May 2012 - moab-dev - mailman3.cels.anl.gov

Testing configuration of MOAB itself
by Mark Miller 30 May '12

30 May '12

Hi MOAB Developers, I am just curious about something now. I am pretty sure MOAB uses buildbot somehow. But, I am wondering whether and how much of configuration of MOAB itself is tested and, in particular, the variety of different (and perhaps incompatible ways) MOAB can be configured. I am just curious. I don't think we do this with VisIt per se but we do have enough different people building it in different ways that a very large set of configuration permutations does wind up being 'tested' and I am just wonder if there is any explicit effort to do this on a project as large as MOAB? Mark -- Mark C. Miller, Lawrence Livermore National Laboratory ================!!LLNL BUSINESS ONLY!!================ miller86(a)llnl.gov urgent: miller86(a)pager.llnl.gov T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511

2 2

--enable-igeom vs. --disable-imesh
by Mark Miller 30 May '12

30 May '12

Hi MOAB Developers, I think by default MOAB builds WITH iMesh support and so the configure option is to disable it with --disable-imesh. However, I just build 4.5 branch and did NOT specify --enable-igeom (such as './configure --help' indicates is necessary for iGeom support) and nonetheless, I am still able to compile iGeom clients in itaps/igeom directory. I mention it only because I am wondering if there are one or two issues here? Does MOAB build iGeom by default too? If so, the configure switch for it probably ought to be --disable-igeom much as it is for iMesh support. If MOAB doesn't build iGeom by default, how is it that 'make check' in itaps/igeom dir succeeded in building iGeom clients? Mark -- Mark C. Miller, Lawrence Livermore National Laboratory ================!!LLNL BUSINESS ONLY!!================ miller86(a)llnl.gov urgent: miller86(a)pager.llnl.gov T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511

2 1

Re: [MOAB-dev] make check on 4.5 branch with gcc-4.1.2
by Tim Tautges 30 May '12

30 May '12

[cc'ing to moab-dev in case others are interested...] Yes, you should configure --with-cgm=, since those will be read through cgm. Once you've done that, it should work fine (I've used that to viz OCC files in Paraview, for example). - tim On 05/30/2012 01:09 PM, Mark Miller wrote: > Ok, thats what I thought. > > Another question. Should I expect the igeom test codes in itaps/igeom, > like testSmooth, to be able to read bricks.stp? I am getting segv's with > it whereas it is reading the default .h5m file ok I guess. > > Also, I'v obtained a slew of other .stp files for testing my VisIt > plugin and am wondering if there are any gotchas I need to be aware of > reading them into MOAB via iGeom. > > I did NOT configure with CGM. Do I need to? > > Mark > > On Wed, 2012-05-30 at 11:03 -0700, Tim Tautges wrote: >> Not the fortran examples. That only became possible with gcc4.3 and newer. >> >> - tim >> >> On 05/30/2012 12:44 PM, Mark Miller wrote: >>> Hi Tim, >>> >>> Should I expect a 'make check' in the itaps dir for MAOB Version4.5 >>> branch to compile correctly for gcc-4.1.2? >>> >>> I am seeing... >>> >>> SET=tr1/unordered_set -O2 -fcray-pointer -c -o ScdMeshF90.o ScdMeshF90.F90 >>> In file ScdMeshF90.F90:58 >>> >>> call iMesh_createStructuredMesh(%VAL(mesh), local_dims, global_dims, %VAL(0),%V >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:61 >>> >>> call iMesh_getRootSet(%VAL(mesh), root_set, ier); if (0 .ne. ier) call exit(1); >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:63 >>> >>> call iMesh_getGeometricDimension(%VAL(mesh), geom_dim, ier); if (0 .ne. ier) ca >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:65 >>> >>> call iMesh_getNumOfType(%VAL(mesh), %VAL(root_set), %VAL(iBase_FACE), num_regio >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:67 >>> >>> call iMesh_getNumOfType(%VAL(mesh), %VAL(root_set), %VAL(iBase_VERTEX), num_ver >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:69 >>> >>> call iMesh_initEntArrIter(%VAL(mesh), %VAL(root_set), %VAL(iBase_FACE), %VAL(iM >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:72 >>> >>> call iMesh_createTagWithOptions(%VAL(mesh), "XM1", "moab:TAG_STORAGE_TYPE=DENSE >>> 1 >>> Error: Syntax error in argument list at (1) >>> In file ScdMeshF90.F90:75 >>> >>> call iMesh_tagIterate(%VAL(mesh), %VAL(tagh), %VAL(iter), rpxm1, count, ier); i >>> 1 >>> Error: Syntax error in argument list at (1) >>> make[3]: *** [ScdMeshF90.o] Error 1 >>> >>> >> -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

