From 2281eb34dca09f067ea77b1906cfac15d7b8955c Mon Sep 17 00:00:00 2001 From: Jan Huwald Date: Mon, 11 Jan 2016 12:52:36 +0100 Subject: Initial release of the HRTC library diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..4394a32 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "integer_encoding_library"] + path = integer_encoding_library + url = https://github.com/biosystemanalysis/integer_encoding_library.git diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..cb214e9 --- /dev/null +++ b/Makefile @@ -0,0 +1,92 @@ +CXX=g++ -std=c++11 -O3 -march=native -mtune=native -Wall -Wextra +CXXFLAGS=-I./integer_encoding_library/include +LIBFLAGS= -I../tng/include -fPIC -DHRTC_VERSION=$(shell git log | head -n1 | cut -f2 -d' ') +BINFLAGS=-lboost_program_options -fwhole-program +LDFLAGS=$(wildcard ./integer_encoding_library/src/*.o) \ + $(wildcard ./integer_encoding_library/src/compress/*.o) \ + $(wildcard ./integer_encoding_library/src/compress/table/*.o) \ + $(wildcard ./integer_encoding_library/src/io/*.o) +SHELL=/bin/bash + +all: bin lib + +.PHONY: bin +bin: hrtc + +.PHONY: lib +lib: hrtc_wrapper.o + +.PHONY: clean +clean: + -rm hrtc *~ test/*{~,.{compr,loop,ident,line_count}} *.o + +%: %.cpp $(wildcard *.hpp) + $(CXX) $(CXXFLAGS) $(LDFLAGS) $(BINFLAGS) $< -o $@ + +hrtc_wrapper.o: hrtc_wrapper.cpp $(wildcard *.hpp) + $(CXX) -c $(CXXFLAGS) $(LIBFLAGS) $< -o $@ + + +### TESTS + +IDENT_TESTS := one_frame three_frames alternate manycol longtrans longrand +LINECOUNT_TESTS := rand + +TEST_BOUND := 100 +TEST_ERROR := 0.1 + +.PHONY: test +test: hrtc \ + $(patsubst %,test/%.ident,$(IDENT_TESTS)) \ + $(patsubst %,test/%.line_count,$(LINECOUNT_TESTS)) + +pass = (echo -e "\033[42m\033[37m\033[1m PASS \033[0m $@") +fail = (echo -e "\033[41m\033[37m\033[1m FAIL \033[0m $@" && false) +col_count = $(shell head -n1 $1 | tr "\t" "\n" | wc -l) + +test/test_num: test_num + time ./$< + touch $@ + +.PRECIOUS: test/%.compr +test/%.compr: test/% hrtc + @echo -e "Compress\t$<" + ./hrtc --src $< --numtraj $(call col_count,$<) --bound $(TEST_BOUND) --error $(TEST_ERROR) --format=tsvfloat --compress >$@~ + mv $@~ $@ + echo foo + +.PRECIOUS: test/%.loop +test/%.loop: test/%.compr hrtc + @echo -e "Decompress\t$<" + ./hrtc --src $< --numtraj $(call col_count,$(patsubst %.compr,%,$<)) --bound $(TEST_BOUND) --error $(TEST_ERROR) --format=tsvfloat --decompress >$@~ + mv $@~ $@ + +test/%.ident: test/% test/%.loop + @[ "$$(md5sum <$<)" == "$$(md5sum <$<.loop)" ] || $(fail) + @$(pass) + +test/%.line_count: test/% test/%.loop + @[ "$$(wc <$<)" == "$$(wc <$<.loop)" ] || $(fail) + @$(pass) + + +### benchmarks + +.PRECIOUS: bench/%.time_size +bench/%.time_size: bench/% hrtc + set -o pipefail; \ + for encoding in $$(seq 0 7; seq 9 17); do \ + (time (echo -en "code\t$$encoding\nsize\t"; ./hrtc --numtraj 429 --compress --bound 2 --error 0.04 --integer-encoding $$encoding <$< | wc -c)) 2>&1 \ + | grep -e ^user -e ^size -e ^code | cut -f2 | sed 's/m/*60 + /' | sed 's/s//' | bc | tr '\n' '\t'; \ + echo; \ + done > $@~ + mv $@~ $@ + +bench/%.time_size.pdf: bench/%.time_size + (echo "set terminal pdf;" \ + "set output '$@~';" \ + "set xlabel 'size [B]';" \ + "set ylabel 'time [s]';" \ + "set title 'size and time requirements of different integer encoders';" \ + "plot '$<' using (175718400/"'$$'"2):3:1 with labels point offset 1 title ''") | gnuplot + mv $@~ $@ diff --git a/README.org b/README.org new file mode 100644 index 0000000..bd6dcd3 --- /dev/null +++ b/README.org @@ -0,0 +1,64 @@ +#+TITLE: High Resolution Trajectory Compression + +* Overview + High Resolution Trajectory