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Finalized MPI Subgraphing and Data Collection Script Updates

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hammer 2022-02-18 12:45:24 -06:00
parent 831c80e74e
commit 83687f097c
12 changed files with 6256 additions and 6285 deletions
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74
build/Makefile
View File

@ -48,19 +48,19 @@ cmake_force:
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BIN
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Binary file not shown.

4
build/ag_run.sh
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@ -19,8 +19,8 @@ TYPE=${2:-sync}
CARS=${3:-2} CARS=${3:-2}
DBNAME=${4:-tmp} DBNAME=${4:-tmp}
NUM_THREADS=${5:-1} NUM_THREADS=${5:-1}
NODES=${6:-1} NODES=${6:-12}
MPI_TYPE=${7:-def} MPI_TYPE=${7:-subgraphing}
module load graphviz module load graphviz

166
build/compile_commands.json
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@ -1,142 +1,132 @@
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"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\"", "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/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/tasks.cpp" "file": "/home/nschrick/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"
} }
] ]

12194
build/states.txt
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File diff suppressed because it is too large Load Diff

41
build/sync_data_col.sh
View File

@ -19,30 +19,39 @@ TIMESTR=`date +"%s"`
DBNAME="${folder}_${TIMESTR}" DBNAME="${folder}_${TIMESTR}"
#nodelist=compute01,compute04,compute07,compute10,compute11,compute12 #nodelist=compute01,compute04,compute07,compute10,compute11,compute12
NODES=(2 3 4 5 6 7 8 9 10 11 12) NODES=(2 3 4 5 6 7 8 9 10 11 12)
MPI_TYPE="serial"
pwd=`pwd` pwd=`pwd`
#one=1 #one=1
#4,8,16,32 thr #4,8,16,32 thr
thrds=(4 8 16 32) 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) thrds=(1)
else else
thrds=(4 8 16 32) thrds=(4 8 16 32)
fi fi
if [[ "$folder" != mpisubgraphing || "$folder" != mpitasking ]]; then if [[ "$folder" != "mpisubgraphing" || "$folder" != "mpitasking" ]]; then
NODES=(1) NODES=(1)
fi fi
if [[ "$folder" == "mpisubgraphing" ]]; then
MPI_TYPE="subgraphing"
elif [[ "$folder" == "mpitasking" ]]; then
MPI_TYPE="tasking"
else
MPI_TYPE="serial"
fi
QSIZE=1 QSIZE=1
SKIPSYNC=false SKIPSYNC=false
if [[ "$folder" == serialnosync ]]; then if [[ "$folder" == "serialnosync" ]]; then
SKIPSYNC=true SKIPSYNC=true
fi fi
if [[ "$folder" == ompnosync ]]; then if [[ "$folder" == "ompnosync" ]]; then
SKIPSYNC=true SKIPSYNC=true
fi fi
@ -50,17 +59,17 @@ if [[ "$SKIPSYNC" == false ]]; then
for thrd in "${thrds[@]}" for thrd in "${thrds[@]}"
do do
if [[ "$folder" == serial ]]; then if [[ "$folder" == "serial" ]]; then
thrd=1 thrd=1
nodelist=compute05 nodelist=compute05
fi fi
if [[ "$folder" == serialnosync ]]; then if [[ "$folder" == "serialnosync" ]]; then
thrd=1 thrd=1
nodelist=compute07 nodelist=compute07
fi fi
if [[ "$folder" == ompnosync ]]; then if [[ "$folder" == "ompnosync" ]]; then
nodelist=compute08 nodelist=compute08
fi fi
@ -72,7 +81,7 @@ if [[ "$SKIPSYNC" == false ]]; then
QSIZE=$((thrd*qmult)) QSIZE=$((thrd*qmult))
fi fi
if [[ "$folder" == serial ]]; then if [[ "$folder" == "serial" ]]; then
QSIZE=1 QSIZE=1
fi fi
@ -82,13 +91,13 @@ if [[ "$SKIPSYNC" == false ]]; then
echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/sync_data.txt echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/sync_data.txt
#1..4 (or 1..10)Services #1..4 (or 1..10)Services
for i in {1..6} for i in {1..4}
do do
for node in "${NODES[@]}" for node in "${NODES[@]}"
do do
SKIP_FLAG=0 SKIP_FLAG=0
#Dispatch the job and get the output ("Submitted batch job <jobid> #Dispatch the job and get the output ("Submitted batch job <jobid>
JOB=`sbatch --nodelist="$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 #Pull the jobid
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'` JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`
@ -129,11 +138,11 @@ if [[ "$SKIPSYNC" == false ]]; then
#Get runtime and states from the output #Get runtime and states from the output
#RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'` #RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'`
RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'` RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'`
DUP=`cat "$FILE" | grep -oP '(?<=Duplicated States that had to be removed: )[^ ]*'`
STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'` STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'`
if ! test -s "$ERR" || test "$SKIP_FLAG" -eq 1 ; then 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","$RUNTIME" str="$i","$STATES","$RUNTIME"
echo $str >> ./slurm_reports/"$folder"/sync_data.csv echo $str >> ./slurm_reports/"$folder"/sync_data.csv
else else
@ -186,13 +195,13 @@ if [[ "$SKIPSYNC" == false ]]; then
echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/non-sync_data.txt echo "----------------------------------- "$cars" cars -----------------------------------" >> ./slurm_reports/"$folder"/non-sync_data.txt
#1..4 (or 1..10)Services #1..4 (or 1..10)Services
for i in {1..6} for i in {1..4}
do do
for node in "${NODES[@]}" for node in "${NODES[@]}"
do do
SKIP_FLAG=0 SKIP_FLAG=0
#Dispatch the job and get the output ("Submitted batch job <jobid> #Dispatch the job and get the output ("Submitted batch job <jobid>
JOB=`sbatch --nodelist="$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 #Pull the jobid
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'` JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`
@ -233,11 +242,11 @@ if [[ "$SKIPSYNC" == false ]]; then
#Get runtime and states from the output #Get runtime and states from the output
#RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'` #RUNTIME=`cat "$FILE" | grep -oP '(?<=total run time is )[^ ]*'`
RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'` RUNTIME=`cat "$FILE" | grep -oP '(?<=AG TOOK )[^ ]*'`
DUP=`cat "$FILE" | grep -oP '(?<=Duplicated States that had to be removed: )[^ ]*'`
STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'` STATES=`cat "$FILE" | grep -oP '(?<=Total States: )[^ ]*'`
if ! test -s "$ERR" || test "$SKIP_FLAG" -eq 1 ; then 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","$RUNTIME" str="$i","$STATES","$RUNTIME"
echo $str >> ./slurm_reports/"$folder"/non-sync_data.csv echo $str >> ./slurm_reports/"$folder"/non-sync_data.csv
else else

