June 2017 - moab-dev - mailman3.cels.anl.gov

MOAB v5.0 major release candidate available
by Vijay S. Mahadevan 11 Jun '17

11 Jun '17

Dear MOAB users, The consolidated release of SIGMA v1.3 is available now, and contains the MOAB 5.0 major release candidate. The release tarball can be downloaded at: ftp://ftp.mcs.anl.gov/pub/fathom/moab-5.0.0.tar.gz. We would also like to thank our users and contributors (refer to AUTHORS file) for making this release possible. The notable changes in MOAB v5.0 are: * PyMOAB -- This interface now directly exposes Python modules to access common MOAB functionality in order to load, query and manipulate structured/unstructured meshes in memory. It also includes interfaces to some specific classes such as the ScdInterface and its associated classes along with the TopoUtil tool. We have also added support for Tags, Range, Skinner modules that can be used to build more advanced capabilities as needed. Currently, this interface only supports serial configuration and we intend to support parallelism through `mpi4py` dependencies in the next release. Several useful tests and examples have also been added for users to get started. * Mesquite Support -- Add Mesquite optimization support to MOAB so that mesh optimization algorithms can be natively run on a MOAB mesh. It can also use the geometry information when MOAB is configured with CGM (through Lasso relational databases in MOAB). * *PR #248, #290, * Require Eigen3 or BLAS/LAPACK -- Add support for the Eigen3 BLAS/LAPACK header libraries; Now BLAS/LAPACK are required dependencies for MOAB in order to support high-performance de nse solver support for various algorithms * Trivial partitioning -- Add capability to load an "*unpartitioned*" mesh file through a trivial partition with the parallel option: `PARALLEL=BCAST_DELETE;PARTITION=TRIVIAL`; This works for any mesh format and so we are no longer restricted to just our parallel h5m native mesh. * Discrete Geometry Module -- Higher order curve and surface reconstruction strategies based on local polynomial fittings along with integrated support for recursive uniform refinement. * Conservative solution transfer -- Add support for computing high-order, conservative, multi-mesh projection weights with the **TempestRemap** library. Several optimizations have been implemented for the advancing-front algorithm to compute the intersections between two unstructured meshes on a sphere. In addition to this, the integration with Tempest library enables computation of the projection weights between FV/cGLL/dGLL discretizations seamlessly in a scalable fashion, even though Tempest itself is a serial library! * HEX8 (linear) to HEX27 (quadratic) mesh conversion utility * Considerable DagMC related enhancements and refactoring of the tool Please refer to the following link to find all changes in the SIGMA components and more specifically, information about the fixes and enhancements in MOAB as part of this release. http://sigma.mcs.anl.gov/news/sigma-release-1-3/ Let us know if you have any questions or encounter any issues during your upgrade. Best, The SIGMA team

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Re: [MOAB-dev] What is the current recommendation for building through meshkit?
by jain＠mcs.anl.gov 06 Jun '17

06 Jun '17

Hi John, Autotools is still our No.#1 build system. See configure step for the builds here: http://gnep.mcs.anl.gov:8010/Example: http://gnep.mcs.anl.gov:8010/builders/meshkit-occ-par-sta/builds/430/steps/… (look at the ./configure line) CMake is supported on master (we will have a release with CMake support for all packages this month).Not all external dependencies are supported via CMake for MeshKit. --Rajeev JainMathematics and Computer Science Argonne National Laboratory1134, Bldg 240, Chicago IL USA 60439O: 630-252-3176 jain(a)mcs.anl.gov From: JR Cary <cary(a)txcorp.com> To: "moab-dev(a)mcs.anl.gov" <moab-dev(a)mcs.anl.gov> Sent: Tuesday, June 6, 2017 10:22 AM Subject: [MOAB-dev] What is the current recommendation for building through meshkit? CGM: CMake MOAB: CMake MeshKit: CMake ????? Thx....John

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What is the current recommendation for building through meshkit?
by JR Cary 06 Jun '17

06 Jun '17

CGM: CMake MOAB: CMake MeshKit: CMake ????? Thx....John

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MPI issue (possibly a link issue) with h5m mesh files
by Lorenzo Botti 06 Jun '17

06 Jun '17

Dear all, I’m stuck with this problem since some time and I like to know if someone has a solution, or just a hint of what is going wrong. If I compile MOAB with HDF5 support I’m forced to use an outdated version of the latter (hdf5 1.8.12 works just fine) because a newer version (I tried both 1.8.18 and 1.10.1) produces the following runtime error *** The MPI_Comm_dup() function was called before MPI_INIT was invoked. *** This is disallowed by the MPI standard. *** Your MPI job will now abort. [dlm249-158.unibg.it:1072] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! This happens when the MOAB function load_file(filename.h5m,...) gets called from my application. All the MOAB tests run just fine, in particular the parallel tests involving hdf5 are successful. I guess that’s a linking issue but I really don’t know how to solve it. My makefile is really basic I do MOAB_LIB_DIR = /Users/digihabia/src2/moab-4.9.2/moab/ include $(MOAB_LIB_DIR)/lib/moab.make … I compile my library spafedte with %.o : %.cpp @echo "Compiling ("$(CXX)") "$<" " @$(CXX) $(spafedte_INCLUDE) $(petsc_INCLUDE) ${MOAB_INCLUDES} $(muparser_INCLUDE) $(metis_INCLUDE) $(mgridgen_INCLUDE) $(eigen_INCLUDE) -c $< -o $@ And build the executable with laplace_test : $(objects) @echo "Linking "$(CURDIR)"/"$@ @$(CXX) $(objects) -o $@ $(spafedte_LIB) $(PETSC_SNES_LIB) $(MOAB_LIBS_LINK) $(MGRIDGEN_LIB) $(METIS_LIB) Any help is appreciated. Bests Lorenzo

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src/verdict/moab missing in master branch.
by Madhusudhan Kundrapu 02 Jun '17

02 Jun '17

Hello, The header files folder is missing at MOAB/src/verdict/ Is this intentional.. -Madhu

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