July 2014 - moab-dev - mailman3.cels.anl.gov

msh -> cub -> h5m
by kanaev＠ibrae.ac.ru 19 Aug '14

19 Aug '14

Hello MOAB-dev, I got simple geometry/mesh Cubit file brick1x1x2.cub, i can simply convert it to .h5m with mbconvert I do export to .MSH format in Cubit, and then import it back and save as .cub file again, when i do mbconvert i got message "Element ids are not contiguous!" though it writes .h5m file but GLOBAL_ID tag values for geometry sets are lost (e.g. for Surfaces) I realise it's mostly Cubit/msh import problem but i'd appreciate any advise on that! Anton

2 1

Re: [MOAB-dev] 137GB mesh file
by Rajeev Jain 31 Jul '14

31 Jul '14

I don't have parallel partitions, I'm looking into HelloMOABPar example. Thanks. Rajeev ----- Original Message ----- From: "Grindeanu, Iulian R." <iulian(a)mcs.anl.gov> To: Vijay S. Mahadevan <vijay.m(a)gmail.com> Cc: "Jain, Rajeev" <jain(a)mcs.anl.gov>; MOAB Dev <moab-dev(a)mcs.anl.gov> Sent: Thursday, July 31, 2014 10:12 AM Subject: RE: [MOAB-dev] 137GB mesh file mbconvert is parallel-capable mbpart is not mbsize "is" , but it needs improvements for output agree we need to review all tools ________________________________________ From: Vijay S. Mahadevan [vijay.m(a)gmail.com] Sent: Thursday, July 31, 2014 9:36 AM To: Grindeanu, Iulian R. Cc: Jain, Rajeev; MOAB Dev Subject: Re: [MOAB-dev] 137GB mesh file > I think we need to modify mbsize to run better in parallel (for example, to > gather all counts from each processor, for the owned entities) and print > only once , something like HelloParMOAB Hmm ok. Make all the tools parallel capable then ? mbsize, mbpart, mbconvert etc. Iulian, we need to make a list of things TODO and then we can prioritize what's needed right now. I'll also get started on a list in parallel and we can consolidate. Vijay On Thu, Jul 31, 2014 at 9:30 AM, Grindeanu, Iulian R. <iulian(a)mcs.anl.gov> wrote: > Hi Rajeev, > You can use mbsize -p0 option > This will load the file in parallel, but the printout will be mangled > between processors, each processor will write its count (-p1 will resolve > shared entities, too), -p2 will exchange a layer of ghost elements) > > so you can do something like this > mpiexec -np 64 mbsize -p0 <file_name> > > How many partitions do you have? > > Do you have partitions? (parallel partitions?) > > You can also modify HelloParMOAB example for you needs (harder) > > LoadPartial example can load only a few partitions, and write a smaller > file, it can be run in serial > > Something like > ./LoadPartial <file_name> PARALLEL_PARTITION 0 1 5 > > This will load only partitions 0, 1 and 5, in serial, and write a part.h5m > file, for which you can do an mbsize in serial (if it is small enough) > > All these methods will ensure at least that you have a "readable" file . > > I think we need to modify mbsize to run better in parallel (for example, to > gather all counts from each processor, for the owned entities) and print > only once , something like HelloParMOAB > > Iulian > > ________________________________ > From: moab-dev-bounces(a)mcs.anl.gov [moab-dev-bounces(a)mcs.anl.gov] on behalf > of Rajeev Jain [jain(a)mcs.anl.gov] > Sent: Wednesday, July 30, 2014 11:40 PM > To: MOAB Dev > Subject: [MOAB-dev] 137GB mesh file > > I have an ABTR model (billions of hex elements, created by MeshKit/rgg) that > is 137GB on fusion@ANL: > /homes/jain/sigma/moab/lasso/meshkit/rgg/test/c_abtr_sh > > I'm unable to do mbsize on it -> any suggestions? > Just want to make sure if this is a valid file, also want to know > material/boundary sets contained in it. > > Rajeev >

2 1

137GB mesh file
by Rajeev Jain 31 Jul '14

31 Jul '14

I have an ABTR model (billions of hex elements, created by MeshKit/rgg) that is 137GB on fusion@ANL: /homes/jain/sigma/moab/lasso/meshkit/rgg/test/c_abtr_sh I'm unable to do mbsize on it -> any suggestions? Just want to make sure if this is a valid file, also want to know material/boundary sets contained in it. Rajeev