Compression (HRTC) is a method for + efficient storage of trajectories from particle simulators + (e.g. molecular dynamics, or agent based systems). + + This code builds a stand-alone program and a library for integration + into other programs. Both are fully functional research prototypes. + +* Installation +** Dependencies + - integer-encoding-library (included as sub-module) + - for the stand-alone program: libboost-program-options (part of [[https://boost.org][boost]]) + - for the library: our fork of [[https://github.com/biosystemanalysis/tng][trajectory-ng]], residing in the same + parent directory as this repository + + The software has only been tested on 64bit GNU/Linux systems using GCC. + +** Building + First set up the integer-encoding-library: +#+BEGIN_SRC sh +git submodule init +git submodule update +(cd integer_encoding_library && make) +#+END_SRC + + Then run ~make bin~, ~make lib~, or just ~make~ to build the + stand-alone program (~hrtc~), the library (~hrtc_wrapper.o~), or + both, respectively. + +* Usage + As uncompressed I/O format ~hrtc~ uses either tab-separated-values + (one time-step per line) or an awkward yet-to-document binary + format. + + Use +#+BEGIN_SRC sh +./hrtc --compress --format tsvfloat --numtraj 42 --bound 23 --error 0.1 \ + --src original_file --dst compressed_file +#+END_SRC + to compress and +#+BEGIN_SRC sh +./hrtc --decompress --format tsvfloat --numtraj 42 --bound 23 --error 0.1 \ + --src compressed_file --dst uncompressed_file +#+END_SRC + to decompress your data. The number of trajectories (rows per line) + has to be specified with ~--numtraj~ as well as the maximal absolute + value occurring in the trajectory (e.g. your bounding box) with + ~--bound~. Most important is the ~--error~ which specifies the + maximal distance of a particle between compressed and original + representation. + + Further parameters that can be tuned are ~--blocksize~, + ~--integer-encoding~, and the ~--qp-ratio~. The last is a value + between 0 and 1 the specifies how the error budget is split between + quantization error and approximation error. + +* License + The code is released under the GPL version 3 license (see file + LICENSE). + +* Contact + The authors can be contacted via email and jabber at jh@sotun.de. diff --git a/common.hpp b/common.hpp new file mode 100644 index 0000000..af59258 --- /dev/null +++ b/common.hpp @@ -0,0 +1,159 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include +#include +#include +#include +#include +#include +using namespace std; + +#include +#include +#include +#include +using boost::dynamic_bitset; +using boost::optional; +namespace prog_options = boost::program_options; + + +#include +using integer_encoding::EncodingPtr; + + +// space time points +typedef uint64_t Time; +const Time maxTime = Time(1) << 48; + +typedef uint16_t TId; +const TId maxTId = -1; + +union STP { + uint64_t raw; + struct { + Time time : 48; + TId id : 16; // trajectory id + }; + STP& operator= (STP const &s) { raw = s.raw; return *this; } + bool operator== (STP const &s) const { return raw == s.raw; } + +}; + +#define GEN(op) \ + bool operator op (STP p1, STP p2) { \ + static_assert(sizeof(p1) == sizeof(p1.raw), "STP not packed"); \ + return (p1.time op p2.time) || ((p1.time == p2.time) && (p1.id op p2.id)); \ + } +GEN(<) +GEN(>) +#undef GEN + +// support vector +struct SVI { + // To save space using the variable length encoding, dt-1 is + // stored. This works as dt >= 1 is guaranteed. + uint32_t dt; + // Signed difference, encoded via signed2unsigned + uint32_t v; +}; + +// A buffer that stores