=$(nc-config --prefix)
+export GC_BIN=${NETCDF_HOME}/bin
+export GC_INCLUDE=${NETCDF_HOME}/include
+export GC_LIB=${NETCDF_HOME}/lib
+
+# Environment variables for passing NetCDF-Fortran paths to GEOS-Chem
+export NETCDF_F_HOME=$(nf-config --prefix)
+export GC_F_BIN=${NETCDF_F_HOME}/bin
+export GC_F_INCLUDE=${NETCDF_F_HOME}/include
+export GC_F_LIB=${NETCDF_F_HOME}/lib
+
+# GEOS-Chem input data # NOTE: Edit if you are storing this somewhere else
+export ROOT=${ModelE_Support}/prod_input_files/ExtData/HEMCO/
+
+# Add modelE tools to path
+export PATH=${HOME}/software/tools/mk_diags:${PATH}
+```
+
+> [!WARNING] Don't `source` the script yet because we need to set up Spack first.
+
+
+#### Step 2: Setup Spack environment for GISS-GC
+
+> [!INFO] Do this the first time only.
+
+Install the Spack package manager using the [instructions](https://spack-tutorial.readthedocs.io/en/latest/tutorial_basics.html) online, if you don't already have it. I put it in `~/software/spack`.
+
+Create a Spack configuration in `${GISS_HOME}/spack.yaml` and copy and paste the
+following code block into it. Note that you may need to adjust the compiler,
+compiler version, and operating system.
+```yaml
+spack:
+  packages:
+    all:
+      compiler: [[email protected]]
+  container:
+    images:
+      os: ubuntu:22.04
+      spack: '0.21'
+  specs:
+  - cmake
+  - gmake
+  - hdf5
+  - netcdf-c+mpi+parallel-netcdf
+  - netcdf-fortran
+  - openmpi
+  concretizer:
+    unify: true
+  config:
+    install_missing_compilers: true
+  compilers:
+  - compiler:
+      spec: gcc@=11.4.0
+      paths:
+        cc: /bin/gcc
+        cxx: /bin/g++
+        f77: /bin/gfortran
+        fc: /bin/gfortran
+      flags: {}
+      operating_system: ubuntu22.04
+      target: x86_64
+      modules: []
+      environment: {}
+      extra_rpaths: []
+```
+Note that this will create a file `~/.spack/linux/compilers.yaml` containing the
+compiler specification.
+
+Create a Spack environment off the YAML file with
+```sh
+cd ${GISS_HOME}
+spack env create giss-gc spack.yaml
+```
+
+With the Spack environment active, install the packages required by the Spack
+environment with
+```sh
+spack install
+```
+This may take an hour or so.
+
+Run
+```sh
+source ${GISS_HOME}/setup.sh
+```
+and check that `${MPI_ROOT}`, `${NETCDF_HOME}`, and `${NETCDF_F_HOME}` (for example) are valid paths. The activation of the Spack environment should result in your command line prompt being prefaced with `[giss-gc]`, possibly in a different colour.
+
+
+#### Step 3: Build GISS tools and put them in the path
+
+> [!INFO] Do this the first time only.
+
+GISS comes with some tools (e.g., for post-processing diagnostics) which need to be compiled.
+We already added this location to the path in `setup.sh`.
+```sh
+# source ${GISS_HOME}/setup.sh
+cp -rp ${GISS_HOME}/model/mk_diags ${HOME}/software/tools
+cd ${HOME}/software/tools/mk_diags
+/bin/bash compscr
+```
+
+#### Step 4: Create `~/.modelErc`
+
+> [!INFO] Do this the first time only.
+
+GISS is configured using a global `~/.modelErc` file. This is created as follows:
+```sh
+# source ${GISS_HOME}/setup.sh
+cd ${GISS_HOME}/decks
+make config COMPILER=${FC} ModelE_Support=${ModelE_Support}
+```
+
+Tweak `~/.modelErc` as follows:
+```diff
+# This file contains global options for modelE. 
+# By default it assumes that the directory structure for modelE runs
+# is set under /scratch/jwallwo2/run .
+
+## Directory structure ##
+
+# DECKS_REPOSITORY - a directory for permanenet storage of run info.
+# All rundecks that you create will be copied to this directory. 
+-DECKS_REPOSITORY=/scratch/jwallwo2/run/prod_decks
++DECKS_REPOSITORY=${ModelE_Support}/prod_decks
+
+# CMRUNDIR - directory to which all run directories will be linked.
+# This directory will be searched by most scripts for locations of 
+# specific runs.
+-CMRUNDIR=/scratch/jwallwo2/run/prod_runs
++CMRUNDIR=${ModelE_Support}/prod_runs
+
+# GCMSEARCHPATH - directory to search for gcm input files.
+# All necessary input files should be copied or linked to this directory.
