December 2023 Release of SEAVEAtk

FabSim3 – v3.76

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

Plugins: https://fabsim3.readthedocs.io/en/latest/plugins/

Code and tutorialshttps://github.com/djgroen/FabSim3/releases/tag/v3.76

New Features

  • Support for Python 3.12
  • New plugins: FabNESO, FabGuard, FabECO and FabOasis
  • Support for dry runs for diagnostic purposes.
  • Added command to wipe remote directories.

Updates

  • Introduced a dynamic polling interval when waiting for completion (initially often, and reducing frequency as time passes)
  • Fixed obsolete tests
  • Updated literature references in documentation
  • Various security fixes
  • Fixes to autocomplete functionality
  • Removed various obsolete defaults in machines.yml
  • Improved implementation of SSHPass authentication method, which is slightly more secure.

Tutorials and plugins

 

MUSCLE3 – v0.7.1

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

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

Added

  • Support for Python 3.11 (working already, now official)
  • Enabled type checking support for the libmuscle Python API

Improved

  • Easier crash debugging due to improved root cause detection
  • Fixed crash in profiling timeline plot
  • Better performance of timeline plot
  • Better visual quality of timeline plot
  • Improved profiling of shutdown process
  • Fixed crash in profiler for large simulations
  • Fixed several (harmless) compiler warnings
  • Small documentation rendering improvements

 

RADICAL-Cybertools

Overview: https://github.com/radical-cybertools

Code: The latest RCT stack consists of the following releases:

Features:

  • New features for the various RCT modules are described in each of the links above.

 

EasySurrogate – v0.19

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

Code: https://github.com/wedeling/EasySurrogate

 Updates:

 

EasyVVUQ – v1.2.1

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

Code: https://github.com/UCL-CCS/EasyVVUQ/releases/tag/v1.2.1

Fixes and updates

  • Fixed several tests for newer Python versions.
  • Updated integration with QCG-PilotJob

Tutorials

 

QCG-PilotJob – v0.14.0

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

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

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

 

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:

  • Up to date

July 2023 Release of SEAVEAtk

FabSim3 – v3.75

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

Code and tutorialshttps://github.com/djgroen/FabSim3/releases/tag/v3.75

New Features

  • Support for upsampling replicated ensemble simulations, i.e. add additional replications for individual instances.
  • Added more pages to the documentation
    • Testing
    • Getting Started
    • APIs for plugin developers
    • New plugin: FabDynamics

Updates

  • Fixed a number of test cases.
  • A range of major extensions and improvements to the documentation.

Tutorials and plugins

MUSCLE3 – v0.7.0

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

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

Added

  • Checkpointing is now supported in C++ and Fortran as well
  • Added built-in profiling feature
  • New object-oriented Fortran API (existing API also still available)
  • New Instance.list_settings() function
  • Build support for macOS with CLang and G++/GFortran
  • Build support for Cray machines and compilers

Improved

  • Compiling with MPI and linking without or vice versa is now impossible
  • Fixed MessagePack build failure on old OSes
  • Fixed resource allocation for instance sets
  • Planner now detects F_INIT -> O_F loops and gives an error
  • Manager correctly handles instances that never register
  • Last lines of log now printer to screen on error for smoother problem solving
  • Various small fixes and improvements

EasyVVUQ – v1.2.1

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

Code: https://github.com/UCL-CCS/EasyVVUQ/releases/tag/v1.2.1

Fixes and updates

  • Fixed several tests for newer Python versions.
  • Updated integration with QCG-PilotJob

Tutorials

QCG-PilotJob – v0.14.0

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

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

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

EasySurrogate – v0.19

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

Code: https://github.com/wedeling/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:

  • no new updates

RADICAL-Cybertools

Overview: https://github.com/radical-cybertools

Code: The current RCT stack consists of the following releases:

Features:

  • The main changes over the last couple of releases have been improved integration and stability of the Raptor subsystem (fast function execution at scale), improved documentation, and support for new NSF and DOE resources.
  • The next set of releases will remove MongoDB as a dependency. That will simplify deployment and sysop significantly and remove some scalability bottlenecks. Release is expected in August 2023.

March 2023 Release of SEAVEAtk

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.

Month 12 Release of SEAVEAtk

EasyVVUQ v1.1.2

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

QCG PilotJob v0.13.1

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

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

FabSim3 v3.2

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:

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

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

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