Skip to content
Snippets Groups Projects
Commit c1f7f7e1 authored by wenqing's avatar wenqing
Browse files

[PMesh] Done some changes according to Dima's suggestion and removed one unused cmd arguement

parent 15e9e7c2
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt
+ 6
− 7
View file @ c1f7f7e1
###
add_executable(partmesh PartitionMesh.cpp MeshPartitioning.h MeshPartitioning.cpp)
set_target_properties(partmesh PROPERTIES FOLDER Utilities)
target_link_libraries(partmesh FileIO)
if(UTILS_PARTMESH_BUILD_WITH_METIS) if(UTILS_PARTMESH_BUILD_WITH_METIS)
include_directories(${METIS_PATH}/libmetis) include_directories(${METIS_PATH}/libmetis)
include_directories(${METIS_PATH}/programs) include_directories(${METIS_PATH}/programs)
...@@ -11,13 +16,7 @@ if(UTILS_PARTMESH_BUILD_WITH_METIS) ...@@ -11,13 +16,7 @@ if(UTILS_PARTMESH_BUILD_WITH_METIS)
) )
ADD_LIBRARY(METIS_Lib STATIC ${METIS_SOURCES} ) ADD_LIBRARY(METIS_Lib STATIC ${METIS_SOURCES} )
add_executable(partmesh PartitionMesh.cpp MeshPartitioning.h MeshPartitioning.cpp) target_link_libraries(partmesh METIS_Lib metis)
set_target_properties(partmesh PROPERTIES FOLDER Utilities)
target_link_libraries(partmesh FileIO METIS_Lib metis)
else()
add_executable(partmesh PartitionMesh.cpp MeshPartitioning.h MeshPartitioning.cpp)
set_target_properties(partmesh PROPERTIES FOLDER Utilities)
target_link_libraries(partmesh FileIO)
endif() endif()
ADD_VTK_DEPENDENCY(partmesh) ADD_VTK_DEPENDENCY(partmesh)
......
Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.cpp
+ 34
− 35
View file @ c1f7f7e1
...@@ -50,7 +50,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -50,7 +50,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
std::ifstream npart_in(fname_parts.data()); std::ifstream npart_in(fname_parts.data());
if (!npart_in.is_open()) if (!npart_in.is_open())
{ {
ERR("Error: cannot open file %s. It may not exist !", fname_parts.data()); ERR("Error: cannot open file %s. It may not exist! ", fname_parts.data());
abort(); abort();
} }
...@@ -68,7 +68,6 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -68,7 +68,6 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
npart_in.close(); npart_in.close();
//TEST std::remove(fname_parts.c_str()); //TEST std::remove(fname_parts.c_str());
// -- Open files for output // -- Open files for output
// //
// for ASCII output // for ASCII output
...@@ -119,10 +118,10 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -119,10 +118,10 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
os_subd.setf(std::ios::scientific); os_subd.setf(std::ios::scientific);
} }
MyInt global_node_id_offset = 0; PetscInt global_node_id_offset = 0;
std::vector<bool> nodes_part_reserved; std::vector<bool> nodes_part_reserved;
nodes_part_reserved.reserve(nnodes); nodes_part_reserved.reserve(nnodes);
std::vector<MyInt> node_global_ids; std::vector<PetscInt> node_global_ids;
node_global_ids.reserve(nnodes); node_global_ids.reserve(nnodes);
for (std::size_t i=0; i<nnodes; i++) for (std::size_t i=0; i<nnodes; i++)
{ {
...@@ -137,8 +136,8 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -137,8 +136,8 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
std::vector<std::size_t> partition_end_node_id(npartitions); std::vector<std::size_t> partition_end_node_id(npartitions);
std::vector<std::size_t> end_non_ghost_node_id(npartitions); std::vector<std::size_t> end_non_ghost_node_id(npartitions);
const MyInt num_headers = 14; const PetscInt num_headers = 14;
MyInt head[num_headers]; PetscInt head[num_headers];
// node rank offset // node rank offset
head[10] = 0; head[10] = 0;
// element rank offset // element rank offset
