Julian Giordani julesghub

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.

	### Build this images on top of the `ubuntu:20.04` docker image.
	### Docker searches for ubuntu:20.04 on the hub.docker
	FROM ubuntu:20.04

	### use ubuntu's package manager system `apt-get` to install compilers
	RUN apt-get update -qq && \
	apt-get install -yq gcc
	### add anyother packages you want above

	ARG WITH_DEBUG

	#!/bin/bash
	#PBS -P BGH
	#PBS -N UW_Run
	#PBS -l select=1:ncpus=4:mem=3GB
	#PBS -l walltime=00:20:00
	#PBS -q defaultQ

	source /project/RDS-FSC-BGH-RW/codes/UWGeodynamics_2.10.1.sh

	cd $PBS_O_WORKDIR

	#!/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()

	## 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 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