+-GCMSEARCHPATH=/scratch/jwallwo2/run/prod_input_files
++CMSEARCHPATH=${ModelE_Support}/prod_input_files
+
+# EXECDIR - path to directory with modelE scripts and with some
+# executables. This directory should contain the scripts from modelE/exec.
+-EXECDIR=/scratch/jwallwo2/run/exec
++EXECDIR=${ModelE_Support}/exec
+
+# SAVEDISK - a directory where all run directories (which will contain
+# all output files such as rsf, acc etc.) will be created. This should
+# be big enough to accomodate all model output.
+-SAVEDISK=/scratch/jwallwo2/run/huge_space
++SAVEDISK=${ModelE_Support}/huge_space
+
+## External libraries ##
+
+# Some of these options can be provided by environment modules (if you 
+# use them). Specify here only what is necessary. Options specified 
+# here will overwrite options proviided by environment modules.
+
+# NETCDFHOME - path to location of netcdf installation directory.
+-# NETCDFHOME=/opt/netcdf/3.6.3
++NETCDFHOME=${NETCDF_F_HOME}
+
+# MPI - set to YES if you want to compile the model for parallel 
+# execution on multiple CPU cores. Keep in mind, that functional 
+# MPI library should be installed on your computer and its type 
+# and location should be specified below.
+# This option can be overwritten from the compile line.
+-MPI=NO
++MPI=YES
+
+# MPIDISTR - the MPI distribution you are using. Currently supported 
+# distributions are: 'intel, 'openmpi', 'mpich2', 'mvapich2', 'SCALI',
+# 'mpt' 
+-# MPIDISTR=openmpi
++MPIDISTR=openmpi
+
+# MPIDIR - path to the MPI installation directory. (Needs to be set
+# only if compiler can't find correct MPI library and include files by
+# default)
+-# MPIDIR=/opt/openmpi
++MPIDIR=${MPI_ROOT}
+
+# MPILIBDIR - path to the location of MPI library. Set it only if 
+# it is different from the default $MPIDIR/lib
+# MPILIBDIR=/opt/openmpi/lib
+
+# MPIINCLUDEDIR - path to location of MPI include files. Set it only
+# if it is different from the default $MPIDIR/include
+# MPIINCLUDEDIR=/opt/openmpi/include
+
+# ESMF5_DIR - path to the installation directory of ESMF (version 5)
+# library. (Required only for Cubed Sphere simulations)
+# ESMF5_DIR=
+
+# ESMF_BOPT - optimization level of ESMF library. (Should only be used
+# togeteher with ESMF5_DIR)
+# ESMF_BOPT=O
++ESMF=NO
+
+## Architecture and compiler
+
+# ABI - Application Binary Interfaces. This variable specifies the
+# architecture you are using. The valid values are '64' and '32'. 
+# On most modern systems you should use '64'. Use '32' if your
+# hardware or compiler support only 32-bit binaries.
+ABI=64
+
+# COMPILER - specifies the Fortran compiler you are using. Currently
+# only 'intel' and 'gfortran' are supported. ('nag' has partial
+# support on development branch.) If you are using Modules for
+# Environment Management, then this variable may already be set in the
+# environment. In this case you don't need to set it here.
+-# COMPILER=gfortran
++COMPILER=gfortran
+
+## General User Preferences ##
+
+# MAILTO - email address of the user. When the program ends/crashes
+# all notifications will be sent to this address. Leave empty 
+# or unset if you don't want to receive these emails
+MAILTO=
+
+# UMASK - the value of 'umask' you want to use for model runs. The files
+# inside the run directory will have permissions set according to this
+# mask.
+UMASK=002
+
+# OVERWRITE - can "gmake rundeck" overwrite files already in repository?
+# (i.e. in the directory DECKS_REPOSITORY)
+OVERWRITE=NO
+
+# OUTPUT_TO_FILES - if set to YES all errors and warnings will be sent
+# to files with the names <source_name>.ERR
+OUTPUT_TO_FILES=NO
+
+# VERBOSE_OUTPUT - if set to YES gmake will show compilation commands
+# and some other information. Otherwise most of the output will be
+# suppressed
+VERBOSE_OUTPUT=YES
+```
+
+#### Step 5: Get the rundeck
+
+> [!INFO] Do this the first time only.
+
+GISS uses 'rundecks' for configuring the model, including setting up preprocessors. These should live within the `${GISS_HOME}/decks` subdirectory. Currently, we are using the `GISS_GC_14.R` rundeck.
+This can be found at `.github/rundecks/GISS_GC_14.R`.
+
+
+#### Step 6: Download the data
+
+> [!INFO] Do this the first time only.
