diff options
| -rw-r--r-- | training/mpi_batch_optimize.cc | 35 | ||||
| -rw-r--r-- | utils/filelib.cc | 19 | ||||
| -rw-r--r-- | utils/filelib.h | 5 | ||||
| -rw-r--r-- | utils/stringlib.cc | 363 | ||||
| -rw-r--r-- | utils/stringlib.h | 3 | ||||
| -rw-r--r-- | utils/ts.cc | 6 |
6 files changed, 427 insertions, 4 deletions
diff --git a/training/mpi_batch_optimize.cc b/training/mpi_batch_optimize.cc index cc5953f6..0ba8c530 100644 --- a/training/mpi_batch_optimize.cc +++ b/training/mpi_batch_optimize.cc @@ -22,6 +22,7 @@ namespace mpi = boost::mpi; #include "ff_register.h" #include "decoder.h" #include "filelib.h" +#include "stringlib.h" #include "optimize.h" #include "fdict.h" #include "weights.h" @@ -42,6 +43,7 @@ bool InitCommandLine(int argc, char** argv, po::variables_map* conf) { ("correction_buffers,M", po::value<int>()->default_value(10), "Number of gradients for LBFGS to maintain in memory") ("gaussian_prior,p","Use a Gaussian prior on the weights") ("means,u", po::value<string>(), "File containing the means for Gaussian prior") + ("per_sentence_grammar_scratch,P", po::value<string>(), "(Optional) location of scratch space to copy per-sentence grammars for fast access, useful if a RAM disk is available") ("sigma_squared", po::value<double>()->default_value(1.0), "Sigma squared term for spherical Gaussian prior"); po::options_description clo("Command line options"); clo.add_options() @@ -186,6 +188,36 @@ struct VectorPlus : public binary_function<vector<T>, vector<T>, vector<T> > { } }; +void MovePerSentenceGrammars(const string& root, int size, int rank, vector<string>* c) { + if (!DirectoryExists(root)) { + cerr << "Can't find scratch space at " << root << endl; + abort(); + } + ostringstream os; + os << root << "/psg." << size << "_of_" << rank; + const string path = os.str(); + MkDirP(path); + string sent; + map<string, string> attr; + for (unsigned i = 0; i < c->size(); ++i) { + sent = (*c)[i]; + attr.clear(); + ProcessAndStripSGML(&sent, &attr); + map<string, string>::iterator it = attr.find("grammar"); + if (it != attr.end()) { + string src_file = it->second; + bool is_gzipped = (src_file.size() > 3) && (src_file.rfind(".gz") == (src_file.size() - 3)); + string new_name = path + "/" + md5(sent); + if (is_gzipped) new_name += ".gz"; + CopyFile(src_file, new_name); + it->second = new_name; + } + ostringstream ns; + ns << SGMLOpenSegTag(attr) << ' ' << sent << " </seg>"; + (*c)[i] = ns.str(); + } +} + int main(int argc, char** argv) { #ifdef HAVE_MPI mpi::environment env(argc, argv); @@ -257,6 +289,9 @@ int main(int argc, char** argv) { ReadTrainingCorpus(conf["training_data"].as<string>(), rank, size, &corpus); assert(corpus.size() > 0); + if (conf.count("per_sentence_grammar_scratch")) + MovePerSentenceGrammars(conf["per_sentence_grammar_scratch"].as<string>(), rank, size, &corpus); + TrainingObserver observer; while (!converged) { observer.Reset(); diff --git a/utils/filelib.cc b/utils/filelib.cc index a0969b1a..d206fc19 100644 --- a/utils/filelib.cc +++ b/utils/filelib.cc @@ -2,6 +2,12 @@ #include <unistd.h> #include <sys/stat.h> +#include <sys/types.h> +#include <sys/socket.h> +#include <cstdlib> +#include <cstdio> +#include <sys/stat.h> +#include <sys/types.h> using namespace