The latest release of NCI-geophys is 23.11. Some selected packages are listed below for Python, R and Julia environments.
Python packages
To see all Python packages available in NCI-geophysics:
$ module use /g/data/up99/modulefiles $ module load NCI-geophys/24.08 $ conda list
Some selected Python packages are listed below. Newer packages in comparing with those in the earlier release (22.06, 22.11) are highlighted.
Geophys environments | 22.06 | 22.11 | 23.03 | 23.11 | 24.04 | 24.08 |
|---|---|---|---|---|---|---|
| Python | 3.9 | 3.9 | 3.9 | 3.9 | 3.10.8 | 3.10.8 |
| Selected Packages oftware | ||||||
| Obspy: A Python framework for Seismology | 1.3.0 | 1.3.1 | 1.4.0 | 1.4.0 | 1.4.0 | 1.4.1 |
| Pyrocko: A seismology toolbox and library written in Python | 2022.04.28 | 2022.06.10 | 2023.01.20 | 2023.10.11 | 2024.01.10 | 2024.01.10 |
| SimPEG: Simulation and gradient based parameter estimation in geophysical applications | 0.17.0 | 0.17.0 | 0.18.1 | 0.20.0 | 0.20.0 | 0.20.0 |
| MTpy: Toolbox for magnetotelluric data processing, analysis, modelling and visualisation | 1.1.5 | 1.1.5 | 1.1.5 | REMOVED | ||
| MTpy-v2: A Python Toolbox for working with Magnetotelluric (MT) Data | 2.0.5 | 2.0.5 | 2.0.7 | |||
| MTH5: Package for reading/writing/manipulating MTH5 files | 0.2.5 | 0.3.0 | 0.3.1 | 0.4.1 | 0.4.2 | 0.4.5 |
| mt_metadata: A tool to standardise metadata for magnetotelluric data | 0.1.9 | 0.1.9 | 0.2.1 | 0.3.3 | 0.3.4 | 0.3.7 |
| PyGEOS: A c/Python library with vectorised geometry functions | 0.12.0 | 0.13 | 0.14 | 0.14 | 0.14 | 0.14 |
| ParaView: Data analysis and visualization application | 5.10.1 | 5.10.1 | 5.11.0 | REMOVED | ||
| geopandas: adds support for geographic data to pandas objects | 0.10.2 | 0.12.1 | 0.12.2 | 0.14.1 | 0.14.3 | 0.14.4 |
| cartopy: geospatial data processing package | 0.20.2 | 0.21.0 | 0.21.1 | 0.22.0 | 0.22.0 | 0.23.0 |
| ipyleaflet: interactive maps in the Jupyter notebook | 0.16.0 | 0.17.2 | 0.17.2 | 0.17.4 | 0.18.2 | 0.19.2 |
| geoplotlib: toolbox for visualizing geographical data and making maps | 0.3.2 | 0.5.1 | 0.5.1 | 0.5.1 | 0.5.1 | 0.5.1 |
| geopy: Python client for several popular geocoding web services | 2.2.0 | 2.2.0 | 2.3.0 | 2.4.0 | 2.4.1 | 2.4.1 |
| intake: a lightweight package for finding, investigating, loading and disseminating data | 0.6.5 | 0.6.6 | 0.6.6 | 0.7.0 | 2.0.4 | 2.0.6 |
| PyGMT: A python interface for the Generic Mapping Tools | 0.6.1 | 0.7.0 | 0.8.0 | 0.10.0 | 0.11.0 | 0.12.0 |
| gdal: a translator library for raster and vector geospatial data formats | 3.4.2 | 3.5.3 | 3.6.0 | 3.6.0 | 3.6.0 | 3.6.0 |
| hvplot: A high-level plotting API for the PyData ecosystem built on HoloViews | 0.8.0 | 0.8.1 | 0.8.2 | 0.9.0 | 0.9.2 | 0.10.0 |
| DASK: Scalable analytics in Python | 2022.5.2 | 2022.7.1 | 2022.7.1 | 2023.9.3 | 2024.1.1 | 2024.8.1 |
| xarray: N-D labeled arrays and datasets in Python | 2022.3.0 | 2022.11.0 | 2023.1.0 | 2023.10.1 | 2024.3.0 | 2024.3.0 |
| tsg-xr: A tool for loading TSG datasets into Xarray | 0.2.5 | 0.2.5 | ||||
| nvcl-kit: A Python package that provides access to Australia's NVCL (National Virtual Core Library) | 1.1.9 | |||||
| aurora: Python library for processing natural source electromagnetic data. | 0.3.13 |
Julia packages
Since Nov 2023, We provide Julia support in seperate singularity images under NCI-geophys modules with the suffix `._jl`, for example `NCI-geophys/23.11_jl`
To list all Julia packages available in NCI-geophysics:
$ module use /g/data/up99/modulefiles $ module load NCI-geophys/24.10_jl $ julia _ _ _ _(_)_ | Documentation: https://docs.julialang.org (_) | (_) (_) | _ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 1.10.5 (2024-08-27) _/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release |__/ | (@v1.10) pkg> st Status `/opt/julia/environments/v1.10/Project.toml` [c3fe647b] AbstractAlgebra v0.43.5 ⌅ [c9ce4bd3] ArchGDAL v0.8.5
Some selected Julia packages are listed below. Newer packages in comparison with those in the earlier release are highlighted in dark grey. Sometimes, some packages have to be removed or reverted back to an earlier version to allow installation. We highlight those scenarios in red and orange, respectively. Discontinued packages that merged into other packages are in green.
