November 2011 - moab-dev - mailman3.cels.anl.gov

r5232 - in MOAB/trunk: . itaps/igeom
by jvporter＠wisc.edu 29 Nov '11

29 Nov '11

Author: jvporter Date: 2011-11-29 17:27:19 -0600 (Tue, 29 Nov 2011) New Revision: 5232 Added: MOAB/trunk/itaps/igeom/FBiGeom-Defs.inc.in MOAB/trunk/itaps/igeom/FBiGeom.h MOAB/trunk/itaps/igeom/FBiGeom_MOAB.cpp MOAB/trunk/itaps/igeom/FBiGeom_MOAB.hpp MOAB/trunk/itaps/igeom/FBiGeom_f.h Removed: MOAB/trunk/itaps/igeom/iGeom-Defs.inc.in MOAB/trunk/itaps/igeom/iGeom.h MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp MOAB/trunk/itaps/igeom/iGeom_MOAB.hpp MOAB/trunk/itaps/igeom/iGeom_f.h Modified: MOAB/trunk/configure.ac MOAB/trunk/itaps/igeom/Makefile.am MOAB/trunk/itaps/igeom/testSmooth.cc MOAB/trunk/itaps/igeom/testgeom.cc Log: Rename iGeom interface to FBiGeom to prevent collisions with CGM's iGeom Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2011-11-29 22:35:07 UTC (rev 5231) +++ MOAB/trunk/configure.ac 2011-11-29 23:27:19 UTC (rev 5232) @@ -1148,7 +1148,7 @@ itaps/imesh/Makefile itaps/imesh/iMesh-Defs.inc itaps/igeom/Makefile - itaps/igeom/iGeom-Defs.inc + itaps/igeom/FBiGeom-Defs.inc tools/Makefile tools/refiner/Makefile tools/mbcoupler/Makefile Copied: MOAB/trunk/itaps/igeom/FBiGeom-Defs.inc.in (from rev 5229, MOAB/trunk/itaps/igeom/iGeom-Defs.inc.in) =================================================================== --- MOAB/trunk/itaps/igeom/FBiGeom-Defs.inc.in (rev 0) +++ MOAB/trunk/itaps/igeom/FBiGeom-Defs.inc.in 2011-11-29 23:27:19 UTC (rev 5232) @@ -0,0 +1,23 @@ +FBIGEOM_CXXFLAGS = @CXXFLAGS@ +FBIGEOM_CFLAGS = @CFLAGS@ +FBIGEOM_LDFLAGS = @EXPORT_LDFLAGS@ + +FBIGEOM_FC = @FC@ +FBIGEOM_FCFLAGS = @FCFLAGS@ + +FBIGEOM_FCDEFS = @DEFS@ + +FBIGEOM_CPPFLAGS = -I$(FBIGEOM_INCLUDEDIR) $(FBIGEOM_INCLUDEDIR2) + +# This definition is deprecated; use IMESH_CPPFLAGS instead +FBIGEOM_INCLUDES = $(FBIGEOM_CPPFLAGS) + +FBIGEOM_LIBS = $(FBIGEOM_LDFLAGS) -L$(MOAB_LIBDIR) \ + -L$(FBIGEOM_LIBDIR) -liMesh -lMOAB \ + @NETCDF_LIBS@ @HDF5_LIBS@ @LIBS@ \ + @CGM_LDFLAGS@ @CGM_LIBS@ + +FBIGEOM_INCLUDEDIR1 = @abs_srcdir@ +FBIGEOM_INCLUDEDIR2 = -I@abs_top_builddir@ +FBIGEOM_LIBDIR = @abs_builddir@/.libs +MOAB_LIBDIR = @abs_builddir@/../../.libs Copied: MOAB/trunk/itaps/igeom/FBiGeom.h (from rev 5229, MOAB/trunk/itaps/igeom/iGeom.h) =================================================================== --- MOAB/trunk/itaps/igeom/FBiGeom.h (rev 0) +++ MOAB/trunk/itaps/igeom/FBiGeom.h 2011-11-29 23:27:19 UTC (rev 5232) @@ -0,0 +1,3978 @@ +#ifndef _ITAPS_FBiGeom +#define _ITAPS_FBiGeom +

