// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // llil4judy.cc // A Judy SL demonstration. // https://www.perlmonks.org/?node_id=11149800 // // April 25, 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 // // Authors // Mario Roy - C++ demonstration with parallel capabilities // eyepopslikeamosquito - Co-author, learning C++ at PerlMonks.com // // See also, memory efficient variant // https://gist.github.com/marioroy/d02881b96b20fa1adde4388b3e216163 // // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // OpenMP Little Book - https://nanxiao.gitbooks.io/openmp-little-book // // This requires the boost library: boost::static_strings::basic_static_string. // // Obtain, build, and install the Judy array library. // I downloaded two patch files from the gentoo site. // https://judy.sourceforge.net/index.html // https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-libs/judy // https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-libs/judy/files // // tar xf ~/Downloads/Judy-1.0.5.tar.gz // cd judy-1.0.5 // // patch -p0 < ~/Downloads/judy-1.0.5-parallel-make.patch // patch -p1 < ~/Downloads/judy-1.0.5-gcc49.patch // // sed -i 's/automake-1.9/automake/' bootstrap // sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac // // ./configure --enable-64-bit // // # Omit passing the -j option to make. It may fail due to parallel build. // make // sudo make install // sudo rm /usr/local/lib/libJudy.la // sudo ldconfig // // Compile on Linux (clang++ or g++): // clang++ -o llil4judy -std=c++20 -fopenmp -Wall -O3 llil4judy.cc -I/usr/local/include -L/usr/local/lib -lJudy // // 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 // // 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: llil4judy big1.txt big2.txt big3.txt >out.txt // NUM_THREADS=3 llil4judy ... // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static_assert(sizeof(size_t) == sizeof(int64_t), "size_t too small, need a 64-bit compile"); // Specify 0/1 to use boost's parallel sorting algorithm; faster than __gnu_parallel::sort. // https://www.boost.org/doc/libs/1_85_0/libs/sort/doc/html/sort/parallel.html // https://www.boost.org/doc/libs/1_85_0/libs/sort/doc/papers/block_indirect_sort_en.pdf // 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) #define USE_BOOST_PARALLEL_SORT 1 #if USE_BOOST_PARALLEL_SORT #ifdef __clang__ #pragma clang diagnostic push #pragma clang diagnostic ignored "-Wunused-parameter" #pragma clang diagnostic ignored "-Wshadow" #include #pragma clang diagnostic pop #else #include #endif #endif #ifdef _OPENMP #include #endif class spinlock_mutex { // https://rigtorp.se/spinlock/ // https://vorbrodt.blog/2019/02/12/fast-mutex/ public: // Assignment is disabled. spinlock_mutex& operator=(const spinlock_mutex& rhs) = delete; 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; }; // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // Judy wrappers // // The Judy C macros are not compatible with C++, so created wrappers. // One of the difficulties in using the Judy function calls lies in // determining whether to pass a pointer or the address of a pointer. // I looked up the functions in /usr/local/include/Judy.h. // inline PWord_t judysl_ins( Pvoid_t &(array), const char* index ) { return (PWord_t) ::JudySLIns(&(array), (const uint8_t *) index, NULL); } inline Word_t judysl_freearray( Pvoid_t &(array) ) { return (Word_t) ::JudySLFreeArray(&(array), NULL); } inline PWord_t judysl_get( Pcvoid_t array, const char* index ) { return (PWord_t) ::JudySLGet(array, (const uint8_t *) index, NULL); } inline PWord_t judysl_first( Pcvoid_t array, char* index ) { return (PWord_t) ::JudySLFirst(array, (uint8_t *) index, NULL); } inline PWord_t judysl_next( Pcvoid_t array, char* index ) { return (PWord_t) ::JudySLNext(array, (uint8_t *) index, NULL); } // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 #include using hash_type = uint32_t; using str_type = boost::static_strings::basic_static_string; #else using hash_type = uint64_t; using str_type = std::basic_string; #endif using str_int_type = std::pair; using vec_str_int_type = std::vector; // Mimic the Perl get_properties subroutine ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // convert positive number from string to uint32_t inline uint32_t fast_atoll64(const char* str) { uint32_t val = 0; uint8_t digit; while ((digit = uint8_t(*str++ - '0')) <= 9) val = val * 10 + digit; return 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; } inline