Geophys environments | 22.06 | 22.11 | 23.03 | 23.11_jl | 24.10_jl |
|---|---|---|---|---|---|
| Julia | 1.7.2 | 1.7.3 | 1.8.5 | 1.9.3 | 1.10.5 |
| Selected Packages | |||||
| ArchGDAL A high level API for GDAL - Geospatial Data Abstraction Library | v0.7.4 | v0.7.4 | v0.7.4 | V0.8.5 | v0.8.5 |
| BenchmarkTools A benchmarking framework for the Julia language | v1.3.1 | V1.3.2 | v1.3.2 | v1.3.2 | V1.5.0 |
| CFTime Julia library for decoding time units conforming to the Climate and Forecasting (CF) netCDF conventions | v0.1.2 | v0.1.2 | v0.1.2 | v0.1.2 | V0.1.3 |
| CoordinateTransformations A fresh approach to coordinate transformations | v0.6.2 | v0.6.2 | v0.6.2 | V0.6.3 | v0.6.3 |
| DataFrames In-memory tabular data in Julia | v1.3.4 | V1.3.6 | v1.3.6 | v1.3.6 | V1.7.0 |
| Distributions A Julia package for probability distributions and associated functions. | v0.25.62 | V0.25.77 | V0.25.86 | V0.25.103 | V0.25.112 |
| Elemental Julia interface to the Elemental linear algebra library. | v0.6.0 | v0.6.0 | v0.6.0 | REMOVED | |
| GADM A Julia package for obtaining geographical data from the GADM dataset | v0.2.4 | v0.2.4 | v0.2.4 | v0.2.4 | v0.2.4 |
| GDAL Thin Julia wrapper for GDAL - Geospatial Data Abstraction Library | v1.4.0 | v1.4.0 | V1.5.1 | V1.6.1 | v1.6.1 |
| GeoArrays Simple geographical raster interaction built on top of ArchGDAL, GDAL and CoordinateTransformations | v0.7.5 | v0.7.5 | v0.7.5 | V0.7.9 | v0.7.9 |
| GeoData Standardising geospatial data in the Julia language | v0.6.1 | v0.6.1 | v0.6.1 | REPLACED BY RASTERS.JL | |
| GeoDataFrames Simple geographical vector interaction built on top of ArchGDAL | v0.2.0 | v0.2.0 | v0.2.0 | V0.2.4 | v0.2.4 |
| GeoDatasets Common geographic data sets | v0.1.6 | V0.1.7 | v0.1.7 | V0.1.8 | v0.1.8 |
| GeoFormatTypes Wrapper types for spatial data formats like well known text, KML, Proj4 strings. | v0.3.0 | v0.3.0 | v0.3.0 | V0.4.2 | v0.4.2 |
| GeoInterface A Julia Protocol for Geospatial Data | v0.5.7 | v0.5.7 | v0.5.7 | v0.5.7 | v0.5.7 |
| GeoJSON Utilities for working with GeoJSON data in Julia | v0.5.1 | v0.5.1 | v0.5.1 | v0.5.1 | v0.5.1 |
| GeoStats An extensible framework for high-performance geostatistics in Julia | v0.31.6 | V0.31.7 | v0.31.7 | v0.31.7 |
|
| Geodesy Work with points defined in various coordinate systems | v1.1.0 | v1.1.0 | v1.1.0 | v1.1.0 | v1.1.0 |
| GeometryBasics Basic Geometry Types | v0.4.2 | v0.4.2 | v0.4.2 | v0.4.2 | v0.4.2 |
| GeometryTypes Geometry types for Julia | v0.8.5 | v0.8.5 | v0.8.5 | v0.8.5 | v0.8.5 |
| GeophysicalFlows Geophysical fluid dynamics pseudospectral solvers with Julia and FourierFlows.jl | v0.14.0 | V0.15.0 | V0.15.2 | V0.15.3 | V0.16.2 |
| Geophysics Planetary science data for atmospheric geophysical models | v0.3.6 | v0.3.6 | v0.3.6 | V0.3.7 | V0.3.8 |
| Graphs Working with graphs in Julia | v1.7.0 | V1.7.4 | V1.8.0 | V1.9.0 | V1.12.0 |
| HiQGA A general purpose package for spatial statistical inference, geophysical forward modeling, Bayesian inference and inversion (both deterministic and probabilistic) | v0.1.0 | V0.2.2 | V0.3.4 | V0.3.13 | V0.4.9 |
