Finalized MPI Subgraphing and Data Collection Script Updates
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"command": "/usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -pthread -o CMakeFiles/ag_gen.dir/src/util/str_array.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/str_array.c\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/str_array.c"
|
||||
"directory": "/home/nschrick/ag_parallel/build",
|
||||
"command": "/opt/apps/gcc/8.2.0/bin/gcc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -I/usr/include/postgresql -I/home/nschrick/ag_parallel/src -isystem /home/nschrick/pkg/boost/1.77.0/include -isystem /storage/home/nschrick/pkg/openmpi/4.1.2/include -isystem /home/nschrick/pkg/openmpi/4.1.2/include -g -pthread -o CMakeFiles/ag_gen.dir/src/util/str_array.c.o -c /home/nschrick/ag_parallel/src/util/str_array.c",
|
||||
"file": "/home/nschrick/ag_parallel/src/util/str_array.c"
|
||||
},
|
||||
{
|
||||
"directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build",
|
||||
"command": "/usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -pthread -o CMakeFiles/ag_gen.dir/src/util/vector.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/vector.c\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/vector.c"
|
||||
"directory": "/home/nschrick/ag_parallel/build",
|
||||
"command": "/opt/apps/gcc/8.2.0/bin/gcc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -I/usr/include/postgresql -I/home/nschrick/ag_parallel/src -isystem /home/nschrick/pkg/boost/1.77.0/include -isystem /storage/home/nschrick/pkg/openmpi/4.1.2/include -isystem /home/nschrick/pkg/openmpi/4.1.2/include -g -pthread -o CMakeFiles/ag_gen.dir/src/util/vector.c.o -c /home/nschrick/ag_parallel/src/util/vector.c",
|
||||
"file": "/home/nschrick/ag_parallel/src/util/vector.c"
|
||||
},
|
||||
{
|
||||
"directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build",
|
||||
"command": "/usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -std=c++14 -fopenmp -DREDIS -g -g -O0 -ggdb -Wall -fopenmp -pedantic -pthread -o CMakeFiles/ag_gen.dir/src/mpi/serialize.cpp.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/serialize.cpp\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/serialize.cpp"
|
||||
"directory": "/home/nschrick/ag_parallel/build",
|
||||
"command": "/opt/apps/gcc/8.2.0/bin/g++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -I/usr/include/postgresql -I/home/nschrick/ag_parallel/src -isystem /home/nschrick/pkg/boost/1.77.0/include -isystem /storage/home/nschrick/pkg/openmpi/4.1.2/include -isystem /home/nschrick/pkg/openmpi/4.1.2/include -std=c++14 -fopenmp -g -g -O0 -ggdb -Wall -fopenmp -pedantic -pthread -o CMakeFiles/ag_gen.dir/src/mpi/serialize.cpp.o -c /home/nschrick/ag_parallel/src/mpi/serialize.cpp",
|
||||
"file": "/home/nschrick/ag_parallel/src/mpi/serialize.cpp"
|
||||
},
|
||||
{
|
||||
"directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build",
|
||||
"command": "/usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -std=c++14 -fopenmp -DREDIS -g -g -O0 -ggdb -Wall -fopenmp -pedantic -pthread -o CMakeFiles/ag_gen.dir/src/mpi/tasks.cpp.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/tasks.cpp\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/tasks.cpp"
|
||||
},
|
||||
{
|
||||
"directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build",
|
||||
"command": "/usr/bin/cc -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -o CMakeFiles/dynstr_test.dir/src/util/mem.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/mem.c\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/mem.c"
|
||||
},
|
||||
{
|
||||
"directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build",
|
||||
"command": "/usr/bin/cc -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -o CMakeFiles/dynstr_test.dir/src/tests/mem_test.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/tests/mem_test.c\"",
|
||||
"file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/tests/mem_test.c"
