UTulsa-Research/ag_gen
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MPI incorp with serialization unit testing

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This commit is contained in:
Noah L. Schrick 2021-12-07 14:17:38 -06:00
parent e93a940e80
commit 88a4d057a2
8 changed files with 572 additions and 357 deletions
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14
CMakeLists.txt
View File

@ -21,7 +21,7 @@ set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -g -Wall -
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O1 -fopenmp")
set(PostgreSQL_TYPE_INCLUDE_DIR "9.5")
set(PostgreSQL_ADDITIONAL_VERSIONS "10.1" "10" "9.5")
set(PostgreSQL_ADDITIONAL_VERSIONS "12.4" "10.1" "10" "9.5")
find_program(LSB_RELEASE lsb_release)
execute_process(COMMAND ${LSB_RELEASE} -is
@ -42,13 +42,15 @@ set(ENV{PKG_CONFIG_PATH} "/usr/local/lib/pkgconfig")
find_package(PkgConfig REQUIRED)
find_package(PostgreSQL REQUIRED)
find_package(OpenMP)
find_package(MPI)
find_package(BISON 2.4 REQUIRED)
find_package(FLEX REQUIRED)
find_package(Boost REQUIRED serialization graph)
find_package(Boost REQUIRED mpi serialization graph)
include_directories(${Boost_INCLUDE_DIR})
find_package(OpenSSL)
find_package(Doxygen)
@ -65,6 +67,12 @@ if(OpenMP_CXX_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
if(MPI_CXX_FOUND)
INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH})
LIST(APPEND SCR_EXTERNAL_LIBS ${MPI_CXX_LIBRARIES})
#set(CMAKE_CXX_COMPILER "mpic++")
endif()
if(DOXYGEN_FOUND)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
add_custom_target(doc ALL ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
@ -126,7 +134,7 @@ add_executable(ag_gen "${CMAKE_SOURCE_DIR}/src/main.cpp"
${FLEX_nm_scanner_OUTPUTS} ${BISON_nm_parser_OUTPUTS}
${FLEX_xp_scanner_OUTPUTS} ${BISON_xp_parser_OUTPUTS}
${ag_gen_src} ${utils_src} ${mpi_src})
target_link_libraries(ag_gen ${PostgreSQL_LIBRARIES} Boost::serialization)
target_link_libraries(ag_gen ${PostgreSQL_LIBRARIES} Boost::serialization Boost::mpi ${MPI_C_LIBRARIES})
add_executable(decode "${CMAKE_SOURCE_DIR}/src/tools/decode.cpp"
${ag_gen_src} ${utils_src})

196
build/Makefile
View File

@ -1,5 +1,5 @@
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# Generated by "Unix Makefiles" Generator, CMake Version 3.22
# Default target executed when no arguments are given to make.
default_target: all
@ -65,16 +65,6 @@ CMAKE_BINARY_DIR = "/home/noah/Documents/School/Thesis Work/ag_parallel/build"
#=============================================================================
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@ -85,6 +75,16 @@ edit_cache:
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]

24
build/run.sh
View File

@ -1,9 +1,25 @@
sudo -u postgres -i sh -c "dropdb ag_gen" || true
sudo -u postgres -i sh -c "createdb ag_gen ag_gen"
psql ag_gen < schema.sql
#!/usr/bin/env bash
DBNAME="testing4"
if sudo -u postgres -i sh -c "psql -q ${DBNAME} -c '\q'" 2>&1; then
echo "Database ${DBNAME} exists. Dropping and recreating from dump."
sudo -u postgres -i sh -c "dropdb "$DBNAME"" || true
sudo -u postgres -i sh -c "createdb "$DBNAME" ag_gen"
psql -q "$DBNAME" < schema.sql
else
echo "Database ${DBNAME} does not exist. Creating and importing from dump."
sudo -u postgres -i sh -c "createdb "$DBNAME" ag_gen"
psql -q "$DBNAME" < schema.sql
fi
#sudo -u postgres -i sh -c "dropdb ag_gen" || true
#sudo -u postgres -i sh -c "createdb ag_gen ag_gen"
#psql ag_gen < schema.sql
#./ag_gen -n ../car_examples/generic_timeline_maintenance.nm -x ../car_examples/tmp.xp -g DOTFILE.dot -t 1 -q 1
#./ag_gen -n ../car_examples/generic_maintenance.nm -x ../car_examples/generic_maintenance.xp -g DOTFILE.dot -t 1 -q 1
./ag_gen -n ../fpga_examples/Network_1/car_network1.nm -x ../fpga_examples/Network_1/car_network1.xp -g DOTFILE.dot -t 1 -q 1 -p -a .20
./ag_gen -n ../fpga_examples/Network_1/car_network1.nm -x ../fpga_examples/Network_1/car_network1.xp -g DOTFILE.dot -t 1 -q 1 -p -a .20 -m 1 -z "$DBNAME"
#./ag_gen -n ../car_examples/generic_timeline_maintenance.nm -x ../car_examples/sync_timeline_maintenance.xp -g DOTFILE.dot -t 1 -q 1
# python3 ../tools/color_code.py ../build/states.txt DOTFILE.dot new.dot

