Underworld 2 & 3 Setonix baremetal run scripts

install_uw2.16.sh

#!/bin/bash -l

# Installation script installing Underworld (baremetal) on Setonix
# A python virtual environment is made under your $PAWSEY_PROJECT directory, ie,
#     /software/projects/$PAWSEY_PROJECT/setonix/venv/py311

## installing latest uw2 on setonix
module load petsc/3.20.1-nocomplex py-pip/23.1.2-py3.11.6 py-h5py/3.8.0

# Now create a python virtual directory
python -m venv /software/projects/$PAWSEY_PROJECT/setonix/venv/py311/
# Activate and install all requirements (think I got them all)
source /software/projects/$PAWSEY_PROJECT/setonix/venv/py311/bin/activate
sg $PAWSEY_PROJECT -c "pip install wheel"
sg $PAWSEY_PROJECT -c "pip install badlands@git+https://github.com/badlands-model/badlands.git@c9b7f672ef84e0f5799b9bda74dbab14ac6c3eb4#subdirectory=badlands"

# install underworld branch to the virtual env
pip install --no-build-isolation git+https://github.com/underworldcode/underworld2@v2.16.x

export PIPVENV=`pip show underworld | grep "Location:" | cut -d ':' -f2 | xargs`

# check the install is as expected
export PYTHONPATH=$PIPVENV:$PYTHONPATH
python -c "import underworld as uw; print(uw.__version__)"

requirements.txt

aiohttp==3.9.3
aiosignal==1.3.1
anyio==4.3.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
async-timeout==4.0.3
attrs==23.2.0
beautifulsoup4==4.12.3
bleach==6.1.0
cffi==1.16.0
defusedxml==0.7.1
exceptiongroup==1.2.0
fastjsonschema==2.19.1
fqdn==1.5.1
frozenlist==1.4.1
idna==3.6
isoduration==20.11.0
Jinja2==3.1.3
jsonpointer==2.4
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter-events==0.9.0
jupyter_client==8.6.0
jupyter_core==5.7.1
jupyter_server==2.12.5
jupyter_server_proxy==4.1.0
jupyter_server_terminals==0.5.2
jupyterlab_pygments==0.3.0
lavavu==1.8.62
MarkupSafe==2.1.5
mistune==3.0.2
meshplex @ git+https://github.com/kinnala/meshplex@09f25dc16501803685eea8b9a50d963a5e0169ee
multidict==6.0.5
nbclient==0.9.0
nbconvert==7.16.1
nbformat==5.9.2
overrides==7.7.0
packaging==23.2
pandocfilters==1.5.1
Pint==0.23
platformdirs==4.2.0
prometheus_client==0.20.0
ptyprocess==0.7.0
pycparser==2.21
Pygments==2.17.2
python-dateutil==2.8.2
python-json-logger==2.0.7
PyYAML==6.0.1
pyzmq==25.1.2
referencing==0.33.0
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.18.0
Send2Trash==1.8.2
simpervisor==1.0.0
six==1.16.0
sniffio==1.3.0
soupsieve==2.5
swig==4.2.0.post0
terminado==0.18.0
tinycss2==1.2.1
tornado==6.4
traitlets==5.14.1
types-python-dateutil==2.8.19.20240106
typing_extensions==4.9.0
uri-template==1.3.0
webcolors==1.13
webencodings==0.5.1
websocket-client==1.7.0
wheel==0.42.0
yarl==1.9.4

runner_uw2.16.sh

#!/bin/bash -l
 
## User required input
#SBATCH --account=pawsey0407
#SBATCH --job-name=bobthejob
#SBATCH --ntasks=3
#SBATCH --time=00:20:00

## Setup job conditions and run environment
#SBATCH --ntasks-per-node=64  # found this is needed ~Apr2023
#SBATCH --cpus-per-task=1     # OMP_NUM_THREADS equivalent

# Note we avoid any inadvertent OpenMP threading by setting
export OMP_NUM_THREADS=1

# load system packages: 
module load petsc/3.21.2-zmhjwb7 py-pip/23.1.2-py3.11.6 py-h5py/3.8.0

# Use the python virtual environment indirectly, provent mishaps
export UWENV=/software/projects/pawsey0407/setonix/venv/py311/
source $UWENV/bin/activate

