November 2013 - moab-dev - mailman3.cels.anl.gov

commit/MOAB: tautges: Create a Fortran90 example that pushes mesh into parallel MOAB, then resolves shared entities
by commits-noreply＠bitbucket.org 15 Nov '13

15 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/4f4f66bf24ff/ Changeset: 4f4f66bf24ff Branch: tautges/push-parallel-mesh-example User: tautges Date: 2013-11-15 18:46:32 Summary: Create a Fortran90 example that pushes mesh into parallel MOAB, then resolves shared entities and exchanges a ghost layer of elements. This required a change to MOAB's iMeshP implementation of iMeshP_syncMeshAll, where a call is made to resolve_shared_ents. This also removes ParallelComm::update_shared_mesh, which was an empty function called from syncMeshAll but didn't do anything. Affected #: 5 files diff --git a/examples/PushParMeshIntoMoabF90.F90 b/examples/PushParMeshIntoMoabF90.F90 new file mode 100644 index 0000000..131d19c --- /dev/null +++ b/examples/PushParMeshIntoMoabF90.F90 @@ -0,0 +1,281 @@ +! PushParMeshIntoMoabF90: push parallel mesh into moab, F90 version +! +! This program shows how to push a mesh into MOAB in parallel from Fortran90, with sufficient +! information to resolve boundary sharing and exchange a layer of ghost information. +! To successfully link this example, you need to specify FCFLAGS that include: +! a) -DUSE_MPI, and +! b) flags required to link Fortran90 MPI programs with the C++ compiler; these flags +! can often be found on your system by inspecting the output of 'mpif90 -show' +! For example, using gcc, the link line looks like: +! make MOAB_DIR=<moab install dir> FCFLAGS="-DUSE_MPI -I/usr/lib/openmpi/include -pthread -I/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl" PushParMeshIntoMoabF90 +! +! Usage: PushParMeshIntoMoab + +program PushParMeshIntoMoab + + use ISO_C_BINDING + implicit none + +#ifdef USE_MPI +# include "iMeshP_f.h" +#else +# include "iMesh_f.h" +#endif + + ! declarations + ! imesh is the instance handle + iMesh_Instance imesh + ! NUMV, NUME, NVPERE are the hardwired here; these are for the whole mesh, + ! local mesh determined later + integer NUMV, NUME, NVPERE + parameter (NUMV = 8) ! # vertices in whole mesh + parameter (NUME = 6) ! # elements in whole mesh + parameter (NVPERE = 4) ! # vertices per element + ! ents, verts will be arrays storing vertex/entity handles + iBase_EntityHandle, pointer :: ents, verts + iBase_EntitySetHandle root_set + TYPE(C_PTR) :: vertsPtr, entsPtr + ! storage for vertex positions, element connectivity indices, global vertex ids + real*8 coords(0:3*NUMV-1) + integer iconn(0:4*NUME-1), gids(0:NUMV-1) + ! + ! local variables + integer lgids(0:NUMV-1), lconn(0:4*NUME-1) + real*8 lcoords(0:3*NUMV-1) + integer lnumv, lvids(0:NUMV-1), gvids(0:NUMV-1) + integer lvpe, ltp ! lvpe = # vertices per entity, ltp = element type + integer ic, ie, iv, istart, iend, ierr, indv, lnume, rank, sz + +#ifdef USE_MPI + ! local variables for parallel runs + iMeshP_PartitionHandle imeshp + integer MPI_COMM_WORLD +#endif + + ! vertex positions, latlon coords, (lat, lon, lev), fortran ordering + ! (first index varying fastest) + data coords / & + 0.0, -45.0, 0.0, 90.0, -45.0, 0.0, 180.0, -45.0, 0.0, 270.0, -45.0, 0.0, & + 0.0, 45.0, 0.0, 90.0, 45.0, 0.0, 180.0, 45.0, 0.0, 270.0, 45.0, 0.0 / + + ! quad index numbering, each quad ccw, sides then bottom then top + data iconn / & + 0, 1, 5, 4, & + 1, 2, 6, 5, & + 2, 3, 7, 6, & + 3, 0, 4, 7, & + 0, 3, 2, 1, & + 4, 5, 6, 7 / + + data lvpe /4/ ! quads in this example + data ltp / iMesh_QUADRILATERAL / ! from iBase_f.h + + ! initialize global vertex ids + do iv = 0, NUMV-1 + lgids(iv) = iv+1 + end do + +#ifdef USE_MPI + ! init the parallel partition + call MPI_INIT(ierr) + call MPI_COMM_SIZE(MPI_COMM_WORLD, sz, ierr) + call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierr) + ! compute starting/ending element numbers + lnume = NUME / sz + istart = rank * lnume + iend = istart + lnume - 1 + if (rank .eq. sz-1) then + iend = NUME-1 + lnume = iend - istart + 1 + endif +#else + ! set the starting/ending element numbers + istart = 0 + iend = NUME-1 + lnume = NUME +#endif + + ! for my elements, figure out which vertices I use and accumulate local indices and coords + ! lvids stores the local 0-based index for each vertex; -1 means vertex i isn't used locally + ! also build up connectivity indices for local elements, in lconn + do iv = 0, NUMV-1 + lvids(iv) = -1 + end do + lnumv = -1 + do ie = istart, iend + do iv = 0, lvpe-1 + indv = iconn(lvpe*ie + iv) + if (lvids(indv) .eq. -1) then + lnumv = lnumv + 1 ! increment local # verts + do ic = 0, 2 ! cache local coords + lcoords(3*lnumv+ic) = coords(3*indv+ic) + end do + lvids(indv) = lnumv + gvids(lnumv) = 1+indv + end if + lconn(lvpe*(ie-istart)+iv) = lvids(indv) + end do ! do iv + end do ! do ie + + lnumv = lnumv + 1 + + ! now create the mesh; this also initializes parallel sharing and ghost exchange + imesh = 0 + imeshp = 0 + call create_mesh(imesh, imeshp, MPI_COMM_WORLD, lnumv, lnume, gvids, lvpe, ltp, lcoords, lconn, & + vertsPtr, entsPtr, ierr) + call c_f_pointer(vertsPtr, verts, [lnumv]) + call c_f_pointer(entsPtr, ents, [lnume]) + + ! get/report number of vertices, elements + call iMesh_getRootSet(%VAL(imesh), root_set, ierr) + iv = 0 + ie = 0 +#ifdef USE_MPI + call iMeshP_getNumOfTypeAll(%VAL(imesh), %VAL(imeshp), %VAL(root_set), %VAL(iBase_VERTEX), iv, ierr) + call iMeshP_getNumOfTypeAll(%VAL(imesh), %VAL(imeshp), %VAL(root_set), %VAL(iBase_FACE), ie, ierr) + if (rank .eq. 0) then + write(0,*) "Number of vertices = ", iv + write(0,*) "Number of entities = ", ie + endif +#else + call iMesh_getNumOfTypeAll(%VAL(imesh), %VAL(root_set), %VAL(iBase_VERTEX), iv, ierr) + call iMesh_getNumOfTypeAll(%VAL(imesh), %VAL(root_set), %VAL(iBase_FACE), ie, ierr) + write(0,*) "Number of vertices = ", iv + write(0,*) "Number of entities = ", ie +#endif + + ! from here, can use verts and ents as (1-based) arrays of entity handles for input to other iMesh functions + + call MPI_FINALIZE(ierr) + stop +end program PushParMeshIntoMoab + +subroutine create_mesh( & + ! interfaces + imesh, imeshp, & + ! input + comm, numv, nume, vgids, nvpe, tp, posn, iconn, & + ! output + vertsPtr, entsPtr, ierr) + ! + ! create a mesh with numv vertices and nume elements, with elements of type tp + ! vertices have positions in posn (3 coordinates each, interleaved xyzxyz...), indexed from 0 + ! elements have nvpe vertices per entity, with connectivity indices stored in iconn, referencing + ! vertices using 0-based indices; vertex and entity handles are output in arrays passed in + ! + ! if imesh/imeshp are 0, imesh/imeshp are initialized in this subroutine + ! + + use ISO_C_BINDING + implicit none + +#ifdef USE_MPI +# include "iMeshP_f.h" +# include "mpif.h" +#else +# include "iMesh_f.h" +#endif + + ! subroutine arguments + iMesh_Instance imesh + TYPE(C_PTR) :: vertsPtr, entsPtr + integer numv, nume, nvpe, vgids(0:*), iconn(0:*), ierr, tp + real*8 posn(0:*) +#ifdef USE_MPI + iMeshP_PartitionHandle imeshp + integer comm +#endif + + ! local variables + integer comm_sz, comm_rank, numa, numo, iv, ie + TYPE(C_PTR) :: statsPtr + integer, allocatable, target :: stats(:) + iBase_TagHandle tagh + integer i + iBase_EntityHandle, pointer :: verts(:), ents(:) + iBase_EntityHandle, allocatable :: conn(:) + iBase_EntitySetHandle root_set +#ifdef USE_MPI + IBASE_HANDLE_T mpi_comm_c + TYPE(C_PTR) :: partsPtr + iMeshP_PartHandle, pointer :: parts(:) + iMeshP_PartHandle part + integer partsa, partso +#endif + + ! create the Mesh instance + if (imesh .eq. 0) then + call iMesh_newMesh("MOAB", imesh, ierr) + end if + +#ifdef USE_MPI + if (imeshp .eq. 0) then + call iMeshP_getCommunicator(%VAL(imesh), MPI_COMM_WORLD, mpi_comm_c, ierr) + call iMeshP_createPartitionAll(%VAL(imesh), %VAL(mpi_comm_c), imeshp, ierr) + call iMeshP_createPart(%VAL(imesh), %VAL(imeshp), part, ierr) + else + partsa = 0 + call iMeshP_getLocalParts(%VAL(imesh), %VAL(imeshp), partsPtr, partsa, partso, ierr) + call c_f_pointer(partsPtr, parts, [partso]) + part = parts(1) + end if + call MPI_COMM_RANK(comm, comm_rank, ierr) + call MPI_COMM_SIZE(comm, comm_sz, ierr) +#endif + + ! create the vertices, all in one call + numa = 0 + call iMesh_createVtxArr(%VAL(imesh), %VAL(numv), %VAL(iBase_INTERLEAVED), posn, %VAL(3*numv), & + vertsPtr, numa, numo, ierr) + + ! fill in the connectivity array, based on indexing from iconn + allocate (conn(0:nvpe*nume-1)) + call c_f_pointer(vertsPtr, verts, [numv]) + do i = 0, nvpe*nume-1 + conn(i) = verts(1+iconn(i)) + end do + ! create the elements + numa = 0 + allocate(stats(0:nume-1)) + statsPtr = C_LOC(stats(0)) + call iMesh_createEntArr(%VAL(imesh), %VAL(tp), conn, %VAL(nvpe*nume), & + entsPtr, numa, numo, statsPtr, numa, numo, ierr) + deallocate(stats) + deallocate(conn) + +#ifdef USE_MPI + ! take care of parallel stuff + + ! add entities to part, using iMesh + call c_f_pointer(entsPtr, ents, [numo]) + call iMesh_addEntArrToSet(%VAL(imesh), ents, %VAL(numo), %VAL(part), ierr) + ! set global ids on vertices, needed for sharing between procs + call iMesh_getTagHandle(%VAL(imesh), "GLOBAL_ID", tagh, ierr, %VAL(9)) + if (iBase_SUCCESS .ne. ierr) then + ! didn't get handle, need to create the tag + call iMesh_createTag(%VAL(imesh), "GLOBAL_ID", %VAL(iBase_INTEGER), tagh, ierr, %VAL(9)) + end if + call iMesh_setIntArrData(%VAL(imesh), verts, %VAL(numv), %VAL(tagh), vgids, %VAL(numv), ierr) + + ! now resolve shared verts and exchange ghost cells + call iMeshP_syncMeshAll(%VAL(imesh), %VAL(imeshp), ierr) + call iMesh_getRootSet(%VAL(imesh), root_set, ierr) + call iMeshP_getNumOfTypeAll(%VAL(imesh), %VAL(imeshp), %VAL(root_set), %VAL(iBase_VERTEX), iv, ierr) + call iMeshP_getNumOfTypeAll(%VAL(imesh), %VAL(imeshp), %VAL(root_set), %VAL(iBase_FACE), ie, ierr) + if (comm_rank .eq. 0) then + write(0,*) "After syncMeshAll:" + write(0,*) " Number of vertices = ", iv + write(0,*) " Number of entities = ", ie + endif + + call iMeshP_createGhostEntsAll(%VAL(imesh), %VAL(imeshp), %VAL(2), %VAL(1), %VAL(1), %VAL(0), ierr) + if (comm_rank .eq. 0) then + write(0,*) "After createGhostEntsAll:" + write(0,*) " Number of vertices = ", iv + write(0,*) " Number of entities = ", ie + endif +#endif + + return +end subroutine create_mesh diff --git a/examples/makefile b/examples/makefile index ff5876c..cd6339e 100644 --- a/examples/makefile +++ b/examples/makefile @@ -9,7 +9,7 @@ MESH_DIR="../MeshFiles/unittest" EXAMPLES = HelloMOAB GetEntities SetsNTags StructuredMeshSimple DirectAccessWithHoles DirectAccessNoHoles PAREXAMPLES = HelloParMOAB ReduceExchangeTags LloydRelaxation -F90EXAMPLES = DirectAccessNoHolesF90 +F90EXAMPLES = DirectAccessNoHolesF90 PushParMeshIntoMoabF90 EXOIIEXAMPLES = TestExodusII default: ${EXAMPLES} @@ -50,12 +50,15 @@ TestExodusII: TestExodusII.o point_in_elem_search: point_in_elem_search.o ${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK} +PushParMeshIntoMoabF90: PushParMeshIntoMoabF90.o + ${MOAB_CXX} -o $@ $< ${IMESH_LIBS} -lgfortran -L/usr/lib/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl + clean: rm -rf *.o ${EXAMPLES} ${PAREXAMPLES} ${EXOIIEXAMPLES} .cpp.o : - ${MOAB_CXX} ${MOAB_CXXFLAGS} ${MOAB_INCLUDES} -DMESH_DIR=\"${MESH_DIR}\" -c $< + ${MOAB_CXX} ${CXXFLAGS} ${MOAB_CXXFLAGS} ${MOAB_INCLUDES} -DMESH_DIR=\"${MESH_DIR}\" -c $< .F90.o : - ${IMESH_FC} ${IMESH_FCFLAGS} ${IMESH_INCLUDES} ${IMESH_FCDEFS} -DMESH_DIR=\"${MESH_DIR}\" -c $< + ${IMESH_FC} ${FCFLAGS} ${IMESH_FCFLAGS} ${IMESH_INCLUDES} ${IMESH_FCDEFS} -DMESH_DIR=\"${MESH_DIR}\" -c $< diff --git a/itaps/imesh/iMeshP_MOAB.cpp b/itaps/imesh/iMeshP_MOAB.cpp index 51254ca..b7e8333 100644 --- a/itaps/imesh/iMeshP_MOAB.cpp +++ b/itaps/imesh/iMeshP_MOAB.cpp @@ -1606,11 +1606,8 @@ void iMeshP_syncMeshAll( iMesh_Instance instance, const iMeshP_PartitionHandle partition_handle, int *err ) { - FIXME; // for now we only sync vertex coordinates - // need to update ParallelComm::update_shared_mesh