69
src/main.cpp
View File

@ -25,6 +25,10 @@
#include <boost/graph/visitors.hpp>
#include <boost/graph/depth_first_search.hpp>
#include <boost/mpi.hpp>
#include <boost/mpi/environment.hpp>
#include <boost/mpi/communicator.hpp>
#include "ag_gen/ag_gen.h"
#include "util/db_functions.h"
#include "util/build_sql.h"
@ -38,6 +42,9 @@
#include "util/redis_manager.h"
#endif // REDIS
namespace mpi = boost::mpi;
template<typename GraphEdge>
class ag_visitor : public boost::default_dfs_visitor {
std::vector<std::pair<GraphEdge, int>> &to_delete;
@ -411,11 +418,13 @@ const std::string read_file(const std::string &fn) {
// and error if an unknown flag is provided. It then uses the database given in
// the "config.txt" file to generate an attack graph.
int main(int argc, char *argv[]) {
//------------------------------
//Program block 1: initialization and database connection
//------------------------------
//int thread_count=strtol(argv[5],NULL,10);
//int init_qsize=strtol(argv[6],NULL,10);
struct timeval ts1,tf1,ts2,tf2,ts3,tf3;
gettimeofday(&ts1,NULL);
if (argc < 2) {
@ -429,8 +438,11 @@ int main(int argc, char *argv[]) {
std::string opt_config;
std::string opt_graph;
std::string opt_batch;
std::string db_name = "ag_gen";
int thread_count;
int init_qsize;
int mpi_nodes;
bool should_graph = false;
bool no_cycles = false;
@ -441,7 +453,7 @@ int main(int argc, char *argv[]) {
double alpha = 0.5;
int opt;
while ((opt = getopt(argc, argv, "rb:g:dhc:n:x:t:q:pa:")) != -1) {
while ((opt = getopt(argc, argv, "rb:g:dhc:n:x:t:q:pa:m:z:")) != -1) {
switch (opt) {
case 'g':
should_graph = true;
@ -482,6 +494,12 @@ int main(int argc, char *argv[]) {
//Save a 10% buffer for PSQL ops
alpha = atof(optarg) - 0.1;
break;
case 'm':
mpi_nodes = atoi(optarg);
break;
case 'z':
db_name = optarg;
break;
case '?':
if (optopt == 'c')
fprintf(stderr, "Option -%c requires an argument.\n", optopt);
@ -495,6 +513,35 @@ int main(int argc, char *argv[]) {
exit(EXIT_FAILURE);
}
}
std::cout << "Arguments parsed." << std::endl;
/*
// Initialize the MPI environment
MPI_Init(NULL, NULL);
// Get the number of processes
MPI_Comm_size(MPI_COMM_WORLD, &mpi_nodes);
// Get the rank of the process
int world_rank;
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
// Get the name of the processor
char processor_name[MPI_MAX_PROCESSOR_NAME];
int name_len;
MPI_Get_processor_name(processor_name, &name_len);
// Print off a hello world message
printf("Hello from processor %s, rank %d out of %d processors\n",
processor_name, world_rank, mpi_nodes);
*/
mpi::environment env;
mpi::communicator world;