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r5230 - MOAB/trunk/tools/mbzoltan
by hongjun＠mcs.anl.gov 29 Nov '11

29 Nov '11

Author: hongjun Date: 2011-11-29 15:58:50 -0600 (Tue, 29 Nov 2011) New Revision: 5230 Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp Log: o geometry surface partition option name is change from "-s" to "-f" o commented lines are removed Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp =================================================================== --- MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-11-29 20:22:44 UTC (rev 5229) +++ MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-11-29 21:58:50 UTC (rev 5230) @@ -55,9 +55,8 @@ opts.addOpt<double>( "imbalance,i", "Imbalance tolerance (used in PHG/Hypergraph method)"); opts.addOpt<int>( "power,m", "Generate multiple partitions, in powers of 2, up to 2^(pow)"); opts.addOpt<void>( "reorder,R", "Reorder mesh to group entities by partition"); - //opts.addOpt<void>( "geom,g", "Specify if partition geometry."); opts.addOpt<double>( "geom,g", "Specify if partition geometry and mesh size."); - opts.addOpt<void>( "surf,s", "Specify if partition geometry surface."); + opts.addOpt<void>( "surf,f", "Specify if partition geometry surface."); opts.addOpt<void>( "ghost,h", "Specify if partition ghost geometry body."); opts.addOpt<int>( "vertex_w,v", "Number of weights associated with a graph vertex."); opts.addOpt<int>( "edge_w,e", "Number of weights associated with an edge."); @@ -68,7 +67,6 @@ opts.parseCommandLine( argc, argv ); MBZoltan *tool = NULL; - //bool part_geom = false; double part_geom_mesh_size = -1.0; bool part_surf = false; bool ghost = false; @@ -83,14 +81,13 @@ bool print_time = opts.getOpt<void>(",T",0); // check if partition geometry, if it is, should get mesh size for the geometry - //part_geom = opts.numOptSet("geom") > 0; if (opts.getOpt( "geom", &part_geom_mesh_size )) { if (part_geom_mesh_size < 0.0) { std::cerr << part_geom_mesh_size << ": invalid geometry partition mesh size." << std::endl; return 1; } } - //if (!part_geom) { // partition mesh + if (part_geom_mesh_size < 0.) { // partition mesh tool = new MBZoltan (&mb, false, argc, argv); } @@ -152,7 +149,6 @@ clock_t t = clock(); const char* options = NULL; - //if (part_geom) options = "FACET_DISTANCE_TOLERANCE=0.1"; if (part_geom_mesh_size) options = "FACET_DISTANCE_TOLERANCE=0.1"; ErrorCode rval = mb.load_file( input_file.c_str(), 0, options ); if (MB_SUCCESS != rval) {

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r5229 - MOAB/trunk/tools/mbzoltan
by hongjun＠mcs.anl.gov 29 Nov '11

29 Nov '11

Author: hongjun Date: 2011-11-29 14:22:44 -0600 (Tue, 29 Nov 2011) New Revision: 5229 Modified: MOAB/trunk/tools/mbzoltan/MBZoltan.cpp MOAB/trunk/tools/mbzoltan/MBZoltan.hpp MOAB/trunk/tools/mbzoltan/mbpart.cpp Log: o reinforce mesh generation time and mesh communication time estimation functions o -g option takes argument of mesh size for geometry partition o added debug statements o passes make check Modified: MOAB/trunk/tools/mbzoltan/MBZoltan.cpp =================================================================== --- MOAB/trunk/tools/mbzoltan/MBZoltan.cpp 2011-11-28 19:01:46 UTC (rev 5228) +++ MOAB/trunk/tools/mbzoltan/MBZoltan.cpp 2011-11-29 20:22:44 UTC (rev 5229) @@ -237,7 +237,7 @@ return MB_SUCCESS; } -ErrorCode MBZoltan::partition_mesh_geom(const bool part_geom, +ErrorCode MBZoltan::partition_mesh_geom(const double part_geom_mesh_size, const int nparts, const char *zmethod, const char *other_method, @@ -283,7 +283,7 @@ // short-circuit everything if RR partition is requested if (!strcmp(zmethod, "RR")) { - if (!part_geom) { + if (part_geom_mesh_size < 0.) { // get all elements result = mbImpl->get_entities_by_dimension(0, 3, elems); RR; @@ -311,13 +311,14 @@ return result; } - if (!part_geom) { + if (part_geom_mesh_size < 0.) { + //if (!part_geom) { result = assemble_graph(part_dim, pts, ids, adjs, length, elems); RR; } else { #ifdef CGM result = assemble_graph(part_dim, pts, ids, adjs, length, obj_weights, - edge_weights, entities); RR; + edge_weights, entities, part_geom_mesh_size); RR; if (debug) { int n_ids = ids.size(); @@ -440,7 +441,8 @@ if (ZOLTAN_OK != retval) return MB_FAILURE; // take results & write onto MOAB partition sets - if (!part_geom) { + if (part_geom_mesh_size < 0.) { + //if (!part_geom) { result = write_partition(nparts, elems, assign_parts, write_as_sets, write_as_tags); } @@ -549,7 +551,8 @@ std::vector<int> &length,