3 4

Re: [MOAB-dev] make check on 4.5 branch with gcc-4.1.2
by Tim Tautges 30 May '12

30 May '12

Not the fortran examples. That only became possible with gcc4.3 and newer. - tim On 05/30/2012 12:44 PM, Mark Miller wrote: > Hi Tim, > > Should I expect a 'make check' in the itaps dir for MAOB Version4.5 > branch to compile correctly for gcc-4.1.2? > > I am seeing... > > SET=tr1/unordered_set -O2 -fcray-pointer -c -o ScdMeshF90.o ScdMeshF90.F90 > In file ScdMeshF90.F90:58 > > call iMesh_createStructuredMesh(%VAL(mesh), local_dims, global_dims, %VAL(0),%V > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:61 > > call iMesh_getRootSet(%VAL(mesh), root_set, ier); if (0 .ne. ier) call exit(1); > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:63 > > call iMesh_getGeometricDimension(%VAL(mesh), geom_dim, ier); if (0 .ne. ier) ca > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:65 > > call iMesh_getNumOfType(%VAL(mesh), %VAL(root_set), %VAL(iBase_FACE), num_regio > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:67 > > call iMesh_getNumOfType(%VAL(mesh), %VAL(root_set), %VAL(iBase_VERTEX), num_ver > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:69 > > call iMesh_initEntArrIter(%VAL(mesh), %VAL(root_set), %VAL(iBase_FACE), %VAL(iM > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:72 > > call iMesh_createTagWithOptions(%VAL(mesh), "XM1", "moab:TAG_STORAGE_TYPE=DENSE > 1 > Error: Syntax error in argument list at (1) > In file ScdMeshF90.F90:75 > > call iMesh_tagIterate(%VAL(mesh), %VAL(tagh), %VAL(iter), rpxm1, count, ier); i > 1 > Error: Syntax error in argument list at (1) > make[3]: *** [ScdMeshF90.o] Error 1 > > -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

1 0

Edges at the ends of a periodic mesh?
by Robert Jacob 25 May '12

25 May '12

Hi, If I have a 2D rectangular mesh which is periodic in one direction, lets say the j direction, then the leftmost and rightmost edge of the mesh are really the same edge. Do they both need to be declared in MOAB? Or does the periodic property mean you only need to describe one of the edges and the other end will know its adjacent to it? Thanks, Rob

