EasyVVUQ – v1.2

Documentation: https://easyvvuq.readthedocs.io/en/latest/

Code: https://github.com/UCL-CCS/EasyVVUQ/releases/tag/v1.2

New features:

• New Simplex Stochastic Collocation sampler for irregular outputs, e.g. with discontinuities or high gradients in the stochastic input space. Works for scalar QoI only thus far.
• Grid-Search sampler, (e.g. for neural-network hyper parameter tuning).
• HDF5 decoder to allow for reading HDF5 output files, useful when dealing with outputs of different size.

Tutorials:

• SSC tutorial: https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/simplex_stochastic_collocation_tutorial.ipynb
• Hyperparameter tuning tutorial, local sampling: https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/hyperparameter_tuning_tutorial.ipyn
• Hyperparameter tuning tutorial, remote sampling with FabSim3: https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/hyperparameter_tuning_tutorial_with_fabsim.ipynb

Usability updates:

• Make it more obvious how to import a pandas dataframe containing cases to be considered
• Make it more obvious how to massage the results from the runs before performing the PCE/SC/MC analysis

FabSim3 – v3.71

Documentation: https://fabsim3.readthedocs.io/en/latest/ 

Code and tutorials: https://github.com/djgroen/FabSim3/releases/tag/v3.71

New features:

• New VVP tutorials in the readthedocs site.
• More HPC access modes for automated access.
• Extended multiplexing documentation.
• Improved support and documentation for QCG-Pilotjob installation on remote machines.
• Add support for continuing replicated simulation runs by using the replica_start_number argument in run_ensemble.
• Plugin developments
  ○ Initial version of FabParticleDA.
  ○ Initial version of FabDynamics
  ○ FabFlee: added built-in visualization tools, and updated to support Flee 3.0

QCG-PilotJob – v0.14.0

Documentation: https://qcg-pilotjob.readthedocs.io

Code: https://github.com/psnc-qcg/QCG-PilotJob/releases/tag/v0.14.0

New features:

• Support for QCG-PJ on the ARCHER2 supercomputer.
• High level interface with EasyVVUQ for novice users.
• Improved handling of custom arguments for LocalManager in QCGPJExecutor
• Fixed dependencies of zmq package
• Improved script element handling of in various parallel modes
• Changed the method of gathering available CPU identifiers
• A range of minor improvements

Bugfixes:

• Improved handling of custom arguments for LocalManager in QCGPJExecutor
• Fixed dependencies of zmq package
• Improved script element handling of in various parallel modes
• Fixed bug undefined variable
• Typo in service arguments

Other Improvements

• Changed the method of gathering available CPU identifiers

MUSCLE3 – v0.6.0

Documentation: https://muscle3.readthedocs.io/en/latest/

Code: https://github.com/multiscale/muscle3/releases/

Updates:

•  Connecting multiple conduits to outgoing ports
• Initial checkpointing support (Python only preview)
• Support for Intel compilers & clang.
• TCP latency improvements
• Small improvements to error messages and documentationEasySurrogate

EasySurrogate

Updates:

• Added Dropout regularization. Tutorial and documentation on this feature is forthcoming

MOGP – v0.72

Documentation: https://github.com/alan-turing-institute/mogp-emulator/tree/main/mogp_emulator/demos

Code: https://github.com/alan-turing-institute/mogp-emulator/releases/tag/v0.7.2

Updates:

• Bugfix release to fix a few outstanding issues. Fixes issues #241 and #242. Changes in this release:
• Update to Dimension Reduction to improve memory usage with some additional tests
• Update to documentation to reflect new dependency requirements
• Improvements to GPU build script in setup.py to remove outdated shared object library files.

EasyVVUQ v1.1.2

• Documentation: https://easyvvuq.readthedocs.io/en/latest/
• Code: http://www.github.com/UCL-CCS/EasyVVUQ

Updates

Overhaul of SC sampler / analysis class:

• Made isotropic sparse-grid subroutines more scalable to higher input dimensions. Reused dimension-adaptive subroutines for this purpose, instead of having (slower) separate isotropic routines.
• Rewrote dimension-adaptive SC expansion as a standard PCE expansion with generalized PCE coefficients. See adaptive sparse-grid tutorial.

