Julian Giordani julesghub

Guide to setting up and installing a bare metal underworld install on [email protected]

1st - Setup python venv

FOO=/some/path/in/scratch

module load petsc/3.21.3 python3/3.12.1 openmpi/4.1.7 python3-as-python swig/4.0.2 hdf5/1.12.2p
export CC='mpicc' CXX='mpicxx' F90='mpifort' F77='mpifort' LD='mpicc' LDSHARED='mpicc -shared'
python -mvenv --system-site-packages $FOO/venv/uw_env

HPC commands to download and run the Underworld sigularity container.

REMEMBER to change the following strings:

/FOO/BAR/ to your desired path, i.e gdata or scratch.
IMAGE-NAME.sif to what you want the container file to be called.

These two strings MUST match up with the same strings in runner scripts.

For Gadi gadi.nci.org.au - Info on gadi.

Jump on gadi with account the has write access to /d/gdata/m18/.
Immediately start a tmux session to always remin connected.
Load dependency modules. python, swig, petsc, etc.
Initialise a virtualenv: python -m venv /g/data/m18/software/underworld/<version>
Activate venv: source /g/data/m18/software/underworld/<version>/bin/activate
install all python packages in this environment which is separate from the system python environment, include lavavu & badlands
Write a correctponding modulefile in /g/data/m18/modulefiles/underworld/ that setups the runtime environment required to use the installation without activating the venv.

	#!/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

	#!/usr/bin/env python3
	# coding: utf-8

	##from underworld.UWGeodynamics.surfaceProcesses import SedimentationThreshold
	##from UWGeodynamics import visualisation as vis


	import underworld as uw
	from underworld import UWGeodynamics as GEO
	from underworld import function as fn

	## bash to install a virtual environment iwth uw3 on Gadi - 30Jan25

	```
	module load python3/3.11.7 python3-as-python openmpi/4.1.3 hdf5/1.12.1p petsc/3.21.3 gmsh/4.13.1
	export CC='mpicc' CXX='mpicxx' F90='mpifort' F77='mpifort' LD='mpicc' LDSHARED='-shared'
	python3 -mvenv --system-site-packages /foo/bar
	source /foo/bar/bin/activate
	pip3 install --no-binary :mpi4py: --no-cache-dir --no-build-isolation mpi4py
	HDF5_DIR= HDF5_LIBDIR=/apps/hdf5/1.12.1p/lib/ompi3 HDF5_INCLUDEDIR=/apps/hdf5/1.12.1p/include/ HDF5_MPI=ON HDF5_VERSION=1.12.1 pip3 install --no-build-isolation --no-binary :all: --no-cache-dir --no-build-isolation h5py
	LDSHARED='-shared' pip3 install --no-build-isolation --no-cache-dir petsc4py==3.21.3

	#!/usr/bin/env python
	# coding: utf-8

	# In[3]:


	import underworld as uw
	from underworld import function as fn
	import underworld.visualisation as vis
	uw.utils.matplotlib_inline()