std::cout << "\nHello from process " << world.rank() << " of " << world.size()
<< "." << std::endl;
if(world.rank() == 0){
printf("Finished init\n");
std::string config_section = (opt_config.empty()) ? "default" : opt_config;
@ -515,6 +562,11 @@ int main(int argc, char *argv[]) {
std::cout<<username<<std::endl;
std::cout<<password<<std::endl;
//init_db("postgresql://" + username + ":" + password + "@" + host + ":" + port + "/" + dbName); //only to connect to the db, not query or update yet!!!
if(db_name != "ag_gen"){
std::cout << "\nThe given database differs from that specified in the config file. Overriding config database name." << std::endl;
init_db("dbname="+db_name+" user="+username+" host="+host+" port="+port+" password="+password);
}
else
init_db("dbname="+dbName+" user="+username+" host="+host+" port="+port+" password="+password);
gettimeofday(&tf2,NULL);
double tdiff2=(tf2.tv_sec-ts1.tv_sec)*1000.0+(tf2.tv_usec-ts1.tv_usec)/1000.0;
@ -524,13 +576,12 @@ int main(int argc, char *argv[]) {
}
else
{
std::cout << "Error: Not yet implemented. Database must be used.\
Please use the '-p' argument when running this program." << std::endl;
return(1);
}
}
//--------------------------------------------
//program block 2: read in network model and exploit pattern and store them in local database
//--------------------------------------------
@ -558,6 +609,8 @@ int main(int argc, char *argv[]) {
}
parsedxp = parse_xp(opt_xp);
}
printf("\n");
printf("=====parsed nm=====\n");
std::cout << parsednm <<"\n";
@ -568,7 +621,7 @@ int main(int argc, char *argv[]) {
if (batch_process)
batch_size = std::stoi(opt_batch);
if (use_postgres) {
if (use_postgres && world.rank() == 0) {
std::cout << "Importing Models and Exploits into Database: ";
import_models(parsednm, parsedxp); //directly use the strings parsednm and parsedxp as SQL commands
gettimeofday(&tf3,NULL);
@ -578,11 +631,6 @@ int main(int argc, char *argv[]) {
printf("\n");
}
else
{
std::cout << "Importing into Mock" << std::endl;
}
//------------------------------------------
//program block 3:
//------------------------------------------
@ -633,7 +681,7 @@ int main(int argc, char *argv[]) {
postinstance = gen.generate(batch_process, batch_size, thread_count, init_qsize, alpha); //The method call to generate the attack graph, defined in ag_gen.cpp.
//Serialization Unit Testing on Postinstance Data
serialization_unit_testing(postinstance);
serialization_unit_testing(postinstance, world);
std::cout << "Done\n";
@ -702,3 +750,4 @@ int main(int argc, char *argv[]) {
printf("%lf\n",tdiff4);
*/
}

