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ok it works

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This commit is contained in:
Michael Zhang 2023-11-25 02:05:20 +00:00
parent a373fd4b83
commit ca96bf8b2d
10 changed files with 3312262 additions and 126 deletions
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1
Dockerfile
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@ -15,6 +15,7 @@ RUN apt update -y && apt install -y --no-install-recommends \
git \
libomp-dev \
libopenmpi-dev \
libfmt-dev \
openmpi-bin \
pandoc \
pkg-config \

14
assignments/03/Makefile
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@ -1,7 +1,13 @@
.PHONY: run
.PHONY: run clean
lpa: lpa.c
mpicc -o $@ -g $<
CFLAGS += -DFMT_HEADER_ONLY
LDFLAGS += $(shell pkg-config --libs fmt)
clean:
rm lpa
lpa: lpa.cpp
mpic++ $(CFLAGS) $(LDFLAGS) -o $@ -g $<
run:
watchexec -c clear 'make lpa && mpirun -n 4 ./lpa dataset/1000.txt'
watchexec -c clear 'make lpa && mpirun -n 4 ./lpa dataset/both_1000.txt'

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assignments/03/dataset/both_1000.txt Normal file
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assignments/03/dataset/both_10000.txt Normal file
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assignments/03/dataset/both_100000.txt Normal file
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assignments/03/dataset/both_1000000.txt Normal file
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assignments/03/dataset/both_EZ.txt Normal file
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@ -0,0 +1,5 @@
4 4
0 1
1 0
2 3
3 2

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assignments/03/dataset/gen.py Normal file
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import sys
with open(sys.argv[1]) as f:
num_nodes, num_edges = map(int, f.readline().strip().split(" "))
all_edges = set()
for _ in range(num_edges):
from_edge, to_edge = map(int, f.readline().strip().split(" "))
all_edges.add((from_edge, to_edge))
all_edges.add((to_edge, from_edge))
all_edges = sorted(list(all_edges))
new_num_edges = len(all_edges)
with open(sys.argv[2], "w") as f:
f.write(f"{num_nodes} {new_num_edges}\n")
for from_edge, to_edge in all_edges:
f.write(f"{from_edge} {to_edge}\n")

122
assignments/03/lpa.c
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@ -1,122 +0,0 @@
#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <unistd.h>
typedef struct {
int fst;
int snd;
} pair;
void init_pair_type(MPI_Datatype *out);
int main(int argc, char **argv) {
MPI_Init(&argc, &argv);
int rank, p;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &p);
MPI_Datatype IntPairType;
init_pair_type(&IntPairType);
// One process reads the file and distributes the data to the other processes
// using a 1D decomposition (each rank gets approx same number of vertices).
#pragma region
FILE *fp;
char *line = NULL;
size_t len;
ssize_t read;
pair params;
if (rank == 0) {
printf("Hello\n");
fp = fopen(argv[1], "r");
if ((read = getline(&line, &len, fp)) != -1)
sscanf(line, "%d %d", &params.fst, &params.snd);
}
// Send this pair
MPI_Bcast(&params, 1, IntPairType, 0, MPI_COMM_WORLD);
int num_nodes = params.fst;
int num_edges = params.snd;
int max_num_my_edges = (num_edges / p) + p;
pair my_edges[max_num_my_edges];
// Read the edges
pair edges[num_edges];
int my_count;
int counts[p], displs[p];
if (rank == 0) {
line = NULL;
for (int i = 0; i < num_edges; ++i) {
getline(&line, &len, fp);
sscanf(line, "%d %d", &edges[i].fst, &edges[i].snd);
}
int step = num_edges / p;
for (int i = 0; i < p; ++i) {
int start = i * step;
int end = i == p - 1 ? num_edges : start + step;
int count = end - start;
counts[i] = count;
displs[i] = start;
}
}
MPI_Scatter(counts, 1, MPI_INT, &my_count, 1, MPI_INT, 0, MPI_COMM_WORLD);
printf("[%d] #: %d\n", rank, my_count);
MPI_Scatterv(edges, counts, displs, IntPairType, my_edges, my_count,
IntPairType, 0, MPI_COMM_WORLD);
if (rank == 0) {
fclose(fp);
if (line)
free(line);
}
#pragma endregion
// Each process analyzes the non-local edges that are contained in its portion
// of the graph.