| Hwloc A Julia API for hwloc | v2.0.0 | V2.8.0+1 | V2.2.0 | v2.2.0 | V3.3.0 |
| IJulia Julia kernel for Jupyter | v1.23.3 | v1.23.3 | V1.24.0 | V1.24.2 | V1.25.0 |
| JOLI Julia Operators LIbrary | v0.8.0 | V0.8.1 | V0.8.5 | v0.8.5 | v0.8.5 |
| JUDI Julia Devito inversion. | v3.1.1 | V3.1.13 | V3.2.3 | V3.3.8 | V3.4.7 |
| LasIO Julia package for reading and writing the LAS lidar format | v0.3.7 | v0.3.7 | v0.3.7 | v0.3.7 | v0.3.7 |
| LibGEOS Julia package for manipulation and analysis of planar geometric objects | v0.6.12 | v0.6.12 | v0.6.12 | v0.6.12 | v0.6.12 |
| LibSpatialIndex A library for spatially indexing kD bounding box data (based on libspatialindex) | v0.2.0 | v0.2.0 | v0.2.0 | v0.2.0 | v0.2.0 |
| MPI MPI wrappers for Julia | v0.19.2 | V0.20.4 | V0.19.2 | V0.20.10 | V0.20.8 |
| NCDatasets Load and create NetCDF files in Julia | v0.11.9 | v0.11.9 | v0.11.9 | V0.12.17 | v0.12.17 |
| NearestNeighbors High performance nearest neighbor data structures and algorithms for Julia | v0.4.10 | V0.4.12 | V0.4.13 | v0.4.13 | V0.4.20 |
| NetCDF NetCDF support for the julia programming language | v0.11.5 | v0.11.5 | V0.11.4 | V0.11.7 | V0.11.8 |
| Oceananigans Fast and friendly fluid dynamics on CPUs and GPUs | v0.76.1 | V0.90.1 | V0.91.6 | ||
| OpenStreetMapX OpenStreetMap (*.osm) support for Julia 1.0 and up | v0.3.2 | V0.3.3 | v0.3.3 | V0.4.1 | v0.4.1 |
| Plots Powerful convenience for Julia visualizations and data analysis | v1.29.1 | V1.32.0 | v1.32.0 | v1.32.0 | v1.32.0 |
| Proj4 Julia wrapper for the PROJ cartographic projections library | v0.6.0 | v0.6.0 | v0.6.0 | V0.5.0 | v0.5.0 |
| QuakeML Read and write QuakeML in Julia | v0.1.1 | v0.1.1 | v0.1.1 | V0.1.2 | v0.1.2 |
| RasterDataSources Easily download and use raster data sets in Julia | v0.5.4 | v0.5.4 | V0.5.7 | v0.5.7 | V0.5.8 |
| Rasters defines common types and methods for reading, writing and manipulating rasterized spatial data | v0.1.1 | v0.1.1 | v0.1.1 | V0.2.2 | v0.2.2 |
| RegionTrees Quadtrees, Octrees, and more in Julia | v0.3.2 | v0.3.2 | v0.3.2 | v0.3.2 | v0.3.2 |
| SeisModels Seismic models of the interior of the Earth and other planets | v1.4.0 | V1.5.0 | v1.5.0 | V1.6.0 | V1.6.1 |
| Shapefile Parsing .shp files in Julia | v0.7.4 | v0.7.4 | v0.7.4 | v0.7.4 | v0.7.4 |
| Turf A Julia port of Turf.js | v0.2.1 | v0.2.1 | v0.2.1 | v0.2.1 | v0.2.1 |
R packages
To list all R packages available in NCI-geophysics:
$ module use /g/data/up99/modulefiles $ module load NCI-geophys/23.11 $ R R version 4.2.2 (2022-10-31) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-conda-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > installed.packages() License_restricts_use OS_type MD5sum NeedsCompilation Built License_restricts_use OS_type MD5sum NeedsCompilation Built Rmpi NA NA NA "yes" "4.2.2" abind NA NA NA "no" "4.2.1" acepack NA NA NA "yes" "4.2.1" ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... zCompositions NA NA NA "no" "4.2.1" zip NA NA NA "yes" "4.2.1" zoo NA NA NA "yes" "4.2.1"
Some selected R packages are listed below. Newer packages in comparing with those in the earlier release (22.06, 22.11) are highlighted.
