Build & Run GEOS on desktop

Requirements

tcsh for GEOS workflow
A gcc/g++/gfortran compiler (gcc-12 is our current workhorse in Linux. macOS has been tested using gcc-14 via Homebrew)
- As of macOS Sequoia 15.5, clang/clang++ can also be used in place of gcc/g++.
If using macOS, Homebrew is needed to install certain packages

# *** If building on Linux ***
sudo apt install g++ gcc gfortran
# If you have multiple installation, you might have to set the preferred
# compiler using the combo:
# sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12
# sudo update-alternatives --config gcc

# *** If building on macOS, use Homebrew to install gcc-14 to access gfortran***
brew install gcc@14

A cuda toolkit if GPU backends will be used. (nvhpc/23.5+ or appropriate for your hardware)
Use lmod to manipulate the stack with module like on HPCs: https://lmod.readthedocs.io/en/latest/030_installing.html

sudo apt install -y lua5.3 lua-bit32 lua-posix lua-posix-dev liblua5.3-0 liblua5.3-dev tcl tcl-dev tcl8.6 tcl8.6-dev libtcl8.6
wget https://github.com/TACC/Lmod/archive/refs/tags/8.7.37.tar.gz
tar -xvf 8.7.37.tar.gz
cd Lmod-8.7.37/
sudo ./configure --prefix=/opt/apps
sudo make install
sudo ln -s /opt/apps/lmod/lmod/init/profile        /etc/profile.d/z00_lmod.sh
sudo ln -s /opt/apps/lmod/lmod/init/cshrc          /etc/profile.d/z00_lmod.csh
sudo ln -s /opt/apps/lmod/lmod/init/profile.fish   /etc/fish/conf.d/z00_lmod.fish

# On macOS, lmod can be installed via Homebrew without the above commands
brew install lmod

For macOS, install the following additional packages via Homebrew
- brew install automake autoconf libtool texinfo m4 cmake wget boost
- IMPORTANT : Examine brew info libtool and brew info m4 to access libtool and m4 easily on macOS

Build our software stack

Copy code from SMT-Nebulae from the main branch on the sw_stack/discover/sles15
Change all /discover path to local
In build_0_on-node.sh remove the --with-gdrcopy= line for UCX (you don't have it installed or/and it doesn't matter outside of HPCs)
Then run the pipeline

./download.sh
./build_0_on-node.sh
./build_1_on-login.sh

The stack will take some time to install, especially the baselibs part of it. To check that baselibs has been built and installed, you can run

./verify_baselibs.sh

which should output

-------+---------+---------+--------------
Config | Install |  Check  |   Package
-------+---------+---------+--------------
  ok   |   ok    |   --    | jpeg
  ok   |   ok    |   --    | zlib
  ok   |   ok    |   --    | szlib
  ok   |   ok    |   --    | hdf5
  ok   |   ok    |   --    | netcdf
  ok   |   ok    |   --    | netcdf-fortran
  ok   |   ok    |   --    | udunits2
  ok   |   ok    |   --    | fortran_udunits2
  ok   |   ok    |   --    | esmf
  ok   |   ok    |   --    | GFE
-------+---------+---------+--------------

macOS Notes on building Software stack

Use the SMT-Nebulae branch called feature/functional_mac_build that contains build scripts specific to macOS.
Adjust basics.sh as follows

-source /Users/ckropiew/SMT-Nebulae/sw_stack/local/modulefiles/SMTStack/2024.08.LOCAL.sh
+source <YOUR PATH TO SMT-Nebulae>/sw_stack/local/modulefiles/SMTStack/2024.08.LOCAL.sh

-export DSLSW_BASELIBS_VER=7.27.0
+export DSLSW_BASELIBS_VER=8.14.0

-export DSLSW_BOOST_VER=1.76.0
-export DSLSW_BOOST_VER_STR=1_76_0 
+export DSLSW_BOOST_VER=1.88.0
+export DSLSW_BOOST_VER_STR=1_88_0

-export DSLSW_BASE=/Users/ckropiew/SMT-Nebulae/sw_stack/local/src/build
+export DSLSW_BASE=<YOUR PATH TO SMT-Nebulae>/sw_stack/local/src/build

Adjust 2024.08.LOCAL.sh as follows

-install_dir="/Users/ckropiew/GEOS_dependencies/install"
-ser_pkgdir="/Users/ckropiew/GEOS_dependencies/install/serialbox"
+install_dir="<YOUR PATH TO SMT-Nebulae>/sw_stack/local/src/install"
+ser_pkgdir="<YOUR PATH TO SMT-Nebulae>/sw_stack/local/src/install/serialbox"

