Subgraphing v1.1

This commit is contained in:
hammer 2022-02-07 22:25:19 -06:00
parent 851b032830
commit 0f8debb7aa
7 changed files with 3267 additions and 17360 deletions

View File

@ -48,19 +48,19 @@ cmake_force:
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@ -3,11 +3,12 @@
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#SBATCH --exclude=compute02,compute03,compute09 #SBATCH --exclude=compute02,compute03,compute09
#SBATCH --export=ALL #SBATCH --export=ALL
#SBATCH --nodelist=compute10,compute11,compute12
export LD_LIBRARY_PATH=/home/nschrick/pkg/postgresql/13.4/lib export LD_LIBRARY_PATH=/home/nschrick/pkg/postgresql/13.4/lib
MPICH_NEMESIS_NETMOD=ofi MPICH_NEMESIS_NETMOD=ofi
MPIEXEC_TIMEOUT=129600 MPIEXEC_TIMEOUT=129600

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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/serialize.cpp.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/serialize.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/serialize.cpp.o -c /home/nschrick/ag_parallel/src/mpi/serialize.cpp",
"file": "/home/noah/Documents/School/Thesis Work/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", "directory": "/home/nschrick/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\"", "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"
} }
] ]

View File

@ -57,7 +57,10 @@ if [ "$TYPE" == "$strval1" ]; then
if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then
mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Sync/6_Exploits/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -s -l 20 #4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Sync/4_Exploits/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -s -l 20
#6 Exploit Option
#mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Sync/6_Exploits/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -s -l 20
else else
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Sync/4_Exploits/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -s -l 20 -a 0.6 -g DOTFILE.dot -z "$DBNAME" mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Sync/4_Exploits/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -s -l 20 -a 0.6 -g DOTFILE.dot -z "$DBNAME"
fi fi