4 11

r5533 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 25 May '12

25 May '12

Author: tautges Date: 2012-05-25 03:47:26 -0500 (Fri, 25 May 2012) New Revision: 5533 Added: MOAB/trunk/src/io/DamselUtil.hpp Modified: MOAB/trunk/src/io/ReadDamsel.cpp MOAB/trunk/src/io/ReadDamsel.hpp MOAB/trunk/src/io/WriteDamsel.cpp Log: Updating Damsel work. Added: MOAB/trunk/src/io/DamselUtil.hpp =================================================================== --- MOAB/trunk/src/io/DamselUtil.hpp (rev 0) +++ MOAB/trunk/src/io/DamselUtil.hpp 2012-05-25 08:47:26 UTC (rev 5533) @@ -0,0 +1,75 @@ +#ifndef READDAMSEL_HPP +#define READDAMSEL_HPP + +#include "moab/Forward.hpp" +#include "DebugOutput.hpp" + +#include "damsel.h" + +namespace moab { + +class DamselUtil +{ +public: + //! needs to be a constructor to initialize dtom_data_type + DamselUtil(); + + static damsel_data_type mtod_data_type[MB_MAX_DATA_TYPE]; + + std::map<damsel_data_type,DataType> dtom_data_type; + + static enum damsel_entity_type mtod_entity_type[MBMAXTYPE]; + + static enum EntityType dtom_entity_type[DAMSEL_ENTITY_ALL_TYPES]; +}; + +damsel_entity_type DamselUtil::mtod_entity_type[] = { + DAMSEL_ENTITY_TYPE_VERTEX, // MBVERTEX + DAMSEL_ENTITY_TYPE_EDGE, // MBEDGE + DAMSEL_ENTITY_TYPE_TRI, // MBTRI + DAMSEL_ENTITY_TYPE_QUAD, // MBQUAD + DAMSEL_ENTITY_TYPE_POLYGON, // MBPOLYGON + DAMSEL_ENTITY_TYPE_TET,// MBTET + DAMSEL_ENTITY_TYPE_PYRAMID, // MBPYRAMID + DAMSEL_ENTITY_TYPE_PRISM, // MBPRISM + DAMSEL_ENTITY_TYPE_UNDEFINED, // MBKNIFE + DAMSEL_ENTITY_TYPE_HEX, // MBHEX, + DAMSEL_ENTITY_TYPE_POLYHEDRON, // MBPOLYHEDRON + DAMSEL_ENTITY_TYPE_UNDEFINED, // MBENTITYSET + DAMSEL_ENTITY_TYPE_ALL_TYPES // MBMAXTYPE /**< +}; + +EntityType DamselUtil::dtom_entity_type[] = { + MBVERTEX, // MBVERTEX + MBEDGE, // MBEDGE + MBTRI, // MBTRI + MBQUAD, // MBQUAD

1 0

r5532 - MOAB/trunk/src/moab
by iulian＠mcs.anl.gov 23 May '12

23 May '12

Author: iulian Date: 2012-05-23 16:30:09 -0500 (Wed, 23 May 2012) New Revision: 5532 Modified: MOAB/trunk/src/moab/ScdInterface.hpp Log: compute factors a little faster Modified: MOAB/trunk/src/moab/ScdInterface.hpp =================================================================== --- MOAB/trunk/src/moab/ScdInterface.hpp 2012-05-23 18:48:20 UTC (rev 5531) +++ MOAB/trunk/src/moab/ScdInterface.hpp 2012-05-23 21:30:09 UTC (rev 5532) @@ -783,11 +783,13 @@ } else { std::vector<double> pfactors, ppfactors; - for (int i = 2; i <= np; i++) + for (int i = 2; i <= np/2; i++) if (!(np%i)) { pfactors.push_back(i); ppfactors.push_back(((double)(i*i))/np); } + pfactors.push_back(np); + ppfactors.push_back( (double)np); // ideally, Px/Py = I/J double ijratio = ((double)(gijk[3]-gijk[0]))/((double)(gijk[4]-gijk[1]));