-boost_pkgdir="$homebrew_install_dir/boost/1.86.0_1"
+boost_pkgdir="$homebrew_install_dir/boost/1.88.0"

-baselibs_pkgdir="$install_dir/baselibs-7.27.0/install/"
+baselibs_pkgdir="$install_dir/baselibs-8.14.0/install/"

-export PYTHONPATH="$ser_pkgdir/python":$PYTHONPATH
+#export PYTHONPATH="$ser_pkgdir/python":$PYTHONPATH

-py_pkgdir="/Library/Frameworks/Python.framework/Versions/3.11"
-export PATH="$py_pkgdir/bin":$PATH
-export LD_LIBRARY_PATH="$py_pkgdir/lib":$LD_LIBRARY_PATH
-export LD_LIBRARY_PATH="$py_pkgdir/lib64":$LD_LIBRARY_PATH
+py_pkgdir="<YOUR PATH TO miniconda>/envs/venv"
+#export PATH="$py_pkgdir/bin":$PATH
+#export LD_LIBRARY_PATH="$py_pkgdir/lib":$LD_LIBRARY_PATH
+#export LD_LIBRARY_PATH="$py_pkgdir/lib64":$LD_LIBRARY_PATH

# *** If clang/clang++ is the C/C++ compiler, make the changes below
-export CC=/opt/homebrew/opt/gcc@14/bin/gcc-14
-export CXX=/opt/homebrew/opt/gcc@14/bin/g++-14
+export CC=clang
+export CXX=clang++

Install miniconda for access to Python
- In the terminal, retrieve the installation file for miniconda via curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o miniconda.sh
- Run minconda.sh to set up miniconda
- Create a virtual Python v3.11.7 environment via miniconda. The command below will create a virtual environment called venv.
  - conda create -n venv python=3.11.7
- Whenever you want to activate the environment, run conda activate venv
If you are using clang and clang++ in place of gcc and g++ for compiling, modify the setup of Baselibs in build_baselibs.sh as follows.

make -j ESMF_COMM=openmpi \
-    ESMF_COMPILER=gfortran \
+    ESMF_COMPILER=gfortranclang \

Install OpenMPI by running the build_ompi.sh script
Install serialbox by running the build_serialbox.sh script
Install Baselibs by running the build_baselibs.sh script
Install NDSL by running the build_ndsl.sh script
Check that Baselibs is installed properly by running ./verify_baselibs.sh and see if you get the output shown above when running ./verify_baselibs.sh.

⚠️ cffi, venv and embedded Python interpreter ⚠️ Due to a non standard approach of non-Posix or Posix-adjacent (Darwin, Windows...) file pathing, the venv can be misdetected when using an embedded Python interpreter via CPython. The CPython crew is aware of the issue but noe fix is ready. To test build the following:

#include <stdio.h>
#include <Python.h>

int main(void)
{
    Py_InitializeEx(0);
    PyObject *f = PySys_GetObject((char *)"stderr");
    PyFile_WriteString("\nsys.path: ", f);
    PyFile_WriteObject(PySys_GetObject((char *)"path"), f, 0);
    PyFile_WriteString("\n\n", f);
    return 0;
}

with (replace the path to include & lib of Python)

gcc -o pex \
    -I/home/fgdeconi/.pyenv/versions/3.11.9/include/python3.11/ \
    run_python.c \
    -L/home/fgdeconi/.pyenv/versions/3.11.9/lib -lpython3.11

Then run ./pex. This will print the python sys.path which should have your virtual environement sites-packages in there. If it doesn't then it's the bug.

Our workaround is to use conda which seems to use a different approach, more sandboxy, which goes around the issue.

macOS Note: You may have to set the DYLD_LIBRARY_PATH environment variable to the lib path related to your conda Python environment to run the pex binary.

Some reference: https://github.com/PyO3/pyo3/issues/1741

Notes on building Software stack with Linux Kernel v6.8+

Make the following adjustments before running the above pipeline...