std; @@ -32,3 +38,16 @@ void MkDirP(const string& dir) { } } +#if 0 +void CopyFile(const string& inf, const string& outf) { + WriteFile w(outf); + CopyFile(inf,*w); +} +#else +void CopyFile(const string& inf, const string& outf) { + ofstream of(outf.c_str(), fstream::trunc|fstream::binary); + ifstream in(inf.c_str(), fstream::binary); + of << in.rdbuf(); +} +#endif + diff --git a/utils/filelib.h b/utils/filelib.h index a8622246..bb6e7415 100644 --- a/utils/filelib.h +++ b/utils/filelib.h @@ -113,9 +113,6 @@ inline void CopyFile(std::string const& inf,std::ostream &out) { CopyFile(*r,out); } -inline void CopyFile(std::string const& inf,std::string const& outf) { - WriteFile w(outf); - CopyFile(inf,*w); -} +void CopyFile(std::string const& inf,std::string const& outf); #endif diff --git a/utils/stringlib.cc b/utils/stringlib.cc index ade02ca9..3a56965c 100644 --- a/utils/stringlib.cc +++ b/utils/stringlib.cc @@ -90,3 +90,366 @@ void ProcessAndStripSGML(string* pline, map<string, string>* out) { } } +string SGMLOpenSegTag(const map<string, string>& attr) { + ostringstream os; + os << "<seg"; + for (map<string,string>::const_iterator it = attr.begin(); it != attr.end(); ++it) + os << ' ' << it->first << '=' << '"' << it->second << '"'; + os << '>'; + return os.str(); +} + +class MD5 { +public: + typedef unsigned int size_type; // must be 32bit + + MD5(); + MD5(const std::string& text); + void update(const unsigned char *buf, size_type length); + void update(const char *buf, size_type length); + MD5& finalize(); + std::string hexdigest() const; + +private: + void init(); + typedef unsigned char uint1; // 8bit + typedef unsigned int uint4; // 32bit + enum {blocksize = 64}; // VC6 won't eat a const static int here + + void transform(const uint1 block[blocksize]); + static void decode(uint4 output[], const uint1 input[], size_type len); + static void encode(uint1 output[], const uint4 input[], size_type len); + + bool finalized; + uint1 buffer[blocksize]; // bytes that didn't fit in last 64 byte chunk + uint4 count[2]; // 64bit counter for number of bits (lo, hi) + uint4 state[4]; // digest so far + uint1 digest[16]; // the result + + // low level logic operations + static inline uint4 F(uint4 x, uint4 y, uint4 z); + static inline uint4 G(uint4 x, uint4 y, uint4 z); + static inline uint4 H(uint4 x, uint4 y, uint4 z); + static inline uint4 I(uint4 x, uint4 y, uint4 z); + static inline uint4 rotate_left(uint4 x, int n); + static inline void FF(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac); + static inline void GG(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac); + static inline void HH(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac); + static inline void II(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac); +}; + +// Constants for MD5Transform routine. +#define S11 7 +#define S12 12 +#define S13 17 +#define S14 22 +#define S21 5 +#define S22 9 +#define S23 14 +#define S24 20 +#define S31 4 +#define S32 11 +#define S33 16 +#define S34 23 +#define S41 6 +#define S42 10 +#define S43 15 +#define S44 21 + +/////////////////////////////////////////////// + +// F, G, H and I are basic MD5 functions. +inline MD5::uint4 MD5::F(uint4 x, uint4 y, uint4 z) { + return (x&y) | (~x&z); +} + +inline