From b7d9fb5b13780cceb64ba5f8e1bf660751ab69ce Mon Sep 17 00:00:00 2001
From: Wenqing Wang <wenqing.wang@ufz.de>
Date: Wed, 22 Jun 2016 10:38:19 +0200
Subject: [PATCH] [PMesh] Let mpmetis be called via system() and changed METIS
repository.
---
.gitmodules | 2 +-
.../PartitionMesh/CMakeLists.txt | 40 ++++++++++--------
.../PartitionMesh/MeshPartitioning.cpp | 18 ++++----
.../PartitionMesh/MetisSetup.cmake | 2 +
.../PartitionMesh/PartitionMesh.cpp | 41 ++++++++-----------
CMakeLists.txt | 4 ++
ThirdParty/metis | 1 +
scripts/cmake/SubmoduleSetup.cmake | 6 +++
8 files changed, 63 insertions(+), 51 deletions(-)
create mode 160000 ThirdParty/metis
diff --git a/.gitmodules b/.gitmodules
index d5696e4418f..c6296f99e94 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -24,4 +24,4 @@
url = https://github.com/ufz/vtkGUISupportQt.git
[submodule "ThirdParty/metis"]
path = ThirdParty/metis
- url = https://github.com/envinf/metis.git
+ url = https://github.com/scibuilder/metis.git
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt b/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt
index 097b8707b57..f1c3a152bd7 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt
@@ -1,23 +1,7 @@
###
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)
- include_directories(${METIS_PATH}/libmetis)
- include_directories(${METIS_PATH}/programs)
-
- set(METIS_SOURCES
- ${METIS_PATH}/programs/mpmetis.c
- ${METIS_PATH}/programs/cmdline_mpmetis.c
- ${METIS_PATH}/programs/io.c
- ${METIS_PATH}/programs/stat.c
- metis_main.h
- )
- ADD_LIBRARY(METIS_Lib STATIC ${METIS_SOURCES} )
-
- target_link_libraries(partmesh METIS_Lib metis)
-endif()
+target_link_libraries(partmesh MeshLib)
ADD_VTK_DEPENDENCY(partmesh)
@@ -31,3 +15,25 @@ cpack_add_component(ogs_partmesh
DESCRIPTION "Mesh partitioning tool."
GROUP Utilities
)
+
+## Compile mpmetis
+add_definitions(-DSVNINFO="${SVNREV}")
+include_directories(${METIS_PATH}/libmetis)
+include_directories(${METIS_PATH}/programs)
+set(METIS_SOURCES
+ ${METIS_PATH}/programs/mpmetis.c
+ ${METIS_PATH}/programs/cmdline_mpmetis.c
+ ${METIS_PATH}/programs/io.c
+ ${METIS_PATH}/programs/stat.c
+ )
+add_executable(mpmetis ${METIS_SOURCES})
+
+target_link_libraries(mpmetis metis)
+
+install(TARGETS mpmetis RUNTIME DESTINATION bin COMPONENT ogs_metis)
+
+cpack_add_component(ogs_metis
+ DISPLAY_NAME "mpmetis"
+ DESCRIPTION "METIS."