Adjust basics.sh as follows

-export DSLSW_OMPI_MAJOR_VER=4.1
-export DSLSW_OMPI_VER=${DSLSW_OMPI_MAJOR_VER}.6
+export DSLSW_OMPI_MAJOR_VER=5.0
+export DSLSW_OMPI_VER=${DSLSW_OMPI_MAJOR_VER}.2

-export DSLSW_BASELIBS_VER=7.17.1
+export DSLSW_BASELIBS_VER=7.23.0

-export DSLSW_BOOST_VER=1.76.0
-export DSLSW_BOOST_VER_STR=1_76_0
+export DSLSW_BOOST_VER=1.86.0
+export DSLSW_BOOST_VER_STR=1_86_0

+#CUDA_DIR=/usr/local/other/nvidia/hpc_sdk/Linux_x86_64/23.9/cuda/

-export FC=gfortran
+export FC=gfortran-12
-export CC=gcc
+export CC=gcc-12
-export CXX=g++
+export CXX=g++-12

Modify the command to configure OpenMPI in build_0_on-node.sh

-./configure --prefix=$DSLSW_INSTALL_DIR/ompi \
-            --disable-libxml2 \
-            --disable-wrapper-rpath \
-            --disable-wrapper-runpath \
-            --with-pmix \
-            --with-cuda=$CUDA_DIR \
-            --with-cuda-libdir=$CUDA_DIR/lib64/stubs \
-            --with-ucx=$DSLSW_INSTALL_DIR/ucx \
-            --with-slurm \
-            --enable-mpi1-compatibility

+./configure --disable-wrapper-rpath --disable-wrapper-runpath \
+    CC=gcc-12 CXX=g++-12 FC=gfortran-12 \
+           --with-hwloc=internal --with-libevent=internal --with-pmix=internal --prefix=$DSLSW_INSTALL_DIR/ompi

As of September 6th, 2024, there is a fix that needs to be applied to ESMF file ESMCI_Time.C to resolve a GEOS runtime issue.

diff --git a/src/Infrastructure/TimeMgr/src/ESMCI_Time.C b/src/Infrastructure/TimeMgr/src/ESMCI_Time.C
index 78c21bce04..ab40a39379 100644
--- a/src/Infrastructure/TimeMgr/src/ESMCI_Time.C
+++ b/src/Infrastructure/TimeMgr/src/ESMCI_Time.C
@@ -1479,7 +1479,10 @@ namespace ESMCI{
      if (sN != 0) {
         sprintf(timeString, "%s%02d:%lld/%lld", timeString, s, sN, sD);
       } else { // no fractional seconds, just append integer seconds
-        sprintf(timeString, "%s%02d", timeString, s);
+       char *tmpstr;
+       tmpstr = strdup(timeString);
+        sprintf(timeString, "%s%02d", tmpstr, s);
+       free(tmpstr);

Build GEOS

Get and setup mepo which is pre-installed on Discover
- mepo stands for "Multiple rEPOsitory": a Python tool held by Matt T in the SI team that handles the GEOS multi-repository strategy. It can be installed using pip.

pip install mepo

Git clone the root of GEOS then using mepo, you clone the rest of the components which pull on the components.yaml at the root of GEOSgcm
- There is two sources for a component the default and the develop source
- v11.5.2 is our baseline, but we have dsl/develop branch where needed
- We do not use develop for GEOSgcm_App or cmake since those have been setup for OpenACC but are not up-to-date for v11.5.2

git clone -b dsl/develop git@github.com:GEOS-ESM/GEOSgcm.git geos
cd geos
mepo clone --partial blobless
mepo develop env GEOSgcm GEOSgcm_GridComp FVdycoreCubed_GridComp pyFV3

CMake GEOS, using the stack, our custom build baselibs and turning on the interface to pyFV3 for the dynamical core
Then make install. Grab a coffee (or 2)
- We override the compiler with their mpi counterpart to make sure libmpi is pulled properly. CMake should deal with that, but there's some failure floating around.

module use -a SW_STACK/modulefiles
ml SMTStack/2024.04.00
export BASEDIR=SW_STACK/src/2024.04.00/install/baselibs-7.17.1/install/x86_64-pc-linux-gnu
# *** Note: Above BASEDIR path will be different for macOS ***

mkdir -f build
cd build
export TMP=GEOS_DIR/geos/build/tmp
export TMPDIR=$TMP
export TEMP=$TMP
mkdir $TMP
echo $TMP

export FC=mpif90
export CC=mpicc
export CXX=mpic++

cmake .. -DBASEDIR=$BASEDIR/Linux \
         -DCMAKE_Fortran_COMPILER=mpif90 \
         -DBUILD_PYFV3_INTERFACE=ON \
         -DCMAKE_BUILD_TYPE=Debug \
         -DCMAKE_INSTALL_PREFIX=../install \
         -DPython3_EXECUTABLE=`which python3`