MD5::uint4 MD5::G(uint4 x, uint4 y, uint4 z) { + return (x&z) | (y&~z); +} + +inline MD5::uint4 MD5::H(uint4 x, uint4 y, uint4 z) { + return x^y^z; +} + +inline MD5::uint4 MD5::I(uint4 x, uint4 y, uint4 z) { + return y ^ (x | ~z); +} + +// rotate_left rotates x left n bits. +inline MD5::uint4 MD5::rotate_left(uint4 x, int n) { + return (x << n) | (x >> (32-n)); +} + +// FF, GG, HH, and II transformations for rounds 1, 2, 3, and 4. +// Rotation is separate from addition to prevent recomputation. +inline void MD5::FF(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac) { + a = rotate_left(a+ F(b,c,d) + x + ac, s) + b; +} + +inline void MD5::GG(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac) { + a = rotate_left(a + G(b,c,d) + x + ac, s) + b; +} + +inline void MD5::HH(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac) { + a = rotate_left(a + H(b,c,d) + x + ac, s) + b; +} + +inline void MD5::II(uint4 &a, uint4 b, uint4 c, uint4 d, uint4 x, uint4 s, uint4 ac) { + a = rotate_left(a + I(b,c,d) + x + ac, s) + b; +} + +////////////////////////////////////////////// + +// default ctor, just initailize +MD5::MD5() +{ + init(); +} + +////////////////////////////////////////////// + +// nifty shortcut ctor, compute MD5 for string and finalize it right away +MD5::MD5(const std::string &text) +{ + init(); + update(text.c_str(), text.length()); + finalize(); +} + +////////////////////////////// + +void MD5::init() +{ + finalized=false; + + count[0] = 0; + count[1] = 0; + + // load magic initialization constants. + state[0] = 0x67452301; + state[1] = 0xefcdab89; + state[2] = 0x98badcfe; + state[3] = 0x10325476; +} + +////////////////////////////// + +// decodes input (unsigned char) into output (uint4). Assumes len is a multiple of 4. +void MD5::decode(uint4 output[], const uint1 input[], size_type len) +{ + for (unsigned int i = 0, j = 0; j < len; i++, j += 4) + output[i] = ((uint4)input[j]) | (((uint4)input[j+1]) << 8) | + (((uint4)input[j+2]) << 16) | (((uint4)input[j+3]) << 24); +} + +////////////////////////////// + +// encodes input (uint4) into output (unsigned char). Assumes len is +// a multiple of 4. +void MD5::encode(uint1 output[], const uint4 input[], size_type len) +{ + for (size_type i = 0, j = 0; j < len; i++, j += 4) { + output[j] = input[i] & 0xff; + output[j+1] = (input[i] >> 8) & 0xff; + output[j+2] = (input[i] >> 16) & 0xff; + output[j+3] = (input[i] >> 24) & 0xff; + } +} + +////////////////////////////// + +// apply MD5 algo on a block +void MD5::transform(const uint1 block[blocksize]) +{ + uint4 a = state[0], b = state[1], c = state[2], d = state[3], x[16]; + decode (x, block, blocksize); + + /* Round 1 */ + FF (a, b, c, d, x[ 0], S11, 0xd76aa478); /* 1 */ + FF (d, a, b, c, x[ 1], S12, 0xe8c7b756); /* 2 */ + FF (c, d, a, b, x[ 2], S13, 0x242070db); /* 3 */ + FF (b, c, d, a, x[ 3], S14, 0xc1bdceee); /* 4 */ + FF (a, b, c, d, x[ 4], S11, 0xf57c0faf); /* 5 */ + FF (d, a, b, c, x[ 5], S12, 0x4787c62a); /* 6 */ + FF (c, d, a, b, x[ 6], S13, 0xa8304613); /* 7 */ + FF (b, c, d, a, x[ 7], S14, 0xfd469501); /* 8 */ + FF (a, b, c, d, x[ 8], S11, 0x698098d8); /* 9 */ + FF (d, a, b, c, x[ 9], S12, 0x8b44f7af); /* 10 */ + FF (c, d, a, b, x[10], S13, 0xffff5bb1); /* 11 */ + FF (b, c, d, a, x[11], S14, 0x895cd7be); /* 12 */ + FF (a, b, c, d, x[12], S11, 0x6b901122); /* 13 */ + FF (d, a, b, c, x[13], S12, 0xfd987193); /* 14 */ + FF (c, d, a, b, x[14], S13, 0xa679438e); /* 15 */ + FF (b, c, d, a, x[15], S14, 0x49b40821); /* 16 */ + + /* Round 2 */ + GG (a, b, c, d, x[ 1], S21, 0xf61e2562); /* 17 */ + GG (d, a, b, c, x[ 6], S22, 0xc040b340); /* 18 */ + GG (c, d, a, b, x[11], S23, 0x265e5a51); /* 19 */ + GG (b, c, d, a, x[ 0], S24, 0xe9b6c7aa); /* 20 */ + GG (a, b, c, d, x[ 5], S21, 0xd62f105d); /* 21 */ + GG (d, a, b, c, x[10], S22, 0x2441453); /* 22 */ + GG (c, d, a, b, x[15], S23, 0xd8a1e681); /* 23 */ + GG (b, c, d, a, x[ 4], S24, 0xe7d3fbc8); /* 24 */ + GG (a, b, c, d, x[ 9], S21, 0x21e1cde6); /* 25 */ + GG (d, a, b, c, x[14], S22, 0xc33707d6); /* 26 */ + GG (c, d, a, b, x[ 3], S23, 0xf4d50d87); /* 27 */ + GG (b, c, d, a, x[ 8], S24, 0x455a14ed); /* 28 */ + GG (a, b, c, d, x[13], S21, 0xa9e3e905); /* 29 */ + GG (d, a, b, c, x[ 2], S22, 0xfcefa3f8); /* 30 */ + GG (c, d, a, b, x[ 7], S23, 0x676f02d9); /* 31 */ + GG (b, c, d, a, x[12], S24, 0x8d2a4c8a); /* 32 */ + + /* Round 3 */ + HH (a, b, c, d, x[ 5], S31, 0xfffa3942); /* 33 */ + HH (d, a, b, c, x[ 8], S32, 0x8771f681); /* 34 */ + HH (c, d, a, b, x[11], S33, 0x6d9d6122); /* 35 */ + HH (b, c, d, a, x[14], S34, 0xfde5380c); /* 36 */ + HH (a, b, c, d, x[ 1], S31, 0xa4beea44); /* 37 */ + HH (d, a, b, c, x[ 4], S32, 0x4bdecfa9); /* 38 */ + HH (c, d, a, b, x[ 7], S33, 0xf6bb4b60); /* 39 */ + HH (b, c, d, a, x[10], S34, 0xbebfbc70); /* 40 */ + HH (a, b, c, d, x[13], S31, 0x289b7ec6); /* 41 */ + HH (d, a, b, c, x[ 0], S32, 0xeaa127fa); /* 42 */ + HH (c, d, a, b, x[ 3], S33, 0xd4ef3085); /* 43 */ + HH (b, c, d, a, x[ 6], S34, 0x4881d05); /* 44 */ + HH (a, b, c, d, x[ 9], S31, 0xd9d4d039); /* 45 */ + HH (d, a, b, c, x[12], S32, 0xe6db99e5); /* 46 */ + HH (c, d, a, b, x[15], S33, 0x1fa27cf8); /* 47 */ + HH (b, c, d, a, x[ 2], S34, 0xc4ac5665); /* 48 */ + + /* Round 4 */ + II (a, b, c, d, x[ 0], S41, 0xf4292244); /* 49 */ + II (d, a, b, c, x[ 7], S42, 0x432aff97); /* 50 */ + II (c, d, a, b, x[14], S43, 0xab9423a7); /* 51 */ + II (b, c, d, a, x[ 5], S44, 0xfc93a039); /* 52 */ + II (a, b, c, d, x[12], S41, 0x655b59c3); /* 53 */ + II (d, a, b, c, x[ 3], S42, 0x8f0ccc92); /* 54 */ + II (c, d, a, b, x[10], S43, 0xffeff47d); /* 55 */ + II (b, c, d, a, x[ 1], S44, 0x85845dd1); /* 56 */ + II (a, b, c, d, x[ 8], S41, 0x6fa87e4f); /* 57 */ + II (d, a, b, c, x[15], S42, 0xfe2ce6e0); /* 58 */ + II (c, d, a, b, x[ 6], S43, 0xa3014314); /* 59 */ + II (b, c, d, a, x[13], S44, 0x4e0811a1); /* 60 */ + II (a, b, c, d, x[ 4], S41, 0xf7537e82); /* 61 */ + II (d, a, b, c, x[11], S42, 0xbd3af235); /* 62 */ + II (c, d, a, b, x[ 2], S43, 0x2ad7d2bb); /* 63 */ + II (b, c, d, a, x[ 9], S44, 0xeb86d391); /* 64 */ + + state[0] += a; + state[1] += b; + state[2] += c; + state[3] += d; + + // Zeroize sensitive information. + memset(x, 0, sizeof x); +} + +////////////////////////////// + +// MD5 block update operation. Continues an MD5 message-digest +// operation, processing another message block +void MD5::update(const unsigned char input[], size_type length) +{ + // compute number of bytes mod 64 + size_type index = count[0] / 8 % blocksize; + + // Update number of