to fix this - ParallelComm* pcomm = PCOMM; - ErrorCode rval = pcomm->update_shared_mesh(); + ErrorCode rval = pcomm->resolve_shared_ents(itaps_cast<EntityHandle>(partition_handle), -1, -1); CHKERR(rval,"update failed"); RETURN (iBase_SUCCESS); } diff --git a/src/parallel/ParallelComm.cpp b/src/parallel/ParallelComm.cpp index d92d9b1..bcc555a 100644 --- a/src/parallel/ParallelComm.cpp +++ b/src/parallel/ParallelComm.cpp @@ -7569,146 +7569,6 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, } */ - ErrorCode ParallelComm::update_shared_mesh() - { - // ErrorCode result; - // int success; - - // ,,, - /* - - // get all procs interfacing to this proc - std::set<unsigned int> iface_procs; - result = get_interface_procs(iface_procs); - RRA("Failed to get iface sets, procs"); - - // post ghost irecv's for all interface procs - // index greqs the same as buffer/sharing procs indices - std::vector<MPI_Request> recv_reqs(2*MAX_SHARING_PROCS, MPI_REQUEST_NULL); - std::vector<MPI_Status> gstatus(MAX_SHARING_PROCS); - std::set<unsigned int>::iterator sit; - for (sit = iface_procs.begin(); sit != iface_procs.end(); sit++) { - int ind = get_buffers(*sit); - success = MPI_Irecv(&ghostRBuffs[ind][0], ghostRBuffs[ind].size(), - MPI_UNSIGNED_CHAR, *sit, - MB_MESG_ANY, procConfig.proc_comm(), - &recv_reqs[ind]); - if (success != MPI_SUCCESS) { - result = MB_FAILURE; - RRA("Failed to post irecv in ghost exchange."); - } - } - - // pack and send vertex coordinates from this proc to others - // make sendReqs vector to simplify initialization - std::fill(sendReqs, sendReqs+2*MAX_SHARING_PROCS, MPI_REQUEST_NULL); - Range recd_ents[MAX_SHARING_PROCS]; - - for (sit = iface_procs.begin(); sit != iface_procs.end(); sit++) { - int ind = get_buffers(*sit); - - Range vertices; - for (Range::iterator rit = interfaceSets.begin(); rit != interfaceSets.end(); - rit++) { - if (!is_iface_proc(*rit, *sit)) - continue; - - result = mbImpl->get_entities_by_type( *rit, MBVERTEX, vertices ); - RRA("Bad interface set."); - } - std::map<unsigned int,Range>::iterator ghosted = ghostedEnts.find(*sit); - if (ghosted != ghostedEnts.end()) { - Range::iterator e = ghosted->second.upper_bound(MBVERTEX); - vertices.merge( ghosted->second.begin(), e ); - } - - // pack-send; this also posts receives if store_remote_handles is true - Range sent; - result = pack_send_entities(*sit, vertices, false, false, - false, true, - ownerSBuffs[ind], ownerRBuffs[MAX_SHARING_PROCS+ind], - sendReqs[ind], recv_reqs[MAX_SHARING_PROCS+ind], - sent); - RRA("Failed to pack-send in mesh update exchange."); - } - - // receive/unpack entities - // number of incoming messages depends on whether we're getting back - // remote handles - int num_incoming = iface_procs.size(); - - while (num_incoming) { - int ind; - MPI_Status status; - success = MPI_Waitany(2*MAX_SHARING_PROCS, &recv_reqs[0], &ind, &status); - if (MPI_SUCCESS != success) { - result = MB_FAILURE; - RRA("Failed in waitany in ghost exchange."); - } - - // ok, received something; decrement incoming counter - num_incoming--; - - std::vector<EntityHandle> remote_handles_v, sent_ents_tmp; - Range remote_handles_r; - int new_size; - - // branch on message type - switch (status.MPI_TAG) { - case MB_MESG_SIZE: - // incoming message just has size; resize buffer and re-call recv, - // then re-increment incoming count - assert(ind < MAX_SHARING_PROCS); - new_size = *((int*)&ghostRBuffs[ind][0]); - assert(0 > new_size); - result = recv_size_buff(buffProcs[ind], ghostRBuffs[ind], recv_reqs[ind], - MB_MESG_ENTS); - RRA("Failed to resize recv buffer."); - num_incoming++; - break; - case MB_MESG_ENTS: - // incoming ghost entities; process - result = recv_unpack_entities(buffProcs[ind], true, - false, - ghostRBuffs[ind], ghostSBuffs[ind], - sendReqs[ind], recd_ents[ind]); - RRA("Failed to recv-unpack message."); - break; - } - } - - // ok, now wait if requested - MPI_Status status[2*MAX_SHARING_PROCS]; - success = MPI_Waitall(2*MAX_SHARING_PROCS, &sendReqs[0], status); - if (MPI_SUCCESS != success) { - result = MB_FAILURE; - RRA("Failure in waitall in ghost exchange."); - } - - return MB_SUCCESS; - } - ErrorCode ParallelComm::update_iface_sets(Range &sent_ents, - std::vector<EntityHandle> &remote_handles, - int from_proc) - { - std::vector<EntityHandle>::iterator remote_it = remote_handles.begin(); - Range::iterator sent_it = sent_ents.begin(); - Range ents_to_remove; - for (; sent_it != sent_ents.end(); sent_it++, remote_it++) { - if (!*remote_it) ents_to_remove.insert(*sent_it); - } - - for (Range::iterator set_it = interfaceSets.begin(); set_it != interfaceSets.end(); set_it++) { - if (!is_iface_proc(*set_it, from_proc)) continue; - ErrorCode result = mbImpl->remove_entities(*set_it, ents_to_remove); - RRA("Couldn't remove entities from iface set in update_iface_sets."); - } - - */ - - return MB_SUCCESS; - } - //! return sharedp tag Tag ParallelComm::sharedp_tag() { diff --git a/src/parallel/moab/ParallelComm.hpp b/src/parallel/moab/ParallelComm.hpp index e4217ce..3424c51 100644 --- a/src/parallel/moab/ParallelComm.hpp +++ b/src/parallel/moab/ParallelComm.hpp @@ -697,10 +697,6 @@ namespace moab { int& num_part_ids_out, EntityHandle remote_handles[MAX_SHARING_PROCS] = 0); - // Propogate mesh modification amongst shared entities - // from the onwing processor to any procs with copies. - ErrorCode update_shared_mesh(); - /** Filter the entities by pstatus tag. * op is one of PSTATUS_ AND, OR, NOT; an entity is output if: * AND: all bits set in pstatus_val are also set on entity Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: tautges: Merge branch 'tautges/par-owner-fix'
by commits-noreply＠bitbucket.org 15 Nov '13

15 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/ded02f43e94d/ Changeset: ded02f43e94d Branch: master User: tautges Date: 2013-11-15 18:33:46 Summary: Merge branch 'tautges/par-owner-fix' Conflicts: test/parallel/parallel_unit_tests.cpp Affected #: 3 files diff --git a/src/parallel/ParallelComm.cpp b/src/parallel/ParallelComm.cpp index 8efc777..d92d9b1 100644 --- a/src/parallel/ParallelComm.cpp +++ b/src/parallel/ParallelComm.cpp @@ -2093,7 +2093,19 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, if (new_h && store_remote_handles) { unsigned char new_pstat = 0x0; - if (is_iface) new_pstat = PSTATUS_INTERFACE; + if (is_iface) { + new_pstat = PSTATUS_INTERFACE; + // here, lowest rank proc should be first + int idx = std::min_element(&ps[0], &ps[0]+num_ps) - &ps[0]; + if (idx) { + std::swap(ps[0], ps[idx]); + std::swap(hs[0], hs[idx]); + } + // set ownership based on lowest rank; can't be in update_remote_data, because + // there we don't know whether it resulted from ghosting or not + if ((num_ps > 1 && ps[0] != (int) rank())) + new_pstat |= PSTATUS_NOT_OWNED; + } else if (created_here) { if (created_iface) new_pstat = PSTATUS_NOT_OWNED; else new_pstat = PSTATUS_GHOST | PSTATUS_NOT_OWNED; @@ -2542,17 +2554,14 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, } // add myself, if it isn't there already - idx = 0; - if (new_ps[0] != (int)rank()) { - idx = std::find(&new_ps[0], &new_ps[0] + new_numps, rank()) - &new_ps[0]; - if (idx == new_numps) { - new_ps[new_numps] = rank(); - new_hs[new_numps] = new_h; - new_numps++; - } - else if (!new_hs[idx] && new_numps > 2) - new_hs[idx] = new_h; + idx = std::find(&new_ps[0], &new_ps[0] + new_numps, rank()) - &new_ps[0]; + if (idx == new_numps) { + new_ps[new_numps] = rank(); + new_hs[new_numps] = new_h; + new_numps++; } + else if (!new_hs[idx] && new_numps > 2) + new_hs[idx] = new_h; // proc list is complete; update for shared, multishared if (new_numps > 1) { @@ -2560,18 +2569,6 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, new_pstat |= PSTATUS_SHARED; } - // if multishared, not ghost or interface, and not not_owned, I'm owned, and should be the first proc - assert(new_ps[idx] == (int)rank()); - if ((new_numps > 2 && !(new_pstat&(PSTATUS_INTERFACE|PSTATUS_GHOST|PSTATUS_NOT_OWNED))) || - (new_pstat&PSTATUS_INTERFACE && !(new_pstat&PSTATUS_NOT_OWNED)) - ) { - idx = std::min_element(&new_ps[0], &new_ps[0] + new_numps) - &new_ps[0]; - std::swap(new_ps[0], new_ps[idx]); - std::swap(new_hs[0], new_hs[idx]); - if (new_ps[0] != (int)rank()) - new_pstat |= PSTATUS_NOT_OWNED; - } - /* plist("new_ps", new_ps, new_numps); plist("new_hs", new_hs, new_numps); @@ -3723,15 +3720,21 @@ ErrorCode ParallelComm::resolve_shared_ents(EntityHandle this_set, return result; } } - - // get the entities in the partition sets - for (Range::iterator rit = partitionSets.begin(); rit != partitionSets.end(); rit++) { - Range tmp_ents; - result = mbImpl->get_entities_by_handle(*rit, tmp_ents, true); + + if (0 == this_set) { + // get the entities in the partition sets + for (Range::iterator rit = partitionSets.begin(); rit != partitionSets.end(); rit++) { + Range tmp_ents; + result = mbImpl->get_entities_by_handle(*rit, tmp_ents, true); + if (MB_SUCCESS != result) return result; + proc_ents.merge(tmp_ents); + } + } + else { + result = mbImpl->get_entities_by_handle(this_set, proc_ents, true); if (MB_SUCCESS != result) return result; - proc_ents.merge(tmp_ents); } - + // resolve dim is maximal dim of entities in proc_ents if (-1 == resolve_dim) { if (proc_ents.empty()) @@ -8414,7 +8417,8 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, continue; } - if (!shents.empty()) check_my_shared_handles(shents); + if (!shents.empty()) + result = check_my_shared_handles(shents); done = true; } @@ -8586,6 +8590,7 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, Range bad_ents, local_shared; std::vector<SharedEntityData>::iterator vit; + unsigned char tmp_pstat; for (unsigned int i = 0; i < shents.size(); i++) { int other_proc = buffProcs[i]; result = get_shared_entities(other_proc, local_shared); @@ -8596,6 +8601,11 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, result = get_remote_handles(true, &localh, &dumh, 1, other_proc, dum_vec); if (MB_SUCCESS != result || dumh != remoteh) bad_ents.insert(localh); + result = get_pstatus(localh, tmp_pstat); + if (MB_SUCCESS != result || + (!tmp_pstat&PSTATUS_NOT_OWNED && vit->owner != rank()) || + (tmp_pstat&PSTATUS_NOT_OWNED && vit->owner == rank())) + bad_ents.insert(localh); } if (!local_shared.empty()) @@ -8603,10 +8613,9 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, } if (!bad_ents.empty()) { - if (prefix) { + if (prefix) std::cout << prefix << std::endl; - list_entities(bad_ents); - } + list_entities(bad_ents); return MB_FAILURE; } diff --git a/test/parallel/parallel_unit_tests.cpp b/test/parallel/parallel_unit_tests.cpp index 85cc3b8..d2d4c5b 100644 --- a/test/parallel/parallel_unit_tests.cpp +++ b/test/parallel/parallel_unit_tests.cpp @@ -1445,12 +1445,11 @@ template <typename T> ErrorCode check_shared_ents(ParallelComm &pcomm, Tag tagh, for (rit = shared_ents.begin(); rit != shared_ents.end(); rit++, i++) { rval = pcomm.get_sharing_data(*rit, &shprocs[0], &shhandles[0], pstatus, np); CHKERR(rval); if (1 == np && shprocs[0] != (int) pcomm.proc_config().proc_rank()) np++; + bool with_root = std::find(&shprocs[0], &shprocs[np], 0)-&shprocs[0] != np || !pcomm.rank(); if (mpi_op == MPI_SUM) {if (dum_vals[i] != fact*np) return MB_FAILURE;} else if (mpi_op == MPI_PROD) {if (dum_vals[i] != pow(fact, np)) return MB_FAILURE;} - else if (mpi_op == MPI_MAX) {if (pcomm.rank() && std::find(&shprocs[0],&shprocs[np], 0) != &shprocs[np] && - dum_vals[i] != fact) return MB_FAILURE;} - else if (mpi_op == MPI_MIN) {if (pcomm.rank() && std::find(&shprocs[0],&shprocs[np], 0) != &shprocs[np] && - dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MAX) {if (with_root && dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MIN) {if (with_root && dum_vals[i] != fact) return MB_FAILURE;} else return MB_FAILURE; } diff --git a/test/parallel/structured3.cpp b/test/parallel/structured3.cpp index 17ad177..daf065b 100644 --- a/test/parallel/structured3.cpp +++ b/test/parallel/structured3.cpp @@ -14,6 +14,12 @@ using namespace moab; // Number of cells in each direction: int NC; + +/* This mesh creates a box that is NCxNCxNC in global dimension, partitioned among processors + * automatically using ScdInterface's SQIJK algorithm. It checks to make sure there are enough + * procs to support this partition method. After mesh creation, shared vertex resolution is done, + * then ghost exchange is done. + */ const int ITERS = 50; void create_parallel_mesh(); @@ -60,7 +66,7 @@ void create_parallel_mesh() times[0] = MPI_Wtime(); rval = scdi->construct_box(HomCoord(), HomCoord(), NULL, 0, // no vertex positions new_box, NULL, // not locally periodic - &par_data, true, false); // assign global ids & resolve shared verts + &par_data, true, false); // assign global ids, don't resolve shared verts CHECK_ERR(rval); // get global id tag Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: tautges: Put some comments in structured3 about what kind of mesh is created.
