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Make CGNS code C++11 compliant #393

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Make CGNS code C++11 compliant #393

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0134d3f
TEMP from PR #391 fix: Correct CGNS_ENUMV usage
jrwrigh Jul 20, 2023
a2a7e4d
Make CGNS files C++11 compliant
jrwrigh Jul 21, 2023
a1a512d
Have MESHES resolve to abosolute path, change nprocs
jrwrigh Jul 21, 2023
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26 changes: 16 additions & 10 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,7 @@ option(USE_XSDK_DEFAULTS "enable the XDSK v0.3.0 default configuration" NO)
#requre c++11 without extensions
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSION OFF)
if(NOT ENABLE_CGNS)
set(CMAKE_CXX_STANDARD 11)
endif()
set(CMAKE_CXX_STANDARD 11)

xsdk_begin_package()
bob_begin_package()
Expand All @@ -27,8 +25,7 @@ if(USE_XSDK_DEFAULTS)
xsdk_compiler_flags()
endif()

# require c++14
option(ENABLE_CGNS "Enable the CGNS reader: requires c++14 extensions" OFF)
option(ENABLE_CGNS "Enable the CGNS reader" OFF)
message(STATUS "ENABLE_CGNS: ${ENABLE_CGNS}")

# Set some default compiler flags that should always be used
Expand All @@ -37,10 +34,7 @@ if(NOT USE_XSDK_DEFAULTS)
bob_begin_cxx_flags()
bob_end_cxx_flags()
set(CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS}")
if(ENABLE_CGNS) #takes precedence over SCOREC_ENABLE_CXX11
message(STATUS "enabling cxx14")
bob_cxx14_flags()
elseif(SCOREC_ENABLE_CXX11)
if(SCOREC_ENABLE_CXX11)
bob_cxx11_flags()
endif()
endif()
Expand All @@ -60,6 +54,8 @@ message(STATUS "IS_TESTING: ${IS_TESTING}")

set(MESHES "${CMAKE_SOURCE_DIR}/pumi-meshes" CACHE STRING "Directory of test meshes")
message(STATUS "MESHES: ${MESHES}")
get_filename_component(MESHES ${MESHES} ABSOLUTE)
message(STATUS "Using absolute file path MESHES: ${MESHES}")

option(BUILD_EXES "Build executables" ON)
message(STATUS "BUILD_EXES: ${BUILD_EXES}")
Expand Down Expand Up @@ -142,6 +138,14 @@ if(ENABLE_CGNS)
set(SCOREC_USE_HDF5_DEFAULT ${ENABLE_CGNS})
bob_public_dep(HDF5)
add_definitions(-DHAVE_CGNS)
else()
set(SCOREC_USE_CGNS_DEFAULT ${ENABLE_CGNS})
bob_public_dep(CGNS)
#CGNS does not provide cmake targets :(
include_directories(SYSTEM ${CGNS_INCLUDE_DIR})
set(SCOREC_USE_HDF5_DEFAULT ${ENABLE_CGNS})
bob_public_dep(HDF5)
add_definitions(-DHAVE_CGNS)
endif()

# Include the SCOREC project packages
Expand Down Expand Up @@ -172,8 +176,10 @@ add_library(core INTERFACE)
target_link_libraries(core INTERFACE ${SCOREC_EXPORTED_TARGETS})
if(ENABLE_CGNS)
target_link_libraries(core INTERFACE ${CMAKE_DL_LIBS}) #HDF5 uses dlopen
target_compile_features(core INTERFACE cxx_std_14)
# target_compile_features(core INTERFACE cxx_std_14)
target_compile_features(core INTERFACE cxx_std_11)
else()
target_link_libraries(core INTERFACE ${CMAKE_DL_LIBS}) #HDF5 uses dlopen
target_compile_features(core INTERFACE cxx_std_11)
endif()
scorec_export_library(core)
Expand Down
52 changes: 33 additions & 19 deletions apf/apfCGNS.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
#include "apfNumberingClass.h"
#include "apfShape.h"
#include "apfFieldData.h"
#include <functional>
#include <pcu_util.h>
#include <lionPrint.h>
//
Expand Down Expand Up @@ -269,9 +270,16 @@ void WriteTags(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity *
}
}
*/
void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity *>> &orderedEnts, const std::vector<std::pair<cgsize_t, cgsize_t>> &ranges, const std::vector<apf::MeshEntity *> &orderedVertices, const int &vStart, const int &vEnd, apf::Mesh *m)

