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Switching to 4E run script, and allowing for MPI Typing in script

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hammer 2022-02-16 00:38:07 -06:00
parent 163c00d071
commit 7a8fb705ba
9 changed files with 24230 additions and 24287 deletions
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74
build/Makefile
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@ -48,19 +48,19 @@ cmake_force:
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@ -68,7 +68,7 @@ CMAKE_BINARY_DIR = "/home/noah/Documents/School/Thesis Work/ag_parallel/build"
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@ -814,9 +761,7 @@ help:
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6
build/ag_run.sh
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@ -19,7 +19,9 @@ 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:-13} NODES=${6:-1}
MPI_TYPE=${7:-def}
module load graphviz module load graphviz
module load gcc module load gcc
@ -29,4 +31,4 @@ module load cmake
module load postgresql module load postgresql
#./run.sh 1 sync 2 "$TESTING" 2 #./run.sh 1 sync 2 "$TESTING" 2
./run.sh "$NUM_SERV" "$TYPE" "$CARS" "$DBNAME" "$NUM_THREADS" "$NODES" ./run.sh "$NUM_SERV" "$TYPE" "$CARS" "$DBNAME" "$NUM_THREADS" "$NODES" "$MPI_TYPE"

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/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"
} }
] ]

65
build/run.sh
View File

@ -7,6 +7,7 @@ CARS=${3:-2}
DBNAME=${4:-tmp} DBNAME=${4:-tmp}
NUM_THREADS=${5:-1} NUM_THREADS=${5:-1}
NODES=${6:-2} NODES=${6:-2}
MPI_TYPE=${7-subgraphing}
ITFC="eth0" ITFC="eth0"
@ -47,31 +48,71 @@ else
ITFC="wlp2s0" ITFC="wlp2s0"
fi fi
#./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_5/car_network5.nm -x ../fpga_examples/Network_5/car_network5.xp -g DOTFILE.dot -t 1 -q 1
if [ "$TYPE" == "$strval1" ]; then if [ "$TYPE" == "$strval1" ]; then
#Old
#./ag_gen -n ../Feb_2021/generic_timeline_maintenance.nm -x ../Feb_2021/Sync/"$NUM_SERV"_Serv/sync_timeline_maintenance.xp -g DOTFILE.dot -t 1 -q 1 -p -a 0.9
if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then if [ "$(dnsdomainname)" = "hammer.esg.utulsa.edu" ]; then
if [ "$MPI_TYPE" == subgraphing ]; then
#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 "$DBNAME" -l 200 -s
elif [ "$MPI_TYPE" == tasking ]; 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 "$DBNAME" -l 200 -e mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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
else
#Serial/OMP
#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 "$DBNAME" -l 200
fi #END Hammer
#Local
else else
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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 "$NUM_THREADS" -q 1 -p -a 0.6 -g DOTFILE.dot -z "$DBNAME" -l 200 -s if [ "$MPI_TYPE" == subgraphing ]; then
fi #4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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 "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -s
elif [ "$MPI_TYPE" == tasking ]; then
#4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$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 "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -e
else
#Serial/OMP
#4 Exploit Option
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 -a 0.6 -z "$DBNAME" -l 200
fi #END Non-Hammer
fi #END Sync
elif [ "$TYPE" == "$strval2" ]; then elif [ "$TYPE" == "$strval2" ]; then
#4 Exploit Option if [ "$(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/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" if [ "$MPI_TYPE" == subgraphing ]; then
#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/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -s
elif [ "$MPI_TYPE" == tasking ]; then
#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/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -e
else
#OMP/Serial
#4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200
fi #END Hammer
#Local
else
if [ "$MPI_TYPE" == subgraphing ]; then
#4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -s
elif [ "$MPI_TYPE" == tasking ]; then
#4 Exploit Option
mpiexec --mca btl_openib_allow_ib 1 --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa -np "$NODES" --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/"$CARS"_car_timeline_maintenance.nm -x ../Oct_2021/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200 -e
else
#OMP/Serial
#4 Exploit Option
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/Non_Sync/4_Exploits/"$NUM_SERV"_Serv/generic_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" -l 200
fi #END Non-Hammer
fi #END Non-Sync
else else
echo "Running default." echo "Running default."
mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/1_car_timeline_maintenance.nm -x ../Oct_2021/Sync/10_Exploits/1_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME" mpiexec --mca btl_openib_allow_ib 1 --mca btl openib,self,vader --mca opal_warn_on_missing_libcuda 0 --bind-to numa --map-by numa --timeout 129600 ./ag_gen -n ../Oct_2021/nm_files/1_car_timeline_maintenance.nm -x ../Oct_2021/Sync/10_Exploits/1_Serv/sync_timeline_maintenance.xp -t "$NUM_THREADS" -q 1 -p -a 0.6 -z "$DBNAME"
fi fi #END Sync/Non-Sync/Default
#Graphviz Strict graphing to avoid duplicate nodes and edges #Graphviz Strict graphing to avoid duplicate nodes and edges

24486
build/states.txt
View File

File diff suppressed because it is too large Load Diff

13
build/sync_data_col.sh
View File

@ -4,9 +4,12 @@
#folder=omp #folder=omp
#nodelist=compute08 #nodelist=compute08
folder=mpi folder=mpitasking
nodelist=compute01,compute04,compute07,compute10,compute11,compute12 nodelist=compute01,compute04,compute07,compute10,compute11,compute12
#folder=mpisubgraphing
#nodelist=compute01,compute04,compute07,compute10,compute11,compute12
#folder=serial #folder=serial
#nodelist=compute05 #nodelist=compute05
@ -22,13 +25,13 @@ pwd=`pwd`
#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 || "$folder" == mpi ]]; then if [[ "$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" != mpi ]]; then if [[ "$folder" != mpisubgraphing || "$folder" != mpitasking ]]; then
NODES=(1) NODES=(1)
fi fi
@ -85,7 +88,7 @@ if [[ "$SKIPSYNC" == false ]]; then
do do
SKIP_FLAG=0 SKIP_FLAG=0
#Dispatch the job and get the output ("Submitted batch job <jobid> #Dispatch the job and get the output ("Submitted batch job <jobid>
JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "sync" "$cars" "$DBNAME" "$thrd" "$node"` JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "sync" "$cars" "$DBNAME" "$thrd" "$node" "tasking"`
#Pull the jobid #Pull the jobid
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'` JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`
@ -189,7 +192,7 @@ if [[ "$SKIPSYNC" == false ]]; then
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"` JOB=`sbatch --nodelist="$nodelist" ag_run.sh "$i" "non-sync" "$cars" "$DBNAME" "$thrd" "$node" "tasking"`
#Pull the jobid #Pull the jobid
JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'` JOB=`echo "$JOB" | grep -oP '(?<=job )[^ ]*'`

10
src/mpi/tasks.cpp
View File

@ -553,11 +553,11 @@ void state_merge(std::vector<Factbase> node_factbases, std::vector<Edge> node_ed
else{ else{
//Each MPI Node has its own copy of states and factbases: we need to correct it with the Root's IDs //Each MPI Node has its own copy of states and factbases: we need to correct it with the Root's IDs
int reset_num = instance.factbases.size(); //int reset_num = instance.factbases.size();
if(get_num_states() > 1) //if(get_num_states() > 1)
reset_num += get_num_states()-1; // reset_num += get_num_states()-1;
fb.reset_curr_id(reset_num); //fb.reset_curr_id(reset_num);
fb.set_id(); //fb.set_id();
} }
} }