by commits-noreply＠bitbucket.org 15 Nov '13

15 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/cfbd8c74d184/ Changeset: cfbd8c74d184 Branch: tautges/par-owner-fix User: tautges Date: 2013-11-15 18:28:10 Summary: Put some comments in structured3 about what kind of mesh is created. Affected #: 1 file diff --git a/test/parallel/structured3.cpp b/test/parallel/structured3.cpp index 17ad177..daf065b 100644 --- a/test/parallel/structured3.cpp +++ b/test/parallel/structured3.cpp @@ -14,6 +14,12 @@ using namespace moab; // Number of cells in each direction: int NC; + +/* This mesh creates a box that is NCxNCxNC in global dimension, partitioned among processors + * automatically using ScdInterface's SQIJK algorithm. It checks to make sure there are enough + * procs to support this partition method. After mesh creation, shared vertex resolution is done, + * then ghost exchange is done. + */ const int ITERS = 50; void create_parallel_mesh(); @@ -60,7 +66,7 @@ void create_parallel_mesh() times[0] = MPI_Wtime(); rval = scdi->construct_box(HomCoord(), HomCoord(), NULL, 0, // no vertex positions new_box, NULL, // not locally periodic - &par_data, true, false); // assign global ids & resolve shared verts + &par_data, true, false); // assign global ids, don't resolve shared verts CHECK_ERR(rval); // get global id tag Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: tautges: 1. In unpack_entities, for interface entities, make sure lowest-rank proc is first.
by commits-noreply＠bitbucket.org 15 Nov '13

15 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/2dab7c2381f9/ Changeset: 2dab7c2381f9 Branch: tautges/par-owner-fix User: tautges Date: 2013-11-15 18:03:42 Summary: 1. In unpack_entities, for interface entities, make sure lowest-rank proc is first. 2. If # sharing procs > 1 and 1st proc is not my rank, set PSTATUS_NOT_OWNED bit. These two things implement the rule in resolve_shared_ents that interface entities are owned by lowest-rank proc sharing them. Implemented here and not in update_remote_data because there you can't tell whether call is from ghosting or interface resolution. 3. In update_remote_data, search for my proc even when it's the first one, to make sure check for 0 handle is done even when I'm the owner. 4. Correct parallel_unit_test test for reduce_tags and max/min; in case where np > 2, you may not be sharing with root, in such case you won't see max/min Affected #: 2 files diff --git a/src/parallel/ParallelComm.cpp b/src/parallel/ParallelComm.cpp index 8efc777..d92d9b1 100644 --- a/src/parallel/ParallelComm.cpp +++ b/src/parallel/ParallelComm.cpp @@ -2093,7 +2093,19 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, if (new_h && store_remote_handles) { unsigned char new_pstat = 0x0; - if (is_iface) new_pstat = PSTATUS_INTERFACE; + if (is_iface) { + new_pstat = PSTATUS_INTERFACE; + // here, lowest rank proc should be first + int idx = std::min_element(&ps[0], &ps[0]+num_ps) - &ps[0]; + if (idx) { + std::swap(ps[0], ps[idx]); + std::swap(hs[0], hs[idx]); + } + // set ownership based on lowest rank; can't be in update_remote_data, because + // there we don't know whether it resulted from ghosting or not + if ((num_ps > 1 && ps[0] != (int) rank())) + new_pstat |= PSTATUS_NOT_OWNED; + } else if (created_here) { if (created_iface) new_pstat = PSTATUS_NOT_OWNED; else new_pstat = PSTATUS_GHOST | PSTATUS_NOT_OWNED; @@ -2542,17 +2554,14 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, } // add myself, if it isn't there already - idx = 0; - if (new_ps[0] != (int)rank()) { - idx = std::find(&new_ps[0], &new_ps[0] + new_numps, rank()) - &new_ps[0]; - if (idx == new_numps) { - new_ps[new_numps] = rank(); - new_hs[new_numps] = new_h; - new_numps++; - } - else if (!new_hs[idx] && new_numps > 2) - new_hs[idx] = new_h; + idx = std::find(&new_ps[0], &new_ps[0] + new_numps, rank()) - &new_ps[0]; + if (idx == new_numps) { + new_ps[new_numps] = rank(); + new_hs[new_numps] = new_h; + new_numps++; } + else if (!new_hs[idx] && new_numps > 2) + new_hs[idx] = new_h; // proc list is complete; update for shared, multishared if (new_numps > 1) { @@ -2560,18 +2569,6 @@ ErrorCode ParallelComm::recv_entities(std::set<unsigned int>& recv_procs, new_pstat |= PSTATUS_SHARED; } - // if multishared, not ghost or interface, and not not_owned, I'm owned, and should be the first proc - assert(new_ps[idx] == (int)rank()); - if ((new_numps > 2 && !(new_pstat&(PSTATUS_INTERFACE|PSTATUS_GHOST|PSTATUS_NOT_OWNED))) || - (new_pstat&PSTATUS_INTERFACE && !(new_pstat&PSTATUS_NOT_OWNED)) - ) { - idx = std::min_element(&new_ps[0], &new_ps[0] + new_numps) - &new_ps[0]; - std::swap(new_ps[0], new_ps[idx]); - std::swap(new_hs[0], new_hs[idx]); - if (new_ps[0] != (int)rank()) - new_pstat |= PSTATUS_NOT_OWNED; - } - /* plist("new_ps", new_ps, new_numps); plist("new_hs", new_hs, new_numps); @@ -3723,15 +3720,21 @@ ErrorCode ParallelComm::resolve_shared_ents(EntityHandle this_set, return result; } } - - // get the entities in the partition sets - for (Range::iterator rit = partitionSets.begin(); rit != partitionSets.end(); rit++) { - Range tmp_ents; - result = mbImpl->get_entities_by_handle(*rit, tmp_ents, true); + + if (0 == this_set) { + // get the entities in the partition sets + for (Range::iterator rit = partitionSets.begin(); rit != partitionSets.end(); rit++) { + Range tmp_ents; + result = mbImpl->get_entities_by_handle(*rit, tmp_ents, true); + if (MB_SUCCESS != result) return result; + proc_ents.merge(tmp_ents); + } + } + else { + result = mbImpl->get_entities_by_handle(this_set, proc_ents, true); if (MB_SUCCESS != result) return result; - proc_ents.merge(tmp_ents); } - + // resolve dim is maximal dim of entities in proc_ents if (-1 == resolve_dim) { if (proc_ents.empty()) @@ -8414,7 +8417,8 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, continue; } - if (!shents.empty()) check_my_shared_handles(shents); + if (!shents.empty()) + result = check_my_shared_handles(shents); done = true; } @@ -8586,6 +8590,7 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, Range bad_ents, local_shared; std::vector<SharedEntityData>::iterator vit; + unsigned char tmp_pstat; for (unsigned int i = 0; i < shents.size(); i++) { int other_proc = buffProcs[i]; result = get_shared_entities(other_proc, local_shared); @@ -8596,6 +8601,11 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, result = get_remote_handles(true, &localh, &dumh, 1, other_proc, dum_vec); if (MB_SUCCESS != result || dumh != remoteh) bad_ents.insert(localh); + result = get_pstatus(localh, tmp_pstat); + if (MB_SUCCESS != result || + (!tmp_pstat&PSTATUS_NOT_OWNED && vit->owner != rank()) || + (tmp_pstat&PSTATUS_NOT_OWNED && vit->owner == rank())) + bad_ents.insert(localh); } if (!local_shared.empty()) @@ -8603,10 +8613,9 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, } if (!bad_ents.empty()) { - if (prefix) { + if (prefix) std::cout << prefix << std::endl; - list_entities(bad_ents); - } + list_entities(bad_ents); return MB_FAILURE; } diff --git a/test/parallel/parallel_unit_tests.cpp b/test/parallel/parallel_unit_tests.cpp index 45ef1c5..944c845 100644 --- a/test/parallel/parallel_unit_tests.cpp +++ b/test/parallel/parallel_unit_tests.cpp @@ -1445,10 +1445,11 @@ template <typename T> ErrorCode check_shared_ents(ParallelComm &pcomm, Tag tagh, for (rit = shared_ents.begin(); rit != shared_ents.end(); rit++, i++) { rval = pcomm.get_sharing_data(*rit, &shprocs[0], &shhandles[0], pstatus, np); CHKERR(rval); if (1 == np && shprocs[0] != (int) pcomm.proc_config().proc_rank()) np++; + bool with_root = std::find(&shprocs[0], &shprocs[np], 0)-&shprocs[0] != np; if (mpi_op == MPI_SUM) {if (dum_vals[i] != fact*np) return MB_FAILURE;} else if (mpi_op == MPI_PROD) {if (dum_vals[i] != pow(fact, np)) return MB_FAILURE;} - else if (mpi_op == MPI_MAX) {if (dum_vals[i] != fact) return MB_FAILURE;} - else if (mpi_op == MPI_MIN) {if (dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MAX) {if (with_root && dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MIN) {if (with_root && dum_vals[i] != fact) return MB_FAILURE;} else return MB_FAILURE; } Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: 2 new changesets
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

2 new commits in MOAB: https://bitbucket.org/fathomteam/moab/commits/d7a5a2be5184/ Changeset: d7a5a2be5184 Branch: None User: tautges Date: 2013-11-14 22:33:51 Summary: Fix parallel_unit_test so it works for 4 procs as well as 2 (not all entities are only pairwise-shared). Add an MPI_Finalize to scdtest in case of error. Affected #: 2 files diff --git a/test/parallel/parallel_unit_tests.cpp b/test/parallel/parallel_unit_tests.cpp index 45ef1c5..85cc3b8 100644 --- a/test/parallel/parallel_unit_tests.cpp +++ b/test/parallel/parallel_unit_tests.cpp @@ -1447,8 +1447,10 @@ template <typename T> ErrorCode check_shared_ents(ParallelComm &pcomm, Tag tagh, if (1 == np && shprocs[0] != (int) pcomm.proc_config().proc_rank()) np++; if (mpi_op == MPI_SUM) {if (dum_vals[i] != fact*np) return MB_FAILURE;} else if (mpi_op == MPI_PROD) {if (dum_vals[i] != pow(fact, np)) return MB_FAILURE;} - else if (mpi_op == MPI_MAX) {if (dum_vals[i] != fact) return MB_FAILURE;} - else if (mpi_op == MPI_MIN) {if (dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MAX) {if (pcomm.rank() && std::find(&shprocs[0],&shprocs[np], 0) != &shprocs[np] && + dum_vals[i] != fact) return MB_FAILURE;} + else if (mpi_op == MPI_MIN) {if (pcomm.rank() && std::find(&shprocs[0],&shprocs[np], 0) != &shprocs[np] && + dum_vals[i] != fact) return MB_FAILURE;} else return MB_FAILURE; } diff --git a/test/parallel/scdtest.cpp b/test/parallel/scdtest.cpp index 3202621..5338b81 100644 --- a/test/parallel/scdtest.cpp +++ b/test/parallel/scdtest.cpp @@ -49,6 +49,7 @@ int main(int argc, char *argv[]) MPI_Comm_size(MPI_COMM_WORLD, &size); if (size != 4 && size != 2) { cerr << "Run this with 2 or 4 processes\n"; + MPI_Finalize(); exit(1); } https://bitbucket.org/fathomteam/moab/commits/7c37ce441fdd/ Changeset: 7c37ce441fdd Branch: master User: tautges Date: 2013-11-14 22:34:11 Summary: Merge branch 'master' of bitbucket.org:fathomteam/moab Affected #: 8 files diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index be91ef8..ebf149c 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -10,10 +10,10 @@ #include "MBTagConventions.hpp" #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} #define ERRORS(err, str) \ - if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} + if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} namespace moab { @@ -315,8 +315,10 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData vd = (*mit).second; - // This variable will not be read - if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end()) + // No need to read ignored variables. Upon creation of dummy variables, + // tag values have already been set + if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end() || + dummyVarNames.find(vd.varName) != dummyVarNames.end()) continue; if (vd.entLoc == ReadNC::ENTLOCSET) @@ -331,8 +333,10 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std if (mit != varInfo.end()) { ReadNC::VarData vd = (*mit).second; - // This variable will not be read - if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end()) + // No need to read ignored variables. Upon creation of dummy variables, + // tag values have already been set + if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end() || + dummyVarNames.find(vd.varName) != dummyVarNames.end()) continue; if (vd.entLoc == ReadNC::ENTLOCSET) @@ -382,7 +386,6 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, std::vector<int>& tstep_nums) { - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; Interface*& mbImpl = _readNC->mbImpl; DebugOutput& dbgOut = _readNC->dbgOut; @@ -392,11 +395,6 @@ ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, s // Finally, read into that space int success; for (unsigned int i = 0; i < vdatas.size(); i++) { - // This is a dummy variable for a dimension with no corresponding coordinate variable - // No need to set its tag data - if (dummyVarNames.find(vdatas[i].varName) != dummyVarNames.end()) - continue; - for (unsigned int t = 0; t < tstep_nums.size(); t++) { void* data = vdatas[i].varDatas[t]; @@ -719,56 +717,63 @@ ErrorCode NCHelper::create_attrib_string(const std::map<std::string, ReadNC::Att return MB_SUCCESS; } -void NCHelper::init_dims_with_no_coord_vars_info() +ErrorCode NCHelper::create_dummy_variables() { + Interface*& mbImpl = _readNC->mbImpl; std::vector<std::string>& dimNames = _readNC->dimNames; - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; + std::vector<int>& dimLens = _readNC->dimLens; std::map<std::string, ReadNC::VarData>& varInfo = _readNC->varInfo; DebugOutput& dbgOut = _readNC->dbgOut; // Hack: look at all dimensions, and see if we have one that does not appear in the list of varInfo names - // Right now, candidates are from unstructured meshes, such as ncol(HOMME) and nCells(MPAS) - // For them, create dummy tags + // Right now, candidates are from unstructured meshes, such as ncol (HOMME) and nCells (MPAS) + // For each of them, create a dummy variable with a sparse tag to store the dimension length for (unsigned int i = 0; i < dimNames.size(); i++) { - // If there is a variable with this dimension name, skip, we are fine; if not, create a dummy varInfo + // If there is a variable with this dimension name, skip if (varInfo.find(dimNames[i]) != varInfo.end()) continue; + // Create a dummy variable int sizeTotalVar = varInfo.size(); std::string var_name(dimNames[i]); ReadNC::VarData& data = varInfo[var_name]; data.varName = std::string(var_name); data.varId = sizeTotalVar; data.varTags.resize(1, 0); - data.varDataType = NC_DOUBLE; // Could be int, actually, but we do not really need the type + data.varDataType = NC_INT; data.varDims.resize(1); data.varDims[0] = (int)i; data.numAtts = 0; data.entLoc = ReadNC::ENTLOCSET; - dbgOut.tprintf(2, "Dummy varInfo created for dimension %s\n", dimNames[i].c_str()); dummyVarNames.insert(dimNames[i]); + dbgOut.tprintf(2, "Dummy variable created for dimension %s\n", dimNames[i].c_str()); + + // Create a sparse tag to store the dimension length + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(dimNames[i].c_str(), 1, MB_TYPE_INTEGER, tagh, + MB_TAG_SPARSE | MB_TAG_CREAT | MB_TAG_EXCL); + // If the tag already exists, skip + if (MB_ALREADY_ALLOCATED == rval) + continue; + ERRORR(rval, "Failed to create dimension tag."); + + rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &dimLens[i]); + ERRORR(rval, "Failed to set data for dimension tag."); + + dbgOut.tprintf(2, "Sparse tag created for dimension %s\n", dimNames[i].c_str()); } + + return MB_SUCCESS; } ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& vdatas, std::vector<int>& tstep_nums) { - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; std::vector<int>& dimLens = _readNC->dimLens; DebugOutput& dbgOut = _readNC->dbgOut; ErrorCode rval = MB_SUCCESS; for (unsigned int i = 0; i < vdatas.size(); i++) { - // This is a dummy variable for a dimension with no corresponding coordinate variable - // No need to allocate memory to read it - if (dummyVarNames.find(vdatas[i].varName) != dummyVarNames.end()) { - if (!vdatas[i].varTags[0]) { - rval = get_tag_to_set(vdatas[i], 0, vdatas[i].varTags[0]); - ERRORR(rval, "Trouble getting dummy tag."); - } - continue; - } - if ((std::find(vdatas[i].varDims.begin(), vdatas[i].varDims.end(), tDim) != vdatas[i].varDims.end())) vdatas[i].has_t = true; @@ -893,7 +898,7 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) ScdParData& parData = _readNC->parData; Range tmp_range; - ScdBox *scd_box; + ScdBox* scd_box; ErrorCode rval = scdi->construct_box(HomCoord(lDims[0], lDims[1], lDims[2], 1), HomCoord(lDims[3], lDims[4], lDims[5], 1), NULL, 0, scd_box, locallyPeriodic, &parData, true); @@ -1050,8 +1055,6 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: #endif for (unsigned int i = 0; i < vdatas.size(); i++) { - vdatas[i].numLev = nLevels; - for (unsigned int t = 0; t < tstep_nums.size(); t++) { dbgOut.tprintf(2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); @@ -1074,17 +1077,14 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: vdatas[i].readStarts[t].push_back(tstep_nums[t]); vdatas[i].readCounts[t].push_back(1); - // Next: numLev - if (vdatas[i].numLev != 1) { - vdatas[i].readStarts[t].push_back(0); - vdatas[i].readCounts[t].push_back(vdatas[i].numLev); - } + // Next: numLev, even if it is 1 + vdatas[i].readStarts[t].push_back(0); + vdatas[i].readCounts[t].push_back(vdatas[i].numLev); // Finally: y and x switch (vdatas[i].entLoc) { case ReadNC::ENTLOCVERT: // Vertices - // Only structured mesh has j parameter that multiplies i to get total # vertices vdatas[i].readStarts[t].push_back(lDims[1]); vdatas[i].readCounts[t].push_back(lDims[4] - lDims[1] + 1); vdatas[i].readStarts[t].push_back(lDims[0]); @@ -1101,8 +1101,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: case ReadNC::ENTLOCFACE: // Faces vdatas[i].readStarts[t].push_back(lCDims[1]); - vdatas[i].readStarts[t].push_back(lCDims[0]); vdatas[i].readCounts[t].push_back(lCDims[4] - lCDims[1] + 1); + vdatas[i].readStarts[t].push_back(lCDims[0]); vdatas[i].readCounts[t].push_back(lCDims[3] - lCDims[0] + 1); assert(vdatas[i].readStarts[t].size() == vdatas[i].varDims.size()); #ifdef USE_MPI @@ -1245,6 +1245,7 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& rval = tmp_rval; } } + // Debug output, if requested if (1 == dbgOut.get_verbosity()) { dbgOut.printf(1, "Read variables: %s", vdatas.begin()->varName.c_str()); diff --git a/src/io/NCHelper.hpp b/src/io/NCHelper.hpp index dcb006e..817257c 100644 --- a/src/io/NCHelper.hpp +++ b/src/io/NCHelper.hpp @@ -55,18 +55,18 @@ protected: ErrorCode get_tag_to_nonset(ReadNC::VarData& var_data, int tstep_num, Tag& tagh, int num_lev); - //! Create a character string attString of attMap. with '\0' + //! Create a character string attString of attMap. with '\0' //! terminating each attribute name, ';' separating the data type //! and value, and ';' separating one name/data type/value from - //! the next'. attLen stores the end position for each name/data + //! the next'. attLen stores the end position for each name/data //! type/ value. ErrorCode create_attrib_string(const std::map<std::string, ReadNC::AttData>& attMap, std::string& attString, std::vector<int>& attLen); - //! Initialize information for dimensions that don't have corresponding - //! coordinate variables - this information is used for creating dummy tags - void init_dims_with_no_coord_vars_info(); + //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), + //! create a dummy variable with a sparse tag to store the dimension length + ErrorCode create_dummy_variables(); private: //! Used by read_variable_to_set() @@ -90,8 +90,11 @@ protected: //! Dimension numbers for time and level int tDim, levDim; - //! Skip unexpected variables + //! Ignored variables std::set<std::string> ignoredVarNames; + + //! Dummy variables + std::set<std::string> dummyVarNames; }; //! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp index 48056c6..b117921 100644 --- a/src/io/NCHelperEuler.cpp +++ b/src/io/NCHelperEuler.cpp @@ -6,10 +6,10 @@ #include <sstream> #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} #define ERRORS(err, str) \ - if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} + if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} namespace moab { @@ -319,13 +319,21 @@ ErrorCode NCHelperEuler::init_mesh_vals() dbgOut.tprintf(1, "%d elements, %d vertices\n", (lDims[3] - lDims[0]) * (lDims[4] - lDims[1]), (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1)); - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), jCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCFACE; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } // For Eul models, slon and slat are "virtual" dimensions (not defined in the file header) @@ -451,8 +459,9 @@ ErrorCode NCHelperEuler::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create dummy tags, if needed, for dimensions with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create dummy variables, if needed, for dimensions with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp index 253d598..7725b55 100644 --- a/src/io/NCHelperFV.cpp +++ b/src/io/NCHelperFV.cpp @@ -6,7 +6,7 @@ #include <sstream> #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} namespace moab { @@ -315,19 +315,27 @@ ErrorCode NCHelperFV::init_mesh_vals() dbgOut.tprintf(1, "%d elements, %d vertices\n", (lDims[3] - lDims[0]) * (lDims[4] - lDims[1]), (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1)); - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), jCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), iCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCNSEDGE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), iDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCEWEDGE; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCFACE; + else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCNSEDGE; + else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), iDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCEWEDGE; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } std::vector<std::string> ijdimNames(4); @@ -452,8 +460,9 @@ ErrorCode NCHelperFV::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create dummy tags, if needed, for dimensions with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create dummy variables, if needed, for dimensions with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperHOMME.cpp b/src/io/NCHelperHOMME.cpp index be4d93f..25c4441 100644 --- a/src/io/NCHelperHOMME.cpp +++ b/src/io/NCHelperHOMME.cpp @@ -151,17 +151,25 @@ ErrorCode NCHelperHOMME::init_mesh_vals() tVals.push_back((double)t); } - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), levDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCVERT; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCVERT; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } - // Hack: create dummy tags for dimensions (like ncol) with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create dummy variables for dimensions (like ncol) with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } @@ -540,11 +548,9 @@ ErrorCode NCHelperHOMME::read_ucd_variable_to_nonset_allocate(std::vector<ReadNC vdatas[i].readStarts[t].push_back(tstep_nums[t]); vdatas[i].readCounts[t].push_back(1); - // Next: numLev - if (vdatas[i].numLev != 1) { - vdatas[i].readStarts[t].push_back(0); - vdatas[i].readCounts[t].push_back(vdatas[i].numLev); - } + // Next: numLev, even if it is 1 + vdatas[i].readStarts[t].push_back(0); + vdatas[i].readCounts[t].push_back(vdatas[i].numLev); // Finally: nVertices switch (vdatas[i].entLoc) { diff --git a/src/io/NCHelperMPAS.cpp b/src/io/NCHelperMPAS.cpp index a326e52..c803bf3 100644 --- a/src/io/NCHelperMPAS.cpp +++ b/src/io/NCHelperMPAS.cpp @@ -26,8 +26,22 @@ NCHelperMPAS::NCHelperMPAS(ReadNC* readNC, int fileId, const FileOptions& opts, , numCellGroups(0) , createGatherSet(false) { - // Hack: ignore 4D variable tracers(Time, nCells, nVertLevels, nTracers) - ignoredVarNames.insert("tracers"); + // Ignore variables containing topological information + ignoredVarNames.insert("nEdgesOnEdge"); + ignoredVarNames.insert("nEdgesOnCell"); + ignoredVarNames.insert("edgesOnVertex"); + ignoredVarNames.insert("cellsOnVertex"); + ignoredVarNames.insert("verticesOnEdge"); + ignoredVarNames.insert("edgesOnEdge"); + ignoredVarNames.insert("cellsOnEdge"); + ignoredVarNames.insert("verticesOnCell"); + ignoredVarNames.insert("edgesOnCell"); + ignoredVarNames.insert("cellsOnCell"); + + // Ignore variables for index conversion + ignoredVarNames.insert("indexToVertexID"); + ignoredVarNames.insert("indexToEdgeID"); + ignoredVarNames.insert("indexToCellID"); } bool NCHelperMPAS::can_read_file(ReadNC* readNC) @@ -144,42 +158,41 @@ ErrorCode NCHelperMPAS::init_mesh_vals() } } - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels for (vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit) { ReadNC::VarData& vd = (*vmit).second; - vd.entLoc = ReadNC::ENTLOCSET; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCVERT; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), eDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCEDGE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), cDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; - } + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCVERT; + else if (std::find(vd.varDims.begin(), vd.varDims.end(), eDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCEDGE; + else if (std::find(vd.varDims.begin(), vd.varDims.end(), cDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCFACE; + } - // Determine number of levels of a variable - for (vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit) { - ReadNC::VarData& vd = (*vmit).second; vd.numLev = 1; - - if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) vd.numLev = nLevels; - continue; - } - - for (unsigned int i = 0; i < opt_lev_dims.size(); i++) { - if (std::find(vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i]) != vd.varDims.end()) { - vd.numLev = dimLens[opt_lev_dims[i]]; - break; + else { + // If nVertLevels dimension is not found, try other optional levels such as nVertLevelsP1 + for (unsigned int i = 0; i < opt_lev_dims.size(); i++) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i]) != vd.varDims.end()) { + vd.numLev = dimLens[opt_lev_dims[i]]; + break; + } } } + + // Hack: ignore variables with more than 3 dimensions, e.g. tracers(Time, nCells, nVertLevels, nTracers) + if (vd.varDims.size() > 3) + ignoredVarNames.insert(vd.varName); } - // Hack: create dummy tags for dimensions (like nCells) with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create dummy variables for dimensions (like nCells) with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp index e930930..a0e02b4 100644 --- a/src/io/ReadNC.cpp +++ b/src/io/ReadNC.cpp @@ -132,16 +132,16 @@ ErrorCode ReadNC::load_file(const char* file_name, const EntityHandle* file_set, return rval; } else { - // Read dimension variable by default, the ones that are also variables - std::vector<std::string> filteredDimNames; + // Read dimension variables by default (the dimensions that are also variables) + std::vector<std::string> dim_var_names; for (unsigned int i = 0; i < dimNames.size(); i++) { std::map<std::string, VarData>::iterator mit = varInfo.find(dimNames[i]); if (mit != varInfo.end()) - filteredDimNames.push_back(dimNames[i]); + dim_var_names.push_back(dimNames[i]); } - if (!filteredDimNames.empty()) { - rval = myHelper->read_variables(filteredDimNames, tstep_nums); + if (!dim_var_names.empty()) { + rval = myHelper->read_variables(dim_var_names, tstep_nums); if (MB_FAILURE == rval) return rval; } @@ -302,7 +302,7 @@ ErrorCode ReadNC::read_header() ERRORR(result, "Getting attributes."); dbgOut.tprintf(1, "Read %u attributes\n", (unsigned int) globalAtts.size()); - // Read in dimensions into dimVals + // Read in dimensions into dimNames and dimLens result = get_dimensions(fileId, dimNames, dimLens); ERRORR(result, "Getting dimensions."); dbgOut.tprintf(1, "Read %u dimensions\n", (unsigned int) dimNames.size()); diff --git a/src/io/ReadNC.hpp b/src/io/ReadNC.hpp index fc75140..c452716 100644 --- a/src/io/ReadNC.hpp +++ b/src/io/ReadNC.hpp @@ -165,9 +165,6 @@ private: //! Dimension lengths std::vector<int> dimLens; - //! These should be taken out when we fix the dummy var info things - std::set<std::string> dummyVarNames; - //! Global attribs std::map<std::string, AttData> globalAtts; Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: danwu: For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME, nCells for MPAS), besides a sparse tag to store the dimension length, a dummy variable in ReadNC::varInfo is still needed to create some conventional tags like __<var_name>_DIMS.
by commits-noreply＠bitbucket.org 14 Nov '13

14 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/2d57da1edae8/ Changeset: 2d57da1edae8 Branch: master User: danwu Date: 2013-11-14 22:13:37 Summary: For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME, nCells for MPAS), besides a sparse tag to store the dimension length, a dummy variable in ReadNC::varInfo is still needed to create some conventional tags like __<var_name>_DIMS. Affected #: 7 files diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index 18905a0..ebf149c 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -315,8 +315,10 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData vd = (*mit).second; - // This variable will not be read - if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end()) + // No need to read ignored variables. Upon creation of dummy variables, + // tag values have already been set + if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end() || + dummyVarNames.find(vd.varName) != dummyVarNames.end()) continue; if (vd.entLoc == ReadNC::ENTLOCSET) @@ -331,8 +333,10 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std if (mit != varInfo.end()) { ReadNC::VarData vd = (*mit).second; - // This variable will not be read - if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end()) + // No need to read ignored variables. Upon creation of dummy variables, + // tag values have already been set + if (ignoredVarNames.find(vd.varName) != ignoredVarNames.end() || + dummyVarNames.find(vd.varName) != dummyVarNames.end()) continue; if (vd.entLoc == ReadNC::ENTLOCSET) @@ -713,7 +717,7 @@ ErrorCode NCHelper::create_attrib_string(const std::map<std::string, ReadNC::Att return MB_SUCCESS; } -ErrorCode NCHelper::create_tags_for_dims_with_no_coord_vars() +ErrorCode NCHelper::create_dummy_variables() { Interface*& mbImpl = _readNC->mbImpl; std::vector<std::string>& dimNames = _readNC->dimNames; @@ -723,12 +727,28 @@ ErrorCode NCHelper::create_tags_for_dims_with_no_coord_vars() // Hack: look at all dimensions, and see if we have one that does not appear in the list of varInfo names // Right now, candidates are from unstructured meshes, such as ncol (HOMME) and nCells (MPAS) - // For each of them, create a sparse tag with the dimension name to store the dimension length + // For each of them, create a dummy variable with a sparse tag to store the dimension length for (unsigned int i = 0; i < dimNames.size(); i++) { // If there is a variable with this dimension name, skip if (varInfo.find(dimNames[i]) != varInfo.end()) continue; + // Create a dummy variable + int sizeTotalVar = varInfo.size(); + std::string var_name(dimNames[i]); + ReadNC::VarData& data = varInfo[var_name]; + data.varName = std::string(var_name); + data.varId = sizeTotalVar; + data.varTags.resize(1, 0); + data.varDataType = NC_INT; + data.varDims.resize(1); + data.varDims[0] = (int)i; + data.numAtts = 0; + data.entLoc = ReadNC::ENTLOCSET; + dummyVarNames.insert(dimNames[i]); + dbgOut.tprintf(2, "Dummy variable created for dimension %s\n", dimNames[i].c_str()); + + // Create a sparse tag to store the dimension length Tag tagh; ErrorCode rval = mbImpl->tag_get_handle(dimNames[i].c_str(), 1, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT | MB_TAG_EXCL); diff --git a/src/io/NCHelper.hpp b/src/io/NCHelper.hpp index e4d37cb..817257c 100644 --- a/src/io/NCHelper.hpp +++ b/src/io/NCHelper.hpp @@ -55,18 +55,18 @@ protected: ErrorCode get_tag_to_nonset(ReadNC::VarData& var_data, int tstep_num, Tag& tagh, int num_lev); - //! Create a character string attString of attMap. with '\0' + //! Create a character string attString of attMap. with '\0' //! terminating each attribute name, ';' separating the data type //! and value, and ';' separating one name/data type/value from - //! the next'. attLen stores the end position for each name/data + //! the next'. attLen stores the end position for each name/data //! type/ value. ErrorCode create_attrib_string(const std::map<std::string, ReadNC::AttData>& attMap, std::string& attString, std::vector<int>& attLen); - //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create - //! a sparse tag with the dimension name to store the dimension length - ErrorCode create_tags_for_dims_with_no_coord_vars(); + //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), + //! create a dummy variable with a sparse tag to store the dimension length + ErrorCode create_dummy_variables(); private: //! Used by read_variable_to_set() @@ -90,8 +90,11 @@ protected: //! Dimension numbers for time and level int tDim, levDim; - //! Skip unexpected variables + //! Ignored variables std::set<std::string> ignoredVarNames; + + //! Dummy variables + std::set<std::string> dummyVarNames; }; //! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp index f70ded1..b117921 100644 --- a/src/io/NCHelperEuler.cpp +++ b/src/io/NCHelperEuler.cpp @@ -459,9 +459,9 @@ ErrorCode NCHelperEuler::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create tags, if needed, for dimensions with no corresponding coordinate variables - rval = create_tags_for_dims_with_no_coord_vars(); - ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); + // Hack: create dummy variables, if needed, for dimensions with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp index b640298..7725b55 100644 --- a/src/io/NCHelperFV.cpp +++ b/src/io/NCHelperFV.cpp @@ -460,9 +460,9 @@ ErrorCode NCHelperFV::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create tags, if needed, for dimensions with no corresponding coordinate variables - rval = create_tags_for_dims_with_no_coord_vars(); - ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); + // Hack: create dummy variables, if needed, for dimensions with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperHOMME.cpp b/src/io/NCHelperHOMME.cpp index dc586c5..25c4441 100644 --- a/src/io/NCHelperHOMME.cpp +++ b/src/io/NCHelperHOMME.cpp @@ -167,9 +167,9 @@ ErrorCode NCHelperHOMME::init_mesh_vals() vd.numLev = nLevels; } - // Hack: create tags for dimensions (like ncol) with no corresponding coordinate variables - rval = create_tags_for_dims_with_no_coord_vars(); - ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); + // Hack: create dummy variables for dimensions (like ncol) with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperMPAS.cpp b/src/io/NCHelperMPAS.cpp index b79fafb..c803bf3 100644 --- a/src/io/NCHelperMPAS.cpp +++ b/src/io/NCHelperMPAS.cpp @@ -190,9 +190,9 @@ ErrorCode NCHelperMPAS::init_mesh_vals() ignoredVarNames.insert(vd.varName); } - // Hack: create tags for dimensions (like nCells) with no corresponding coordinate variables - rval = create_tags_for_dims_with_no_coord_vars(); - ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); + // Hack: create dummy variables for dimensions (like nCells) with no corresponding coordinate variables + rval = create_dummy_variables(); + ERRORR(rval, "Failed to create dummy variables."); return MB_SUCCESS; } diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp index d48612d..a0e02b4 100644 --- a/src/io/ReadNC.cpp +++ b/src/io/ReadNC.cpp @@ -132,16 +132,16 @@ ErrorCode ReadNC::load_file(const char* file_name, const EntityHandle* file_set, return rval; } else { - // Read dimension variable by default, the ones that are also variables - std::vector<std::string> filteredDimNames; + // Read dimension variables by default (the dimensions that are also variables) + std::vector<std::string> dim_var_names; for (unsigned int i = 0; i < dimNames.size(); i++) { std::map<std::string, VarData>::iterator mit = varInfo.find(dimNames[i]); if (mit != varInfo.end()) - filteredDimNames.push_back(dimNames[i]); + dim_var_names.push_back(dimNames[i]); } - if (!filteredDimNames.empty()) { - rval = myHelper->read_variables(filteredDimNames, tstep_nums); + if (!dim_var_names.empty()) { + rval = myHelper->read_variables(dim_var_names, tstep_nums); if (MB_FAILURE == rval) return rval; } Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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Questions about side_number