typedef std::vector<apf::MeshEntity *> VecMeshEntity_t;
typedef std::pair<cgsize_t, cgsize_t> CGRange_t;

void WriteFields(const CGNS &cgns, const std::vector<VecMeshEntity_t> &orderedEnts, const std::vector<CGRange_t> &ranges, const VecMeshEntity_t &orderedVertices, const int &vStart, const int &vEnd, apf::Mesh *m)
{
const auto writeField = [&m, &cgns](apf::Field *f, const auto &orderedEnts, const int &solIndex, const auto &inner, const auto &post, const int &numComponents, const int &component, const std::string &fieldName, const int &start, const int &end, int &fieldIndex) {
typedef std::function<void (apf::MeshEntity *elem, apf::FieldDataOf<double> *fieldData, std::vector<double> &ddata, const int &numComponents, const int &component)> innerLambda_t;
typedef std::function<void (const int &solIndex, std::vector<double> &ddata, const cgsize_t *rmin, const cgsize_t *rmax, const int &globalSize, const int &fieldIndex)> postLambda_t;

const auto writeField = [&m, &cgns](apf::Field *f, const VecMeshEntity_t &orderedEnt, const int &solIndex, const innerLambda_t &inner, const postLambda_t &post, const int &numComponents, const int &component, const std::string &fieldName, const int &start, const int &end, int &fieldIndex) {
std::vector<double> data;

cgsize_t rmin[3];
Expand All @@ -281,7 +289,7 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
rmax[0] = end;

apf::FieldDataOf<double> *fieldData = f->getData();
for (const auto &e : orderedEnts)
for (const auto &e : orderedEnt)
{
if (fieldData->hasEntity(e) && m->isOwned(e))
{
Expand Down Expand Up @@ -310,7 +318,7 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
}
};

const auto loopCellFields = [&m, &writeField](const auto &orderedEnts, const int &solIndex, const auto &inner, const auto &post, const auto &ranges) {
const auto loopCellFields = [&m, &writeField](const std::vector<VecMeshEntity_t> &orderedEnts, const int &solIndex, const innerLambda_t &inner, const postLambda_t &post, const std::vector<CGRange_t> &ranges) {
for (int i = 0; i < m->countFields(); ++i)
{
apf::Field *f = m->getField(i);
Expand All @@ -335,7 +343,7 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
}
};

const auto loopVertexFields = [&m, &writeField](const auto &orderedEnts, const int &solIndex, const auto &inner, const auto &post, const int &vStart, const int &vEnd) {
const auto loopVertexFields = [&m, &writeField](const VecMeshEntity_t &orderedVertices, const int &solIndex, const innerLambda_t &inner, const postLambda_t &post, const int &vStart, const int &vEnd) {
for (int i = 0; i < m->countFields(); ++i)
{
apf::Field *f = m->getField(i);
Expand All @@ -352,12 +360,12 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
fieldNameNew += "_[" + std::to_string(component) + "]";

//std::cout << "VERTEX " << fieldNameNew << " " << fieldName << " " << component << " " << numComponents << std::endl;
writeField(f, orderedEnts, solIndex, inner, post, numComponents, component, fieldNameNew, vStart, vEnd, fieldIndex);
writeField(f, orderedVertices, solIndex, inner, post, numComponents, component, fieldNameNew, vStart, vEnd, fieldIndex);
}
}
};

const auto postLambda = [&cgns](const int &solIndex, std::vector<double> &ddata, const cgsize_t *rmin, const cgsize_t *rmax, const int &globalSize, const int &fieldIndex) {
const postLambda_t postLambda = [&cgns](const int &solIndex, std::vector<double> &ddata, const cgsize_t *rmin, const cgsize_t *rmax, const int &globalSize, const int &fieldIndex) {
if (globalSize > 0)
{
if (cgp_field_write_data(cgns.index, cgns.base, cgns.zone, solIndex, fieldIndex, &rmin[0], &rmax[0],
Expand All @@ -366,7 +374,7 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
}
};

const auto innerLambda = [](apf::MeshEntity *elem, apf::FieldDataOf<double> *fieldData, std::vector<double> &ddata, const int &numComponents, const int &component) {
const innerLambda_t innerLambda = [](apf::MeshEntity *elem, apf::FieldDataOf<double> *fieldData, std::vector<double> &ddata, const int &numComponents, const int &component) {
std::vector<double> vals(numComponents, -12345);
fieldData->get(elem, vals.data());
//std::cout << numComponents << " " << component << " " << vals[0] << std::endl;
Expand All @@ -390,7 +398,7 @@ void WriteFields(const CGNS &cgns, const std::vector<std::vector<apf::MeshEntity
}
}