#pragma region
#pragma endregion
// Each process determines which processors stores the non-local vertices
// corresponding to the non-local edges.
#pragma region
#pragma endregion
// All the processes are communicating to figure out which process needs to
// send what data to the other processes.
#pragma region
#pragma endregion
// The processes perform the transfers of non-local labels and updates of
// local labels until convergence.
#pragma region
#pragma endregion
// The results are gathered to a single process, which writes them to the
// disk.
#pragma region
#pragma endregion
MPI_Finalize();
return 0;
}
void init_pair_type(MPI_Datatype *out) {
int blocklengths[2] = {1, 1};
MPI_Datatype types[2] = {MPI_INT, MPI_INT};
MPI_Aint offsets[2];
offsets[0] = offsetof(pair, fst);
offsets[1] = offsetof(pair, snd);
MPI_Type_create_struct(2, blocklengths, offsets, types, out);
MPI_Type_commit(out);
}

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assignments/03/lpa.cpp Normal file
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#include <algorithm>
#include <array>
#include <cstring>
#include <functional>
#include <limits>
#include <map>
#include <set>
#include <vector>
#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <unistd.h>
#include <utility>
#include <fmt/format.h>
#include <fmt/ranges.h>
#define TAG_SEND_NUM_EDGES 1001
#define TAG_SEND_EDGES 1002
#define TAG_SEND_FINAL_RESULT 1003
typedef struct {
int fst;
int snd;
} pair;
void init_pair_type(MPI_Datatype *out);
int main(int argc, char **argv) {
MPI::Init(argc, argv);
int rank = MPI::COMM_WORLD.Get_rank(), p = MPI::COMM_WORLD.Get_size();
MPI_Datatype IntPairType;
init_pair_type(&IntPairType);
// One process reads the file and distributes the data to the other processes
// using a 1D decomposition (each rank gets approx same number of vertices).
#pragma region
FILE *fp;
char *line = NULL;
size_t len;
ssize_t read;
pair params;
if (rank == 0) {
printf("Hello\n");
fp = fopen(argv[1], "r");
if ((read = getline(&line, &len, fp)) != -1)
sscanf(line, "%d %d", &params.fst, &params.snd);
}
// Send the params
MPI_Bcast(&params, 1, IntPairType, 0, MPI::COMM_WORLD);
int total_num_nodes = params.fst;
int total_num_edges = params.snd;
int each_num_nodes = total_num_nodes / p;
// Calculate exactly how many nodes my current process holds
int num_my_nodes =
rank == p - 1 ? total_num_nodes - rank * each_num_nodes : each_num_nodes;
int my_nodes[num_my_nodes];
std::function<std::pair<int, int>(int)> node_range =
[p, total_num_nodes, each_num_nodes](int process) {
int start = process * each_num_nodes;
int end = process == p - 1 ? total_num_nodes : start + each_num_nodes;
return std::make_pair(start, end);
};
// Read the edges
int num_my_edges;
pair *my_edges;
int counts[p], displs[p];
if (rank == 0) {
line = NULL;
pair all_edges[total_num_edges];
// For the current process, what's the last node we're expecting to see?