File diff suppressed because it is too large Load Diff

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@ -1246,6 +1246,8 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
int finished_signal = 0; int finished_signal = 0;
int send_msg = 0; int send_msg = 0;
int state_count = 0; int state_count = 0;
int first_loop = 1;
int msg_sends = 0;
std::random_device rd; // obtain a random number from hardware std::random_device rd; // obtain a random number from hardware
std::mt19937 gen(rd()); // seed the generator std::mt19937 gen(rd()); // seed the generator
@ -1259,25 +1261,33 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
if(world.rank() == 0){ if(world.rank() == 0){
//2 offset for root node and db node //2 offset for root node and db node
for (int w = 0; w < std::min((int)world.size()-2, (int)localFrontier.size()); w++){ for (int w = 0; w < std::min((int)world.size()-2, (int)localFrontier.size()); w++){
localFrontier.front().force_set_id(localFrontier.front().get_hash(instance.facts));
mpi::request state_req = world.isend(w+2, 1, localFrontier.front()); mpi::request state_req = world.isend(w+2, 1, localFrontier.front());
localFrontier.pop_front(); localFrontier.pop_front();
state_req.wait(); state_req.wait();
} msg_sends++;
std::cout << "Root has sent initial states as a total of " << msg_sends << " messages." << std::endl;
} }
//Main Work Loop std::cout << "World Size: " << world.size() << std::endl;
while((!localFrontier.empty() && !finished_signal) || world.rank() > 0){ }
//Main Work Loop - Just make this a do while instead of first_loop
while(!localFrontier.empty() || finished_signal == 0 || world.rank() > 0 || first_loop == 1){
first_loop = 0;
//Refill localFrontier if needed //Refill localFrontier if needed
if(localFrontier.empty() && world.rank() == 0) { if(localFrontier.empty() && world.rank() == 0) {
task_zero(instance, localFrontier, mem_threshold); task_zero(instance, localFrontier, mem_threshold);
} }
//Don't sync with db node //Don't sync with db node
work_comm.barrier(); //work_comm.barrier();
if (world.rank() > 1){ if (world.rank() > 1){
localFrontier.clear();
//Check for finished signal //Check for finished signal
if(world.iprobe(0, 99)){ if(world.iprobe(0, 99)){
std::cout << "Node " << world.rank() << " received finalize signal" << std::endl;
break; break;
} }
@ -1286,10 +1296,11 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
world.recv(0, 1, current_state); world.recv(0, 1, current_state);
state_count = 0; state_count = 0;
send_msg = 1; send_msg = 1;
localFrontier.emplace_front(current_state);
std::cout << "Node " << world.rank() << " received a new state to explore" << std::endl;
while(!localFrontier.empty()){ while(!localFrontier.empty()){
if (state_count < state_limit){ if (state_count < state_limit){
//Do work //Do work
//Force set NS id to hash
auto current_state = localFrontier.front(); auto current_state = localFrontier.front();
auto current_hash = current_state.get_hash(instance.facts); auto current_hash = current_state.get_hash(instance.facts);
@ -1482,7 +1493,6 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
hash_map.insert(std::make_pair(new_state.get_hash(instance.facts), new_state.get_id())); hash_map.insert(std::make_pair(new_state.get_hash(instance.facts), new_state.get_id()));
localFrontier.emplace_front(new_state); localFrontier.emplace_front(new_state);
Edge ed(current_state.get_hash(instance.facts), new_state.get_id(), exploit, assetGroup); Edge ed(current_state.get_hash(instance.facts), new_state.get_id(), exploit, assetGroup);
ed.set_id(); ed.set_id();
instance.edges.push_back(ed); instance.edges.push_back(ed);
@ -1498,6 +1508,7 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
else else
break; break;
} //for loop for new states ends } //for loop for new states ends
state_count++;
} }
else else
@ -1506,15 +1517,23 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
} }
//Let root node we finished, but only if we have done work since our last message //Let root node we finished, but only if we have done work since our last message
if(send_msg == 1){ if(send_msg == 1){
if(localFrontier.size() != 0){
world.isend(0, 2, 2);
}
else
world.isend(0, 2, 1); world.isend(0, 2, 1);
send_msg = 0; send_msg = 0;
std::cout << "Node " << world.rank() << " finished subgraphing work." << std::endl; std::cout << "Node " << world.rank() << " finished subgraphing work." << std::endl;
if(localFrontier.size() > 0){ if(localFrontier.size() != 0){
world.isend(0, 3, localFrontier); mpi::request lf_req = world.isend(0, 3, localFrontier);
std::cout << "Node " << world.rank() << " has sent a localFrontier of size " << localFrontier.size() << std::endl;
lf_req.wait();
} }
//Send new states and edges, then clear worker instance //Send new states and edges, then clear worker instance
world.isend(0, 10, instance.factbases); mpi::request if_req = world.isend(0, 10, instance.factbases);
world.isend(0, 11, instance.edges); mpi::request ie_req = world.isend(0, 11, instance.edges);
if_req.wait();
ie_req.wait();
std::vector<Factbase>().swap(instance.factbases); std::vector<Factbase>().swap(instance.factbases);
std::vector<FactbaseItems>().swap(instance.factbase_items); std::vector<FactbaseItems>().swap(instance.factbase_items);
std::vector<Edge>().swap(instance.edges); std::vector<Edge>().swap(instance.edges);
@ -1537,6 +1556,7 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
else if (world.rank() == 1){ else if (world.rank() == 1){
//Check for finished signal, assuming we have no more storage requests //Check for finished signal, assuming we have no more storage requests
if(world.iprobe(0, 99) && !world.iprobe(0,7) && !world.iprobe(0,8)){ if(world.iprobe(0, 99) && !world.iprobe(0,7) && !world.iprobe(0,8)){
std::cout << "Node " << world.rank() << " received finalize signal" << std::endl;
break; break;
} }
@ -1569,17 +1589,21 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
//World Rank = 0 //World Rank = 0
else{ else{
std::map<int, int> deque_marker; std::map<int, int> deque_marker;
std::map<int, int> frontier_recv;
int finish_count = 0; int finish_count = 0;
//Receive states and edges when nodes finish //Receive states and edges when nodes finish
while(finish_count != world.size() -2){ //while(finish_count != world.size() -2){
std::cout << "Waiting for " << msg_sends << " total messages." << std::endl;
while(finish_count != msg_sends){