auto WriteVertices(const CGNS &cgns, apf::Mesh *m, apf::GlobalNumbering *gvn)
std::tuple<VecMeshEntity_t, int, int> WriteVertices(const CGNS &cgns, apf::Mesh *m, apf::GlobalNumbering *gvn)
{
int Cx = -1;
int Cy = -1;
Expand All @@ -412,7 +420,7 @@ auto WriteVertices(const CGNS &cgns, apf::Mesh *m, apf::GlobalNumbering *gvn)
cgp_error_exit();
}

std::vector<apf::MeshEntity *> orderedVertices;
VecMeshEntity_t orderedVertices;
cgsize_t vertexMin[3];
cgsize_t vertexMax[3];
cgsize_t contigRange = -1;
Expand Down Expand Up @@ -574,7 +582,10 @@ CellElementReturn WriteElements(const CGNS &cgns, apf::Mesh *m, apf::GlobalNumbe

void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults, const int &cellCount, apf::Mesh *m, const apf::CGNSBCMap &cgnsBCMap, const std::map<apf::Mesh::Type, CGNS_ENUMT(ElementType_t)> &apf2cgns, apf::GlobalNumbering *gvn)
{
const auto EdgeLoop = [&m](const auto &lambda, apf::MeshTag *edgeTag) {
typedef std::function<void(apf::MeshEntity*)> LambdaMeshEntity_t;
typedef std::vector<apf::CGNSInfo> VecCGNSInfo_t;

const auto EdgeLoop = [&m](const LambdaMeshEntity_t &lambda, apf::MeshTag *edgeTag) {
apf::MeshIterator *edgeIter = m->begin(1);
apf::MeshEntity *edge = nullptr;
int vals[1];
Expand All @@ -591,7 +602,7 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
m->end(edgeIter);
};

const auto FaceLoop = [&m](const auto &lambda, apf::MeshTag *faceTag) {
const auto FaceLoop = [&m](const LambdaMeshEntity_t &lambda, apf::MeshTag *faceTag) {
apf::MeshIterator *faceIter = m->begin(2);
apf::MeshEntity *face = nullptr;
int vals[1];
Expand All @@ -608,7 +619,8 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
m->end(faceIter);
};

const auto BCEntityAdder = [&apf2cgns, &m, &cgns, &gvn](const auto &Looper, const auto &bcGroup, int &startingLocation) {

const auto BCEntityAdder = [&apf2cgns, &m, &cgns, &gvn](const std::function<void(LambdaMeshEntity_t, apf::MeshTag*)> &Looper, const apf::CGNSInfo &bcGroup, int &startingLocation) {
std::map<apf::Mesh::Type, std::vector<apf::MeshEntity *>> bcEntTypes;
for (const auto &r : apf2cgns)
bcEntTypes.insert(std::make_pair(r.first, std::vector<apf::MeshEntity *>()));
Expand Down Expand Up @@ -715,7 +727,9 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
PCU_Get_Comm());
};

const auto doVertexBC = [&](const auto &iter) {
typedef std::map<std::basic_string<char>, std::vector<apf::CGNSInfo>>::const_iterator MapCGNSInfo_t;

const auto doVertexBC = [&](const MapCGNSInfo_t &iter) {
for (const auto &p : iter->second)
{
std::vector<cgsize_t> bcList;
Expand Down Expand Up @@ -751,7 +765,7 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
}
};

const auto doEdgeBC = [&](const auto &iter, int &startingLocation) {
const auto doEdgeBC = [&](const MapCGNSInfo_t &iter, int &startingLocation) {
for (const auto &p : iter->second)
{
const auto se = BCEntityAdder(EdgeLoop, p, startingLocation);
Expand All @@ -774,7 +788,7 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
}
};

const auto doFaceBC = [&](const auto &iter, int &startingLocation) {
const auto doFaceBC = [&](const MapCGNSInfo_t &iter, int &startingLocation) {
for (const auto &p : iter->second)
{
const auto se = BCEntityAdder(FaceLoop, p, startingLocation);
Expand All @@ -797,7 +811,7 @@ void AddBocosToMainBase(const CGNS &cgns, const CellElementReturn &cellResults,
}
};

const auto doCellBC = [&](const auto &iter, const int &) {
const auto doCellBC = [&](const MapCGNSInfo_t &iter, const int &) {
for (const auto &p : iter->second)
{
std::vector<cgsize_t> bcList;
Expand Down Expand Up @@ -1051,11 +1065,11 @@ void WriteCGNS(const char *prefix, apf::Mesh *m, const apf::CGNSBCMap &cgnsBCMap
auto communicator = PCU_Get_Comm();
cgp_mpi_comm(communicator);
//
cgp_pio_mode(CGNS_ENUMV(CGP_INDEPENDENT));
cgp_pio_mode(CGP_INDEPENDENT);