int current_process = 0;
std::pair<int, int> current_node_range = node_range(current_process);
int edge_counter = 0;
for (int i = 0; i < total_num_edges; ++i) {
getline(&line, &len, fp);
int fst, snd;
sscanf(line, "%d %d", &fst, &snd);
if (fst >= current_node_range.second) {
if (current_process == 0) {
num_my_edges = edge_counter;
my_edges = (pair *)calloc(num_my_edges, sizeof(pair));
memcpy(my_edges, all_edges, edge_counter * sizeof(pair));
} else {
MPI_Send(&edge_counter, 1, MPI_INT, current_process,
TAG_SEND_NUM_EDGES, MPI::COMM_WORLD);
MPI_Send(all_edges, edge_counter, IntPairType, current_process,
TAG_SEND_EDGES, MPI::COMM_WORLD);
}
// We're starting on the next process
current_process += 1;
current_node_range = node_range(current_process);
edge_counter = 0;
}
all_edges[edge_counter].fst = fst;
all_edges[edge_counter].snd = snd;
edge_counter += 1;
}
// We have to send the last one again here, since it didn't get caught in
// the loop above
MPI_Send(&edge_counter, 1, MPI_INT, current_process, TAG_SEND_NUM_EDGES,
MPI::COMM_WORLD);
MPI_Send(all_edges, edge_counter, IntPairType, current_process,
TAG_SEND_EDGES, MPI::COMM_WORLD);
// int step = num_edges / p;
// for (int i = 0; i < p; ++i) {
// int start = i * step;
// int end = i == p - 1 ? num_edges : start + step;
// int count = end - start;
// counts[i] = count;
// displs[i] = start;
// }
} else {
MPI_Recv(&num_my_edges, 1, MPI_INT, 0, TAG_SEND_NUM_EDGES, MPI::COMM_WORLD,
NULL);
my_edges = (pair *)calloc(num_my_edges, sizeof(pair));
MPI_Recv(my_edges, num_my_edges, IntPairType, 0, TAG_SEND_EDGES,
MPI::COMM_WORLD, NULL);
}
char *buf = (char *)calloc(sizeof(char), 1000);
int offset = 0; // Keep track of the current position in the buffer
for (int i = 0; i < std::min(num_my_edges, 5); i++) {
offset +=
sprintf(buf + offset, "(%d, %d)", my_edges[i].fst, my_edges[i].snd);
if (i < len - 1) {
// Add a separator (e.g., comma or space) if it's not the last
offset += sprintf(buf + offset, " ");
}
}
if (rank == 0) {
fclose(fp);
if (line)
free(line);
}
#pragma endregion
// Each process analyzes the non-local edges that are contained in its portion
// of the graph.
#pragma region
std::map<int, int> node_label_assignment;
std::pair<int, int> my_node_range = node_range(rank);
// Initial node assignment
for (int i = my_node_range.first; i < my_node_range.second; ++i) {
node_label_assignment[i] = i;
}
std::map<int, std::set<int>> adj;
std::set<int> non_local_nodes;
std::set<std::pair<int, int>> non_local_edges;
for (int i = 0; i < num_my_edges; ++i) {
pair edge = my_edges[i];
adj[edge.fst].insert(edge.snd);
if (!(my_node_range.first <= edge.fst && edge.fst < my_node_range.second)) {
non_local_nodes.insert(edge.fst);
non_local_edges.insert(std::make_pair(edge.snd, edge.fst));
}
if (!(my_node_range.first <= edge.snd && edge.snd < my_node_range.second)) {
non_local_nodes.insert(edge.snd);
non_local_edges.insert(std::make_pair(edge.fst, edge.snd));
}
}
#pragma endregion
// Each process determines which processors stores the non-local vertices
// corresponding to the non-local edges.
#pragma region
std::map<int, std::set<int>> send_map;
std::map<int, std::set<int>> recv_map;
for (auto entry : non_local_edges) {
int local_node = entry.first, remote_node = entry.second;
int corresponding_process = remote_node / each_num_nodes;
// The last process gets some extra nodes
if (corresponding_process >= p)
corresponding_process = p - 1;
send_map[corresponding_process].insert(local_node);
recv_map[corresponding_process].insert(remote_node);
}
#pragma endregion
// All the processes are communicating to figure out which process needs to
// send what data to the other processes.
#pragma region
#pragma endregion
// The processes perform the transfers of non-local labels and updates of
// local labels until convergence.