...@@ -176,9 +175,9 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -176,9 +175,9 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
std::vector< std::vector<unsigned> > std::vector< std::vector<unsigned> >
elems_non_ghost_nodes_local_ids(_elements.size()); elems_non_ghost_nodes_local_ids(_elements.size());
const MyInt num_non_ghost_nodes = end_non_ghost_node_id[ipart] const PetscInt num_non_ghost_nodes = end_non_ghost_node_id[ipart]
- partition_start_node_id[ipart]; - partition_start_node_id[ipart];
for (MyInt i=0; i<num_non_ghost_nodes; i++) for (PetscInt i=0; i<num_non_ghost_nodes; i++)
{ {
const unsigned node_id = partition_nodes[ i + partition_start_node_id[ipart] ]->getID(); const unsigned node_id = partition_nodes[ i + partition_start_node_id[ipart] ]->getID();
...@@ -249,7 +248,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -249,7 +248,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
partition_end_node_id[ipart] = partition_nodes.size(); partition_end_node_id[ipart] = partition_nodes.size();
// Renumber // Renumber
MyInt local_id = 0; PetscInt local_id = 0;
std::vector<unsigned> nodes_local_ids_partition; std::vector<unsigned> nodes_local_ids_partition;
nodes_local_ids_partition.reserve(nnodes); nodes_local_ids_partition.reserve(nnodes);
...@@ -276,15 +275,15 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -276,15 +275,15 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
} }
// Count the number of integer variables used to define non-ghost elements // Count the number of integer variables used to define non-ghost elements
const MyInt num_non_ghost_elems = partition_regular_elements.size(); const PetscInt num_non_ghost_elems = partition_regular_elements.size();
MyInt nmb_element_idxs = 3 * num_non_ghost_elems; PetscInt nmb_element_idxs = 3 * num_non_ghost_elems;
for (MyInt j=0; j<num_non_ghost_elems; j++) for (PetscInt j=0; j<num_non_ghost_elems; j++)
{ {
nmb_element_idxs += partition_regular_elements[j]->getNNodes(); nmb_element_idxs += partition_regular_elements[j]->getNNodes();
} }
const MyInt num_ghost_elems = partition_ghost_elements.size(); const PetscInt num_ghost_elems = partition_ghost_elements.size();
MyInt nmb_element_idxs_g = 3 * num_ghost_elems; PetscInt nmb_element_idxs_g = 3 * num_ghost_elems;
for (MyInt j=0; j<num_ghost_elems; j++) for (PetscInt j=0; j<num_ghost_elems; j++)
{ {
nmb_element_idxs_g += partition_ghost_elements[j]->getNNodes(); nmb_element_idxs_g += partition_ghost_elements[j]->getNNodes();
} }
...@@ -292,19 +291,19 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -292,19 +291,19 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
std::string ipart_str = std::to_string(ipart); std::string ipart_str = std::to_string(ipart);
// Number of active elements // Number of active elements
const MyInt offset_e = num_non_ghost_elems + nmb_element_idxs; const PetscInt offset_e = num_non_ghost_elems + nmb_element_idxs;
const MyInt offset_e_g = num_ghost_elems + nmb_element_idxs_g; const PetscInt offset_e_g = num_ghost_elems + nmb_element_idxs_g;
// Reserved for nodes for high order interpolation // Reserved for nodes for high order interpolation
const MyInt num_non_ghost_nodes_extra = 0; const PetscInt num_non_ghost_nodes_extra = 0;
const MyInt num_nodes_linear_element = partition_end_node_id[ipart] const PetscInt num_nodes_linear_element = partition_end_node_id[ipart]
- partition_start_node_id[ipart]; - partition_start_node_id[ipart];
const MyInt num_nodes_quadratic_element = 0; const PetscInt num_nodes_quadratic_element = 0;
const MyInt num_nodes_global_mesh = nnodes; const PetscInt num_nodes_global_mesh = nnodes;
