Month 12 Release of SEAVEAtk

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