9
src/ag_gen/ag_gen.cpp
View File

@ -92,6 +92,7 @@ AGGen::AGGen(AGGenInstance &_instance) : instance(_instance) {
hash_map.insert(std::make_pair(init_state.get_hash(instance.facts), init_id)); hash_map.insert(std::make_pair(init_state.get_hash(instance.facts), init_id));
frontier.push_back(init_state); frontier.push_back(init_state);
use_redis = false; 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); localFrontier.emplace_front(new_state);
//Edge ed(current_state.get_id(), new_state.get_id(), exploit, assetGroup); //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(); ed.set_id();
instance.edges.push_back(ed); instance.edges.push_back(ed);
} //END if (hash_map.find(hash_num) == hash_map.end()) } //END if (hash_map.find(hash_num) == hash_map.end())
else { 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_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(); ed.set_id();
instance.edges.push_back(ed); instance.edges.push_back(ed);
} }
@ -1610,9 +1611,7 @@ int initQSize, double mem_threshold, mpi::communicator &world, int state_limit)
gettimeofday(&t2,NULL); gettimeofday(&t2,NULL);
total_t+=(t2.tv_sec-t1.tv_sec)*1000.0+(t2.tv_usec-t1.tv_usec)/1000.0; 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); printf("AG TOOK %lf ms.\n", total_t);
std::cout << "Instance Edges before adjustment: " << instance.edges.size() << std::endl;
edge_adjustment(instance, hash_map); edge_adjustment(instance, hash_map);
std::cout << "Instance Edges after adjustment: " << instance.edges.size() << std::endl;
auto end = std::chrono::system_clock::now(); auto end = std::chrono::system_clock::now();
std::chrono::duration<double> elapsed_seconds = end - start; std::chrono::duration<double> elapsed_seconds = end - start;

1
src/ag_gen/ag_gen.h
View File

@ -62,6 +62,7 @@ struct AGGenInstance {
std::vector<Exploit> exploits; //init std::vector<Exploit> exploits; //init
std::vector<Edge> edges; std::vector<Edge> edges;
Keyvalue facts; //init Keyvalue facts; //init
unsigned long duplicates;
std::chrono::duration<double> elapsed_seconds; std::chrono::duration<double> elapsed_seconds;
}; };

7
src/ag_gen/edge.cpp
View File

@ -121,8 +121,13 @@ bool Edge::operator==(const Edge& ed2)
{ {
if(get_to_id() == ed2.get_to_id() && if(get_to_id() == ed2.get_to_id() &&
get_from_id() == ed2.get_from_id() && get_from_id() == ed2.get_from_id() &&
get_id() == ed2.get_id()){ get_exploit_id() == ed2.get_exploit_id()){
return true; return true;
} }
else return false; else return false;
} }
void Edge::force_set_id(int i)
{
id = i;
}

2
src/ag_gen/edge.h
View File

@ -63,7 +63,7 @@ class Edge {
bool is_deleted(); bool is_deleted();
bool comparator(Edge& ed2); bool comparator(Edge& ed2);
bool operator==(const Edge& ed2); bool operator==(const Edge& ed2);
void force_set_id(int i);
}; };
#endif // AG_GEN_EDGE_H #endif // AG_GEN_EDGE_H

2
src/main.cpp
View File

@ -713,12 +713,12 @@ int main(int argc, char *argv[]) {
std::cout << "Finished generation." << std::endl; std::cout << "Finished generation." << std::endl;
std::cout << "Saving to Database." << std::endl; std::cout << "Saving to Database." << std::endl;
save_ag_to_db(postinstance, true); 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 Edges: " << get_num_edges() << std::endl;
std::cout << "Total Time: " << postinstance.elapsed_seconds.count() << " seconds\n"; std::cout << "Total Time: " << postinstance.elapsed_seconds.count() << " seconds\n";
//std::cout << "Total States: " << postinstance.factbases.size() << "\n"; //std::cout << "Total States: " << postinstance.factbases.size() << "\n";
std::cout << "Total States: " << get_num_states() << std::endl; 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 << "Saving Attack Graph to Database: " << std::flush;
std::cout << "Done\n"; std::cout << "Done\n";

37
src/mpi/tasks.cpp
View File

@ -550,18 +550,22 @@ void state_merge(std::vector<Factbase> &node_factbases, std::vector<Edge> &node_
i_alpha = i_usage/tot_sys_mem; 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 //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. //every time we want to push new edges back on the frontier - verified through timing for both small and large networks.
for (auto &ed : node_edges){ instance.edges.insert(std::end(instance.edges), std::begin(node_edges), std::end(node_edges));
instance.edges.push_back(ed);
}
} }
//Convert Edge to_hash and from_hash to to_id and from_id //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) 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){ for (auto &ed : instance.edges){
auto itr = hash_map.find(ed.get_to_id()); auto itr = hash_map.find(ed.get_to_id());
if(itr != hash_map.end()){ if(itr != hash_map.end()){
@ -577,7 +581,28 @@ void edge_adjustment(AGGenInstance &instance, std::unordered_map<size_t, int> &h
} }
//Remove duplicates //Remove duplicates
//instance.edges.erase(unique(instance.edges.begin(), instance.edges.end(), [](Edge& ed1, Edge& ed2){return ed1.comparator(ed2);}), instance.edges.end()); //Poor Approach, but functional. Examine replacing instance.edges with a set instead of a vector
instance.edges.erase(unique(instance.edges.begin(), instance.edges.end()), instance.edges.end());
//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++;
}
}
} }