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Fixing early stoppage

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hammer 2022-02-13 13:14:04 -06:00
parent b9735af8cb
commit 88394b7779
10 changed files with 14474 additions and 14531 deletions
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build/Makefile
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@ -48,19 +48,19 @@ cmake_force:
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@ -7,7 +7,7 @@
#SBATCH --exclude=compute02,compute03,compute09 #SBATCH --exclude=compute02,compute03,compute09
#SBATCH --export=ALL #SBATCH --export=ALL
#SBATCH --nodelist=compute10,compute11,compute12 #SBATCH --nodelist=compute10,compute11,compute12,compute07,compute08,compute04,compute05,compute01
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
@ -19,7 +19,7 @@ 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:-4} NODES=${6:-13}
module load graphviz module load graphviz
module load gcc module load gcc

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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"
} }
] ]

6
build/run.sh
View File

@ -58,7 +58,7 @@ if [ "$TYPE" == "$strval1" ]; then
if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then
#4 Exploit Option #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 "$DBNAME" -l 40 -s mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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" -l 200 -e -g DOTFILE.dot
#6 Exploit Option #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 "$DBNAME" -s -l 20 #mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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
@ -81,8 +81,8 @@ fi
#Graphviz Strict graphing to avoid duplicate nodes and edges #Graphviz Strict graphing to avoid duplicate nodes and edges
#echo -n 'strict ' | cat - DOTFILE.dot > temp && mv temp DOTFILE.dot echo -n 'strict ' | cat - DOTFILE.dot > temp && mv temp DOTFILE.dot
#dot -Tsvg new.dot > ag.svg #dot -Tsvg new.dot > ag.svg
#dot -Tsvg DOTFILE.dot > ag.svg dot -Tsvg DOTFILE.dot > ag.svg

10110
build/states.txt
View File

File diff suppressed because it is too large Load Diff

11
src/ag_gen/ag_gen.cpp
View File

@ -309,6 +309,7 @@ double mem_threshold, mpi::communicator &world)
{ {
auto current_state = localFrontier.back(); auto current_state = localFrontier.back();
localFrontier.pop_back(); localFrontier.pop_back();
std::cout << "Sending state ID " << current_state.get_id() << std::endl;
for(int l=0; l < alloc; l++){ for(int l=0; l < alloc; l++){
mpi::request cs_req = world.isend(send_check(world, l), 20, current_state); mpi::request cs_req = world.isend(send_check(world, l), 20, current_state);
cs_req.wait(); cs_req.wait();
@ -361,6 +362,7 @@ double mem_threshold, mpi::communicator &world)
//Have the 0th Task 2 node tell the other world nodes that it's done //Have the 0th Task 2 node tell the other world nodes that it's done
if(ttwo_comm.rank() == 0){ if(ttwo_comm.rank() == 0){
//std::cout << "" << std::endl;
for (int w = 0; w < world.size(); w++) for (int w = 0; w < world.size(); w++)
{ {
//2 Node Edge case //2 Node Edge case
@ -421,6 +423,13 @@ double mem_threshold, mpi::communicator &world)
world.recv(mpi::any_source, 6, current_state); world.recv(mpi::any_source, 6, current_state);
world.recv(mpi::any_source, 10, exploit); world.recv(mpi::any_source, 10, exploit);
world.recv(mpi::any_source, 11, assetGroup); world.recv(mpi::any_source, 11, assetGroup);
std::cout << "Received new state" << std::endl;
if(instance.factbases.size() == 0){
last_known_id = 0;
}
else last_known_id = instance.factbases.size()-1;
if(get_num_states() > 1)
last_known_id += get_num_states()-1;
struct timeval t31,t32; struct timeval t31,t32;
gettimeofday(&t31,NULL); gettimeofday(&t31,NULL);
@ -434,7 +443,7 @@ double mem_threshold, mpi::communicator &world)
} //while probe/instance update ends } //while probe/instance update ends
} //else wait ends } //else wait ends
} }
if(world.rank() == 0) std::cout << "" << std::endl;
//Task Four //Task Four
if (world.rank() == send_check(world, alloc+two_alloc)){ if (world.rank() == send_check(world, alloc+two_alloc)){
if(world.iprobe(0, 7) || world.iprobe(0, 8)){ if(world.iprobe(0, 7) || world.iprobe(0, 8)){