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r5228 - in MOAB/trunk: itaps/igeom src/moab
by iulian＠mcs.anl.gov 28 Nov '11

28 Nov '11

Author: iulian Date: 2011-11-28 13:01:46 -0600 (Mon, 28 Nov 2011) New Revision: 5228 Removed: MOAB/trunk/itaps/igeom/SmoothCurveEval.cpp MOAB/trunk/itaps/igeom/SmoothCurveEval.hpp MOAB/trunk/itaps/igeom/SmoothFaceEval.cpp MOAB/trunk/itaps/igeom/SmoothFaceEval.hpp Modified: MOAB/trunk/itaps/igeom/Makefile.am MOAB/trunk/itaps/igeom/iGeom.h MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp MOAB/trunk/itaps/igeom/iGeom_MOAB.hpp MOAB/trunk/src/moab/FBEngine.hpp Log: restore iGeom moab implementation to its former glory eventually, FBiGeom in meshkit should point to this one. Although FBiGeom looks redundant now, maybe it will go away. igeom in moab is built only if --enable-igeom is used in configuration, so it should not affect yet anybody else Modified: MOAB/trunk/itaps/igeom/Makefile.am =================================================================== --- MOAB/trunk/itaps/igeom/Makefile.am 2011-11-28 16:11:43 UTC (rev 5227) +++ MOAB/trunk/itaps/igeom/Makefile.am 2011-11-28 19:01:46 UTC (rev 5228) @@ -19,9 +19,7 @@ libiGeomMOAB_la_SOURCES = \ iGeom_MOAB.hpp \ - iGeom_MOAB.cpp \ - SmoothCurveEval.hpp SmoothCurveEval.cpp \ - SmoothFaceEval.hpp SmoothFaceEval.cpp + iGeom_MOAB.cpp libiGeomMOAB_la_include_HEADERS = \ iGeom.h \ Deleted: MOAB/trunk/itaps/igeom/SmoothCurveEval.cpp =================================================================== --- MOAB/trunk/itaps/igeom/SmoothCurveEval.cpp 2011-11-28 16:11:43 UTC (rev 5227) +++ MOAB/trunk/itaps/igeom/SmoothCurveEval.cpp 2011-11-28 19:01:46 UTC (rev 5228) @@ -1,425 +0,0 @@ -/* - * SmoothCurveEval.cpp - * - * Created on: Jun 9, 2010 - * Author: iulian - */ - -#include "SmoothCurveEval.hpp" -//#include "SmoothVertex.hpp" -#include "SmoothFaceEval.hpp" -#include "assert.h" - -#include "moab/GeomTopoTool.hpp" - -using namespace moab; - -SmoothCurveEval::SmoothCurveEval(moab::Interface * mb, moab::EntityHandle curve) -{ - //_mbOut->create_meshset(MESHSET_ORDERED, _oSet); - /*_cmlEdgeMesher = new CMLEdgeMesher (this, CML::STANDARD); - _cmlEdgeMesher->set_sizing_function(CML::LINEAR_SIZING);*/ - _leng = 0; // not initialized - _edgeTag = 0; // not initialized - _mb = mb; - _set = curve; -} -SmoothCurveEval::~SmoothCurveEval() { - // TODO Auto-generated destructor stub -} -