// Reserved for nodes for high order interpolation // Reserved for nodes for high order interpolation
const MyInt num_nodes_global_mesh_extra = nnodes; const PetscInt num_nodes_global_mesh_extra = nnodes;
// Write configuration data and elements of this partition // Write configuration data and elements of this partition
head[0] = num_nodes_linear_element + num_nodes_quadratic_element; head[0] = num_nodes_linear_element + num_nodes_quadratic_element;
...@@ -319,35 +318,35 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base, ...@@ -319,35 +318,35 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
head[9] = nmb_element_idxs_g; head[9] = nmb_element_idxs_g;
if (output_binary) if (output_binary)
{ {
fwrite(head, 1, num_headers * sizeof(MyInt), of_bin_cfg); fwrite(head, 1, num_headers * sizeof(PetscInt), of_bin_cfg);
head[10] += head[0] * sizeof(NodeStruct); head[10] += head[0] * sizeof(NodeStruct);
head[11] += offset_e * sizeof(MyInt); head[11] += offset_e * sizeof(PetscInt);
head[12] += offset_e_g * sizeof(MyInt); head[12] += offset_e_g * sizeof(PetscInt);
// Write non-ghost elements // Write non-ghost elements
std::vector<MyInt> ele_info(offset_e); std::vector<PetscInt> ele_info(offset_e);
MyInt counter = num_non_ghost_elems; PetscInt counter = num_non_ghost_elems;
for (MyInt j = 0; j < num_non_ghost_elems; j++) for (PetscInt j = 0; j < num_non_ghost_elems; j++)
{ {
ele_info[j] = counter; ele_info[j] = counter;
getElementIntegerVariables(*partition_regular_elements[j], nodes_local_ids_partition, getElementIntegerVariables(*partition_regular_elements[j], nodes_local_ids_partition,
ele_info, counter); ele_info, counter);
} }
fwrite(&ele_info[0], 1, (offset_e) * sizeof(MyInt), of_bin_ele); fwrite(&ele_info[0], 1, (offset_e) * sizeof(PetscInt), of_bin_ele);
// Write ghost elements // Write ghost elements
ele_info.resize(offset_e_g); ele_info.resize(offset_e_g);
counter = num_ghost_elems; counter = num_ghost_elems;
for (MyInt j = 0; j < num_ghost_elems; j++) for (PetscInt j = 0; j < num_ghost_elems; j++)
{ {
ele_info[j] = counter; ele_info[j] = counter;
getElementIntegerVariables(*partition_ghost_elements[j], nodes_local_ids_partition, getElementIntegerVariables(*partition_ghost_elements[j], nodes_local_ids_partition,
ele_info, counter); ele_info, counter);
} }
fwrite(&ele_info[0], 1, (offset_e_g) * sizeof(MyInt), of_bin_ele_g); fwrite(&ele_info[0], 1, (offset_e_g) * sizeof(PetscInt), of_bin_ele_g);
} }
else else
{ {
...@@ -462,16 +461,16 @@ ElementType MeshPartitioning::getElementType(const Element& elem) ...@@ -462,16 +461,16 @@ ElementType MeshPartitioning::getElementType(const Element& elem)
void MeshPartitioning::getElementIntegerVariables(const Element& elem, void MeshPartitioning::getElementIntegerVariables(const Element& elem,
const std::vector<unsigned>& local_node_ids, const std::vector<unsigned>& local_node_ids,
std::vector<MyInt>& elem_info, std::vector<PetscInt>& elem_info,
MyInt& counter) PetscInt& counter)
{ {
unsigned mat_id = 0; // Materical ID to be set from the mesh data unsigned mat_id = 0; // Materical ID to be set from the mesh data
const MyInt nn = elem.getNNodes();; const PetscInt nn = elem.getNNodes();;
elem_info[counter++] = mat_id; elem_info[counter++] = mat_id;
elem_info[counter++] = static_cast<unsigned>(getElementType(elem)) + 1; elem_info[counter++] = static_cast<unsigned>(getElementType(elem)) + 1;
elem_info[counter++] = nn; elem_info[counter++] = nn;
for(MyInt i=0; i<nn; i++) for(PetscInt i=0; i<nn; i++)
{ {
elem_info[counter++] = local_node_ids[elem.getNodeIndex(i)]; elem_info[counter++] = local_node_ids[elem.getNodeIndex(i)];
} }
......
Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.h
+ 4
− 4
View file @ c1f7f7e1
...@@ -29,7 +29,7 @@ enum class ElementType : unsigned {LINE2, QUAD4, HEX8, TRI3, TET4, PRISM6, PYRAM ...@@ -29,7 +29,7 @@ enum class ElementType : unsigned {LINE2, QUAD4, HEX8, TRI3, TET4, PRISM6, PYRAM
/// A subdomain mesh. /// A subdomain mesh.
class MeshPartitioning : public Mesh class MeshPartitioning : public Mesh
{ {
typedef long MyInt; // for PetscInt typedef long PetscInt;
public: public:
/// Copy constructor /// Copy constructor
MeshPartitioning(const MeshLib::Mesh &mesh) : Mesh(mesh) MeshPartitioning(const MeshLib::Mesh &mesh) : Mesh(mesh)
...@@ -60,8 +60,8 @@ class MeshPartitioning : public Mesh ...@@ -60,8 +60,8 @@ class MeshPartitioning : public Mesh
*/ */
void getElementIntegerVariables(const Element& elem, void getElementIntegerVariables(const Element& elem,
const std::vector<unsigned>& local_node_ids, const std::vector<unsigned>& local_node_ids,
std::vector<MyInt>& elem_info, std::vector<PetscInt>& elem_info,
MyInt& counter); PetscInt& counter);
/*! /*!
\brief Write local indicies of element nodes to a ASCII file \brief Write local indicies of element nodes to a ASCII file
...@@ -74,7 +74,7 @@ class MeshPartitioning : public Mesh ...@@ -74,7 +74,7 @@ class MeshPartitioning : public Mesh
struct NodeStruct struct NodeStruct
{ {
MyInt id; PetscInt id;
double x; double x;
double y; double y;
double z; double z;
......
Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
+ 2
− 13
View file @ c1f7f7e1
...@@ -14,15 +14,13 @@ ...@@ -14,15 +14,13 @@
#include "tclap/CmdLine.h" #include "tclap/CmdLine.h"
#include "logog/include/logog.hpp"
#ifdef BUILD_WITH_METIS #ifdef BUILD_WITH_METIS
extern "C" { extern "C" {
#include "metis_main.h" #include "metis_main.h"
} }
#endif #endif
#include "BaseLib/LogogSimpleFormatter.h" #include "Applications/ApplicationsLib/LogogSetup.h"
#include "BaseLib/FileTools.h" #include "BaseLib/FileTools.h"
#include "MeshLib/IO/readMeshFromFile.h" #include "MeshLib/IO/readMeshFromFile.h"
...@@ -35,10 +33,7 @@ extern "C" { ...@@ -35,10 +33,7 @@ extern "C" {
int main (int argc, char* argv[]) int main (int argc, char* argv[])
{ {
LOGOG_INITIALIZE(); ApplicationsLib::LogogSetup logog_setup;
logog::Cout* logog_cout (new logog::Cout);
BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
logog_cout->SetFormatter(*custom_format);
std::string m_str = "Partition a mesh for parallel computing." std::string m_str = "Partition a mesh for parallel computing."
"The tasks of this tool are in twofold:\n" "The tasks of this tool are in twofold:\n"
...@@ -63,8 +58,6 @@ int main (int argc, char* argv[]) ...@@ -63,8 +58,6 @@ int main (int argc, char* argv[])
cmd.add(asci_flag); cmd.add(asci_flag);
TCLAP::SwitchArg elem_part_flag("e","element_wise","Enable element wise partitioing.", false); TCLAP::SwitchArg elem_part_flag("e","element_wise","Enable element wise partitioing.", false);
cmd.add(elem_part_flag); cmd.add(elem_part_flag);
TCLAP::SwitchArg output_part_flag("o","output_parititon","Enable output partitions.", false);
cmd.add(output_part_flag);
cmd.parse(argc, argv); cmd.parse(argc, argv);
...@@ -130,9 +123,5 @@ int main (int argc, char* argv[]) ...@@ -130,9 +123,5 @@ int main (int argc, char* argv[])
INFO( "Total runtime: %g s.\n", run_timer.elapsed() ); INFO( "Total runtime: %g s.\n", run_timer.elapsed() );
INFO( "Total CPU time: %g s.\n", CPU_timer.elapsed() ); INFO( "Total CPU time: %g s.\n", CPU_timer.elapsed() );
delete custom_format;
delete logog_cout;
LOGOG_SHUTDOWN();
return 0; return 0;
} }
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment