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Add lill4map.cc example. Thank you @marioroy.

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greg7mdp
2024-03-31 18:03:39 -04:00
parent 7ef2e73341
commit 6f5d3ccc0d
2 changed files with 497 additions and 0 deletions
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CMakeLists.txt
Vendored
+17
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@@ -202,6 +202,23 @@ if (PHMAP_BUILD_EXAMPLES)
add_executable(ex_mt_word_counter examples/mt_word_counter.cc phmap.natvis)
add_executable(ex_p_bench examples/p_bench.cc phmap.natvis)
## set(Boost_INCLUDE_DIR /home/greg/dev/boost_1_82_0) # if boost installed in non-standard location
set(Boost_USE_STATIC_LIBS OFF)
set(Boost_USE_MULTITHREADED ON)
set(Boost_USE_STATIC_RUNTIME OFF)
# lill4map.cc - see https://www.perlmonks.com/?node_id=11149643
# -------------------------------------------------------------
find_package(OpenMP)
find_package(Boost 1.70.0)
if (OPENMP_FOUND AND Boost_FOUND AND "cxx_std_20" IN_LIST CMAKE_CXX_COMPILE_FEATURES)
add_executable(ex_lill4map examples/lill4map.cc phmap.natvis)
target_include_directories(ex_lill4map PRIVATE ${Boost_INCLUDE_DIRS})
target_compile_features(ex_lill4map PUBLIC cxx_std_20)
target_link_libraries(ex_lill4map PRIVATE OpenMP::OpenMP_CXX)
target_compile_options(ex_lill4map PRIVATE "${OpenMP_CXX_FLAGS}")
endif()
target_link_libraries(ex_knucleotide Threads::Threads)
target_link_libraries(ex_bench Threads::Threads)
endif()
examples/lill4map.cc
+480
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@@ -0,0 +1,480 @@
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// llil4map.cc (new chunking variant)
// https://www.perlmonks.com/?node_id=11149643
// A phmap::parallel_flat_hash_map demonstration.
// By Mario Roy, March 31, 2024
// Based on llil3m.cpp https://perlmonks.com/?node_id=11149482
// Original challenge https://perlmonks.com/?node_id=11147822
// and summary https://perlmonks.com/?node_id=11150293
// Other demonstrations https://perlmonks.com/?node_id=11149907
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// OpenMP Little Book - https://nanxiao.gitbooks.io/openmp-little-book
//
// Obtain the parallel hashmap library (required dependency):
// git clone --depth=1 https://github.com/greg7mdp/parallel-hashmap
//
// Compile on Linux (clang++ or g++):
// clang++ -o llil4map -std=c++20 -fopenmp -Wall -O3 llil4map.cc -I./parallel-hashmap
//
// On macOS, use g++-12 from https://brew.sh (installation: brew install gcc@12).
// The g++ command also works with mingw C++ compiler (https://sourceforge.net/projects/mingw-w64)
// that comes bundled with Strawberry Perl (C:\Strawberry\c\bin\g++.exe).
//
// Obtain gen-llil.pl and gen-long-llil.pl from https://perlmonks.com/?node_id=11148681
// perl gen-llil.pl big1.txt 200 3 1
// perl gen-llil.pl big2.txt 200 3 1
// perl gen-llil.pl big3.txt 200 3 1
// perl gen-long-llil.pl long1.txt 600
// perl gen-long-llil.pl long2.txt 600
// perl gen-long-llil.pl long3.txt 600
//
// To make random input, obtain shuffle.pl from https://perlmonks.com/?node_id=11149800
// perl shuffle.pl big1.txt >tmp && mv tmp big1.txt
// perl shuffle.pl big2.txt >tmp && mv tmp big2.txt
// perl shuffle.pl big3.txt >tmp && mv tmp big3.txt
//
// Example run: llil4map big1.txt big2.txt big3.txt >out.txt
// NUM_THREADS=3 llil4map ...
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// Specify 0/1 to use boost's parallel sorting algorithm; faster than __gnu_parallel::sort.
// https://www.boost.org/doc/libs/1_81_0/libs/sort/doc/html/sort/parallel.html
// This requires the boost header files: e.g. devpkg-boost bundle on Clear Linux.
// Note: Another option is downloading and unpacking Boost locally.
// (no need to build it because the bits we use are header file only)
#include <string_view>
#define USE_BOOST_PARALLEL_SORT 0
#include <chrono>
#include <thread>
#include <parallel_hashmap/phmap.h>
#include <cstdio>
#include <cstddef>
#include <cstdint>
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <string>
#include <array>
#include <vector>
#include <utility>
#include <iterator>
#include <execution>
#include <algorithm>
#if USE_BOOST_PARALLEL_SORT > 0
#include <boost/sort/sort.hpp>
#endif
#ifdef _OPENMP
#include <omp.h>
#endif
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
static_assert(sizeof(size_t) == sizeof(int64_t), "size_t too small, need a 64-bit compile");
#include <atomic>
#include <cstddef>
class spinlock_mutex {
// https://rigtorp.se/spinlock/
// https://vorbrodt.blog/2019/02/12/fast-mutex/
public:
void lock() noexcept {
for (;;) {
if (!lock_.exchange(true, std::memory_order_acquire))
break;
while (lock_.load(std::memory_order_relaxed))
__builtin_ia32_pause();
}
}
void unlock() noexcept {
lock_.store(false, std::memory_order_release);
}
private:
alignas(4 * sizeof(std::max_align_t)) std::atomic_bool lock_ = false;
};
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
typedef uint32_t int_type;
// All words in big1.txt, big2.txt, big3.txt are <= 6 chars in length.
// big.txt max word length is 6
// long.txt max word length is 208
//
// Based on rough benchmarking, the short fixed string hack below is only
// worth trying for MAX_STR_LEN_L up to about 30.
// See also https://backlinko.com/google-keyword-study
//
// To use (limited length) fixed length strings uncomment the next line.
//#define MAX_STR_LEN_L (size_t) 12
#ifdef MAX_STR_LEN_L
struct str_type : std::array<char, MAX_STR_LEN_L> {
bool operator==( const str_type& o ) const {
return ::memcmp(this->data(), o.data(), MAX_STR_LEN_L) == 0;
}
bool operator<( const str_type& o ) const {
return ::memcmp(this->data(), o.data(), MAX_STR_LEN_L) < 0;
}
};
// inject specialization of std::hash for str_type into namespace std
namespace std {
template<> struct hash<str_type> {
std::size_t operator()( str_type const& v ) const noexcept {
std::basic_string_view<char> bv {
reinterpret_cast<const char*>(v.data()), v.size() * sizeof(char) };
return std::hash<std::basic_string_view<char>>()(bv);
}
};
}
#else
using str_type = std::basic_string<char>;
#endif
using str_int_type = std::pair<str_type, int_type>;
using vec_str_int_type = std::vector<str_int_type>;
// create the parallel_flat_hash_map with mutexes
using map_str_int_type = phmap::parallel_flat_hash_map<
str_type, int_type,
phmap::priv::hash_default_hash<str_type>,
phmap::priv::hash_default_eq<str_type>,
phmap::priv::Allocator<phmap::priv::Pair<const str_type, int_type>>,
12,
spinlock_mutex
>;
// Mimic the Perl get_properties subroutine ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// fast_atoll64
// https://stackoverflow.com/questions/16826422/
// c-most-efficient-way-to-convert-string-to-int-faster-than-atoi
inline int64_t fast_atoll64( const char* str )
{
int64_t val = 0;
int sign = 0;
if (*str == '-') {
sign = 1, ++str;
}
uint8_t digit;
while ((digit = uint8_t(*str++ - '0')) <= 9)
val = val * 10 + digit;
return sign ? -val : val;
}
// Helper function to find a character.
inline char* find_char(char* first, char* last, char c)
{
while (first != last) {
if (*first == c) break;
++first;
}
return first;
}
// Limit chunk size and line length.
inline constexpr size_t CHUNK_SIZE = 32768;
inline constexpr size_t MAX_LINE_LEN = 255;
static int64_t get_properties(
const char* fname, // in : the input file name
const int nthds, // in : the number of threads
map_str_int_type& map_ret) // inout : the map to be updated
{
int64_t num_lines = 0;
std::ifstream fin(fname, std::ifstream::binary);
if (!fin.is_open()) {
std::cerr << "Error opening '" << fname << "' : " << strerror(errno) << '\n';
return num_lines;
}
#pragma omp parallel reduction(+:num_lines)
{
std::string buf; buf.resize(CHUNK_SIZE + MAX_LINE_LEN + 1, '\0');
char *first, *last, *found;
size_t len, klen;
int_type count;
while (fin.good()) {
len = 0;
// Read the next chunk serially.