3 3

MOAB-4.7.0 Release (SIGMA 1.0)
by Vijay S. Mahadevan 25 Jul '14

25 Jul '14

Dear MOAB users, We are pleased to announce the release of MOAB-4.7 which is now part of the Scalable Interfaces for Geometry and Mesh based Applications (SIGMA) tools. The tarball for the release is available for download from http://sigma.mcs.anl.gov/downloads. The release notes for all the packages as part of SIGMA are available at http://sigma.mcs.anl.gov/sigma/sigma-release-1-0. Please upgrade from 4.6.x and lower to the latest version in order for us to help you better use the tools. Some important updates for MOAB include: # Implemented the Array-based Half Facet data structures in MOAB to improve adjacency querying and efficient traversals between related entities (use -enable-ahf during configure) # Co-developed (MOAB and PETSc) to introduce a new native MOAB-mesh based Discretization Manager (DM) implementation in PETSc that supports parallel solution to PDE problems on unstructured grids # Improved configuration and support for CMake based builds # Extensive enhancements in several reader/writer implementations (NC, VTK, HOMME, CAM-Euler, CAM-FV, VTK, MPAS, GCRM, CUBIT) # Improved Paraview plugin support to directly read H5M files # Remove memory leak for point-to-point communication (issue #7), due to reusing of MPIRequest structures # Several other miscellaneous bug fixes, enhancements throughout the library. More information at http://sigma.mcs.anl.gov/sigma/sigma-release-1-0. As always, send us an email at moab-dev(a)mcs.anl.gov, if you have any questions on configuration/build/install procedures. Thank you, Vijay and SIGMA team

1 0

make check returns error when installing moab
by the lily 23 Jul '14

23 Jul '14

Hi everyone, I keep getting an error when I try to install moab, here are the steps I did and the output for each step, Step1: ./configureoutput: configure: WARNING: ************************************************************************* * MOAB has been configured w/out the HDF5 library. * Support for native file format is disabled! ************************************************************************* configure: WARNING: ************************************************************************* * MOAB has been configured w/out the NetCDF library. * Support for ExodusII/Genesis and other file formats is disabled! ************************************************************************* Step2: makeoutput:make[3]: Nothing to be done for `all-am'.Making all in iomake[3]: Nothing to be done for `all'.Making all in dualmake[3]: Nothing to be done for `all'.Making all in obbmake[3]: Nothing to be done for `all'.Making all in perfMaking all in point_locationmake[4]: Nothing to be done for `all'.make[4]: Nothing to be done for `all-am'.Making all in dagmcmake[3]: Nothing to be done for `all'.Making all in oldincmake[3]: Nothing to be done for `all'.Making all in docmake[2]: Nothing to be done for `all'../config.status --version | \ sed -e 's/.*options "$.*$"/\1/p' -e 'd' | \ tr "'" "\n" | \ sed -e '/^ *$/d' > moab.config Step3: make checkoutput:libtool: link: unrecognized option `-O2'libtool: link: Try `libtool --help' for more information.make[4]: *** [ScdMeshF90] Error 1make[3]: *** [check-am] Error 2make[2]: *** [check] Error 2make[1]: *** [check-recursive] Error 1 make: *** [check-recursive] Error 1 I do not know what exactly went wrong, do I need to install any libraries before installing moab? Thank you.

4 16

Re: [MOAB-dev] how to install mbpart in moab installation??
by Rajeev Jain 16 Jul '14

