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@hhijazi
hhijazi committed Sep 25, 2024
1 parent ee55acf commit 7e7fb17
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Showing 3 changed files with 43 additions and 185 deletions.
2 changes: 1 addition & 1 deletion cmake/ExternalH5CPP.cmake
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Expand Up @@ -12,7 +12,7 @@ set(H5CPP_DOWNLOAD_URL https://github.com/ess-dmsc/h5cpp.git)
set(H5CPP_ROOT_DIR ${THIRDPARTY_INSTALL_PATH}/Install/H5CPP/build CACHE INTERNAL "")
ExternalProject_Add(h5cpp
DOWNLOAD_DIR ${THIRDPARTY_INSTALL_PATH}
DOWNLOAD_COMMAND export HTTPS_PROXY=$ENV{HTTPS_PROXY} && git clone ${H5CPP_DOWNLOAD_URL} && rm -fr ./Install/H5CPP && mv H5CPP ./Install/H5CPP && cd ./Install/H5CPP && mkdir build && cd build && cmake .. -DH5CPP_WITH_BOOST=OFF -DH5CPP_CONAN=DISABLE -DH5CPP_DISABLE_TESTS=ON && make
DOWNLOAD_COMMAND export HTTPS_PROXY=$ENV{HTTPS_PROXY} && git clone ${H5CPP_DOWNLOAD_URL} && rm -fr ./Install/H5CPP && mv H5CPP ./Install/H5CPP && cd ./Install/H5CPP && mkdir build && cd build && cmake .. -DH5CPP_WITH_BOOST=ON -DH5CPP_CONAN=DISABLE -DH5CPP_DISABLE_TESTS=ON && make
URL ${H5CPP_DOWNLOAD_URL}
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${H5CPP_ROOT_DIR}
CONFIGURE_COMMAND ""
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3 changes: 2 additions & 1 deletion cmake/FindH5CPP.cmake
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Expand Up @@ -5,10 +5,11 @@ message("Looking for H5CPP in ${H5CPP_ROOT_DIR}")
include(FindPackageHandleStandardArgs)

find_path(H5CPP_INCLUDE_DIR
NAMES hdf5.hpp
NAMES hdf5.hpp
HINTS /usr/local/include
HINTS /usr/local/include/h5cpp
HINTS ${H5CPP_ROOT_DIR}/include
HINTS ${H5CPP_ROOT_DIR}/../src/h5cpp/
HINTS ${H5CPP_ROOT_DIR}/src/h5cpp
HINTS ${PROJECT_SOURCE_DIR}/thirdparty/H5CPP/src
)
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223 changes: 40 additions & 183 deletions examples/Optimization/MILP/sensor_assign2/Sensor_Assign2.cpp
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Expand Up @@ -31,6 +31,7 @@ int main(int argc, const char * argv[]) {
// run_MIP = true;
myModel m = myModel();
auto par = m.readHD5(fname, 1e-8);
return;
// vector<param<double>> par = m.readData(argc, argv, 1, 2);
// m.readH5SolStats(sol_fname, par[0], par[1], par[2]);
auto start = high_resolution_clock::now();
Expand Down Expand Up @@ -81,196 +82,52 @@ int main(int argc, const char * argv[]) {

vector<param<double>> myModel::readHD5(const string& fname, double wThrsh){

vector<param<double>> par (3);
#ifdef USE_H5CPP
auto hd5file = file::open(fname);
auto RootGroup = hd5file.root();
/* Read agent names */
auto agents_group = RootGroup.get_group("agents");
auto agents_names = agents_group.get_dataset("agent_name");
agents = indices("agents");
dataspace::Simple Dataspace(agents_names.dataspace());
auto Dimensions = Dataspace.current_dimensions();
auto nb_agents = Dimensions[0];
// budget.resize(nb_agents);
// auto budget_set = agents_group.get_dataset("budget");
// budget_set.read(budget);
auto MaxDimensions = Dataspace.maximum_dimensions();
std::vector<string> AllElements(Dataspace.size());
agents_names.read(AllElements);
for (auto Value : AllElements) {
agents.insert("Agent_"+to_string(agents.size()));
}
/* Read objects */
auto objects_group = RootGroup.get_group("objects");
auto object_names_set = objects_group.get_dataset("object_name");
auto priority_set = objects_group.get_dataset("priority");
dataspace::Simple object_names_space(object_names_set.dataspace());
objects = indices("objects");
auto nb_objects = object_names_space.size();
std::vector<string> object_names(nb_objects);
object_names_set.read(object_names);
for (auto name : object_names) {
objects.insert("Object_"+to_string(objects.size()));
}
auto pr_size = priority_set.dataspace().size();
assert(pr_size==nb_objects*nb_agents);
vector<double> priority(pr_size);
sleep(1);
priority_set.read(priority);
if(priority.size() != pr_size){
throw invalid_argument("priority size should be " + to_string(pr_size) + ". After reading h5 file, it is being set to " + to_string(priority.size()));
}
/* Read sensors */
auto sensors_group = RootGroup.get_group("sensors");
auto sensors_names_set = sensors_group.get_dataset("sensor_name");
auto agent_own_set = sensors_group.get_dataset("agent_id");
dataspace::Simple sensors_names_space(sensors_names_set.dataspace());
dataspace::Simple agent_own_space(agent_own_set.dataspace());
sensors = indices("sensors");
own_sens = indices("own_sens");

auto nb_sensors = sensors_names_space.size();
owner.resize(nb_sensors);/*< vector storing ownership of each sensor */
vector<string> sensors_names(nb_sensors);
sensors_names_set.read(sensors_names);
for (auto name : sensors_names) {
sensors.insert("Sensor_"+to_string(sensors.size()));
}
vector<int> agent_own(nb_sensors);
agent_own_set.read(agent_own);
int s_id = 0;
for (auto agent_id : agent_own) {
owner[s_id] = agent_id;
owner_map[sensors.get_key(s_id)] = agent_id;
own_sens.insert(sensors.get_key(s_id++)+","+agents.get_key(agent_id));
}
// agents.print();
// objects.print();
// sensors.print();
// own_sens.print();
/* Read arcs */
auto arcs_group = RootGroup.get_group("arcs");
auto object_id_set = arcs_group.get_dataset("object_id");
auto sensor_id_set = arcs_group.get_dataset("sensor_id");
auto quality_set = arcs_group.get_dataset("quality");
auto nb_arcs = object_id_set.dataspace().size();
vector<int> object_ids(nb_arcs), sensor_ids(nb_arcs);
vector<double> quality(nb_arcs);
object_id_set.read(object_ids);
sensor_id_set.read(sensor_ids);
quality_set.read(quality);
Node* node = NULL;
Arc* arc = NULL;
string src, dest;


for (int i = 0; i <nb_objects; i++){
node = new Node(objects.get_key(i),graph.nodes.size());
graph.add_node(node);
}
for (int i = 0; i <nb_sensors; i++){
node = new Node(sensors.get_key(i),graph.nodes.size());
node->owner_id = owner[i];
graph.add_node(node);
}


for (int i = 0; i < nb_arcs; i++) {
src = sensors.get_key(sensor_ids[i]);
dest = objects.get_key(object_ids[i]);
arc = new Arc(src + "," + dest);
arc->_id = i;
arc->_src = graph.get_node(src);
arc->_dest= graph.get_node(dest);
arc->weight = quality[i];
graph.add_arc(arc);
arc->connect(false);
}
// graph.print();
DebugOn("Done reading h5 file and building graph" << endl);
DebugOn("Graph has " << graph.nodes.size() << " nodes" << endl);
DebugOn("Graph has " << graph.arcs.size() << " arcs" << endl);
DebugOn("Number of objects = " << nb_objects << endl);
DebugOn("Number of sensors = " << nb_sensors << endl);
DebugOn("Number of agents = " << nb_agents << endl);
N = nb_sensors;
M = nb_objects;
K = nb_agents;

/* Graph nodes are indexed in {0,...,n+m-1})*/
assert(N + M == graph.nodes.size());/* Make sure we have the right number of nodes */
arcs = indices("arcs");
own_arcs = indices("own_arcs");
bought_arcs = indices("bought_arcs");