|
||||
"directory": "/home/nschrick/ag_parallel/build",
|
||||
"command": "/opt/apps/gcc/8.2.0/bin/g++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -I/usr/include/postgresql -I/home/nschrick/ag_parallel/src -isystem /home/nschrick/pkg/boost/1.77.0/include -isystem /storage/home/nschrick/pkg/openmpi/4.1.2/include -isystem /home/nschrick/pkg/openmpi/4.1.2/include -std=c++14 -fopenmp -g -g -O0 -ggdb -Wall -fopenmp -pedantic -pthread -o CMakeFiles/ag_gen.dir/src/mpi/tasks.cpp.o -c /home/nschrick/ag_parallel/src/mpi/tasks.cpp",
|
||||
"file": "/home/nschrick/ag_parallel/src/mpi/tasks.cpp"
|
||||
}
|
||||
]
|
||||
12194
build/states.txt
12194
build/states.txt
File diff suppressed because it is too large
Load Diff
@ -19,30 +19,39 @@ TIMESTR=`date +"%s"`
|
||||
DBNAME="${folder}_${TIMESTR}"
|
||||
#nodelist=compute01,compute04,compute07,compute10,compute11,compute12
|
||||
NODES=(2 3 4 5 6 7 8 9 10 11 12)
|
||||
MPI_TYPE="serial"
|
||||
|
||||
pwd=`pwd`
|
||||
#one=1
|
||||
#4,8,16,32 thr
|
||||
thrds=(4 8 16 32)
|
||||
|
||||
if [[ "$folder" == serial || "$folder" == serialnosync || "$folder" == mpitasking || "$folder" == mpisubgraphing ]]; then
|
||||
if [[ "$folder" == "serial" || "$folder" == "serialnosync" || "$folder" == "mpitasking" || "$folder" == "mpisubgraphing" ]]; then
|
||||
thrds=(1)
|
||||
else
|
||||
thrds=(4 8 16 32)
|
||||
fi
|
||||
|
||||
if [[ "$folder" != mpisubgraphing || "$folder" != mpitasking ]]; then
|
||||
if [[ "$folder" != "mpisubgraphing" || "$folder" != "mpitasking" ]]; then
|
||||
NODES=(1)
|
||||
fi
|
||||
|
||||
if [[ "$folder" == "mpisubgraphing" ]]; then
|
||||
MPI_TYPE="subgraphing"
|
||||
elif [[ "$folder" == "mpitasking" ]]; then
|
||||
MPI_TYPE="tasking"
|
||||
else
|
||||
MPI_TYPE="serial"
|
||||
fi
|
||||
|
||||
QSIZE=1
|
||||
SKIPSYNC=false
|
||||
|
||||
if [[ "$folder" == serialnosync ]]; then
|
||||
if [[ "$folder" == "serialnosync" ]]; then
|
||||
SKIPSYNC=true
|
||||
fi
|
||||
|
||||
if [[ "$folder" == ompnosync ]]; then
|
||||
if [[ "$folder" == "ompnosync" ]]; then
|
||||
SKIPSYNC=true
|
||||
fi
|
||||
|
||||
@ -50,17 +59,17 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
|
||||
for thrd in "${thrds[@]}"
|
||||
do
|
||||
if [[ "$folder" == serial ]]; then
|
||||
if [[ "$folder" == "serial" ]]; then
|
||||
thrd=1
|
||||
nodelist=compute05
|
||||
fi
|
||||
|
||||
if [[ "$folder" == serialnosync ]]; then
|
||||
if [[ "$folder" == "serialnosync" ]]; then
|
||||
thrd=1
|
||||
nodelist=compute07
|
||||
fi
|
||||
|
||||
if [[ "$folder" == ompnosync ]]; then
|
||||
if [[ "$folder" == "ompnosync" ]]; then
|
||||
nodelist=compute08
|
||||
fi
|
||||
|
||||
@ -72,7 +81,7 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
QSIZE=$((thrd*qmult))
|
||||
fi
|
||||
|
||||
if [[ "$folder" == serial ]]; then
|
||||
if [[ "$folder" == "serial" ]]; then
|
||||
QSIZE=1
|
||||
fi
|
||||
|
||||
@ -82,13 +91,13 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
|
||||
echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/sync_data.txt
|
||||
#1..4 (or 1..10)Services
|
||||
for i in {1..6}
|
||||
for i in {1..4}
|
||||
do
|
||||
for node in "${NODES[@]}"
|
||||
do
|
||||
SKIP_FLAG=0
|
||||
#Dispatch the job and get the output ("Submitted batch job <jobid>
|
||||
JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "sync" "$cars" "$DBNAME" "$thrd" "$node" "tasking"`
|
||||
JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "sync" "$cars" "$DBNAME" "$thrd" "$node" "$MPI_TYPE"`
|
||||
#Pull the jobid
|
||||
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`
|
||||
|
||||
@ -129,11 +138,11 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
#Get runtime and states from the output
|
||||
#RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'`
|
||||
RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'`
|
||||
|
||||
DUP=`cat "$FILE" | grep -oP '(?<=Duplicated States that had to be removed: )[^ ]*'`
|
||||
STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'`