CGNS cgns;
cgns.fname = std::string(prefix);
if (cgp_open(prefix, CGNS_ENUMV(CG_MODE_WRITE), &cgns.index))
if (cgp_open(prefix, CG_MODE_WRITE, &cgns.index))
cgp_error_exit();

{
Expand Down
14 changes: 7 additions & 7 deletions mds/mdsCGNS.cc
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Expand Up @@ -177,19 +177,19 @@ struct MeshDataGroup
if (components.size() == 1)
{
std::cout << "Scalar Group has " << components.size() << " related componenets: " << std::endl;
for (const auto m : components)
for (const auto &m : components)
std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
}
else if (components.size() == 3)
{
std::cout << "Vector Group has " << components.size() << " related componenets: " << std::endl;
for (const auto m : components)
for (const auto &m : components)
std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
}
else if (components.size() == 9)
{
std::cout << "Matrix Group has " << components.size() << " related componenets: " << std::endl;
for (const auto m : components)
for (const auto &m : components)
std::cout << "Field " << m.second.name << " @ " << m.second.si << " " << m.second.fi << std::endl;
}
else
Expand Down Expand Up @@ -265,7 +265,7 @@ void Kill(const int fid)
}
}

auto ReadCGNSCoords(int cgid, int base, int zone, int ncoords, int nverts, const std::vector<cgsize_t> &, const apf::GlobalToVert &globalToVert)
std::map<int, std::array<double, 3>> ReadCGNSCoords(int cgid, int base, int zone, int ncoords, int nverts, const std::vector<cgsize_t> &, const apf::GlobalToVert &globalToVert)
{
// Read min required as defined by consecutive range
// make one based as ReadElements makes zero based
Expand Down Expand Up @@ -389,7 +389,7 @@ void SimpleElementPartition(std::vector<cgsize_t> &numberToReadPerProc, std::vec
using Pair = std::pair<cgsize_t, cgsize_t>;
using LocalElementRanges = std::vector<Pair>; // one based

auto ReadElements(int cgid, int base, int zone, int section, int el_start /* one based */, int el_end, int numElements, int verticesPerElement, LocalElementRanges &localElementRanges)
std::tuple<std::vector<cgsize_t>, cgsize_t> ReadElements(int cgid, int base, int zone, int section, int el_start /* one based */, int el_end, int numElements, int verticesPerElement, LocalElementRanges &localElementRanges)
{
std::vector<cgsize_t> numberToReadPerProc;
std::vector<cgsize_t> startingIndex;
Expand Down Expand Up @@ -1056,8 +1056,8 @@ apf::Mesh2 *DoIt(gmi_model *g, const std::string &fname, apf::CGNSBCMap &cgnsBCM
int cgid = -1;
auto comm = PCU_Get_Comm();
cgp_mpi_comm(comm);
cgp_pio_mode(CGNS_ENUMV(CGP_INDEPENDENT));
cgp_open(fname.c_str(), CGNS_ENUMV(CG_MODE_READ), &cgid);
cgp_pio_mode(CGP_INDEPENDENT);
cgp_open(fname.c_str(), CG_MODE_READ, &cgid);

int nbases = -1;
cg_nbases(cgid, &nbases);
Expand Down
2 changes: 1 addition & 1 deletion test/cgns.cc
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Expand Up @@ -119,7 +119,7 @@ pMesh toPumi(const std::string &prefix, gmi_model *g, apf::Mesh2 *mesh)
return pm;
}

auto additional(const std::string &prefix, gmi_model *g, apf::Mesh2 *mesh)
std::function<void()> additional(const std::string &prefix, gmi_model *g, apf::Mesh2 *mesh)
{
// seems essential to make pm first before calling balance or reorder...
auto pm = toPumi(prefix, g, mesh);
Expand Down
2 changes: 1 addition & 1 deletion test/testing.cmake
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Expand Up @@ -560,7 +560,7 @@ mpi_test(cgns_3d_2 ${numProcs}
#
# 3D BCS tests
#
set(numProcs 5)
set(numProcs 4)
#
set(CGNSDIR ${MESHES}/cgns/withBCS/3D)
#
Expand Down