# *** To add Serialbox serialization to GEOS, add the following two flags to the above cmake command
#     1) -DBUILD_SERIALBOX_SER=ON 
#     2) -DSERIALBOX_ROOT=<Path to Serialbox Installation>

# *** If MKL isn't found by cmake, add the following flag to the above cmake command: -DMKL_INCLUDE_DIR=<MKL Include Path>

make -j48 install

Note: There may be an error that occurs when building GEOS on macOS that refers to ./src/Shared/@GMAO_Shared/LANL_Shared/CICE4/bld/makdep.c. This error points out that the main routine in makdep.c is missing a type. Simply put int in front of main to resolve this problem (ex: int main).

macOS Note: To build GEOS using clang/clang++, there are additional OpenMP files needed that macOS does not have. Here is how to get those files and set up the environment variables needed for building GEOS using clang/clang++ on macOS.

Use Homebrew to get the libomp package : brew install libomp
Set up the following environment variables
- export OPENMP_CPPFLAGS="-I/opt/homebrew/opt/libomp/include
- export OPENMP_LDFLAGS="-L/opt/homebrew/opt/libomp/lib -lomp -Xpreprocessor -fopenmp
- export GT4PY_EXTRA_COMPILE_OPT_FLAGS="-fbracket-depth=512

⚠️ MKL Dependency⚠️

Some code in GEOS requires MKL. It's unclear which (apart from a random number generator in Radiation) and it seems to be an optional dependency. The cmake process will look for it. If you want to install it follow steps for the standalone OneAPI MKL installer

Get data (curtesy of Matt T.) in it's most compact form: TinyBC
- WARNING: TinyBC is Matt way to move around a small example and/or develop on desktop, it's fragile and we shall treat it as a dev tool, offer help when needed.
- Do not rename it

wget https://portal.nccs.nasa.gov/datashare/astg/smt/geos-fp/restarts/TinyBCs-GitV10.2024Apr04.tar.gz
tar -xvf TinyBCs-GitV10.2024Apr04.tar.gz
rm TinyBCs-GitV10.2024Apr04.tar.gz
cd TinyBCs-GitV10

Make experiment, using TinyBC. First we will make our live easier by aliasing the relevant script. In your .bashrc (remember to re-bash)

alias tinybc_create_exp=PATH_TO/TinyBCs-GitV10/scripts/create_expt.py
alias tinybc_makeoneday=PATH_TO/TinyBCs-GitV10/scripts/makeoneday.bash

Then we can make experiment for c24

cd PATH_TO_GEOS/install/bin
tinybc_create_exp --horz c24 --vert 72 --nonhydro --nooserver --gocart C --moist GFDL --link --expdir /PATH_TO_EXPERIMENT/ TBC_C24_L72
cd /PATH_TO_EXPERIMENT/TBC_C24_L72
tinybc_makeoneday noext # Temporary: we deactivate ExtData to go around a crash

⚠️ ⚠️ ⚠️ Bash might not work, if you see errors try to run under tcsh. Prefer a PATH_TO_EXPERIMENT outside of GEOS to not mix experiment data & code. ⚠️ ⚠️ ⚠️

The simulation is ready to run a 24h simulation (with the original Fortran) with

module load SMTStack/2024.04.04
./gcm_run.j

To run the pyFV3 version, modification to the AGCM.rc and gcm_run.j needs to be done after the tinybc_makeoneday. This runs the numpy backend.

AGCM.rc

###########################################################
# dynamics options
# ----------------------------------------
DYCORE: FV3
 FV3_CONFIG: HWT
+ RUN_PYFV3: 1
AdvCore_Advection: 0

gcm_run.j

setenv RUN_CMD "$GEOSBIN/esma_mpirun -np "

setenv GCMVER `cat $GEOSETC/.AGCM_VERSION`
echo   VERSION: $GCMVER

+setenv FV3_DACEMODE           Python
+setenv GEOS_PYFV3_BACKEND     numpy
+setenv PACE_CONSTANTS         GEOS
+setenv PACE_FLOAT_PRECISION   32
+setenv PYTHONOPTIMIZE         1
+setenv PACE_LOGLEVEL          Debug

+setenv FVCOMP_DIR PATH_TO_GEOS/src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSsuperdyn_GridComp/@FVdycoreCubed_GridComp/
+setenv PYTHONPATH $FVCOMP_DIR/python/interface:$FVCOMP_DIR/python/@pyFV3


#######################################################################
#             Experiment Specific Environment Variables
######################################################################

Remove the source $GEOSBIN/g5_modules to make sure your local environment is left clean.