by Chris Eldred 13 Nov '13

13 Nov '13

Hey Moab-Dev, I wanted to clarify my understanding of the side_number function for polygon meshes in 2D. Specifically, given a parent-child element pair; the function returns three parameters: side number, sense and offset. For a face-edge pair, these parameters represent: Side_number =the index of the edge in the array (NOT range) returned by get_adjacencies(face,1,1,edges_associated_with_face) Sense = the orientation of the normal of the edge with respect to the face (ie positive for outward, negative for inward) For a face-vertex pair, these parameter represent: Side_number = the index of the vertex in the array (NOT range) returned by get_adjacencies(face,1,0,vertices_associated_with_face) Sense = 0 For an edge-vertex pair, these parameters represent: Side_number = the index of the vertex in the array (NOT range) returned by get_adjacencies(edge,1,0,vertices_associated_with_edge) Sense = the orientation of the tangent of the edge with respect to the vertex (ie positive for towards, negative for away) Questions: 1) Is this understanding correct? 2) What does the offset parameter represent in these cases? 3) Is side_number working for meshes that contain polygons with repeated vertices (like those used in MPAS)? My preliminary testing based on the above understanding says no, but I wanted to check. If not, will it be working soon? 4) Is there an iMESH function (or MOAB specific extension) that would return similar information to side_number. I need to get access to the information returned by side_number via Fortran 90 and iMESH is what I am currently using to access MOAB via Fortran. Thanks, Chris Eldred -- Chris Eldred DOE Computational Science Graduate Fellow Graduate Student, Atmospheric Science, Colorado State University B.S. Applied Computational Physics, Carnegie Mellon University, 2009 chris.eldred(a)gmail.com / celdred(a)atmos.colostate.edu

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commit/MOAB: danwu: Take out legacy dummy var info things. For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME, nCells for MPAS), create a sparse tag with the dimension name to store the dimension length. This is done directly in NCHelper::create_tags_for_dims_with_no_coord_vars(), and ReadNC::dummyVarNames is no longer used.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/d96979b3285b/ Changeset: d96979b3285b Branch: master User: danwu Date: 2013-11-13 22:33:13 Summary: Take out legacy dummy var info things. For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME, nCells for MPAS), create a sparse tag with the dimension name to store the dimension length. This is done directly in NCHelper::create_tags_for_dims_with_no_coord_vars(), and ReadNC::dummyVarNames is no longer used. Affected #: 8 files diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index db0bfd4..18905a0 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -382,7 +382,6 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, std::vector<int>& tstep_nums) { - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; Interface*& mbImpl = _readNC->mbImpl; DebugOutput& dbgOut = _readNC->dbgOut; @@ -392,11 +391,6 @@ ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, s // Finally, read into that space int success; for (unsigned int i = 0; i < vdatas.size(); i++) { - // This is a dummy variable for a dimension with no corresponding coordinate variable - // No need to set its tag data - if (dummyVarNames.find(vdatas[i].varName) != dummyVarNames.end()) - continue; - for (unsigned int t = 0; t < tstep_nums.size(); t++) { void* data = vdatas[i].varDatas[t]; @@ -719,56 +713,47 @@ ErrorCode NCHelper::create_attrib_string(const std::map<std::string, ReadNC::Att return MB_SUCCESS; } -void NCHelper::init_dims_with_no_coord_vars_info() +ErrorCode NCHelper::create_tags_for_dims_with_no_coord_vars() { + Interface*& mbImpl = _readNC->mbImpl; std::vector<std::string>& dimNames = _readNC->dimNames; - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; + std::vector<int>& dimLens = _readNC->dimLens; std::map<std::string, ReadNC::VarData>& varInfo = _readNC->varInfo; DebugOutput& dbgOut = _readNC->dbgOut; // Hack: look at all dimensions, and see if we have one that does not appear in the list of varInfo names - // Right now, candidates are from unstructured meshes, such as ncol(HOMME) and nCells(MPAS) - // For them, create dummy tags + // Right now, candidates are from unstructured meshes, such as ncol (HOMME) and nCells (MPAS) + // For each of them, create a sparse tag with the dimension name to store the dimension length for (unsigned int i = 0; i < dimNames.size(); i++) { - // If there is a variable with this dimension name, skip, we are fine; if not, create a dummy varInfo + // If there is a variable with this dimension name, skip if (varInfo.find(dimNames[i]) != varInfo.end()) continue; - int sizeTotalVar = varInfo.size(); - std::string var_name(dimNames[i]); - ReadNC::VarData& data = varInfo[var_name]; - data.varName = std::string(var_name); - data.varId = sizeTotalVar; - data.varTags.resize(1, 0); - data.varDataType = NC_DOUBLE; // Could be int, actually, but we do not really need the type - data.varDims.resize(1); - data.varDims[0] = (int)i; - data.numAtts = 0; - data.entLoc = ReadNC::ENTLOCSET; - dbgOut.tprintf(2, "Dummy varInfo created for dimension %s\n", dimNames[i].c_str()); - dummyVarNames.insert(dimNames[i]); + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(dimNames[i].c_str(), 1, MB_TYPE_INTEGER, tagh, + MB_TAG_SPARSE | MB_TAG_CREAT | MB_TAG_EXCL); + // If the tag already exists, skip + if (MB_ALREADY_ALLOCATED == rval) + continue; + ERRORR(rval, "Failed to create dimension tag."); + + rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &dimLens[i]); + ERRORR(rval, "Failed to set data for dimension tag."); + + dbgOut.tprintf(2, "Sparse tag created for dimension %s\n", dimNames[i].c_str()); } + + return MB_SUCCESS; } ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& vdatas, std::vector<int>& tstep_nums) { - std::set<std::string>& dummyVarNames = _readNC->dummyVarNames; std::vector<int>& dimLens = _readNC->dimLens; DebugOutput& dbgOut = _readNC->dbgOut; ErrorCode rval = MB_SUCCESS; for (unsigned int i = 0; i < vdatas.size(); i++) { - // This is a dummy variable for a dimension with no corresponding coordinate variable - // No need to allocate memory to read it - if (dummyVarNames.find(vdatas[i].varName) != dummyVarNames.end()) { - if (!vdatas[i].varTags[0]) { - rval = get_tag_to_set(vdatas[i], 0, vdatas[i].varTags[0]); - ERRORR(rval, "Trouble getting dummy tag."); - } - continue; - } - if ((std::find(vdatas[i].varDims.begin(), vdatas[i].varDims.end(), tDim) != vdatas[i].varDims.end())) vdatas[i].has_t = true; diff --git a/src/io/NCHelper.hpp b/src/io/NCHelper.hpp index dcb006e..e4d37cb 100644 --- a/src/io/NCHelper.hpp +++ b/src/io/NCHelper.hpp @@ -64,9 +64,9 @@ protected: std::string& attString, std::vector<int>& attLen); - //! Initialize information for dimensions that don't have corresponding - //! coordinate variables - this information is used for creating dummy tags - void init_dims_with_no_coord_vars_info(); + //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for HOMME), create + //! a sparse tag with the dimension name to store the dimension length + ErrorCode create_tags_for_dims_with_no_coord_vars(); private: //! Used by read_variable_to_set() diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp index 5082c2e..f70ded1 100644 --- a/src/io/NCHelperEuler.cpp +++ b/src/io/NCHelperEuler.cpp @@ -459,8 +459,9 @@ ErrorCode NCHelperEuler::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create dummy tags, if needed, for dimensions with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create tags, if needed, for dimensions with no corresponding coordinate variables + rval = create_tags_for_dims_with_no_coord_vars(); + ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp index 488a511..b640298 100644 --- a/src/io/NCHelperFV.cpp +++ b/src/io/NCHelperFV.cpp @@ -460,8 +460,9 @@ ErrorCode NCHelperFV::init_mesh_vals() dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } - // Hack: create dummy tags, if needed, for dimensions with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create tags, if needed, for dimensions with no corresponding coordinate variables + rval = create_tags_for_dims_with_no_coord_vars(); + ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperHOMME.cpp b/src/io/NCHelperHOMME.cpp index ba504e6..dc586c5 100644 --- a/src/io/NCHelperHOMME.cpp +++ b/src/io/NCHelperHOMME.cpp @@ -167,8 +167,9 @@ ErrorCode NCHelperHOMME::init_mesh_vals() vd.numLev = nLevels; } - // Hack: create dummy tags for dimensions (like ncol) with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create tags for dimensions (like ncol) with no corresponding coordinate variables + rval = create_tags_for_dims_with_no_coord_vars(); + ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); return MB_SUCCESS; } diff --git a/src/io/NCHelperMPAS.cpp b/src/io/NCHelperMPAS.cpp index 9d50ffe..b79fafb 100644 --- a/src/io/NCHelperMPAS.cpp +++ b/src/io/NCHelperMPAS.cpp @@ -190,8 +190,9 @@ ErrorCode NCHelperMPAS::init_mesh_vals() ignoredVarNames.insert(vd.varName); } - // Hack: create dummy tags for dimensions (like nCells) with no corresponding coordinate variables - init_dims_with_no_coord_vars_info(); + // Hack: create tags for dimensions (like nCells) with no corresponding coordinate variables + rval = create_tags_for_dims_with_no_coord_vars(); + ERRORR(rval, "Failed to create tags for dimensions with no coordinate variables."); return MB_SUCCESS; } diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp index e930930..d48612d 100644 --- a/src/io/ReadNC.cpp +++ b/src/io/ReadNC.cpp @@ -302,7 +302,7 @@ ErrorCode ReadNC::read_header() ERRORR(result, "Getting attributes."); dbgOut.tprintf(1, "Read %u attributes\n", (unsigned int) globalAtts.size()); - // Read in dimensions into dimVals + // Read in dimensions into dimNames and dimLens result = get_dimensions(fileId, dimNames, dimLens); ERRORR(result, "Getting dimensions."); dbgOut.tprintf(1, "Read %u dimensions\n", (unsigned int) dimNames.size()); diff --git a/src/io/ReadNC.hpp b/src/io/ReadNC.hpp index fc75140..c452716 100644 --- a/src/io/ReadNC.hpp +++ b/src/io/ReadNC.hpp @@ -165,9 +165,6 @@ private: //! Dimension lengths std::vector<int> dimLens; - //! These should be taken out when we fix the dummy var info things - std::set<std::string> dummyVarNames; - //! Global attribs std::map<std::string, AttData> globalAtts; Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: danwu: Ignore some MPAS variables such as topological information. For all NC helpers, determine the entity location type and number of levels in init_mesh_vals(), with some minor changes.