16 Jul '14

Just to complete the thread: we've resolved the issue. MOAB was built using mpi option, but serial hdf5 was used, using parallel hdf5 fixes the problems while running Nek5000 in parallel. Rajeev ________________________________ From: "Jain, Rajeev" <jain(a)mcs.anl.gov> To: "Grindeanu, Iulian R." <iulian(a)mcs.anl.gov>; "Vegendla, Surya Narayana Prasad" <svegendla(a)anl.gov> Cc: MOAB Dev <moab-dev(a)mcs.anl.gov> Sent: Wednesday, July 16, 2014 10:01 AM Subject: Re: [MOAB-dev] how to install mbpart in moab installation?? The mesh files are already partitioned for the Nek examples you're trying to run. Let's try to see if it fails loading on multiple processors: /homes/jain/nek5_svn/examples/moab ==> mpiexec -n 2 mbconvert -O PARALLEL=READ_PART -O PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -O PARTITION_DISTRIBUTE -o PARALLEL=WRITE_PART pipe00.h5m t.h5m If this fails then your moab installation has problems. Rajeev ________________________________ From: "Grindeanu, Iulian R." <iulian(a)mcs.anl.gov> To: "Vegendla, Surya Narayana Prasad" <svegendla(a)anl.gov>; "Jain, Rajeev" <jain(a)mcs.anl.gov> Cc: MOAB Dev <moab-dev(a)mcs.anl.gov> Sent: Wednesday, July 16, 2014 9:11 AM Subject: RE: how to install mbpart in moab installation?? you need zoltan, too http://sigma.mcs.anl.gov/?p=409 when you configure with zoltan, mbpart will be compiled, too ________________________________ From: moab-dev-bounces(a)mcs.anl.gov [moab-dev-bounces(a)mcs.anl.gov] on behalf of Vegendla, Surya Narayana Prasad [svegendla(a)anl.gov] Sent: Wednesday, July 16, 2014 8:59 AM To: Jain, Rajeev Cc: MOAB Dev Subject: Re: [MOAB-dev] how to install mbpart in moab installation?? Yes Rajeev, I configured with mpi. Did I miss anything in the following commands? #MOAB## git clone https://bitbucket.org/fathomteam/moab cd moab autoreconf -fi ./configure --with-mpi --with-hdf5=/home/svegendla/install/hdf5 --prefix=/home/svegendla/install/moab/bld make make install Thanks, Prasad From:Rajeev Jain [mailto:[email protected]] Sent: Tuesday, July 15, 2014 8:51 PM To: Vegendla, Surya Narayana Prasad Cc: MOAB Dev Subject: Re: how to install mbpart in moab installation?? MOAB must be configured with MBZoltan for mbpart tool. The .h5m file in Nek repo already has two partitions and it should work well with two processors. The error line you mention is a call to "iMeshP_loadAll" function are you using parallel MOAB? ==> mbsize -t moab_conjht.h5m File moab_conjht.h5m: Tag Name Vertex Hex EntitySet ------------------ -------- -------- --------- MATERIAL_SET 0 0 3 NEUMANN_SET 0 0 6 DIRICHLET_SET 0 0 0 GEOM_DIMENSION 0 0 0 GLOBAL_ID 99 5 11 HAS_MID_NODES 0 0 3 PARALLEL_PARTITION 0 0 2 distFactor 0 0 6 qaRecord 0 0 0 Rajeev ________________________________ From:"Vegendla, Surya Narayana Prasad" <svegendla(a)anl.gov> To: "Jain, Rajeev" <jain(a)mcs.anl.gov> Sent: Tuesday, July 15, 2014 3:56 PM Subject: how to install mbpart in moab installation?? Hi Rajeev, How to install mbpart in MOAB bin directory as similar to mbconvert? And also following errors are seen while running on multi processors blues account, here I used the partition grid from MCS account where mbpart installed your directory (it works well in a single processor). Number of processors: 2 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /home/svegendla/nekFiles/moab_conjhtOld/moab_conjht.rea timer accuracy: 9.5367432E-08 sec read .rea file ASSERT ERROR: 21 in moab.f line 477 ASSERT ERROR: 21 in moab.f line 477 call exitt: dying ... Thanks, Prasad

1 0

Cohesive elements
by Gerd Heber 16 Jul '14

16 Jul '14

Has anyone tried to represent cohesive elements* in MOAB? Should we fall back to (degenerate) polyhedra or just use the built-in triangles and quadrilaterals (and "double up")? Thanks for your comments. G. * Topologically they are pairs of triangles or quadrilaterals with linear or quadratic shape functions. Their constitutive law is such that they seize to carry load beyond a certain limit, at which point they separate. They should be treated like 3D elements, although they have no volume/thickness.

3 2

Conventions for naming entity sets
by Gerd Heber 16 Jul '14

16 Jul '14

It appears that the simplest way to name an entity set is to create a tag with that name and a dummy tag value. (I'm not thinking about large numbers of entity sets, I might have a few dozen.) 1. Am I missing something that's more straightforward? 2. Are there conventions regarding the tag type (sparse, dense) or tag value type (bit, integer)? Thanks for your comments. G.