208
src/mpi/serialize.cpp
View File

@ -35,8 +35,14 @@
#include <boost/serialization/assume_abstract.hpp>
#include <boost/serialization/string.hpp>
#include <boost/mpi.hpp>
#include <boost/mpi/environment.hpp>
#include <boost/mpi/communicator.hpp>
#include <boost/serialization/is_bitwise_serializable.hpp>
namespace mpi = boost::mpi;
void save_quality(const Quality &q, const char * filename){
std::ofstream ofs(filename);
@ -175,10 +181,12 @@ int network_state_check(NetworkState &ns1, NetworkState &ns2){
}
void serialization_unit_testing(AGGenInstance &instance){
void serialization_unit_testing(AGGenInstance &instance, boost::mpi::communicator &world){
if(world.rank() == 0){
printf("\n");
std::cout << "---------STARTING SERIALIZATION UNIT TESTING---------" << std::endl;
}
std::string filename(boost::archive::tmpdir());
filename += "/qualfile.txt";
@ -196,79 +204,210 @@ void serialization_unit_testing(AGGenInstance &instance){
int ns_count = 0;
int ns_corr = 0;
if(world.rank() == 0){
std::cout << "Performing Unit Testing on Quality Serialization." << std::endl;
}
for (auto qual : instance.initial_qualities)
{
//std::cout << "Orginial Quality:" << std::endl;
//qual.print();
//printf("\n");
save_quality(qual, filename.c_str());
//Send Qualities
if(world.rank() == 0){
//Can't use broadcast, since it doesn't send to self.
if(world.size() == 1)
world.isend(0, 0, qual);
else
broadcast(world, qual, 0);
//save_quality(qual, filename.c_str());
}
//Receive Qualities
if(world.rank() > 0 || world.size() == 1){
Quality new_qual;
restore_quality(new_qual, filename.c_str());
mpi::request req;
//std::cout << "Quality after restoring from serialization:" << std::endl;
req = world.irecv(mpi::any_source, mpi::any_tag,new_qual);
do {
boost::optional<mpi::status> stat = req.test();
if(stat){
//std::cout << "New message from " << stat->source() << ":"<< std::endl;
//new_qual.print();
//std::cout << "-------------------------------------------" << std::endl;
//printf("\n");
break;
}
} while(1);
//restore_quality(new_qual, filename.c_str());
qual_count++;
qual_corr += quality_check(qual, new_qual);
}
std::cout << "Quality Unit Testing: " << std::to_string(qual_corr) << "/" << std::to_string(qual_count) << std::endl;
}
int total_qual_corr;
if (world.rank() == 0 && world.size() == 1){
total_qual_corr = qual_corr;
}
if (world.rank() == 0 && world.size() > 1){
reduce(world, qual_corr, total_qual_corr, std::plus<int>(), 0);
}
else if (world.rank() > 0 && world.size() > 1){
reduce(world, qual_corr, std::plus<int>(), 0);
}
if (world.rank() == 0){
std::cout << "Quality Unit Testing: " << std::to_string(total_qual_corr) << "/" << std::to_string(world.size() * qual_count) << std::endl;
printf("\n");
std::cout << "Performing Unit Testing on Topology Serialization." << std::endl;
}
for (auto topo : instance.initial_topologies)
{
//std::cout << "Original Topology: " << std::endl;
//topo.print();
save_topology(topo, filename.c_str());
//Send Topologies
if(world.rank() == 0){
//Can't use broadcast, since it doesn't send to self.
if(world.size() == 1)
world.isend(0, 0, topo);
else
broadcast(world, topo, 0);
//save_quality(qual, filename.c_str());
}
//Receive Topologies
if(world.rank() > 0 || world.size() == 1){
Topology new_top;
restore_topology(new_top, filename.c_str());
mpi::request req;
//std::cout << "Topology after restoring from serialization:" << std::endl;
//new_top.print();
//std::cout << "-------------------------------------------" << std::endl;
//printf("\n");
req = world.irecv(mpi::any_source, mpi::any_tag, new_top);
do {
boost::optional<mpi::status> stat = req.test();
if(stat){
break;
}
} while(1);
//restore_topology(new_top, filename.c_str());
top_count++;
top_corr += topology_check(topo, new_top);
}
std::cout << "Topology Unit Testing: " << std::to_string(top_corr) << "/" << std::to_string(top_count) << std::endl;
}
int total_top_corr;
if(world.rank() ==0 && world.size() == 1){
total_top_corr = top_corr;
}
if (world.rank() == 0 && world.size() > 1){
reduce(world, top_corr, total_top_corr, std::plus<int>(), 0);
}
else if (world.rank() > 0 && world.size() > 1){
reduce(world, top_corr, std::plus<int>(), 0);
}
if (world.rank() == 0){