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Question: Exchange part of mesh so that it is available to all processes
by Markus Mayr 28 Nov '11

28 Nov '11

Dear list, I have got a question regarding a distributed mesh. Although I know this is necessarily inefficient, I would like to make a part of the mesh available to all processes, more precisely the boundary faces and vertices of my volume mesh. I do not know which function I am supposed to use or even if there is a function that does what I want. As far as I can see, send_/recv_ functions send a message from one process to another one, so these functions probably do not what I want. broadcast_entities might be the right thing, maybe something like broadcast_entities(mpi_rank, owned_boundary_entities) results in owned_boundary_entities containing *all* boundary entities? But on the other hand, according to the documentation all processes should know about the whole mesh, which is not the case for me. Apart from that I do not know what remote handles are. The other option would be exchange_owned_mesh(s), I think. Is exchange_procs simply a list of all processes involved and exchange_ents a list containing the local part of each process right after calling that function? What about remote handles? Am I supposed to use exchange_owned_mesh or exchange_owned_meshs? In either case: Can I exchange tags using the exchange_tags functions afterwards? Maybe someone can help me? Thanks! Best regards, Markus Mayr

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r5225 - MOAB/trunk/src/parallel
by hongjun＠mcs.anl.gov 27 Nov '11

27 Nov '11

Author: hongjun Date: 2011-11-27 17:29:02 -0600 (Sun, 27 Nov 2011) New Revision: 5225 Modified: MOAB/trunk/src/parallel/ParallelComm.cpp Log: o remove incorrect shared tag checking code o changed to create interface sets from shared entities o buffer is not deleted and kept for shared processors in exchange_owned mesh function o PSTATUS_NOT_OWNED is added for interface mesh created in unpack_entities Modified: MOAB/trunk/src/parallel/ParallelComm.cpp =================================================================== --- MOAB/trunk/src/parallel/ParallelComm.cpp 2011-11-23 16:47:25 UTC (rev 5224) +++ MOAB/trunk/src/parallel/ParallelComm.cpp 2011-11-27 23:29:02 UTC (rev 5225) @@ -1771,10 +1771,10 @@ // update sharing data and pstatus, adjusting order if iface result = update_remote_data(new_h, &ps[0], &hs[0], num_ps, (is_iface ? PSTATUS_INTERFACE : - (created_here ? (created_iface ? 0 : PSTATUS_GHOST - | PSTATUS_NOT_OWNED) : 0))); + (created_here ? (created_iface ? PSTATUS_NOT_OWNED: + PSTATUS_GHOST | PSTATUS_NOT_OWNED) : 0))); RRA(""); - + // need to send this new handle to all sharing procs if (!is_iface) { for (j = 0; j < num_ps; j++) { @@ -5716,12 +5716,6 @@ exchange_procs_sets.push_back(exchange_procs[i]); } - // check and clean incorrect shared tags - result = clean_shared_tags(exchange_ents); - RRA("Couldn't clean shared tags."); - result = clean_shared_tags(exchange_sets); - RRA("Couldn't clean shared tags."); - // exchange entities first result = exchange_owned_mesh(exchange_procs, exchange_ents, store_remote_handles, wait_all, migrate); @@ -5734,53 +5728,27 @@ for (int i = 0; i < n_proc; i++) delete exchange_sets[i]; - // set shared information - Tag sharedp = sharedp_tag(); - Tag sharedps = sharedps_tag(); - Tag pstatus = pstatus_tag(); - Range tagged_ents; - - // get shared proc tag entities and add shared pstatus - result = mbImpl->get_entities_by_type_and_tag(0, MBMAXTYPE, &sharedp, 0, 1, - tagged_ents); - RRA("Failed to get sharing proc tag in remote_handles."); - - std::vector<int> shared_procs(tagged_ents.size()); - result = mbImpl->tag_get_data(sharedp, tagged_ents, &shared_procs[0]); - Range::iterator it = tagged_ents.begin(); - Range::iterator eit = tagged_ents.end(); - for (int i = 0; it != eit; it++, i++) {