bits + if ((count[0] += (length << 3)) < (length << 3)) + count[1]++; + count[1] += (length >> 29); + + // number of bytes we need to fill in buffer + size_type firstpart = 64 - index; + + size_type i; + + // transform as many times as possible. + if (length >= firstpart) + { + // fill buffer first, transform + memcpy(&buffer[index], input, firstpart); + transform(buffer); + + // transform chunks of blocksize (64 bytes) + for (i = firstpart; i + blocksize <= length; i += blocksize) + transform(&input[i]); + + index = 0; + } + else + i = 0; + + // buffer remaining input + memcpy(&buffer[index], &input[i], length-i); +} + +////////////////////////////// + +// for convenience provide a verson with signed char +void MD5::update(const char input[], size_type length) +{ + update((const unsigned char*)input, length); +} + +////////////////////////////// + +// MD5 finalization. Ends an MD5 message-digest operation, writing the +// the message digest and zeroizing the context. +MD5& MD5::finalize() +{ + static unsigned char padding[64] = { + 0x80, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + + if (!finalized) { + // Save number of bits + unsigned char bits[8]; + encode(bits, count, 8); + + // pad out to 56 mod 64. + size_type index = count[0] / 8 % 64; + size_type padLen = (index < 56) ? (56 - index) : (120 - index); + update(padding, padLen); + + // Append length (before padding) + update(bits, 8); + + // Store state in digest + encode(digest, state, 16); + + // Zeroize sensitive information. + memset(buffer, 0, sizeof buffer); + memset(count, 0, sizeof count); + + finalized=true; + } + + return *this; +} + +////////////////////////////// + +// return hex representation of digest as string +std::string MD5::hexdigest() const +{ + if (!finalized) + return ""; + + char buf[33]; + for (int i=0; i<16; i++) + sprintf(buf+i*2, "%02x", digest[i]); + buf[32]=0; + + return std::string(buf); +} + +////////////////////////////// + +std::string md5(const std::string& str) { + MD5 md5 = MD5(str); + return md5.hexdigest(); +} + diff --git a/utils/stringlib.h b/utils/stringlib.h index 8022bb88..cafbdac3 100644 --- a/utils/stringlib.h +++ b/utils/stringlib.h @@ -249,6 +249,7 @@ inline void SplitCommandAndParam(const std::string& in, std::string* cmd, std::s } void ProcessAndStripSGML(std::string* line, std::map<std::string, std::string>* out); +std::string SGMLOpenSegTag(const std::map<std::string, std::string>& attr); // given the first character of a UTF8 block, find out how wide it is // see http://en.wikipedia.org/wiki/UTF-8 for more info @@ -260,4 +261,6 @@ inline unsigned int UTF8Len(unsigned char x) { else return 0; } +std::string md5(const std::string& in); + #endif diff --git a/utils/ts.cc b/utils/ts.cc index 3694e076..bf4f8f69 100644 --- a/utils/ts.cc +++ b/utils/ts.cc @@ -7,6 +7,7 @@ #include "prob.h" #include "sparse_vector.h" #include "fast_sparse_vector.h" +#include "stringlib.h" using namespace std; @@ -79,6 +80,11 @@ int main() { y -= y; } cerr << "Counted " << c << " times\n"; + + cerr << md5("this is a test") << endl; + cerr << md5("some other ||| string is") << endl; + map<string,string> x; x["id"] = "12"; x["grammar"] = "/path/to/grammar.gz"; + cerr << SGMLOpenSegTag(x) << endl; return 0; } |