1 0

r5527 - MOAB/trunk/src
by iulian＠mcs.anl.gov 18 May '12

18 May '12

Author: iulian Date: 2012-05-18 16:51:19 -0500 (Fri, 18 May 2012) New Revision: 5527 Modified: MOAB/trunk/src/GeomTopoTool.cpp Log: add more debug info when the topological tests are failing for example, Takeda1.h5m has an edge that is oriented the wrong way. Our convention is that the orientation of mesh edges in an edge set is the same, and that mesh edges are oriented along the geometry edge, in order. Modified: MOAB/trunk/src/GeomTopoTool.cpp =================================================================== --- MOAB/trunk/src/GeomTopoTool.cpp 2012-05-18 19:05:02 UTC (rev 5526) +++ MOAB/trunk/src/GeomTopoTool.cpp 2012-05-18 21:51:19 UTC (rev 5527) @@ -1309,7 +1309,7 @@ return MB_SUCCESS; } -#define RETFALSE(a) { std::cout<<a<<"\n"; return false; } +#define RETFALSE(a, b) { std::cout<<a<<"\n"; mdbImpl->list_entity(b); return false; } bool GeomTopoTool::check_model() { // vertex sets should have one node @@ -1321,20 +1321,20 @@ Range nodes; rval = mdbImpl->get_entities_by_handle(vSet, nodes); if (MB_SUCCESS!=rval) - RETFALSE(" failed to get nodes from vertex set ") + RETFALSE(" failed to get nodes from vertex set ", vSet); if (nodes.size()!=1) - RETFALSE(" number of nodes is different from 1 ") + RETFALSE(" number of nodes is different from 1 ", vSet) EntityType type = mdbImpl->type_from_handle(nodes[0]); if (type != MBVERTEX) - RETFALSE(" entity in vertex set is not a node ") + RETFALSE(" entity in vertex set is not a node ", nodes[0]) // get all parents, and see if they belong to geomRanges[1] Range edges; rval = mdbImpl->get_parent_meshsets(vSet, edges); if (MB_SUCCESS!=rval) - RETFALSE(" can't get parent edges for a node set ") + RETFALSE(" can't get parent edges for a node set ", vSet) Range notEdges = subtract(edges, geomRanges[1] ); if (!notEdges.empty()) - RETFALSE(" some parents of a node set are not geo edges ") + RETFALSE(" some parents of a node set are not geo edges ", notEdges[0]) } // edges to be formed by continuous chain of mesh edges, oriented correctly @@ -1344,10 +1344,10 @@ std::vector<EntityHandle> mesh_edges; rval = mdbImpl->get_entities_by_type(edge, MBEDGE, mesh_edges); if (MB_SUCCESS!=rval) - RETFALSE(" can't get mesh edges from edge set") + RETFALSE(" can't get mesh edges from edge set", edge) int num_edges = (int)mesh_edges.size(); if (num_edges==0) - RETFALSE(" no mesh edges in edge set ") + RETFALSE(" no mesh edges in edge set ", edge) EntityHandle firstNode; EntityHandle currentNode; // will also hold the last node in chain of edges

1 0

r5518 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 12 May '12

12 May '12

Author: tautges Date: 2012-05-12 14:15:57 -0500 (Sat, 12 May 2012) New Revision: 5518 Added: MOAB/trunk/src/io/ReadDamsel.cpp MOAB/trunk/src/io/ReadDamsel.hpp Modified: MOAB/trunk/src/io/WriteDamsel.cpp Log: Backing up a start at a Damsel reader; using define_entity_fast instead of define_entity in writer. Added: MOAB/trunk/src/io/ReadDamsel.cpp =================================================================== --- MOAB/trunk/src/io/ReadDamsel.cpp (rev 0) +++ MOAB/trunk/src/io/ReadDamsel.cpp 2012-05-12 19:15:57 UTC (rev 5518) @@ -0,0 +1,241 @@ +#include "ReadDamsel.hpp" + +#include "assert.h" +#include "moab/Interface.hpp" +#include "moab/Core.hpp" +#include "moab/Range.hpp" +#include "moab/Error.hpp" +#include "moab/ReadUtilIface.hpp" +#include "MBTagConventions.hpp" +#include "EntitySequence.hpp" +#include "Internals.hpp" +#include "DenseTag.hpp" + +namespace moab { + + // Some macros to handle error checking (cribbed from WriteHDF5). The + // CHK_MB_ERR_* check the value of an ErrorCode. + // The *_0 macros accept no other arguments. The *_1 + // macros accept a single damsel handle to close on error. + // All macros contain a "return" statement. These macros are coded with a do if while + // to allow statements calling them to be terminated with a ; +#define CHK_MB_ERR( A, B ) \ +do if (MB_SUCCESS != (A)) { \ +mError->set_last_error(B);\ +return error(A);} while(false) + +#define CHK_MB_ERR_2( A, B, C ) \ +do if (MB_SUCCESS != (A )) { \ +mError->set_last_error(B, C); \ +return error(A);} while(false) + +#define CHK_MB_ERR_FINALIZE( A, B ) \ +do if (MB_SUCCESS != (A)) { \ + DMSLlib_finalize(dmslLib); \ + dmslLib = 0; \ + mError->set_last_error(B);\ + return error(A); \ +} while(false) + +#define CHK_DMSL_ERR( A, B ) \ +do if (DMSL_OK.id != A.id) { \ +mError->set_last_error(B);\ +return error(MB_FAILURE); \ +} while(false) + +#define CHK_DMSL_ERR_2( A, B, C ) \