| Geophys environments | 22.06 | 22.11 | 23.03 | 23.11 |
|---|---|---|---|---|
| R | 4.1.3 | 4.2.2 | 4.2.2 | 4.2.2 |
| Selected Packages | ||||
| geoscale - geological time scale plotting | 2.0 | 2.0.1 | 2.0.1 | REMOVED |
| astrochron - a package for conducting, and learning about: (1) paleoclimate time series analysis, (2) astronomical time scale construction, and (3) the statistical integration of astrochronologies with other geochronologic/chronostratigraphic data. | 1.1 | 1.1 | 1.1 | REMOVED |
| GEOmap - Topographic and geologic mapping | 2.5-0 | 2.5-0 | 2.5-0 | 2.5_5 |
| geomapdata- Set of data for use in package GEOmap | 2.0-0 | 2.0-0 | 2.0-0 | 2.0_2 |
| terrainmeshr - Triangulate and simplify 3D terrain meshes | 0.1.0 | 0.1.0 | 0.1.0 | 0.1.0 |
| RSAGA - SAGA geoprocessing and terrain analysis | 1.3.0 | 1.3.0 | 1.4.0 | 1.4.0 |
| earthtones - Derive a color palette from a particular location on Earth | 0.1.1 | 0.1.1 | 0.1.1 | REMOVED |
| rgr - Applied geochemistry exploratory data analysis | 1.1.15 | REMOVED | ||
| OrgMassSpecR - Organic/biological mass spectrometry data analysis | 0.5-3 | 0.5-3 | 0.5-3 | 0.5-3 |
| CHNOSZ -Thermodynamic calculations and diagrams for geochemistry | 1.4.3 | 1.4.3 | 2.0.0 | REMOVED |
| ggtern -An extension to ‘ggplot2’, for the creation of ternary diagrams | 3.3.5 | 3.3.5 | 3.4.1 | 3.4.2 |
| phreeqc -R Interface to Geochemical Modeling Software | 3.7.4 | 3.7.4 | 3.7.5 | REMOVED |
| gear - Geostatistical analysis in R - datasets included | 0.3.4 | 0.3.4 | 0.3.4 | REMOVED |
| gstat - Spatial and spatio-temporal geostatistical modeling, prediction, and simulation | 2.0-9 | 2.1-0 | 2.1-0 | 2.1_1 |
| geostats - An introduction to statistics for geoscientists | 1.4 | 1.5 | 1.6 | REMOVED |
| streamDepletr - Estimate streamflow depletion due to groundwater pumping | 0.1.1 | 0.1.1 | 0.1.1 | REMOVED |
| Rpvt - Estimate the PVT properties of reservoir fluids | 0.1.1 | REMOVED | ||
| tidypaleo - Provides a set of functions with a common framework for age-depth model management, stratigraphic visualization, and common statistical transformations. | 0.1.2 | 0.1.2 | 0.1.3 | REMOVED |
| fossil - Palaeoecological and palaeogeographical analysis tools | 0.4.0 | 0.4.0 | 0.4.0 | REMOVED |
| FossilSim - Simulating taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling | 2.3.0 | 2.3.1 | 2.3.1 | REMOVED |
| strap - Stratigraphic tree analysis for paleontology | 1.6-0 | 1.6-0 | 1.6-0 | REMOVED |
| folio - Datasets for teaching archaeology and paleontology | 1.1.0 | 1.3.0 | 1.3.0 | REMOVED |
| chronosphere -A package to facilitate spatially explicit analyses of (paleo)environmental/ecological research | 0.4.1 | 0.4.1 | 0.4.1 | REMOVED |
| vegan - Ordination methods, diversity analysis and other functions for community and vegetation ecologists. | 2.6-2 | 2.6-4 | 2.6-4 | 2.6-4 |
| fingerPro - Sediment source fingerprinting | 1.1 | 1.1 | 1.1 | REMOVED |
| provenance - Statistical toolbox for sedimentary provenance analysis | 3.3 | 4.0 | 4.1 | REMOVED |
| ETAS - Modeling earthquake data using ‘ETAS’ model | 0.4.9 | 0.4.9 | 0.5.1 | REMOVED |
| GRTo - Tools for the analysis of Gutenberg-Richter distributions of earthquake magnitudes | 1.3 | 1.3 | 1.3 | REMOVED |
| SDAR - A tool for plotting and facilitating the analysis of stratigraphic and sedimentological data | 0.9-55 | 0.9-55 | 0.9-55 | REMOVED |
| coreCT - Programmatic analysis of sediment cores using computed tomography imaging | 1.3.3 | 1.3.3 | 1.3.3 | REMOVED |
| EMMAgeo - End-member modeling of grain-size data | 0.9.7 | 0.9.7 | 0.9.7 | REMOVED |
| DecomposeR - Empirical model decomposition for cyclostratigraphy | 1.0.4 | 1.0.4 | 1.0.6 | REMOVED |