/* Parameters */
vector<param<double>> par (3);
param<double> w0("w0");
param<double> w_own("w_own");
param<double> w_bought("w_bought");
arcs.add(graph.arcs);
w0.in(arcs);
w_own.in(own_arcs);
w_bought.in(bought_arcs);
DebugOn("Building coefficient matrix..." << endl);
string sensor_name, agent_name, object_name;
/*define index sets for weights, then read weights (need owner to sepsrate own and bought weights)*/
for (int k = 0; k < K; k++) {
agent_name = agents.get_key(k);
for (int i = 0; i < N; i++) {
sensor_name = sensors.get_key(i);
auto sensor_node = graph.get_node(sensor_name);
if (owner[i] == k) {
for (const Arc* a: sensor_node->get_out()) {
own_arcs.add(sensor_name + "," + a->_dest->_name + "," + agent_name);
int object = stoi(a->_dest->_name.substr(7, a->_dest->_name.size()));
int tmp = k + object * K;//a->_dest->_id + nb_objects * k;
double wTmp = a->weight*priority[tmp];
if (wTmp > wThrsh) {
w_own.add_val(wTmp);
}
else {
w_own.add_val(0);
}
// for (const Arc* b: a->_dest->get_in()) {
// if (b->_src->owner_id == k) {
// if (b->_src->_id != i) {
// own_rplc.add(a->_src->_name + "," + b->_src->_name + "," + a->_dest->_name + "," + agent_name);
// }
// }
// else {
// oths_rplc.add(sensor_name + "," + b->_src->_name + "," + a->_dest->_name + "," + agent_name);
// }
// }
}
}
else {
bought_sens.add(sensor_name + "," + agent_name);
for (const Arc* a: sensor_node->get_out()) {
bought_arcs.add(a->_src->_name + "," + a->_dest->_name + "," + agent_name);
int object = stoi(a->_dest->_name.substr(7, a->_dest->_name.size()));
int tmp = k + object * K;//a->_dest->_id + nb_objects * k;
if (tmp >= priority.size()) {
cout << "Priority out of range " << tmp << " " << priority.size() << endl;
}
double wTmp = a->weight * priority[tmp];
if (wTmp > wThrsh) {
w_bought.add_val(wTmp);
}
else {
w_bought.add_val(0);
}
}
}
auto att = RootGroup.attributes;
auto natt = att.size();
DebugOn("H5 file has " << natt << " attributes" << endl);
for (auto i = 0; i < natt; i++) {
auto att_i = att[i];
DebugOn("Attribute " << i << "'s name is " << att_i.name() << endl);
auto ds = att_i.dataspace();
auto nbe = ds.size();
DebugOn("Attribute dataspace size: " << nbe << endl);
string att_data;
att_i.read(att_data);
DebugOn("Attribute data: " << att_data << endl);
}
auto nodes = RootGroup.nodes;
auto nnodes = nodes.size();
DebugOn("H5 file has " << nnodes << " nodes" << endl);
for(size_t index = 0; index<nnodes;++index)
{
std::cout<<RootGroup.nodes[index].link().path()<<std::endl;
auto nbnodeatt = RootGroup.nodes[index].attributes.size();
DebugOn("Node has " << nbnodeatt << " attributes" << endl);
for (auto i = 0; i < nbnodeatt; i++) {
auto att_i = RootGroup.nodes[index].attributes[i];
DebugOn("Attribute " << i << "'s name is " << att_i.name() << endl);
// DebugOn("Attribute " << i << "'s datatype is " << att_i.datatype() << endl);
// auto dtype = att_i.datatype();
auto ds = att_i.dataspace();
auto nbe = ds.size();
DebugOn("Attribute dataspace size: " << nbe << endl);


// string att_data;
// att_i.read(att_data);
// DebugOn("Attribute data: " << att_data[0] << endl);
}
}


// graph.print();
DebugOn("Done reading h5 file" << endl);


/*pass weights to init*/
par[0] = w0;
par[1] = w_own;
par[2] = w_bought;

return par;
#else
cerr << "Can't read Hd5 as a solver: this version of Gravity was compiled without H5CPP. Rerun cmake with -DH5CPP=ON." << endl;
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