#pragma omp critical
{
fin.read(&buf[0], CHUNK_SIZE);
if ((len = fin.gcount()) > 0) {
if (buf[len - 1] != '\n' && fin.getline(&buf[len], MAX_LINE_LEN)) {
// Getline discards the newline char and appends null char.
// Therefore, change '\0' to '\n'.
len += fin.gcount();
buf[len - 1] = '\n';
}
}
}
if (!len) break;
buf[len] = '\0';
first = &buf[0];
last = &buf[len];
// Process max Nthreads chunks concurrently.
while (first < last) {
char* beg_ptr{first}; first = find_char(first, last, '\n');
char* end_ptr{first}; ++first, ++num_lines;
if ((found = find_char(beg_ptr, end_ptr, '\t')) == end_ptr) continue;
count = fast_atoll64(found + 1);
#ifdef MAX_STR_LEN_L
str_type s {}; // {} initializes all elements of s to '\0'
klen = std::min(MAX_STR_LEN_L, (size_t)(found - beg_ptr));
::memcpy(s.data(), beg_ptr, klen);
#else
klen = found - beg_ptr;
str_type s(beg_ptr, klen);
#endif
// Use lazy_emplace to modify the map while the mutex is locked.
map_ret.lazy_emplace_l(
s,
[&](map_str_int_type::value_type& p) {
// called only when key was already present
p.second += count;
},
[&](const map_str_int_type::constructor& ctor) {
// construct value_type in place when key not present
ctor(std::move(s), count);
}
);
}
}
}
fin.close();
return num_lines;
}
// Output subroutine ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
size_t divide_up(size_t dividend, size_t divisor)
{
if (dividend % divisor)
return (size_t)(dividend / divisor) + 1;
else
return (size_t)(dividend / divisor);
}
static void out_properties(
const int nthds, // in : the number of threads
vec_str_int_type& vec) // in : the vector to output
{
size_t num_chunks = divide_up(vec.size(), CHUNK_SIZE);
#ifdef _OPENMP
int nthds_out = std::min(nthds, 6);
#endif
#pragma omp parallel for ordered schedule(static, 1) num_threads(nthds_out)
for (size_t chunk_id = 1; chunk_id <= num_chunks; ++chunk_id) {
std::string str(""); str.reserve(2048 * 1024);
auto it = vec.begin() + (chunk_id - 1) * CHUNK_SIZE;
auto it2 = vec.begin() + std::min(vec.size(), chunk_id * CHUNK_SIZE);
for (; it != it2; ++it) {
#ifdef MAX_STR_LEN_L
str.append(it->first.data());
#else
str.append(it->first.data(), it->first.size());
#endif
str.append("\t", 1);
str.append(std::to_string(it->second));
str.append("\n", 1);
}
#pragma omp ordered
std::cout << str << std::flush;
}
}
typedef std::chrono::high_resolution_clock high_resolution_clock;
typedef std::chrono::high_resolution_clock::time_point time_point;
typedef std::chrono::milliseconds milliseconds;
double elaspe_time(
time_point cend,
time_point cstart)
{
return double (
std::chrono::duration_cast<milliseconds>(cend - cstart).count()
) * 1e-3;
}
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
int main(int argc, char* argv[])
{
if (argc < 2) {
if (argc > 0)
std::cerr << "usage: llil4map file1 file2 ... >out.txt\n";
return 1;
}
std::cerr << std::setprecision(3) << std::setiosflags(std::ios::fixed);
#ifdef MAX_STR_LEN_L
std::cerr << "llil4map (fixed string length=" << MAX_STR_LEN_L << ") start\n";
#else
std::cerr << "llil4map start\n";
#endif
#ifdef _OPENMP
std::cerr << "use OpenMP\n";
#else
std::cerr << "don't use OpenMP\n";
#endif
#if USE_BOOST_PARALLEL_SORT == 0
std::cerr << "don't use boost sort\n";
#else
std::cerr << "use boost sort\n";
#endif
time_point cstart1, cend1, cstart2, cend2, cstart3, cend3s, cend3;
cstart1 = high_resolution_clock::now();
#ifdef _OPENMP
// Determine the number of threads.