1 0

r5517 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 12 May '12

12 May '12

Author: tautges Date: 2012-05-12 13:13:50 -0500 (Sat, 12 May 2012) New Revision: 5517 Modified: MOAB/trunk/src/io/WriteDamsel.cpp Log: Updating damsel writer to latest damsel syntax. Modified: MOAB/trunk/src/io/WriteDamsel.cpp =================================================================== --- MOAB/trunk/src/io/WriteDamsel.cpp 2012-05-11 16:38:51 UTC (rev 5516) +++ MOAB/trunk/src/io/WriteDamsel.cpp 2012-05-12 18:13:50 UTC (rev 5517) @@ -212,7 +212,7 @@ DAMSEL_HANDLE_COLLECTION_TYPE_VECTOR); // make a damsel collection - dseth = DMSLcontainer_tree_create(dmslModel, (damsel_handle_ptr)&seth, coll_type); + dseth = DMSLcontainer_tree_create(dmslModel, coll_type); if (DAMSEL_CONTAINER_INVALID == dseth) CHK_MB_ERR_2(MB_FAILURE, "Bad handle returned by Damsel for meshset %lu.", seth); // get all the entities & add @@ -250,8 +250,7 @@ // create a damsel container for these entity handles damsel_container ent_cont; - ent_cont = DMSLhandle_create_sequence(dmslModel, (damsel_handle)&ent_cont, (int)(end_ent-start_ent+1), - start_ent, 1); + ent_cont = DMSLhandle_create_sequence(dmslModel, (int)(end_ent-start_ent+1), start_ent, 1); if (DAMSEL_CONTAINER_INVALID == ent_cont) CHK_MB_ERR(MB_FAILURE, "Bad sequence returned by Damsel."); @@ -264,10 +263,6 @@ int num_connect = rsi.get_sequence()->values_per_entity(); assert(0 < num_connect); - // define the entities to damsel - err = DMSLentity_define(ent_cont, moab_to_damsel_entity_type[etype], num_connect); - CHK_DMSL_ERR_2(err, "DMSLentity_define failed for entities starting with handle %lu.", rsi.get_start_handle()); - // get the connectivity storage location and pass to damsel Range ent_range(start_ent, end_ent); int count; @@ -279,19 +274,16 @@ CHK_MB_ERR_2(MB_FAILURE, "Entity subrange not in the same sequence for entities starting with handle %lu.", rsi.get_start_handle()); - damsel_container conn_cont = DMSLhandle_create_vector(dmslModel, (damsel_handle) &conn_cont, + damsel_container conn_cont = DMSLhandle_create_vector(dmslModel, count*verts_per_ent, (damsel_handle*)connect); + // define the entities to damsel + err = DMSLentity_define(ent_cont, moab_to_damsel_entity_type[etype], num_connect, conn_cont); + CHK_DMSL_ERR_2(err, "DMSLentity_define failed for entities starting with handle %lu.", rsi.get_start_handle()); + // NOTE: THE FOLLOWING CALL SHOULDN'T BE NEEDED AFTER BEN FIXES WRITING SEQUENCES/VECTORS TO FILE err = DMSLmodel_map_handles_inventing_file_handles(conn_cont); - err = DMSLentity_set_connectivity(ent_cont, conn_cont); - CHK_DMSL_ERR(err, "Failure creating connectivity vector container.");

1 0