by commits-noreply＠bitbucket.org 13 Nov '13

13 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/527454d1564f/ Changeset: 527454d1564f Branch: master User: danwu Date: 2013-11-13 20:05:40 Summary: Ignore some MPAS variables such as topological information. For all NC helpers, determine the entity location type and number of levels in init_mesh_vals(), with some minor changes. Affected #: 5 files diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index be91ef8..db0bfd4 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -10,10 +10,10 @@ #include "MBTagConventions.hpp" #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} #define ERRORS(err, str) \ - if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} + if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} namespace moab { @@ -893,7 +893,7 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) ScdParData& parData = _readNC->parData; Range tmp_range; - ScdBox *scd_box; + ScdBox* scd_box; ErrorCode rval = scdi->construct_box(HomCoord(lDims[0], lDims[1], lDims[2], 1), HomCoord(lDims[3], lDims[4], lDims[5], 1), NULL, 0, scd_box, locallyPeriodic, &parData, true); @@ -1050,8 +1050,6 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: #endif for (unsigned int i = 0; i < vdatas.size(); i++) { - vdatas[i].numLev = nLevels; - for (unsigned int t = 0; t < tstep_nums.size(); t++) { dbgOut.tprintf(2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); @@ -1074,17 +1072,14 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: vdatas[i].readStarts[t].push_back(tstep_nums[t]); vdatas[i].readCounts[t].push_back(1); - // Next: numLev - if (vdatas[i].numLev != 1) { - vdatas[i].readStarts[t].push_back(0); - vdatas[i].readCounts[t].push_back(vdatas[i].numLev); - } + // Next: numLev, even if it is 1 + vdatas[i].readStarts[t].push_back(0); + vdatas[i].readCounts[t].push_back(vdatas[i].numLev); // Finally: y and x switch (vdatas[i].entLoc) { case ReadNC::ENTLOCVERT: // Vertices - // Only structured mesh has j parameter that multiplies i to get total # vertices vdatas[i].readStarts[t].push_back(lDims[1]); vdatas[i].readCounts[t].push_back(lDims[4] - lDims[1] + 1); vdatas[i].readStarts[t].push_back(lDims[0]); @@ -1101,8 +1096,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: case ReadNC::ENTLOCFACE: // Faces vdatas[i].readStarts[t].push_back(lCDims[1]); - vdatas[i].readStarts[t].push_back(lCDims[0]); vdatas[i].readCounts[t].push_back(lCDims[4] - lCDims[1] + 1); + vdatas[i].readStarts[t].push_back(lCDims[0]); vdatas[i].readCounts[t].push_back(lCDims[3] - lCDims[0] + 1); assert(vdatas[i].readStarts[t].size() == vdatas[i].varDims.size()); #ifdef USE_MPI @@ -1245,6 +1240,7 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& rval = tmp_rval; } } + // Debug output, if requested if (1 == dbgOut.get_verbosity()) { dbgOut.printf(1, "Read variables: %s", vdatas.begin()->varName.c_str()); diff --git a/src/io/NCHelperEuler.cpp b/src/io/NCHelperEuler.cpp index 48056c6..5082c2e 100644 --- a/src/io/NCHelperEuler.cpp +++ b/src/io/NCHelperEuler.cpp @@ -6,10 +6,10 @@ #include <sstream> #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} #define ERRORS(err, str) \ - if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} + if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} namespace moab { @@ -319,13 +319,21 @@ ErrorCode NCHelperEuler::init_mesh_vals() dbgOut.tprintf(1, "%d elements, %d vertices\n", (lDims[3] - lDims[0]) * (lDims[4] - lDims[1]), (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1)); - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), jCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCFACE; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } // For Eul models, slon and slat are "virtual" dimensions (not defined in the file header) diff --git a/src/io/NCHelperFV.cpp b/src/io/NCHelperFV.cpp index 253d598..488a511 100644 --- a/src/io/NCHelperFV.cpp +++ b/src/io/NCHelperFV.cpp @@ -6,7 +6,7 @@ #include <sstream> #define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} + if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} namespace moab { @@ -315,19 +315,27 @@ ErrorCode NCHelperFV::init_mesh_vals() dbgOut.tprintf(1, "%d elements, %d vertices\n", (lDims[3] - lDims[0]) * (lDims[4] - lDims[1]), (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1)); - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), jCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), iCDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCNSEDGE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), iDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCEWEDGE; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if ((std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCFACE; + else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), iCDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCNSEDGE; + else if ((std::find(vd.varDims.begin(), vd.varDims.end(), jCDim) != vd.varDims.end()) && + (std::find(vd.varDims.begin(), vd.varDims.end(), iDim) != vd.varDims.end())) + vd.entLoc = ReadNC::ENTLOCEWEDGE; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } std::vector<std::string> ijdimNames(4); diff --git a/src/io/NCHelperHOMME.cpp b/src/io/NCHelperHOMME.cpp index be4d93f..ba504e6 100644 --- a/src/io/NCHelperHOMME.cpp +++ b/src/io/NCHelperHOMME.cpp @@ -151,13 +151,20 @@ ErrorCode NCHelperHOMME::init_mesh_vals() tVals.push_back((double)t); } - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels std::map<std::string, ReadNC::VarData>::iterator mit; for (mit = varInfo.begin(); mit != varInfo.end(); ++mit) { ReadNC::VarData& vd = (*mit).second; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) && (std::find(vd.varDims.begin(), - vd.varDims.end(), levDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCVERT; + + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCVERT; + } + + vd.numLev = 1; + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) + vd.numLev = nLevels; } // Hack: create dummy tags for dimensions (like ncol) with no corresponding coordinate variables @@ -540,11 +547,9 @@ ErrorCode NCHelperHOMME::read_ucd_variable_to_nonset_allocate(std::vector<ReadNC vdatas[i].readStarts[t].push_back(tstep_nums[t]); vdatas[i].readCounts[t].push_back(1); - // Next: numLev - if (vdatas[i].numLev != 1) { - vdatas[i].readStarts[t].push_back(0); - vdatas[i].readCounts[t].push_back(vdatas[i].numLev); - } + // Next: numLev, even if it is 1 + vdatas[i].readStarts[t].push_back(0); + vdatas[i].readCounts[t].push_back(vdatas[i].numLev); // Finally: nVertices switch (vdatas[i].entLoc) { diff --git a/src/io/NCHelperMPAS.cpp b/src/io/NCHelperMPAS.cpp index a326e52..9d50ffe 100644 --- a/src/io/NCHelperMPAS.cpp +++ b/src/io/NCHelperMPAS.cpp @@ -26,8 +26,22 @@ NCHelperMPAS::NCHelperMPAS(ReadNC* readNC, int fileId, const FileOptions& opts, , numCellGroups(0) , createGatherSet(false) { - // Hack: ignore 4D variable tracers(Time, nCells, nVertLevels, nTracers) - ignoredVarNames.insert("tracers"); + // Ignore variables containing topological information + ignoredVarNames.insert("nEdgesOnEdge"); + ignoredVarNames.insert("nEdgesOnCell"); + ignoredVarNames.insert("edgesOnVertex"); + ignoredVarNames.insert("cellsOnVertex"); + ignoredVarNames.insert("verticesOnEdge"); + ignoredVarNames.insert("edgesOnEdge"); + ignoredVarNames.insert("cellsOnEdge"); + ignoredVarNames.insert("verticesOnCell"); + ignoredVarNames.insert("edgesOnCell"); + ignoredVarNames.insert("cellsOnCell"); + + // Ignore variables for index conversion + ignoredVarNames.insert("indexToVertexID"); + ignoredVarNames.insert("indexToEdgeID"); + ignoredVarNames.insert("indexToCellID"); } bool NCHelperMPAS::can_read_file(ReadNC* readNC) @@ -144,38 +158,36 @@ ErrorCode NCHelperMPAS::init_mesh_vals() } } - // Determine the entity location type of a variable + // For each variable, determine the entity location type and number of levels for (vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit) { ReadNC::VarData& vd = (*vmit).second; - vd.entLoc = ReadNC::ENTLOCSET; - if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCVERT; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), eDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCEDGE; - else if ((std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) && - (std::find(vd.varDims.begin(), vd.varDims.end(), cDim) != vd.varDims.end())) - vd.entLoc = ReadNC::ENTLOCFACE; - } + vd.entLoc = ReadNC::ENTLOCSET; + if (std::find(vd.varDims.begin(), vd.varDims.end(), tDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), vDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCVERT; + else if (std::find(vd.varDims.begin(), vd.varDims.end(), eDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCEDGE; + else if (std::find(vd.varDims.begin(), vd.varDims.end(), cDim) != vd.varDims.end()) + vd.entLoc = ReadNC::ENTLOCFACE; + } - // Determine number of levels of a variable - for (vmit = varInfo.begin(); vmit != varInfo.end(); ++vmit) { - ReadNC::VarData& vd = (*vmit).second; vd.numLev = 1; - - if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), levDim) != vd.varDims.end()) vd.numLev = nLevels; - continue; - } - - for (unsigned int i = 0; i < opt_lev_dims.size(); i++) { - if (std::find(vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i]) != vd.varDims.end()) { - vd.numLev = dimLens[opt_lev_dims[i]]; - break; + else { + // If nVertLevels dimension is not found, try other optional levels such as nVertLevelsP1 + for (unsigned int i = 0; i < opt_lev_dims.size(); i++) { + if (std::find(vd.varDims.begin(), vd.varDims.end(), opt_lev_dims[i]) != vd.varDims.end()) { + vd.numLev = dimLens[opt_lev_dims[i]]; + break; + } } } + + // Hack: ignore variables with more than 3 dimensions, e.g. tracers(Time, nCells, nVertLevels, nTracers) + if (vd.varDims.size() > 3) + ignoredVarNames.insert(vd.varName); } // Hack: create dummy tags for dimensions (like nCells) with no corresponding coordinate variables Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: 4 new changesets
by commits-noreply＠bitbucket.org 12 Nov '13

12 Nov '13