constexpr size_t CHUNK_SIZE = 32768; inline constexpr size_t MAX_LINE_LEN = 255; inline constexpr size_t NUM_MAPS = 963; static int64_t get_properties( const char* fname, // in : the input file name const int nthds, // in : the number of threads auto& L, // in : the locks array auto& M, // inout : the maps array auto& T) // inout : the totals array { 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'); while (fin.good()) { size_t 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'; char *first = &buf[0]; char *last = &buf[len]; // Process max Nthreads chunks concurrently. while (first < last) { char* beg_ptr{first}; char* end_ptr{find_char(first, last, '\n')}; char* found = find_char(beg_ptr, end_ptr, '\t'); first = end_ptr + 1; if (found == end_ptr) continue; assert(*found == '\t'); int_type count = fast_atoll64(found + 1); #ifdef MAX_STR_LEN_L size_t klen = std::min(MAX_STR_LEN_L, (size_t)(found - beg_ptr)); beg_ptr[klen] = '\0'; #else size_t klen = found - beg_ptr; beg_ptr[klen] = '\0'; #endif size_t hv = std::hash>{}( std::basic_string_view{ reinterpret_cast(beg_ptr), klen }); size_t idx = ( ((hv & 0x000000000000ffffULL) << 16) | ((hv & 0x00000000ffff0000ULL) >> 16) ) % NUM_MAPS; if (nthds == 1) { PWord_t PValue = judysl_get(M[idx], beg_ptr); if (! PValue) { PValue = judysl_ins(M[idx], beg_ptr); ++T[idx]; } (*PValue) += count; } else { L[idx].lock(); PWord_t PValue = judysl_get(M[idx], beg_ptr); if (! PValue) { PValue = judysl_ins(M[idx], beg_ptr); ++T[idx]; } (*PValue) += count; L[idx].unlock(); } ++num_lines; } } } fin.close(); // std::cerr << "getprops done\n"; 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); int nthds_out = 1; #ifdef _OPENMP nthds_out = std::min(nthds, 32); #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(cend - cstart).count() ) * 1e-3; } // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ int main(int argc, char* argv[]) { if (argc < 2) { if (argc > 0) std::cerr << "usage: llil4judy file1 file2 ... >out.txt\n"; return 1; } std::cerr << std::setprecision(3) << std::setiosflags(std::ios::fixed); #ifdef MAX_STR_LEN_L std::cerr << "llil4judy (fixed string length=" << MAX_STR_LEN_L << ") start\n"; #else std::cerr << "llil4judy 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, 12); #else int nthds = 1; int nthds_move = 1; #endif // Get the list of input files from the command line int nfiles = argc - 1; char** fname = &argv[1]; spinlock_mutex L[NUM_MAPS]; Pvoid_t M[NUM_MAPS]; std::size_t T[NUM_MAPS] {}; for (size_t i = 0; i < NUM_MAPS; ++i) M[i] = (Pvoid_t) NULL; int64_t num_lines = 0; for (int i = 0; i < nfiles; ++i) num_lines += get_properties(fname[i], nthds, L, M, T); int64_t num_keys = 0; for (size_t i = 0; i < NUM_MAPS; ++i) num_keys += T[i]; cend1 = high_resolution_clock::now(); double ctaken1 = elaspe_time(cend1, cstart1); std::cerr << "get properties " << std::setw(8) << ctaken1 << " secs\n"; cstart2 = high_resolution_clock::now(); // Store the properties into a vector vec_str_int_type propvec; propvec.resize(num_keys); std::array I; I[0] = propvec.begin(); for (size_t i = 1; i < NUM_MAPS; ++i) I[i] = I[i-1] + T[i-1]; #pragma omp parallel for schedule(static, 1) num_threads(nthds_move) for (size_t i = 0; i < NUM_MAPS; ++i) { char index[MAX_LINE_LEN+1]; index[0] = '\0'; PWord_t PValue; auto it = I[i]; PValue = judysl_first(M[i], index); while (PValue != NULL) { *it++ = std::make_pair(index, *PValue); PValue = judysl_next(M[i], index); } } cend2 = high_resolution_clock::now(); double ctaken2 = elaspe_time(cend2, cstart2); std::cerr << "judy to vector " << std::setw(8) << ctaken2 << " secs\n"; if (!propvec.size()) { std::cerr << "No work, exiting...\n"; return 1; } cstart3 = high_resolution_clock::now(); // Sort the vector by (count) in reverse order, (name) in lexical order auto reverse_order = [](const str_int_type& left, const str_int_type& right) { return left.second != right.second ? left.second > right.second #ifdef MAX_STR_LEN_L : ::memcmp(left.first.data(), right.first.data(), MAX_STR_LEN_L) < 0; #else : left.first < right.first; #endif }; #if USE_BOOST_PARALLEL_SORT == 0 // Standard sort std::sort(propvec.begin(), propvec.end(), reverse_order); #else // Parallel sort boost::sort::block_indirect_sort( propvec.begin(), propvec.end(), reverse_order, #ifdef __NVCOMPILER_LLVM__ std::min(nthds, 32) #else nthds #endif ); #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 " << num_keys << "\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; }