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r5223 - MOAB/trunk/itaps/imesh
by iulian＠mcs.anl.gov 22 Nov '11

22 Nov '11

Author: iulian Date: 2011-11-22 16:56:17 -0600 (Tue, 22 Nov 2011) New Revision: 5223 Added: MOAB/trunk/itaps/imesh/FindAdjacencyF90.F90 Modified: MOAB/trunk/itaps/imesh/Makefile.am Log: more examples with fortran calls: create set, add entities to set, retrieve vertex coordinates, adjacencies Added: MOAB/trunk/itaps/imesh/FindAdjacencyF90.F90 =================================================================== --- MOAB/trunk/itaps/imesh/FindAdjacencyF90.F90 (rev 0) +++ MOAB/trunk/itaps/imesh/FindAdjacencyF90.F90 2011-11-22 22:56:17 UTC (rev 5223) @@ -0,0 +1,125 @@ +! FindAdjacency: Interacting with iMesh +! +! This program shows how to get more information about a mesh, by +! getting connectivity two different ways (as connectivity and as +! adjacent 0-dimensional entities). + +! Usage: FindAdjacency +#define CHECK(a) \ + if (ierr .ne. 0) print *, a + +program findadjacency + implicit none +#include "iMesh_f.h" + + ! declarations + iMesh_Instance mesh + IBASE_HANDLE_T rpents, rpverts, rpallverts, ipoffsets + integer ioffsets + IBASE_HANDLE_T ents, verts, allverts, verths + pointer (rpents, ents(0:*)) + pointer (rpverts, verts(0:*)) + pointer (rpallverts, allverts(0:*)) + pointer (ipoffsets, ioffsets(0:*)) +! for all vertices in one call + iBase_EntityHandle verth + pointer (verths, verth(0:*)) + integer ierr, ents_alloc, ents_size + integer iverts_alloc, iverts_size + integer allverts_alloc, allverts_size + integer offsets_alloc, offsets_size, coords_alloc, coords_size + iBase_EntitySetHandle root_set + integer vert_uses, i, num_ents + real*8 coords + pointer (pcoord, coords(0:*)) +! + iBase_EntitySetHandle :: sethand + + ! create the Mesh instance + call iMesh_newMesh("", mesh, ierr) + CHECK("Problems instantiating interface.") + + ! load the mesh + call iMesh_getRootSet(%VAL(mesh), root_set, ierr) + CHECK("Problems getting root set") + + call iMesh_load(%VAL(mesh), %VAL(root_set), &

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r5222 - MOAB/trunk/examples/itaps
by iulian＠mcs.anl.gov 22 Nov '11

22 Nov '11

Author: iulian Date: 2011-11-22 10:39:45 -0600 (Tue, 22 Nov 2011) New Revision: 5222 Modified: MOAB/trunk/examples/itaps/FindConnectF.F MOAB/trunk/examples/itaps/TagIterateF.F Log: use IBASE_HANDLE_T for pointer to entity handle, and iBase_EntityHandle instead of integer*8, so the test programs work on 32 bit machine too. we will have to fix intel compiler issues separately Modified: MOAB/trunk/examples/itaps/FindConnectF.F =================================================================== --- MOAB/trunk/examples/itaps/FindConnectF.F 2011-11-21 20:47:07 UTC (rev 5221) +++ MOAB/trunk/examples/itaps/FindConnectF.F 2011-11-22 16:39:45 UTC (rev 5222) @@ -11,8 +11,8 @@ c declarations iMesh_Instance mesh - integer*8 ents - integer*8 rpverts, rpallverts, ipoffsets + iBase_EntityHandle ents + IBASE_HANDLE_T rpverts, rpallverts, ipoffsets pointer (rpents, ents(0:*)) pointer (rpverts, verts(0:*)) pointer (rpallverts, allverts(0:*)) Modified: MOAB/trunk/examples/itaps/TagIterateF.F =================================================================== --- MOAB/trunk/examples/itaps/TagIterateF.F 2011-11-21 20:47:07 UTC (rev 5221) +++ MOAB/trunk/examples/itaps/TagIterateF.F 2011-11-22 16:39:45 UTC (rev 5222) @@ -14,7 +14,7 @@ iBase_EntityHandle root_set iBase_EntityArrIterator iter iBase_TagHandle tagh - integer*8 rpents, ents, rpdata + IBASE_HANDLE_T rpents, ents, rpdata real*8 tag_data pointer (rpdata, tag_data(0:*)) pointer (rpents, ents(0:*))