24
src/mpi/tasks.cpp
View File

@ -70,7 +70,7 @@ void task_one(AGGenInstance &instance, NetworkState &current_state,\
int alloc, int two_alloc, int reduc_factor, int num_tasks, mpi::communicator &world,\ int alloc, int two_alloc, int reduc_factor, int num_tasks, mpi::communicator &world,\
mpi::communicator &tcomm){ mpi::communicator &tcomm){
//std::cout << "Process rank " << world.rank() << " with " << alloc << " node(s) allocated has started Task 1." << std::endl; //std::cout << "Process rank " << world.rank() << " with " << alloc << " node(s) allocated has started Task 1 and has a local communicator rank of " << tcomm.rank() << std::endl;
std::vector<std::tuple<Exploit, AssetGroup>> appl_exploits; std::vector<std::tuple<Exploit, AssetGroup>> appl_exploits;
unsigned long esize = exploit_list.size(); unsigned long esize = exploit_list.size();
@ -184,7 +184,7 @@ void task_one(AGGenInstance &instance, NetworkState &current_state,\
if (alloc > two_alloc) if (alloc > two_alloc)
skip_greatest = 1; skip_greatest = 1;
if(world.rank() <= (alloc - skip_greatest)){ if(world.rank() <= (alloc - skip_greatest)){
//std::cout << "Process " << world.rank() << " sending applicable exploit list of size " << appl_exploits.size() <<\ //std::cout << "Process " << world.rank() << " sending Appl exploit list of size " << appl_exploits.size() <<\
" to Process " << send_check(world, world.rank() + alloc -1) << std::endl; " to Process " << send_check(world, world.rank() + alloc -1) << std::endl;
mpi::request appl_req = world.isend(send_check(world, world.rank() + alloc -1), 30, appl_exploits); mpi::request appl_req = world.isend(send_check(world, world.rank() + alloc -1), 30, appl_exploits);
mpi::request cs_req = world.isend(send_check(world, world.rank() + alloc -1), 40, current_state); mpi::request cs_req = world.isend(send_check(world, world.rank() + alloc -1), 40, current_state);
@ -206,7 +206,7 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
world.recv(mpi::any_source, 30, appl_exploits); world.recv(mpi::any_source, 30, appl_exploits);
world.recv(mpi::any_source, 40, current_state); world.recv(mpi::any_source, 40, current_state);
//std::cout << "Process " << world.rank() << " received Task 1 data with Appl exploit size " << appl_exploits.size() << std::endl; std::cout << "Process " << world.rank() << " with local communicator rank " << ttwo_comm.rank() << " received Task 1 data with Appl exploit size " << appl_exploits.size() << " for State ID " << current_state.get_id() << std::endl;
//Check for new fact and new state that caused an update in the hash table and facts //Check for new fact and new state that caused an update in the hash table and facts
while(world.iprobe(mpi::any_source, 3) || world.iprobe(mpi::any_source, 4)){ while(world.iprobe(mpi::any_source, 3) || world.iprobe(mpi::any_source, 4)){
@ -275,7 +275,7 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
sync_vectors[std::get<0>(sync_recv)].insert(std::end(sync_vectors[std::get<0>(sync_recv)]), std::begin(partial_appl_exploits), std::end(partial_appl_exploits)); sync_vectors[std::get<0>(sync_recv)].insert(std::end(sync_vectors[std::get<0>(sync_recv)]), std::begin(partial_appl_exploits), std::end(partial_appl_exploits));
} }
} }
std::cout << "Before the loop, Process " << world.rank() << " has Appl exploit size " << appl_exploits.size() << std::endl;
//loop through the vector //loop through the vector
for(auto itr=appl_exploits.begin(); itr!=appl_exploits.end(); itr++){ for(auto itr=appl_exploits.begin(); itr!=appl_exploits.end(); itr++){
@ -297,7 +297,7 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
auto assetGroup = std::get<1>(e); auto assetGroup = std::get<1>(e);
egroup=exploit.get_group(); egroup=exploit.get_group();
std::cout << "Process " << world.rank() << " for state ID " << current_state.get_id() << " has exploit " << exploit.get_name() << " with group " << egroup << std::endl;