|
||||
|
||||
if ! test -s "$ERR" || test "$SKIP_FLAG" -eq 1 ; then
|
||||
printf "${i} Services Synchronized: ${STATES} states and ${RUNTIME} runtime \n\n" >> ./slurm_reports/"$folder"/sync_data.txt
|
||||
printf "${i} Services Synchronized: ${STATES} states ${RUNTIME} runtime and ${DUP} duplicate states \n\n" >> ./slurm_reports/"$folder"/sync_data.txt
|
||||
str="$i","$STATES","$RUNTIME"
|
||||
echo $str >> ./slurm_reports/"$folder"/sync_data.csv
|
||||
else
|
||||
@ -186,13 +195,13 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
|
||||
echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/non-sync_data.txt
|
||||
#1..4 (or 1..10)Services
|
||||
for i in {1..6}
|
||||
for i in {1..4}
|
||||
do
|
||||
for node in "${NODES[@]}"
|
||||
do
|
||||
SKIP_FLAG=0
|
||||
#Dispatch the job and get the output ("Submitted batch job <jobid>
|
||||
JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "non-sync" "$cars" "$DBNAME" "$thrd" "$node" "tasking"`
|
||||
JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "non-sync" "$cars" "$DBNAME" "$thrd" "$node" "$MPI_TYPE"`
|
||||
#Pull the jobid
|
||||
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`
|
||||
|
||||
@ -233,11 +242,11 @@ if [[ "$SKIPSYNC" == false ]]; then
|
||||
#Get runtime and states from the output
|
||||
#RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'`
|
||||
RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'`
|
||||
|
||||
DUP=`cat "$FILE" | grep -oP '(?<=Duplicated States that had to be removed: )[^ ]*'`
|
||||
STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'`
|
||||
|
||||
if ! test -s "$ERR" || test "$SKIP_FLAG" -eq 1 ; then
|
||||
printf "${i} Services Non-Synchronized: ${STATES} states and ${RUNTIME} runtime \n\n" >> ./slurm_reports/"$folder"/non-sync_data.txt
|
||||
printf "${i} Services Non-Synchronized: ${STATES} states ${RUNTIME} runtime and ${DUP} duplicate states \n\n" >> ./slurm_reports/"$folder"/non-sync_data.txt
|
||||
str="$i","$STATES","$RUNTIME"
|
||||
echo $str >> ./slurm_reports/"$folder"/non-sync_data.csv
|
||||
else
|
||||
|
||||
@ -92,6 +92,7 @@ AGGen::AGGen(AGGenInstance &_instance) : instance(_instance) {
|
||||
hash_map.insert(std::make_pair(init_state.get_hash(instance.facts), init_id));
|
||||
frontier.push_back(init_state);
|
||||
use_redis = false;
|
||||
instance.duplicates = 0;
|
||||
}
|
||||
|
||||
/**
|
||||
@ -1337,15 +1338,15 @@ int initQSize, double mem_threshold, mpi::communicator &world, int state_limit)
|
||||
|
||||
localFrontier.emplace_front(new_state);
|
||||
//Edge ed(current_state.get_id(), new_state.get_id(), exploit, assetGroup);
|
||||
Edge ed(current_state.get_hash(instance.facts), new_state.get_hash(instance.facts), exploit, assetGroup);
|
||||
Edge ed(current_hash, hash_num, exploit, assetGroup);
|
||||
ed.set_id();
|
||||
instance.edges.push_back(ed);
|
||||
} //END if (hash_map.find(hash_num) == hash_map.end())
|
||||
|
||||
else {
|
||||
auto id = hash_map[hash_num];
|
||||
//auto id = hash_map[hash_num];
|
||||
//Edge ed(current_state.get_id(), id, exploit, assetGroup);
|
||||
Edge ed(current_state.get_hash(instance.facts), hash_num, exploit, assetGroup);
|
||||
Edge ed(current_hash, hash_num, exploit, assetGroup);
|
||||
ed.set_id();
|
||||
instance.edges.push_back(ed);
|
||||
}
|
||||
@ -1610,9 +1611,7 @@ int initQSize, double mem_threshold, mpi::communicator &world, int state_limit)
|
||||
gettimeofday(&t2,NULL);
|
||||
total_t+=(t2.tv_sec-t1.tv_sec)*1000.0+(t2.tv_usec-t1.tv_usec)/1000.0;
|
||||
printf("AG TOOK %lf ms.\n", total_t);
|
||||
std::cout << "Instance Edges before adjustment: " << instance.edges.size() << std::endl;
|
||||
edge_adjustment(instance, hash_map);
|
||||
std::cout << "Instance Edges after adjustment: " << instance.edges.size() << std::endl;
|
||||
auto end = std::chrono::system_clock::now();
|
||||
|
||||
std::chrono::duration<double> elapsed_seconds = end - start;
|
||||
|
||||
@ -62,6 +62,7 @@ struct AGGenInstance {
|
||||
std::vector<Exploit> exploits; //init
|
||||
std::vector<Edge> edges;
|
||||
Keyvalue facts; //init
|
||||
unsigned long duplicates;
|
||||
|
||||
std::chrono::duration<double> elapsed_seconds;
|
||||
};
|
||||
|
||||
@ -121,8 +121,13 @@ bool Edge::operator==(const Edge& ed2)
|
||||
{
|
||||
if(get_to_id() == ed2.get_to_id() &&
|
||||
get_from_id() == ed2.get_from_id() &&
|
||||
get_id() == ed2.get_id()){
|
||||
get_exploit_id() == ed2.get_exploit_id()){
|
||||
return true;
|
||||
}
|
||||
else return false;
|
||||
}
|
||||
|
||||
void Edge::force_set_id(int i)
|
||||
{
|
||||
id = i;
|
||||
}
|
||||
|
||||
@ -63,7 +63,7 @@ class Edge {
|
||||
bool is_deleted();
|
||||
bool comparator(Edge& ed2);
|
||||
bool operator==(const Edge& ed2);
|
||||
|
||||
void force_set_id(int i);
|
||||
};
|
||||
|
||||
#endif // AG_GEN_EDGE_H
|
||||
|
||||
@ -713,12 +713,12 @@ int main(int argc, char *argv[]) {
|
||||
std::cout << "Finished generation." << std::endl;
|
||||
std::cout << "Saving to Database." << std::endl;
|
||||
save_ag_to_db(postinstance, true);
|
||||
//std::cout << "PostInstance states: " << postinstance.factbases.size() << std::endl;
|
||||
|
||||
std::cout << "Total Edges: " << get_num_edges() << std::endl;
|
||||
std::cout << "Total Time: " << postinstance.elapsed_seconds.count() << " seconds\n";
|
||||
//std::cout << "Total States: " << postinstance.factbases.size() << "\n";
|
||||
std::cout << "Total States: " << get_num_states() << std::endl;
|
||||
std::cout << "Duplicated States that had to be removed: " << postinstance.duplicates << std::endl;
|
||||
std::cout << "Saving Attack Graph to Database: " << std::flush;
|
||||
std::cout << "Done\n";
|
||||
|
||||
|
||||
@ -550,18 +550,22 @@ void state_merge(std::vector<Factbase> &node_factbases, std::vector<Edge> &node_
|
||||
i_alpha = i_usage/tot_sys_mem;
|
||||
}
|
||||
}
|
||||
else{
|
||||
instance.duplicates++;
|
||||
}
|
||||
}
|
||||
|
||||
//Note: This does add duplicates. Having one duplicate removal sweep at the end is preferable to duplicate checking
|
||||
//every time we want to push new edges back on the frontier.
|
||||
for (auto &ed : node_edges){
|
||||
instance.edges.push_back(ed);
|
||||
}
|
||||
//every time we want to push new edges back on the frontier - verified through timing for both small and large networks.
|
||||
instance.edges.insert(std::end(instance.edges), std::begin(node_edges), std::end(node_edges));
|
||||
|
||||
}
|
||||
|
||||
//Convert Edge to_hash and from_hash to to_id and from_id
|
||||
void edge_adjustment(AGGenInstance &instance, std::unordered_map<size_t, int> &hash_map)
|
||||
{
|
||||
|
||||
// 2 Loops: Can't convert hash->ID while simultaneously checking for duplicates
|
||||
for (auto &ed : instance.edges){
|
||||
auto itr = hash_map.find(ed.get_to_id());
|
||||
if(itr != hash_map.end()){
|
||||
@ -577,7 +581,28 @@ void edge_adjustment(AGGenInstance &instance, std::unordered_map<size_t, int> &h
|
||||
}
|
||||
|
||||
//Remove duplicates
|
||||
//instance.edges.erase(unique(instance.edges.begin(), instance.edges.end(), [](Edge& ed1, Edge& ed2){return ed1.comparator(ed2);}), instance.edges.end());
|
||||
instance.edges.erase(unique(instance.edges.begin(), instance.edges.end()), instance.edges.end());
|
||||
//Poor Approach, but functional. Examine replacing instance.edges with a set instead of a vector
|
||||
|
||||
//Tmp Vector
|
||||
std::vector<Edge> clean;
|
||||
int i = instance.edges.size() + get_num_edges();
|
||||
for(auto itr = instance.edges.begin(); itr != instance.edges.end();){
|
||||
int seen = 0;
|
||||
for(auto eitr = clean.begin(); eitr != clean.end(); eitr++){
|
||||
if((*eitr).operator==(*itr)){
|
||||
seen = 1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if(seen == 1){
|
||||
//Remove duplicate
|
||||
itr = instance.edges.erase(itr);
|
||||
}
|
||||
else{
|
||||
clean.push_back(*itr);
|
||||
(*itr).force_set_id(i);
|
||||
i++;
|
||||
itr++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user