# MPI flags for connection
export MPICH_OFI_STARTUP_CONNECT=1
export MPICH_OFI_VERBOSE=1
export MPICH_OFI_SKIP_NIC_SYMMETRY_TEST=1


## model name and execution
export model="mymod.py"
srun -n ${SLURM_NTASKS} python3 $model

setonix_install_uw2.15.sh

# Installation script installing Underworld (baremetal) on Setonix
# A python virtual environment is made under your $PAWSEY_PROJECT directory, ie,
#     /software/projects/$PAWSEY_PROJECT/setonix/venv/py310

## installing latest uw2 on setonix
module load spack/0.19.0 petsc/3.19.5-nocomplex py-h5py/3.7.0

# old command to install custom petsc
#`spack project install -j24 petsc@3.19.4 +fftw +mumps +hwloc ^python@3.10.10 ^hdf5@1.12.2`

# Now create a python virtual directory
python -m venv /software/projects/$PAWSEY_PROJECT/setonix/venv/py310/
# Activate and install all requirements (think I got them all)
source /software/projects/$PAWSEY_PROJECT/setonix/venv/py310/bin/activate
sg $PAWSEY_PROJECT -c "pip install -r requirements.txt"
sg $PAWSEY_PROJECT -c "pip install badlands@git+https://github.com/badlands-model/badlands.git@c9b7f672ef84e0f5799b9bda74dbab14ac6c3eb4#subdirectory=badlands"

# install underworld branch to the virtual env
pip install --no-build-isolation git+https://github.com/underworldcode/underworld2
### sg <projectcode> -c "" never works for me for UW

export PIPVENV=`pip show underworld | grep "Location:" | cut -d ':' -f2 | xargs`

# check the install is as expected
export PYTHONPATH=$PIPVENV:$PYTHONPATH
python -c "import underworld as uw; print(uw.__version__)"

uw2.15_runner.sh

#!/bin/bash -l
 
## User required input
#SBATCH --account=pawsey0407
#SBATCH --job-name=bobthejob
#SBATCH --ntasks=3
#SBATCH --time=00:20:00

## Setup job conditions and run environment
#SBATCH --ntasks-per-node=64  # found this is needed ~Apr2023
#SBATCH --cpus-per-task=1     # OMP_NUM_THREADS equivalent

# Note we avoid any inadvertent OpenMP threading by setting
export OMP_NUM_THREADS=1

# load system packages: 
module load spack/0.19.0 petsc/3.19.5-nocomplex py-h5py/3.7.0

# Use the python virtual environment indirectly, provent mishaps
export UWENV=/software/projects/pawsey0407/setonix/py310/
export PATH=${UWENV}/bin/:$PATH
export PYTHONPATH=${UWENV}/lib/python3.10/site-packages/:$PYTHONPATH

# MPI flags for connection
export MPICH_OFI_STARTUP_CONNECT=1
export MPICH_OFI_VERBOSE=1
export MPICH_OFI_SKIP_NIC_SYMMETRY_TEST=1

export OMP_NUM_THREADS=1

## model name and execution
export model="mymod.py"
srun -n ${SLURM_NTASKS} python3 $model

uw3.setonix.sh

# load system packages: py3.11, mpi, hdf5 
module load petsc/3.21.2-zmhjwb7 py-pip/23.1.2-py3.11.6 py-h5py/3.8.0 py-cython/3.0.4

# path to virtual environment with petsc4py, underworld and dependencies.
export UWP_DIR=/software/projects/pawsey0407/setonix/venv/py311
source $UWP_DIR/bin/activate

# The following doesn't work for loading the path
##export PYTHONPATH=$UWP_DIR/lib/python3.11/site-packages/:$PYTHONPATH
# To run test you'll need pytest
# pip install --user pytest

# if further python packages are needed activate and modify the virtual env. with 
#   source $UWP_DIR/bin/activate

# Note we avoid any inadvertent OpenMP threading by setting
export OMP_NUM_THREADS=1

# download uw3 from github
#git clone https://github.com/underworldcode/underworld3.git 
#git checkout <branchName>
#cd underworld3.git
#pip install .