2 1

FW: Conventions for naming entity sets
by Grindeanu, Iulian R. 16 Jul '14

16 Jul '14

________________________________________ From: moab-dev-bounces(a)mcs.anl.gov [moab-dev-bounces(a)mcs.anl.gov] on behalf of Gerd Heber [gheber(a)hdfgroup.org] Sent: Wednesday, July 16, 2014 10:42 AM To: moab-dev(a)mcs.anl.gov Subject: [MOAB-dev] Conventions for naming entity sets It appears that the simplest way to name an entity set is to create a tag with that name and a dummy tag value. (I'm not thinking about large numbers of entity sets, I might have a few dozen.) 1. Am I missing something that's more straightforward? 2. Are there conventions regarding the tag type (sparse, dense) or tag value type (bit, integer)? Thanks for your comments. G. Yes, that is the best way; you can use then get_entities_by_type_and_tag http://ftp.mcs.anl.gov/pub/fathom/moab-docs/classmoab_1_1Interface.html#aa5… to retrieve the sets in one sweep, in case you do not cache them in your code. If you use tag values, you can filter by tag value, too; if not, it will retrieve all sets with that tag. Integer tags, sparse are best for this. look at the examples, too Iulian

1 0

Re: [MOAB-dev] how to install mbpart in moab installation??
by Rajeev Jain 16 Jul '14

16 Jul '14

The mesh files are already partitioned for the Nek examples you're trying to run. Let's try to see if it fails loading on multiple processors: /homes/jain/nek5_svn/examples/moab ==> mpiexec -n 2 mbconvert -O PARALLEL=READ_PART -O PARTITION=PARALLEL_PARTITION -O PARALLEL_RESOLVE_SHARED_ENTS -O PARTITION_DISTRIBUTE -o PARALLEL=WRITE_PART pipe00.h5m t.h5m If this fails then your moab installation has problems. Rajeev ________________________________ From: "Grindeanu, Iulian R." <iulian(a)mcs.anl.gov> To: "Vegendla, Surya Narayana Prasad" <svegendla(a)anl.gov>; "Jain, Rajeev" <jain(a)mcs.anl.gov> Cc: MOAB Dev <moab-dev(a)mcs.anl.gov> Sent: Wednesday, July 16, 2014 9:11 AM Subject: RE: how to install mbpart in moab installation?? you need zoltan, too http://sigma.mcs.anl.gov/?p=409 when you configure with zoltan, mbpart will be compiled, too ________________________________ From: moab-dev-bounces(a)mcs.anl.gov [moab-dev-bounces(a)mcs.anl.gov] on behalf of Vegendla, Surya Narayana Prasad [svegendla(a)anl.gov] Sent: Wednesday, July 16, 2014 8:59 AM To: Jain, Rajeev Cc: MOAB Dev Subject: Re: [MOAB-dev] how to install mbpart in moab installation?? Yes Rajeev, I configured with mpi. Did I miss anything in the following commands? #MOAB## git clone https://bitbucket.org/fathomteam/moab cd moab autoreconf -fi ./configure --with-mpi --with-hdf5=/home/svegendla/install/hdf5 --prefix=/home/svegendla/install/moab/bld make make install Thanks, Prasad From:Rajeev Jain [mailto:[email protected]] Sent: Tuesday, July 15, 2014 8:51 PM To: Vegendla, Surya Narayana Prasad Cc: MOAB Dev Subject: Re: how to install mbpart in moab installation?? MOAB must be configured with MBZoltan for mbpart tool. The .h5m file in Nek repo already has two partitions and it should work well with two processors. The error line you mention is a call to "iMeshP_loadAll" function are you using parallel MOAB? ==> mbsize -t moab_conjht.h5m File moab_conjht.h5m: Tag Name Vertex Hex EntitySet ------------------ -------- -------- --------- MATERIAL_SET 0 0 3 NEUMANN_SET 0 0 6 DIRICHLET_SET 0 0 0 GEOM_DIMENSION 0 0 0 GLOBAL_ID 99 5 11 HAS_MID_NODES 0 0 3 PARALLEL_PARTITION 0 0 2 distFactor 0 0 6 qaRecord 0 0 0 Rajeev ________________________________ From:"Vegendla, Surya Narayana Prasad" <svegendla(a)anl.gov> To: "Jain, Rajeev" <jain(a)mcs.anl.gov> Sent: Tuesday, July 15, 2014 3:56 PM Subject: how to install mbpart in moab installation?? Hi Rajeev, How to install mbpart in MOAB bin directory as similar to mbconvert? And also following errors are seen while running on multi processors blues account, here I used the partition grid from MCS account where mbpart installed your directory (it works well in a single processor). Number of processors: 2 REAL wdsize : 8 INTEGER wdsize : 4 Beginning session: /home/svegendla/nekFiles/moab_conjhtOld/moab_conjht.rea timer accuracy: 9.5367432E-08 sec read .rea file ASSERT ERROR: 21 in moab.f line 477 ASSERT ERROR: 21 in moab.f line 477 call exitt: dying ... Thanks, Prasad

1 0