while(world.iprobe(mpi::any_source, 10) || world.iprobe(mpi::any_source, 11)) { while(world.iprobe(mpi::any_source, 10) || world.iprobe(mpi::any_source, 11)) {
std::vector<Factbase> node_factbases; std::vector<Factbase> node_factbases;
std::vector<Edge> node_edges; std::vector<Edge> node_edges;
world.recv(mpi::any_source, 10, node_factbases); world.recv(mpi::any_source, 10, node_factbases);
world.recv(mpi::any_source, 11, node_edges); world.recv(mpi::any_source, 11, node_edges);
std::cout << "Merging states. Starting with: " << instance.factbases.size() << " states." << std::endl;
state_merge(node_factbases, node_edges, hash_map, instance, mem_threshold, world); state_merge(node_factbases, node_edges, hash_map, instance, mem_threshold, world);
std::cout << "Finished merging. Now have: " << instance.factbases.size() << " states." << std::endl;
} }
//Nodes finish //Nodes finish
@ -1588,6 +1612,12 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
if(world.iprobe(w, 2)){ if(world.iprobe(w, 2)){
world.recv(w, 2, dummy_finish); world.recv(w, 2, dummy_finish);
finish_count++; finish_count++;
if(dummy_finish == 2){
frontier_recv[w] = 1;
}
else
frontier_recv[w] = 0;
std::cout << "Root received subgraph finish message from node " << w << std::endl;
} }
} }
@ -1620,52 +1650,92 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
//Receive node frontiers and merge them into root frontier //Receive node frontiers and merge them into root frontier
for(int w = 2; w < world.size(); w++){ for(int w = 2; w < world.size(); w++){
if(world.iprobe(w, 3)){ //if(world.iprobe(w, 3)){
if(frontier_recv[w] == 1){
std::deque<NetworkState> nodeFrontier; std::deque<NetworkState> nodeFrontier;
world.recv(w, 3, nodeFrontier); world.recv(w, 3, nodeFrontier);
localFrontier.insert(localFrontier.begin(), \ localFrontier.insert(localFrontier.begin(), \
std::make_move_iterator(nodeFrontier.begin()),\ std::make_move_iterator(nodeFrontier.begin()),\
std::make_move_iterator(nodeFrontier.end())); std::make_move_iterator(nodeFrontier.end()));
std::cout << "Local Frontier now has size: " << localFrontier.size() << std::endl;
deque_marker[w] = (int)(localFrontier.size()-1); deque_marker[w] = (int)(localFrontier.size()-1);
std::cout << "Deque marker for node " << w << " is " << deque_marker[w] << std::endl;
} }
//If a node doesn't have a specific state to pull, randomly assign it one //If a node doesn't have a specific state to pull, randomly assign it one
if (!deque_marker.count(w)){ if (!deque_marker.count(w)){
//Randomly assign a state index to pop //Randomly assign a state index to pop
std::uniform_int_distribution<> distr(0, localFrontier.size()-1); // define the range std::uniform_int_distribution<> distr(0, localFrontier.size()-1); // define the range
deque_marker[w] = distr(gen); deque_marker[w] = distr(gen);
std::cout << "Random deque marker for node " << w << " is " << deque_marker[w] << std::endl;
} }
} }
std::cout << "Root added a placemarker for all frontier pulls " << std::endl;
msg_sends = 0;
//Send new Network State to all worker nodes, if we have enough unex states to do so //Send new Network State to all worker nodes, if we have enough unex states to do so
//2 offset for root node and db node //2 offset for root node and db node
for (int w = 0; w < world.size()-2; w++){ for (int w = 2; w < world.size(); w++){
std::cout << "Attempting to send a new state to node " << w << std::endl;
int proceed = 0; int proceed = 0;
while(!proceed){ int break_flag = 0;
if(localFrontier.size() > 0){ while(proceed == 0){
if(deque_marker[w+2] > localFrontier.size()) while(deque_marker[w] >= localFrontier.size()){
deque_marker[w+2]--; if(localFrontier.size() == 1 || localFrontier.size() == 0){
deque_marker[w] = 0;
break;
}
deque_marker[w] = localFrontier.size()-1;
}
std::cout << "<While> LF Size: " << localFrontier.size() << std::endl;
if(localFrontier.size() != 0){
//while(deque_marker[w] >= localFrontier.size())
// deque_marker[w]--;
//auto deque_access = localFrontier.begin() + deque_marker[w+2]; //auto deque_access = localFrontier.begin() + deque_marker[w+2];
auto deque_access = deque_marker[w+2]; auto deque_access = deque_marker[w];
NetworkState send_state = localFrontier.at(deque_access); NetworkState send_state = localFrontier.at(deque_access);
std::cout << "Got our state from deque" << std::endl;
//Don't explore on states we already have explored //Don't explore on states we already have explored
if(hash_map.find(send_state.get_id()) != hash_map.end()){ if(hash_map.find(send_state.get_id()) != hash_map.end()){
std::cout << "Already explored this state." << std::endl;
if(localFrontier.size() == 1){
localFrontier.clear();
deque_marker[w] = -1;
std::cout << "Cleared LF, it is now of size: " << localFrontier.size() << std::endl;
}
else{
localFrontier.erase(localFrontier.begin()+deque_access); localFrontier.erase(localFrontier.begin()+deque_access);
deque_marker[w+2]--; deque_marker[w]--;
}
std::cout << "Post hashing LF size: " << localFrontier.size() << std::endl;
}
else{
std::cout << " We have not seen this state yet." << std::endl;
proceed = 1;
} }
if(proceed){ if(proceed == 1){
mpi::request state_req = world.isend(w+2, 1, send_state); std::cout << "Preparing the send to World Rank " << w << std::endl;
mpi::request state_req = world.isend(w, 1, send_state);
localFrontier.erase(localFrontier.begin()+deque_access); localFrontier.erase(localFrontier.begin()+deque_access);
state_req.wait(); state_req.wait();
} msg_sends++;
} std::cout << "Root sent new states to World Rank " << w << std::endl;
} }
} }
//Else localFrontier size = 0
if(localFrontier.empty() && finish_count == world.size() -2){ else{
std::cout << "Frontier is empty. " << std::endl;
break;
}
}
}
std::cout << "Message Sends: " << msg_sends << std::endl;
//if LocalFrontier is empty at this point and we did not send any messages, we're done
if(localFrontier.empty() && msg_sends == 0){
std::cout << "Root is sending finalize signal" << std::endl;
finished_signal = 1; finished_signal = 1;
} }
@ -1675,7 +1745,8 @@ AGGenInstance &AGGen::sg_generate(bool batch_process, int batch_num, int numThrd
//Tell all nodes to finish //Tell all nodes to finish
if(world.rank() == 0){ if(world.rank() == 0){
for(int w = 1; w < world.size(); w++){ for(int w = 1; w < world.size(); w++){
world.send(w, 99, 1); world.isend(w, 99, 1);
std::cout << "Finalize message sent to Node " << w << std::endl;
} }
} }