const char* env_nthds = std::getenv("NUM_THREADS");
int nthds = ( env_nthds && strlen(env_nthds) )
? ::atoi(env_nthds)
: std::thread::hardware_concurrency();
omp_set_dynamic(false);
omp_set_num_threads(nthds);
omp_set_max_active_levels(1);
int nthds_move = std::min(nthds, 6);
#else
int nthds = 1;
#endif
// Get the list of input files from the command line
int nfiles = argc - 1;
char** fname = &argv[1];
// Store the properties into a vector
vec_str_int_type propvec;
int64_t num_lines = 0;
{
// Enclose the map inside a block, so GC releases the object
// immediately after exiting the scope.
map_str_int_type map;
for (int i = 0; i < nfiles; ++i)
num_lines += get_properties(fname[i], nthds, map);
cend1 = high_resolution_clock::now();
double ctaken1 = elaspe_time(cend1, cstart1);
std::cerr << "get properties " << std::setw(8) << ctaken1 << " secs\n";
if (map.size() == 0) {
std::cerr << "No work, exiting...\n";
return 1;
}
cstart2 = high_resolution_clock::now();
if (nthds == 1) {
propvec.reserve(map.size());
for (auto const& x : map)
propvec.emplace_back(std::move(x.first), x.second);
}
else {
propvec.resize(map.size());
std::vector<vec_str_int_type::iterator> I; I.resize(map.subcnt());
I[0] = propvec.begin();
size_t prev_num_keys;
for (size_t i = 0; i < map.subcnt(); ++i) {
map.with_submap(i, [&](const map_str_int_type::EmbeddedSet& set) {
if (i == 0) {
prev_num_keys = set.size();
} else {
I[i] = I[i-1] + prev_num_keys;
prev_num_keys = set.size();
}
});
}
#pragma omp parallel for schedule(static, 1) num_threads(nthds_move)
for (size_t i = 0; i < map.subcnt(); ++i) {
map.with_submap_m(i, [&](map_str_int_type::EmbeddedSet& set) {
auto it = I[i];
for (auto& x : set)
*it++ = std::make_pair(std::move(const_cast<str_type&>(x.first)), x.second);
});
}
}
// phmap's clear() retains capacity until out of scope
// swap map with an empty temporary, which is immediately destroyed
// map.clear();
map_str_int_type().swap(map);
cend2 = high_resolution_clock::now();
double ctaken2 = elaspe_time(cend2, cstart2);
std::cerr << "map to vector " << std::setw(8) << ctaken2 << " secs\n";
}
cstart3 = high_resolution_clock::now();
// Sort the vector by (count) in reverse order, (name) in lexical order
#if USE_BOOST_PARALLEL_SORT == 0
std::sort(
// Standard sort
propvec.begin(), propvec.end(),
[](const str_int_type& left, const str_int_type& right) {
return left.second != right.second
? left.second > right.second
: left.first < right.first;
}
);
#else
boost::sort::block_indirect_sort(
// Parallel sort
propvec.begin(), propvec.end(),
[](const str_int_type& left, const str_int_type& right) {
return left.second != right.second
? left.second > right.second
: left.first < right.first;
},
std::min(nthds, 32)
);
#endif
cend3s = high_resolution_clock::now();
// Output the sorted vector
out_properties(nthds, propvec);
cend3 = high_resolution_clock::now();
double ctaken = elaspe_time(cend3, cstart1);
double ctaken3s = elaspe_time(cend3s, cstart3);
double ctaken3o = elaspe_time(cend3, cend3s);
std::cerr << "vector stable sort " << std::setw(8) << ctaken3s << " secs\n";
std::cerr << "write stdout " << std::setw(8) << ctaken3o << " secs\n";
std::cerr << "total time " << std::setw(8) << ctaken << " secs\n";
std::cerr << " count lines " << num_lines << "\n";
std::cerr << " count unique " << propvec.size() << "\n";
// Hack to see Private Bytes in Windows Task Manager
// (uncomment next line so process doesn't exit too quickly)
// std::this_thread::sleep_for(milliseconds(9000));
return 0;
}