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Creating vertices and putting them in sets.
by Robert Jacob 21 Nov '11

21 Nov '11

Hi again, Assuming I get my Fortran program working, I want to make sure it will do what I intend and that I have the concepts straight. I want to create a couple of sets of vertices, numEl in each set: So first call: iMesh_createVtxArr(...,numEl,...,vetexHandle1,...) Then put the vertices in an entity set: iMesh_CreateEntSet(...,set1,...) iMesh_addEntArrToSet(...,vertexHandle1,...,set1,...) Then inquire to make sure there's NumEl vertices: iMesh_getNumofType(...,set1,iBase_VERTEX, num_vts1,...) Then I'll repeat those 4 calls but with vertexHandle2, set2, num_vts2 At the end, num_vts1 and num_vts2 should each equal NumEl. Right? Currently, num_vts1 is NumEl and then num_vts2 is 2*NumEl. That would make sense (to me) if I was inquiring on the root_set. Unless I'm missing something. Thanks, Rob

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r5221 - in MOAB/trunk: . config
by tautges＠mcs.anl.gov 21 Nov '11

21 Nov '11

Author: tautges Date: 2011-11-21 14:47:07 -0600 (Mon, 21 Nov 2011) New Revision: 5221 Modified: MOAB/trunk/config/compiler.m4 MOAB/trunk/configure.ac Log: Fix compiling of Fortran code and automatic handling of proper compiler flags in autoconf. Modified: MOAB/trunk/config/compiler.m4 =================================================================== --- MOAB/trunk/config/compiler.m4 2011-11-18 18:47:06 UTC (rev 5220) +++ MOAB/trunk/config/compiler.m4 2011-11-21 20:47:07 UTC (rev 5221) @@ -155,6 +155,8 @@ # before setting up libtool so that it can override libtool settings. CFLAGS="$USER_CFLAGS $FATHOM_CC_SPECIAL" CXXFLAGS="$USER_CXXFLAGS $FATHOM_CXX_SPECIAL" +FFLAGS="$USER_FFLAGS $FATHOM_F77_SPECIAL" +FCFLAGS="$USER_FCFLAGS $FATHOM_FC_SPECIAL" # On IBM/AIX, the check for OBJEXT fails for the mpcc compiler. # (Comment out this hack, it should be fixed correctly now) @@ -194,6 +196,11 @@ enable_fc_optimize=yes fi fi + if test "x$enable_f77_optimize" = "x"; then + if test "x$USER_FFLAGS" = "x"; then + enable_f77_optimize=yes + fi + fi fi # Choose compiler flags from CLI args @@ -202,6 +209,7 @@ CXXFLAGS="$CXXFLAGS -g" CFLAGS="$CFLAGS -g" FCFLAGS="$FCFLAGS -g" + FFLAGS="$FFLAGS -g" fi if test "xyes" = "x$enable_cxx_optimize"; then CXXFLAGS="$CXXFLAGS -O2 -DNDEBUG" @@ -212,6 +220,9 @@ if test "xyes" = "x$enable_fc_optimize"; then FCFLAGS="$FCFLAGS -O2" fi +if test "xyes" = "x$enable_f77_optimize"; then + FFLAGS="$FFLAGS -O2" +fi # Check for 32/64 bit. # This requires FATHOM_CXX_FLAGS and FATHOM_CC_FLAGS to have been called first Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2011-11-18 18:47:06 UTC (rev 5220) +++ MOAB/trunk/configure.ac 2011-11-21 20:47:07 UTC (rev 5221) @@ -77,7 +77,7 @@ if test "xyes" = "x$ENABLE_FORTRAN" && test "x" != "x$FC"; then

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