4 new commits in MOAB: https://bitbucket.org/fathomteam/moab/commits/31889427adeb/ Changeset: 31889427adeb Branch: None User: iulian07 Date: 2013-11-13 06:57:34 Summary: use FileOptions class to set up the arguments It is much nicer, and it also has help automatically: for example, diffusion -h does this: diffusion -h Simulate a transport problem in a semi-Lagrangian formulation This program simulates a transport problem on a sphere according to a benchmark from a Nair & Lauritzen paper. It starts with a partitioned mesh on a sphere, add a tracer, and steps through. The flow reverses after half time, and it should return to original configuration, if the integration was exact. Usage: diffusion --help | [options] Options: -h [--help] : Show full help text -g [--gtolerance] <val>: geometric absolute tolerance (used for point concidence on the sphere) -i [--input_file] <arg>: input mesh file, partitioned -O [--extra_read_options] <arg>: extra read options -f [--field_type] <int>: field type-- 1: quasi-smooth; 2: smooth; 3: slotted cylinders (non-smooth) -n [--num_steps] <int>: number of steps -w [--write_debug_files]: write debugging files during simulation -v [--write_velocity_files]: Reorder mesh to group entities by partition -p [--write_result_in_parallel]: write tracer result files Affected #: 1 file diff --git a/tools/mbcslam/diffusion.cpp b/tools/mbcslam/diffusion.cpp index ed1d120..378473e 100644 --- a/tools/mbcslam/diffusion.cpp +++ b/tools/mbcslam/diffusion.cpp @@ -39,6 +39,10 @@ on the sphere; see CSLAM Utils case1 #include "CslamUtils.hpp" +const char BRIEF_DESC[] = + "Simulate a transport problem in a semi-Lagrangian formulation\n"; +std::ostringstream LONG_DESC; + // non smooth scalar field // some input data double gtol = 1.e-9; // this is for geometry tolerance @@ -51,7 +55,7 @@ double T = 5; int case_number = 1; // 1, 2 (non-divergent) 3 divergent moab::Tag corrTag; -bool noWrite = false; +bool writeFiles = false; bool parallelWrite = false; bool velocity = false; int field_type = 1 ; // 1 quasi smooth, 2 - smooth, 3 non-smooth, @@ -395,7 +399,7 @@ ErrorCode compute_tracer_case1(Interface * mb, Intx2MeshOnSphere & worker, Entit // lagr and euler are preserved EntityHandle covering_set; rval = worker.create_departure_mesh_3rd_alg(lagr_set, covering_set); - if (!noWrite) // so if write + if (writeFiles) // so if write { std::stringstream newTracer; newTracer << "Tracer" << rank << "_" << tStep << ".vtk"; @@ -414,7 +418,7 @@ ErrorCode compute_tracer_case1(Interface * mb, Intx2MeshOnSphere & worker, Entit rval = worker.intersect_meshes(covering_set, euler_set, out_set); CHECK_ERR(rval); - if (!noWrite) // so if write + if (writeFiles) // so if write { std::stringstream intx_mesh; intx_mesh << "Intx" << rank << "_" << tStep << ".vtk"; @@ -440,7 +444,7 @@ ErrorCode compute_tracer_case1(Interface * mb, Intx2MeshOnSphere & worker, Entit rval = mb->write_file(resTrace.str().c_str(), 0, "PARALLEL=WRITE_PART", &euler_set, 1, &tagElem, 1); } - if (!noWrite) // so if write + if (writeFiles) // so if write { std::stringstream newIntx; newIntx << "newIntx" << rank << "_" << tStep << ".vtk"; @@ -484,68 +488,49 @@ int main(int argc, char **argv) { MPI_Init(&argc, &argv); + LONG_DESC << "This program simulates a transport problem on a sphere" + " according to a benchmark from a Nair & Lauritzen paper.\n" + << "It starts with a partitioned mesh on a sphere, add a tracer, and steps through.\n" << + "The flow reverses after half time, and it should return to original configuration, if the integration was exact. "; + ProgOptions opts(LONG_DESC.str(), BRIEF_DESC); - std::string extra_read_opts; // read a homme file, partitioned in 16 so far std::string fileN= TestDir + "/HN16.h5m"; const char *filename_mesh1 = fileN.c_str(); - if (argc > 1) - { - int index = 1; - while (index < argc) - { - if (!strcmp(argv[index], "-gtol")) // this is for geometry tolerance - { - gtol = atof(argv[++index]); - } - - if (!strcmp(argv[index], "-input")) - { - filename_mesh1 = argv[++index]; - } - - if (!strcmp(argv[index], "-O")) - { - extra_read_opts = std::string(argv[++index]); - } - - if (!strcmp(argv[index], "-f")) - { - field_type = atoi(argv[++index]); - } - if (!strcmp(argv[index], "-ns")) - { - numSteps = atoi(argv[++index]); - } - - if (!strcmp(argv[index], "-nw")) - { - noWrite = true; - } - - if (!strcmp(argv[index], "-v")) - { - velocity = true; - } - - if (!strcmp(argv[index], "-pw")) - { - parallelWrite = true; - } - - if (!strcmp(argv[index], "-h")) - { - std::cout << "usage: -gtol <tol> -input <file> -O <extra_read_opts> -v (output velocities) \n " - << "-f <field_type> -h (this help) -ns <numSteps> -pw (parallel write) -nw (no dbg write) \n"; - std::cout << " field type: 1: quasi-smooth; 2: smooth; 3: slotted cylinders (non-smooth)\n"; - return 0; - } - index++; - } - } + + opts.addOpt<double>("gtolerance,g", + "geometric absolute tolerance (used for point concidence on the sphere)", &gtol); + + std::string input_file; + opts.addOpt<std::string>("input_file,i", "input mesh file, partitioned", + &input_file); + std::string extra_read_opts; + opts.addOpt<std::string>("extra_read_options,O", "extra read options ", + &extra_read_opts); + //int field_type; + opts.addOpt<int>("field_type,f", + "field type-- 1: quasi-smooth; 2: smooth; 3: slotted cylinders (non-smooth)", &field_type); + + opts.addOpt<int>("num_steps,n", + "number of steps ", &numSteps); + + //bool reorder = false; + opts.addOpt<void>("write_debug_files,w", "write debugging files during simulation ", + &writeFiles); + + opts.addOpt<void>("write_velocity_files,v", "Reorder mesh to group entities by partition", + &velocity); + + opts.addOpt<void>("write_result_in_parallel,p", "write tracer result files", + &parallelWrite); + + opts.parseCommandLine(argc, argv); + + if (!input_file.empty()) + filename_mesh1=input_file.c_str(); // read in parallel, in the "euler_set", the initial mesh - std::string opts = std::string("PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION")+ + std::string optsRead = std::string("PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION")+ std::string(";PARALLEL_RESOLVE_SHARED_ENTS")+extra_read_opts; Core moab; Interface & mb = moab; @@ -554,7 +539,7 @@ int main(int argc, char **argv) rval = mb.create_meshset(MESHSET_SET, euler_set); CHECK_ERR(rval); - rval = mb.load_file(filename_mesh1, &euler_set, opts.c_str()); + rval = mb.load_file(filename_mesh1, &euler_set, optsRead.c_str()); ParallelComm* pcomm = ParallelComm::get_pcomm(&mb, 0); CHECK_ERR(rval); @@ -569,7 +554,7 @@ int main(int argc, char **argv) std::cout << " case 1: use -gtol " << gtol << " -R " << radius << " -input " << filename_mesh1 << " -f " << field_type << " numSteps: " << numSteps << "\n"; - std::cout<<" write debug results: " << (noWrite ? "no" : "yes") << "\n"; + std::cout<<" write debug results: " << (writeFiles ? "yes" : "no") << "\n"; std::cout<< " write tracer in parallel: " << ( parallelWrite ? "yes" : "no") << "\n"; std::cout <<" output velocity: " << (velocity? "yes" : "no") << "\n"; } https://bitbucket.org/fathomteam/moab/commits/ce159c7e5cb7/ Changeset: ce159c7e5cb7 Branch: None User: iulian07 Date: 2013-11-13 06:57:34 Summary: report area of the intersection polygons; Affected #: 1 file diff --git a/tools/mbcslam/Intx2MeshOnSphere.cpp b/tools/mbcslam/Intx2MeshOnSphere.cpp index 7ea5854..a1d786b 100644 --- a/tools/mbcslam/Intx2MeshOnSphere.cpp +++ b/tools/mbcslam/Intx2MeshOnSphere.cpp @@ -452,6 +452,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE std::vector<double> newValues(rs2.size(), 0.);// initialize with 0 all of them // area of the polygon * conc on red (old) current quantity // finaly, divide by the area of the red + double check_intx_area=0.; for (Range::iterator it= polys.begin(); it!=polys.end(); it++) { EntityHandle poly=*it; @@ -465,6 +466,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE // big assumption here, red and blue are "parallel" ;we should have an index from // blue to red (so a deformed blue corresponds to an arrival red) double areap = area_spherical_element(mb, poly, R); + check_intx_area+=areap; // so the departure cell at time t (blueIndex) covers a portion of a redCell // that quantity will be transported to the redCell at time t+dt // the blue corresponds to a red arrival @@ -535,10 +537,17 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE ERRORR(rval, "can't set new values tag"); double total_mass=0.; + double total_intx_area =0; int mpi_err = MPI_Reduce(&total_mass_local, &total_mass, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD); if (MPI_SUCCESS != mpi_err) return MB_FAILURE; + // now reduce total area + mpi_err = MPI_Reduce(&check_intx_area, &total_intx_area, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD); + if (MPI_SUCCESS != mpi_err) return MB_FAILURE; if (my_rank==0) + { std::cout <<"total mass now:" << total_mass << "\n"; + std::cout <<"check: total intersection area: (4 * M_PI * R^2): " << total_intx_area << "\n"; + } if (remote_cells) { https://bitbucket.org/fathomteam/moab/commits/9f8346f39e8a/ Changeset: 9f8346f39e8a Branch: None User: iulian07 Date: 2013-11-13 06:57:34 Summary: side number for padded polygons the only problem is the edge between last node and first node; Affected #: 1 file diff --git a/src/Core.cpp b/src/Core.cpp index ad6bdda..a6e6cfd 100644 --- a/src/Core.cpp +++ b/src/Core.cpp @@ -2971,7 +2971,7 @@ ErrorCode Core::side_number(const EntityHandle parent, return (0 == temp_result ? MB_SUCCESS : MB_FAILURE); } else if (TYPE_FROM_HANDLE(parent) == MBPOLYGON) { - // find location of 1st vertex + // find location of 1st vertex; this works even for padded vertices const EntityHandle *first_v = std::find(parent_conn, parent_conn+num_parent_vertices, child_conn[0]); if (first_v == parent_conn+num_parent_vertices) return MB_ENTITY_NOT_FOUND; @@ -2990,11 +2990,23 @@ ErrorCode Core::side_number(const EntityHandle parent, else return MB_ENTITY_NOT_FOUND; } else if (TYPE_FROM_HANDLE(child) == MBEDGE) { + // determine the actual number of vertices, for the padded case + // the padded case could be like ABCDEFFF; num_parent_vertices=8, actual_num_parent_vertices=6 + int actual_num_parent_vertices = num_parent_vertices; + while(actual_num_parent_vertices>=3 && + (parent_conn[actual_num_parent_vertices-2] ==parent_conn[actual_num_parent_vertices-1] ) ) + actual_num_parent_vertices--; + if (parent_conn[(sd_number+1)%num_parent_vertices] == child_conn[1]) sense = 1; else if (parent_conn[(sd_number+num_parent_vertices-1)%num_parent_vertices] == - child_conn[1]) + child_conn[1]) // this will also cover edge AF for padded case, side will be 0, sense -1 sense = -1; + // if edge FA in above example, we should return sd_number = 5, sense 1 + else if ((sd_number==actual_num_parent_vertices-1) && (child_conn[1]==parent_conn[0])) + sense =1; + else + return MB_ENTITY_NOT_FOUND; return MB_SUCCESS; } } https://bitbucket.org/fathomteam/moab/commits/1bbc73aca065/ Changeset: 1bbc73aca065 Branch: master User: iulian07 Date: 2013-11-13 06:57:34 Summary: use zoltan partitioning for intx_mpas assumes that the build is configured with zoltan it is launched in serial as a test here, so it should not matter for make check Affected #: 1 file diff --git a/tools/mbcslam/intx_mpas.cpp b/tools/mbcslam/intx_mpas.cpp index 6888cb3..570c97f 100644 --- a/tools/mbcslam/intx_mpas.cpp +++ b/tools/mbcslam/intx_mpas.cpp @@ -121,7 +121,7 @@ int main(int argc, char **argv) MPI_Init(&argc, &argv); std::string extra_read_opts; - std::string fileN= TestDir + "/mpas_p8.h5m"; + std::string fileN= TestDir + "/io/mpasx1.642.t.2.nc"; const char *filename_mesh1 = fileN.c_str(); bool flux_form = false; if (argc > 1) @@ -164,8 +164,8 @@ int main(int argc, char **argv) } } // start copy - std::string opts = std::string("PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION")+ - std::string(";PARALLEL_RESOLVE_SHARED_ENTS")+extra_read_opts; + std::string opts = std::string("PARALLEL=READ_PART;PARTITION_METHOD=RCBZOLTAN")+ + std::string(";PARALLEL_RESOLVE_SHARED_ENTS;VARIABLE=;")+extra_read_opts; Core moab; Interface & mb = moab; EntityHandle euler_set; Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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