+
+We aren't actually going to be able to run the model on our laptops, so it's sufficient to just create empty files with the expected names:
+
+```sh
+export DATA=${ModelE_Support}/prod_input_files
+touch ${DATA}/CD144X90.ext.nc
+touch ${DATA}/cloud.epsilon4.72x46
+touch ${DATA}/CO2profile.Jul16-2017.txt
+touch ${DATA}/CROPS_and_pastures_Pongratz_to_Hurtt_144X90N_nocasp.nc
+touch ${DATA}/dH2O_by_CH4_monthly
+touch ${DATA}/GHG.CMIP6.1-2014.txt
+touch ${DATA}/GIC.144X90.DEC01.1.ext_1.nc
+touch ${DATA}/GLMELT_144X90_gas.OCN.nc
+touch ${DATA}/H2Ocont_MT_CKD
+touch ${DATA}/Irrig144x90_1848to2100_FixedFuture_v3.nc
+touch ${DATA}/ISCCP.tautables
+touch ${DATA}/LWCorrTables33k
+touch ${DATA}/LWTables33k_lowH2O_CO2_O3_planck_1-800
+touch ${DATA}/miescatpar.abcdv2
+touch ${DATA}/MSU_SSU_RSS_weights.txt
+touch ${DATA}/NCARIC.144x90.D7712010_ext.nc
+touch ${DATA}/o3_2010_shindell_144x90x49_April1850.nc
+touch ${DATA}/oct2003.relhum.nr.Q633G633.table
+touch ${DATA}/OST_144x90.1876-1885avg.CMIP6.nc
+touch ${DATA}/RD_Fd.nc
+touch ${DATA}/RD_Fd.names.txt
+touch ${DATA}/REG2X2.5
+touch ${DATA}/S144X900098M.ext.nc
+touch ${DATA}/sgpgxg.table8
+touch ${DATA}/SICE_144x90.1876-1885avg.CMIP6.nc
+touch ${DATA}/soil_textures_top30cm_2x2.5
+touch ${DATA}/soilcarb_top30cm_2x2.5.nc
+touch ${DATA}/solar.CMIP6official.ann1850-2299_with_E3_fastJ.nc
+touch ${DATA}/STRATAER.VOL.1850-2014_CMIP6_hdr
+touch ${DATA}/top_index_144x90_a.ij.ext.nc
+touch ${DATA}/topcld.trscat8
+touch ${DATA}/V144x90_EntMM16_height_trimmed_scaled_ext.nc
+touch ${DATA}/V144x90_EntMM16_lai_max_trimmed_scaled_ext.nc
+touch ${DATA}/V144x90_EntMM16_lai_trimmed_scaled_ext.nc
+touch ${DATA}/V144x90_EntMM16_lc_max_trimmed_scaled_nocrops.ext.nc
+touch ${DATA}/Z2HX2fromZ1QX1N.BS1.nc
+touch ${DATA}/ZSIfac_144x90.1876-1885avg.CMIP6.nc
+touch ${DATA}/ZVAR2X25A.nc
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCA
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCB
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCdalbsn
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/DUST
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/NIT
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/O3
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/OCA
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/SSA
+mkdir -p ${DATA}/cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/SUL
+mkdir -p ${DATA}/nudging/merra2
+touch ${DATA}/nudging/merra2/uwnd.2014.MERRA2onGISSE2.nc4
+touch ${DATA}/nudging/merra2/vwnd.2014.MERRA2onGISSE2.nc4
+touch ${DATA}/nudging/merra2/uwnd.2015.MERRA2onGISSE2.nc4
+touch ${DATA}/nudging/merra2/vwnd.2015.MERRA2onGISSE2.nc4
+touch ${DATA}/nudging/merra2/uwnd.2016.MERRA2onGISSE2.nc4
+touch ${DATA}/nudging/merra2/vwnd.2016.MERRA2onGISSE2.nc4
+```
+#### Step 7: Compile
+
+> [!CHECK] Do this every time.
+
+Create an executable `build.sh` script in `${GISS_HOME}` with the following contents:
+```sh
+#!/bin/bash
+
+# Default value for MP
+MP=NO
+
+# Check if an argument is provided
+if [ $# -gt 0 ]; then
+  MP=$1
+fi
+
+# Check the RUNID environment variable is set
+if [ -z "${RUNID}" ]; then
+  echo "Error: RUNID environment variable is not set."
+  exit 1
+fi
+
+cd decks/
+# make clean
+make -j setup RUN=${RUNID} F90=mpif90 GC=YES MP=${MP} MPI=YES
+cd -
+```
+and run it with `./build.sh`.
+
+Notes:
+* Run with `./build.sh MP=YES` to compile with OpenMP shared memory parallelism
+* Uncomment the `make clean` line to build from scratch.
+
+#### Step 8: Run the model
+
+> [!DANGER] Do not attempt to run the model on your laptop - it will require far too much RAM.