SIGMA

Scalable Interfaces for Geometry and Mesh based Applications

SIGMA Release 1.2

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SIGMA v1.2 notable changes

SIGMA v1.2 minor release includes a consolidated packaging of all geometry and mesh related components. Details on compatibility of the different tools and dependent libraries are available separately and all questions can be directed to <package>[email protected].
Current release contains the following SIGMA tools:

  1. Common Geometry Module (CGM) – Version 15.0
  2. Mesh Oriented datABase (MOAB) – Version 4.9.0
  3. MeshKit library (MeshKit) – Version 1.4.0

As part of SIGMA v1.2, the Lasso source package has been integrated completely into MOAB for multiple technical reasons. The primarily motivation is the need to explore uniform and adaptive refinement algorithms that are geometry-aware through the embedded interfaces exposed in Lasso, which are now directly available as part of MOAB. This also simplifies the configuration stack necessary for MeshKit while maintaining backwards compatibility.
Source tarballs can be obtained from either the Bitbucket repository or from the ftp site. For more build instructions, go to the downloads page.
Several combination of compilers, dependencies and versions are constantly being tested after every commit and nightly with our Buildbot system. Continuous Integration (CI) support through dynamic Buildbot reconfiguration is being enabled to improve the workflow of both the developers and contributors to SIGMA. The individual release notes for each of the tools are available below.

Table of contents

CGM Version 15.0

This version of CGM is compatible with Cubit 14.9 and Cubit 15.0 (https://cubit.sandia.gov/public/15.0/Cubit-15.0-announcement.html)

A. Features

  • PR #21: Support for Windows CMake builds
  • PR #25: Add support for OCE 0.17 version (compatible with OCC 6.8.0)

B. Fixes

  • PR #30: Clean up configuration for building on OSX
  • PR #28: Number of models in cubit files for version >=14
  • PR #23: Restore some OCC tests

MOAB Version 4.9.0

A. Features

  • PR #109: Optimized AHF data structure and scalability of parallel uniform mesh refinement now available (Major)
  • PR #140: Merge Lasso sources to MOAB completely (Major)
  • PR #137: Debian builds are available for MOAB out-of-the-box now; Check the link for updates (Major)
  • PR #172: Updated support to load geometry representations (CGM 15.0 + Cubit 14.9/15.0) (Minor)

B. Configuration

CMake

  • PR #166: Missing file in CMakeLists.txt and remove exe flag from sources
  • PR #154: Don’t require METIS_DIR, PARMETIS_DIR to be set
  • PR #150: Improve CMake HDF5 detection
  • PR #146: Remove usage of MPI_DIR, remove config/FindMPI.cmake
  • PR #135: CMake cleanup
  • PR #124: CMake support for verdict, Metis/ParMetis

Autotools

  • PR #168: Remove obsolete code related to netcdf workaround in moab_mpi.h
  • PR #163: Prepare to use CMake run target in examples folder
  • PR #149: Replace the deprecated finite routine (C99 standard)
  • PR #148: Modify obb tests to not be run with regular suite
  • PR #144: Fortran libs for iMeshP test
  • PR #129: Use correct linker flags for Fortran examples in debug mode
  • PR #121: Fixes for examples and upgrade makefile with options to run targets
  • PR #114: Fix compiler warnings related to HAVE_UNORDERED_MAP
  • PR #122: Enable MOAB_HAVE_VSNPRINTF for ErrorOutput.cpp

C. Fixes

General

  • PR #169: Fix for quadratic pyramid adjacency creation, related to order of faces
  • PR #165: GenLargeExample tetra option fix
  • PR #157: Fix metis partitioner for serial builds
  • PR #147: Rename SDIR macro
  • PR #132: CartVect duplicate removal
  • PR #142: Simplify CpuTimer
  • PR #138: Updates to TestUtil and testMatrix3 to make sure eigenvectors (normalized) are checked correctly.
  • PR #136: Add checks for dense double tags
  • PR #130: Fix for the way Eigenvectors are returned in the Eigenvalue decomposition function.
  • PR #133: Face-to-volume Sense Corrections (MOAB)
  • PR #120: Fixed the test_adj.
  • PR #126: Remove redundant definition of CpuTimer in WriteHDF5Parallel.cpp
  • PR #123: Fix element_test issue due to missing mesh files
  • PR #125: Bug in Coupler
  • PR #119: Fix dual_test issue due to missing mesh file

Parallel

  • PR #160: Fix hdf5 parallel reader if number of partitions is too small
  • PR #159: Run more parallel tests when built without HDF5
  • PR #158: Add option to skip augmenting the default sets with ghosts
  • PR #145: Factor in sequence manager for ghosting
  • PR #141: Populate sets with ghost entities
  • PR #131: Merge_all method added to merge mesh class

I/O

  • PR #151: HDF5 parallel reader bug
  • PR #128: HDF5 file with more than 2^32 entities

Memory leaks

  • PR #156: Various fixes for memory leaks in serial and parallel examples
  • PR #153: Valgrind fix for parallel_hdf5_test
  • PR #127: Gen large mesh memory reduction
  • PR #116: Major changes for large mesh example

MeshKit Version 1.4

A. Features:

  • Old MeshKit/algs, MeshKit/utils and MeshKit/rgg are deleted. RGG tools CoreGen and AssyGen are fully functional and adhere to the graph-based scheme.
  • Added a new MeshOp FacetMeshReader.
  • Lasso has been removed as a dependency. MOAB must now be configured –with-irel option for building MeshKit.
  • AssyMesher: A new MeshOp for meshing OCC (.brep) type reactor assembly meshes generated by AssyGen has been added.

B. Enhancements:

  • New AssyGen boundary layer generation feature is added, this has been exposed via RGG GUI by Kitware.
  • MESHTOGEOM tag and o/p file has developed in RGG workflow for PROTEUS to compute ratio of mesh to geometric volume.
  • New routines due to CGM and MOAB updatation.
  • Using quality check from MOAB in PostBL for modified penultimate hexes. Program exits if negative Jacobian is encountered.

C. Fixes

  • A new tools directory is introduced with AssyGen, CoreGen and PostBL as tools.
  • CoreGen has been optimized and found to be 10-20% faster using the graph-based design.
  • Several valgrind and warning fixes have been applied.
  • Bugs found during the development of AssyMesher in TFIMapping and CGM have been fixed.
  • Fix conflicts between multiple instances of OneToOneSwept from existence of tags and marking of shared nodes.
  • Fix multiple layer creation when creating tet layers from prim layers, indices were incorrect.

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