std::cout << "Topology Unit Testing: " << std::to_string(total_top_corr) << "/" << std::to_string(world.size() * top_count) << std::endl;
printf("\n");
std::cout << "Performing Unit Testing on Factbase Serialization." << std::endl;
}
for (auto fb : instance.factbases)
{
save_factbase(fb, filename.c_str());
//Send Factbases
if(world.rank() == 0){
//Can't use broadcast, since it doesn't send to self.
if(world.size() == 1)
world.isend(0, 0, fb);
else
broadcast(world, fb, 0);
}
//Receive Factbases
if(world.rank() > 0 || world.size() == 1){
Factbase new_fb;
restore_factbase(new_fb, filename.c_str());
mpi::request req;
req = world.irecv(mpi::any_source, mpi::any_tag, new_fb);
do {
boost::optional<mpi::status> stat = req.test();
if(stat){
break;
}
} while(1);
fb_count++;
fb_corr += factbase_check(fb, new_fb);
}
}
std::cout << "Factbase Unit Testing: " << std::to_string(fb_corr) << "/" << std::to_string(fb_count) << std::endl;
int total_fb_corr;
if(world.rank() ==0 && world.size() == 1){
total_fb_corr = fb_corr;
}
if (world.rank() == 0 && world.size() > 1){
reduce(world, fb_corr, total_fb_corr, std::plus<int>(), 0);
}
else if (world.rank() > 0 && world.size() > 1){
reduce(world, fb_corr, std::plus<int>(), 0);
}
if (world.rank() == 0){
std::cout << "Factbase Unit Testing: " << std::to_string(total_fb_corr) << "/" << std::to_string(world.size() * fb_count) << std::endl;
printf("\n");
std::cout << "Performing Unit Testing on Network State Serialization." << std::endl;
save_network_state(init_state, filename.c_str());
}
//Send Network State
if(world.rank() == 0){
//Can't use broadcast, since it doesn't send to self.
if(world.size() == 1)
world.isend(0, 0, init_state);
else
broadcast(world, init_state, 0);
}
//Receive Network State
if(world.rank() > 0 || world.size() == 1){
NetworkState new_ns;
restore_network_state(new_ns, filename.c_str());
mpi::request req;
req = world.irecv(mpi::any_source, mpi::any_tag, new_ns);
do {
boost::optional<mpi::status> stat = req.test();
if(stat){
break;
}
} while(1);
ns_count++;
ns_corr += network_state_check(init_state, new_ns);
}
std::cout << "Network State Unit Testing: " << std::to_string(ns_corr) << "/" << std::to_string(ns_count) << std::endl;
int total_ns_corr;
if(world.rank() ==0 && world.size() == 1){
total_ns_corr = ns_corr;
}
if (world.rank() == 0 && world.size() > 1){
reduce(world, ns_corr, total_ns_corr, std::plus<int>(), 0);
}
else if (world.rank() > 0 && world.size() > 1){
reduce(world, ns_corr, std::plus<int>(), 0);
}
if (world.rank() == 0){
std::cout << "Network State Unit Testing: " << std::to_string(total_ns_corr) << "/" << std::to_string(world.size() * ns_count) << std::endl;
printf("\n");
}
if(qual_corr == qual_count)
if(world.rank() == 0){
if(total_qual_corr == world.size() * qual_count)
{
std::cout << "100% Success Rate for Quality Serialization." << std::endl;
}
@ -278,7 +417,7 @@ void serialization_unit_testing(AGGenInstance &instance){
}
if(top_corr == top_count)
if(total_top_corr == world.size() * top_count)
{
std::cout << "100% Success Rate for Topology Serialization." << std::endl;
}
@ -287,7 +426,7 @@ void serialization_unit_testing(AGGenInstance &instance){
e_flag = 1;
}
if(fb_corr == fb_count)
if(total_fb_corr == world.size() * fb_count)
{
std::cout << "100% Success Rate for Factbase Serialization." << std::endl;
}
@ -296,7 +435,7 @@ void serialization_unit_testing(AGGenInstance &instance){
e_flag = 1;
}
if(ns_corr == ns_count)
if(total_ns_corr == world.size() * ns_count)
{
std::cout << "100% Success Rate for Network State Serialization." << std::endl;
}
@ -310,6 +449,9 @@ void serialization_unit_testing(AGGenInstance &instance){
std::cout << "-------------ERRORS OCCURRED DURING SERIALIZATION UNIT TESTING---------------" << std::endl;
std::cout << "---------FINISHED SERIALIZATION UNIT TESTING---------" << std::endl;
printf("\n");
}
//MPI Clean-up
//MPI_Finalize();
return;
}

2
src/mpi/serialize.h
View File

@ -9,7 +9,7 @@ void save_topology(const Topology &t, const char * filename);
void restore_topology(Topology &t, const char * filename);
int topology_check(Topology &t1, Topology &t2);
void serialization_unit_testing(AGGenInstance &instance);
void serialization_unit_testing(AGGenInstance &instance, boost::mpi::communicator &world);
#endif //SERIALIZE_H