#pragma region
while (true) {
// First, exchange the data that needs to be exchanged
std::vector<int> sendbuf;
std::vector<int> send_counts;
std::vector<int> send_displs;
std::vector<int> recv_counts;
std::vector<int> recv_displs;
int recv_total;
{
int offset = 0;
for (int i = 0; i < p; ++i) {
int count = send_map[i].size();
// std::sort(send_map[i].begin(), send_map[i].end());
for (auto k : send_map[i]) {
sendbuf.push_back(node_label_assignment[k]);
}
send_counts.push_back(count);
send_displs.push_back(offset);
offset += count;
}
offset = 0;
for (int i = 0; i < p; ++i) {
int count = recv_map[i].size();
// std::sort(recv_map[i].begin(), recv_map[i].end());
recv_counts.push_back(count);
recv_displs.push_back(offset);
offset += count;
}
recv_total = offset;
}
std::vector<int> recvbuf(recv_total, 0);
// std::cout << fmt::format("[{}] {} \t|| \t{}", rank,
// fmt::join(send_counts, ", "),
// fmt::join(recv_counts, ", "))
// << std::endl;
MPI::COMM_WORLD.Alltoallv(sendbuf.data(), send_counts.data(),
send_displs.data(), MPI_INT, recvbuf.data(),
recv_counts.data(), recv_displs.data(), MPI_INT);
std::map<int, int> total_node_label_assignment(node_label_assignment);
for (int i = 0; i < p; ++i) {
std::vector<int> ouais(recv_map[i].begin(), recv_map[i].end());
for (int j = 0; j < recv_counts[i]; ++j) {
int remote_node = ouais[j];
int remote_value = recvbuf[recv_displs[i] + j];
total_node_label_assignment[remote_node] = remote_value;
}
}
// For each local node, determine the minimum label out of its neighbors
std::map<int, int> new_labels;
for (int i = my_node_range.first; i < my_node_range.second; ++i) {
int current_value = total_node_label_assignment[i];
int min = current_value;
for (auto neighbor : adj[i]) {
if (total_node_label_assignment[neighbor] < min)
min = total_node_label_assignment[neighbor];
}
if (min < current_value) {
new_labels[i] = min;
}
}
// std::cout << fmt::format("[{}] Helloge {}", rank,
// fmt::join(new_labels, ", "))
// << std::endl;
// Have there been any changes in the labels?
int num_changes = new_labels.size();
int total_changes;
MPI::COMM_WORLD.Allreduce(&num_changes, &total_changes, 1, MPI_INT,
MPI::SUM);
std::cout << fmt::format("[{}] # updates: {} ({})", rank, num_changes,
total_changes)
<< std::endl;
if (total_changes == 0) {
break;
}
// Update the original node assignment
for (auto entry : new_labels) {
node_label_assignment[entry.first] = entry.second;
}
}
#pragma endregion
// The results are gathered to a single process, which writes them to the
// disk.
#pragma region
if (rank == 0) {
std::vector<int> all_assignments(total_num_nodes);
std::map<int, int> label_count;
int ctr = 0;
for (int i = 0; i < p; ++i) {
std::pair<int, int> this_node_range = node_range(i);
int count = this_node_range.second - this_node_range.first;
if (i == 0) {
for (int j = 0; j < count; ++j) {
all_assignments[this_node_range.first + j] =
node_label_assignment[this_node_range.first + j];
label_count[all_assignments[this_node_range.first + j]]++;
}
} else {
MPI::COMM_WORLD.Recv(&all_assignments[this_node_range.first], count,
MPI::INT, i, TAG_SEND_FINAL_RESULT);
for (int j = 0; j < count; ++j) {
label_count[all_assignments[this_node_range.first + j]]++;
}
}
}
std::cout << "Done! " << label_count.size() << std::endl;
} else {
std::vector<int> flat_assignments;
for (int i = my_node_range.first; i < my_node_range.second; ++i) {
flat_assignments.push_back(node_label_assignment[i]);
}
MPI::COMM_WORLD.Send(flat_assignments.data(), flat_assignments.size(),
MPI::INT, 0, TAG_SEND_FINAL_RESULT);
}
#pragma endregion
MPI::Finalize();
return 0;
}
void init_pair_type(MPI_Datatype *out) {
int blocklengths[2] = {1, 1};
MPI_Datatype types[2] = {MPI_INT, MPI_INT};
MPI_Aint offsets[2];
offsets[0] = offsetof(pair, fst);
offsets[1] = offsetof(pair, snd);
MPI_Type_create_struct(2, blocklengths, offsets, types, out);
MPI_Type_commit(out);
}