+ GROUP Utilities
+)
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.cpp b/Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.cpp
index 7494757d141..f3719c3b4d2 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.cpp
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/MeshPartitioning.cpp
@@ -30,7 +30,7 @@ void MeshPartitioning :: write2METIS(const std::string& file_name)
os << _elements.size() <<" \n";
for (const auto elem : _elements)
{
- for (unsigned j=0; j<elem->getNNodes(); j++)
+ for (unsigned j=0; j<elem->getNumberOfNodes(); j++)
{
os << elem->getNodeIndex(j) + 1 <<" ";
}
@@ -192,7 +192,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
std::vector<unsigned> nonghost_nodes_local_ids;
unsigned ghost_counter = 0;
- for (unsigned kk=0; kk<elem->getNNodes(); kk++)
+ for (unsigned kk=0; kk<elem->getNumberOfNodes(); kk++)
{
if (nodes_reseved[elem->getNodeIndex(kk)])
{
@@ -225,7 +225,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
// Mark the non-ghost nodes for each ghost element
for (const auto ghost_elem : partition_ghost_elements)
{
- for (unsigned k=0; k<ghost_elem->getNNodes(); k++)
+ for (unsigned k=0; k<ghost_elem->getNumberOfNodes(); k++)
nodes_reseved[ghost_elem->getNodeIndex(k)] = false;
// Mark non-ghost nodes
@@ -236,7 +236,7 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
// Add the ghost nodes to the node vector of this partition
for (const auto ghost_elem : partition_ghost_elements)
{
- for (unsigned k=0; k<ghost_elem->getNNodes(); k++)
+ for (unsigned k=0; k<ghost_elem->getNumberOfNodes(); k++)
{
const unsigned node_id = ghost_elem->getNodeIndex(k);
if (nodes_reseved[node_id])
@@ -279,13 +279,13 @@ void MeshPartitioning :: partitionByNodeMETIS(const std::string& file_name_base,
PetscInt nmb_element_idxs = 3 * num_non_ghost_elems;
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]->getNumberOfNodes();
}
const PetscInt num_ghost_elems = partition_ghost_elements.size();
PetscInt nmb_element_idxs_g = 3 * num_ghost_elems;
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]->getNumberOfNodes();
}
std::string ipart_str = std::to_string(ipart);
@@ -465,7 +465,7 @@ void MeshPartitioning::getElementIntegerVariables(const Element& elem,
PetscInt& counter)
{
unsigned mat_id = 0; // Materical ID to be set from the mesh data
- const PetscInt nn = elem.getNNodes();;
+ const PetscInt nn = elem.getNumberOfNodes();;
elem_info[counter++] = mat_id;
elem_info[counter++] = static_cast<unsigned>(getElementType(elem)) + 1;
elem_info[counter++] = nn;
@@ -481,8 +481,8 @@ void MeshPartitioning::writeLocalElementNodeIndicies(std::ostream& os, const Ele
{
unsigned mat_id = 0; // Materical ID to be set from the mesh data
os << mat_id << " " << static_cast<unsigned>(getElementType(elem)) + 1 << " "
- << elem.getNNodes() <<" ";
- for(unsigned i=0; i<elem.getNNodes(); i++)
+ << elem.getNumberOfNodes() <<" ";
+ for(unsigned i=0; i<elem.getNumberOfNodes(); i++)
{
os << local_node_ids[elem.getNodeIndex(i)] << " ";
}
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/MetisSetup.cmake b/Applications/Utils/ModelPreparation/PartitionMesh/MetisSetup.cmake
index 9a0e5910b8f..e2a1aefa871 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/MetisSetup.cmake
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/MetisSetup.cmake
@@ -1,6 +1,8 @@
MESSAGE( STATUS "The METIS package is copyrighted by the Regents of the University of Minnesota." )
MESSAGE( STATUS "Please read the license of the METIS package carefully before you use the METIS." )
+set(METIS_PATH "${CMAKE_SOURCE_DIR}/ThirdParty/metis")
+
add_definitions(-DUSE_GKREGEX)
set(GKLIB_PATH "${METIS_PATH}/GKlib" CACHE PATH "path to GKlib")
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp b/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
index 999ce5c412a..622e51f18d1 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
@@ -12,13 +12,8 @@
*/
-#include "tclap/CmdLine.h"
-
-#ifdef BUILD_WITH_METIS
-extern "C" {
-#include "metis_main.h"
-}
-#endif
+#include <sstream>
+#include <tclap/CmdLine.h>
#include "Applications/ApplicationsLib/LogogSetup.h"
#include "BaseLib/FileTools.h"
@@ -54,6 +49,8 @@ int main (int argc, char* argv[])
TCLAP::SwitchArg ogs2metis_flag("1", "ogs2metis",
"Indicator to convert the ogs mesh file to METIS input file", cmd, false);
+ TCLAP::SwitchArg exe_metis_flag("m","exe_metis","Call mpmetis inside the programme via system().", false);
+ cmd.add(exe_metis_flag);
TCLAP::SwitchArg asci_flag("a","asci","Enable ASCII output.", false);
cmd.add(asci_flag);
TCLAP::SwitchArg elem_part_flag("e","element_wise","Enable element wise partitioing.", false);
@@ -70,7 +67,7 @@ int main (int argc, char* argv[])
const std::string file_name_base = BaseLib::dropFileExtension(ifile_name);
MeshLib::MeshPartitioning* mesh = static_cast<MeshLib::MeshPartitioning*>
(MeshLib::IO::readMeshFromFile(file_name_base + ".vtu"));
- INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
+ INFO("Mesh read: %d nodes, %d elements.", mesh->getNumberOfNodes(), mesh->getNumberOfElements());
if (ogs2metis_flag.getValue())
{
@@ -89,23 +86,17 @@ int main (int argc, char* argv[])
const int num_partitions = nparts.getValue();
std::string str_nparts = std::to_string(num_partitions);
- // With the metis source code being compiled
- if (num_partitions > 1)
+ // Execute mpmetis via system(...)
