FDSI Summer Program/HONEE
Information for tutorial in HONEE, to be updated as needed.
HONEE, or the High-Order Navier-stokes Equation Evaluator, is a CFD program that combines libCEED and PETSc.
Contents
Building HONEE for Cisco nodes
First, start a job on the Cisco nodes. All the below commands should be run within a terminal on a Cisco node.
Setup Envionment
source /projects/tools/Spackv0.23/share/spack/setup-env.sh spack load gcc@12.3 module load openmpi
Create new directory
mkdir honee_build cd honee_build
Build PETSc
Ordinarily, I'd only recommend doing a git clone, e.g. git clone https://gitlab.com/petsc/petsc.git.
However, the /nobackup/ server is quite slow and this process takes around 20 minutes (normally about a minute on my laptop), so downloading and extracting a tarball may be quicker.
I may cover that later, but for now I'll just cover it via git clone.
git clone https://gitlab.com/petsc/petsc.git cd petsc cp /nobackup/uncompressed/jrwrigh/HONEE_Setup/petsc/reconfigure.py ./reconfigure.py make export PETSC_DIR=$(pwd) PETSC_ARCH=arch-32 cd ..
The reconfigure.py file has the following:
#!/bin/python3
if __name__ == '__main__':
import sys
import os
sys.path.insert(0, os.path.abspath('config'))
import configure
configure_options = [
'--with-64-bit-indices=0',
'--download-hdf5',
'--download-cgns',
'--download-ctetgen=1',
'--download-parmetis=1',
'--download-metis=1',
'--download-ptscotch=1',
'--with-debugging=0',
'--with-fortran-bindings=0',
'--with-fc=0',
'PETSC_ARCH=arch-32',
'COPTFLAGS=-g -O3',
'CXXOPTFLAGS=-g -O3',
]
configure.petsc_configure(configure_options)
Building HONEE
Ensure that PETSC_DIR and PETSC_ARCH are set to the desired PETSc installation.
git clone https://github.com/CEED/libCEED.git cd libCEED make build/fluids-navierstokes -j
The executable build/fluids-navierstokes is then built and ready for running.
Changing HONEE Inputs
HONEE uses PETSc's input argument system for handling inputs. They can be provided either via command-line flags or inside a YAML file. So
./build/fluids-navierstokes -ts_dt 1e-3
is equivalent to
./build/fluids-navierstokes -options_file test.yaml
if test.yaml has this in it:
ts_dt: 1e-3
Note also that PETSc allows for hierarchical flags as well within a YAML file. So instead of writing
ts_dt: 1e-3 ts_type: alpha ts_max_time: 2.3
You can write:
ts: dt: 1e-3 type: alpha max_time: 2.3