Documentation

• Extensive methodological sparse-grid tutorial: https://www.researchgate.net/publication/359296270_Adaptive_sparse-grid_tutorial
• New tutorial on using mathematical expressions involving parameters in template files using the Jinja encoder: https://github.com/UCL-CCS/EasyVVUQ/blob/dev/tutorials/jinja_tutorial.ipynb

QCG PilotJob v0.13.1

• Documentation: https://qcg-pilotjob.readthedocs.io/en/latest/
• Code: https://github.com/vecma-project/QCG-PilotJob

New features

• Additonal environment variables for launching srun jobs from inside a pilot job parallel task

Bugfixes

• Support for different argument names between Slurm versions (Lourense Veen)
• Race condition in wait4all method (LourenseVeen)
• Reporting version in debug logs

Other Improvements

• Enhanced tests (Lourense Veen)
  • support for tests with different Slurm versions
  • updated documentation for tests
  • bugfixes within the testing scripts

EasySurrogate v0.19

• Tutorial: https://github.com/wedeling/EasySurrogate/tree/master/tutorials
• Code: https://github.com/wedeling/EasySurrogate

Updates

Some minor changes have been introduced in the ANN / Deep active subspace methods:

• made it possible to select varying numbers of neurons, to create “constrained” hidden layers. This is used to make a deep-active subspace type of surrogate without orthonormality embedded in network architecture. Instead, orthonormality is computed in a post-processing procedure. Explained in updated tutorials.

Tutorials

• 2 epidemiological deep-active subspace Jupyter notebook tutorials (HIV and COVID 19): https://github.com/wedeling/deep_active_subspace_data

FabSim3 v3.2

• Documentation: https://fabsim3.readthedocs.io/en/latest/
• Code: http://www.github.com/djgroen/FabSim3

New Features

• Two new plugins: FabSCEMa and FabNEPTUNE
• Range of fixes and improvements to the FabMOGP plugin
• Inclusion of the FabSim3 Automated Validation tutorial.
• Added support for multiplexing in the SSH layer, and tutorial documenting it. This greatly reduces the number of times users have to type in passwords.
• (We also submitted a paper describing FabSim3 to a journal)

Updates

• A range of improvements to the documentation.

Tutorials

This version of FabSim3 has been used to enable the following application tutorials:

• • FabFlee (migration modelling) link to tutorial
  • FabMD (molecular dynamics) link to tutorial
  • FabCovid (Covid-19 simulation) link to tutorial
  • FabUQCampaign (basic CFD models) link to tutorial
  • fabmogp (Multi-Output Gaussian Process Emulator) link to tutorial

Muscle3 v0.5.0 (made possible through the Dutch e-Science Center)

• Documentation: http://muscle3.readthedocs.io
• Code: https://github.com/multiscale/muscle3/releases/tag/0.5.0

New Features

• MUSCLE3 now starts submodels and other components (using QCG-PilotJob)
• Automatic resource management for components on HPC

Incompatible changes

• compute_elements are not called components in .ymmsl files

Improved

• Integration with QCG-PilotJob
• Extension of yMMSL language
• Simplification of the installation process by removal of gRPC dependency and automatic detection of MPI availability
• Use latest OpenSSL library when installing it automatically
• Cleaner logging output
• Improved communication performance and scalability.

MOGP Emulator v0.7.0

• Documentation: https://github.com/alan-turing-institute/mogp-emulator/tree/main/mogp_emulator/demos
• Code: https://github.com/alan-turing-institute/mogp-emulator/tree/main/mogp_emulator

New Features

New release incorporating recent work. New features in this release:

• Maxi-min LHC Experimental Designs
• Mulit-output history matching
• Emulator validation
• GPU implementation now supports Priors
• Additional fixes and improvements to documentation and examples

EasyVVUQ v1.1.1

• Documentation: https://easyvvuq.readthedocs.io/en/latest/
• Code: http://www.github.com/UCL-CCS/EasyVVUQ

QCG PilotJob v0.13.0

• Documentation: https://qcg-pilotjob.readthedocs.io/en/latest/
• Code: https://github.com/vecma-project/QCG-PilotJob

EasySurrogate v0.18

• Tutorial: https://github.com/wedeling/EasySurrogate/tree/master/tutorials
• Code: https://github.com/wedeling/EasySurrogate

FabSim3 v3.6

• Documentation: https://fabsim3.readthedocs.io/en/latest/
• Code: http://www.github.com/djgroen/FabSim3

EQI (formerly EasyVVUQ-QCGPilotJob) v0.5.2

• Documentation: https://easyvvuq-qcgpj.readthedocs.io/en/latest/
• Code: https://github.com/vecma-project/easyvvuq-qcgpj

MUSCLE 3 v0.4.0

• Documentation: http://muscle3.readthedocs.io
• Code: https://github.com/multiscale/muscle3/releases/tag/0.4.0

MOGP Emulator v0.6.1

• Documentation: https://github.com/alan-turing-institute/mogp-emulator/tree/main/mogp_emulator/demos
• Code: https://github.com/alan-turing-institute/mogp-emulator/tree/main/mogp_emulator