+ if (num_partitions > 1 && exe_metis_flag.getValue())
{
-#ifdef BUILD_WITH_METIS
INFO("METIS is running ...");
- const int argc_m = 4;
- char *argv_m[argc_m];
- std::string unsc = "-"; // Avoid compilation warning by argv_m[0] = "-";
- argv_m[0] = &unsc[0];
- std::string option = "-gtype=nodal";
- argv_m[1] = &option[0];
- std::string part_mesh_file = file_name_base + ".mesh";
- argv_m[2] = &part_mesh_file[0];
- argv_m[3] = &str_nparts[0];
-
- metis_main(argc_m, argv_m);
-#endif
+ std::stringstream ss;
+ ss << "mpmetis " << " -gtype=nodal "
+ << file_name_base + ".mesh "
+ << nparts.getValue();
+
+ int status = system(ss.str().c_str());
+ INFO("Return value of system calling %d ", status);
}
INFO("Partitioning the mesh in the node wise way ...");
@@ -123,5 +114,7 @@ int main (int argc, char* argv[])
INFO( "Total runtime: %g s.\n", run_timer.elapsed() );
INFO( "Total CPU time: %g s.\n", CPU_timer.elapsed() );
- return 0;
+ delete mesh;
+
+ return EXIT_SUCCESS;
}
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1396b488687..3faf588d928 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -150,6 +150,10 @@ if(OGS_BUILD_TESTS)
set(Data_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/Tests/Data CACHE INTERNAL "")
endif()
+if(OGS_BUILD_UTILS)
+ include(${CMAKE_SOURCE_DIR}/Applications/Utils/ModelPreparation/PartitionMesh/MetisSetup.cmake)
+endif()
+
######################
### Subdirectories ###
######################
diff --git a/ThirdParty/metis b/ThirdParty/metis
new file mode 160000
index 00000000000..0f44bee3cab
--- /dev/null
+++ b/ThirdParty/metis
@@ -0,0 +1 @@
+Subproject commit 0f44bee3cab5d5453d4fff7cd877c0d4b858f72b
diff --git a/scripts/cmake/SubmoduleSetup.cmake b/scripts/cmake/SubmoduleSetup.cmake
index 6a0c9d20625..5331d4cfcbf 100644
--- a/scripts/cmake/SubmoduleSetup.cmake
+++ b/scripts/cmake/SubmoduleSetup.cmake
@@ -12,12 +12,18 @@ set(REQUIRED_SUBMODULES
ThirdParty/tetgen
${OGS_ADDITIONAL_SUBMODULES_TO_CHECKOUT}
)
+
+
+
if(OGS_BUILD_TESTS)
list(APPEND REQUIRED_SUBMODULES Tests/Data)
endif()
if(OGS_BUILD_GUI)
list(APPEND REQUIRED_SUBMODULES ThirdParty/vtkGUISupportQt)
endif()
+if(OGS_BUILD_UTILS)
+ list(APPEND REQUIRED_SUBMODULES ThirdParty/metis)
+endif()
foreach(SUBMODULE ${REQUIRED_SUBMODULES})
execute_process(
--
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