if ((egroup != "null" && group_fired[egroup] == 0) || egroup == "null"){ if ((egroup != "null" && group_fired[egroup] == 0) || egroup == "null"){
NetworkState new_state{current_state}; NetworkState new_state{current_state};
std::vector<std::tuple<Exploit, AssetGroup>> sync_exploits; std::vector<std::tuple<Exploit, AssetGroup>> sync_exploits;
@ -311,10 +311,10 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
//TODO: Does not work if only some assets belong to a group. This only works if //TODO: Does not work if only some assets belong to a group. This only works if
//all assets are in the group //all assets are in the group
if(sync_exploits.size() < instance.assets.size()){ if(sync_exploits.size() < instance.assets.size()){
break; continue;
} }
} }
//std::cout << "Sync exploit size " << sync_exploits.size() << " at Node " << world.rank() << " out of a total of " << appl_exploits.size() << std::endl; std::cout << "Sync exploit size " << sync_exploits.size() << " at Node " << world.rank() << " out of a total of " << appl_exploits.size() << std::endl;
for(auto sync_itr=sync_exploits.begin(); sync_itr!=sync_exploits.end(); sync_itr++){ for(auto sync_itr=sync_exploits.begin(); sync_itr!=sync_exploits.end(); sync_itr++){
e = *sync_itr; e = *sync_itr;
exploit = std::get<0>(e); exploit = std::get<0>(e);
@ -325,7 +325,8 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
auto postconditions = createPostConditions(e, instance.facts); auto postconditions = createPostConditions(e, instance.facts);
auto qualities = std::get<0>(postconditions); auto qualities = std::get<0>(postconditions);
auto topologies = std::get<1>(postconditions); auto topologies = std::get<1>(postconditions);
std::cout << "Exploit " << exploit.get_name() << " is applicable to ID " << current_state.get_id() << std::endl;
for(auto &qual : qualities) { for(auto &qual : qualities) {
auto action = std::get<0>(qual); auto action = std::get<0>(qual);
auto fact = std::get<1>(qual); auto fact = std::get<1>(qual);
@ -395,7 +396,7 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
//<6 Node Edge Case Prevention: Node 0 unable to execute task 3 //<6 Node Edge Case Prevention: Node 0 unable to execute task 3
if(world.rank() != 0){ if(world.rank() != 0){
//std::cout << "Node " << world.rank() << " sending new state data to Node 0" << std::endl; std::cout << "Node " << world.rank() << " sending new state data to Node 0" << std::endl;
mpi::request ns_req = world.isend(0, 5, new_state); mpi::request ns_req = world.isend(0, 5, new_state);
mpi::request cs_req = world.isend(0, 6, current_state); mpi::request cs_req = world.isend(0, 6, current_state);
mpi::request ex_req = world.isend(0, 10, exploit); mpi::request ex_req = world.isend(0, 10, exploit);
@ -420,7 +421,8 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com
} }
else{ else{
//std::cout << "Breaking." << std::endl; //std::cout << "Breaking." << std::endl;
break; //break;
continue;
} }
} }
} }
@ -429,7 +431,7 @@ void task_three(AGGenInstance &instance, NetworkState &new_state, std::deque<Net
double mem_threshold, boost::mpi::communicator &world, int alloc, int two_alloc, NetworkState &current_state,\ double mem_threshold, boost::mpi::communicator &world, int alloc, int two_alloc, NetworkState &current_state,\
Exploit &exploit, AssetGroup &assetGroup, std::unordered_map<size_t, int> &hash_map, int last_known_id){ Exploit &exploit, AssetGroup &assetGroup, std::unordered_map<size_t, int> &hash_map, int last_known_id){
std::cout << "Started Task 3." << std::endl; //std::cout << "Started Task 3." << std::endl;
auto hash_num = new_state.get_hash(instance.facts); auto hash_num = new_state.get_hash(instance.facts);
//although local frontier is updated, the global hash is also updated to avoid testing on explored states. //although local frontier is updated, the global hash is also updated to avoid testing on explored states.