SVI structs (x0, v0), ..., (xn, vn) in memory +// as xn, ..., x0, v0, ..., vn and helps with (de)compression. This +// keeps numbers of the same magnitude proximate in memory while +// compressing only one buffer (storing only one size, not copying +// memory arounds) +// +// ATTENTION pointer mangling: uncompressed stores the center of the +// buffer pointed to by uncompressed_full. Elements are appended by +// growing in both directions. +struct SplitSVIBuffer { + size_t size, compressed_size; // no. of uint32_t, not bytes! + uint32_t *uncompressed_full, + *uncompressed, + *compressed; + EncodingPtr codec; + + // init with max. number of pairs to store + SplitSVIBuffer(EncodingPtr codec, size_t size) + : size(size), + compressed_size(codec->require(2 * size)), + uncompressed_full(new uint32_t[DECODE_REQUIRE_MEM(2 * size)]), + uncompressed(uncompressed_full + size), + compressed(new uint32_t[compressed_size]), + codec(codec) { + } + + void set(size_t pos, SVI val) { + *(uncompressed + pos) = val.dt; + *(uncompressed - pos - 1) = val.v; + } + + SVI get(size_t pos) { + SVI res; + res.dt = *(uncompressed + pos); + res.v = *(uncompressed - pos - 1); + return res; + } + + // return pointer to buf, buf size in uint32_t + tuple encode(size_t numSVI) { + auto res_size = compressed_size; + codec->encodeArray(uncompressed - numSVI, numSVI * 2, compressed, &res_size); + return make_tuple(compressed, res_size); + } + + void decode(size_t numSVI, size_t csize) { + codec->decodeArray(compressed, csize, uncompressed - numSVI, 2 * numSVI); + } + + ~SplitSVIBuffer() { + delete[] uncompressed_full; + delete[] compressed; + } +}; + + +struct ChunkSize { + uint32_t raw; // uncompressed size in bytes + uint32_t compressed; // compressed size in bytes +}; + + +template +Dst bit_convert(Src s) { + static_assert(sizeof(Src) == sizeof(Dst), "bit size mismatch"); + union { + Src s; + Dst d; + } c; + c.s = s; + return c.d; +} + +template +constexpr int bitsizeof() { return 8 * sizeof(T); } + +char* hrtc_version_string() { +#define str(s) #s +#define xstr(s) str(s) + return (char*) xstr(HRTC_VERSION); +#undef str +} diff --git a/compressor.hpp b/compressor.hpp new file mode 100644 index 0000000..3963f9d --- /dev/null +++ b/compressor.hpp @@ -0,0 +1,278 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include "common.hpp" +#include "num_util.hpp" + +// state of one trajectory during compression +template +struct TrajState { + Real x0, x1, vmin, vmax; + int64_t qx0; // store the quantized x0 as reference so that + // numerical error of support vector position does not + // accumulate + uint32_t dt; + + // The first point added initialises the data structure. + // The quantised integer to be stored is returned + uint32_t add_first(Real x, Real, Real quantum) { + qx0 = quantize(x, quantum); + x0 = quant2real(qx0, quantum), + x1 = x, + vmin = -numeric_limits::infinity(), + vmax = numeric_limits::infinity(), + dt = 0; + + return signed2unsigned(quantize(x, quantum)); + } + + optional add(Real x, Real e, Real quantum) { + // compute new error bound + Real vmin2((x - x0 - e) / (dt + 1)), + vmax2((x - x0 + e) / (dt + 1)); + vmin2 = max(vmin, vmin2); + vmax2 = min(vmax, vmax2); + + if (vmin2 > vmax2) { + // if new point does not fit in the existing error bound, store + // a linear segment up to the previous point and start a new + // segment + SVI res = flush(quantum); + // qx0 and x0 are set by flush + x1 = x; + dt = 1; + vmin = x1 - x0 - e; + vmax = x1 - x0 + e; + return res; + }else{ + // extend the linear segment by the current point otherwise + x1 = x; + vmin = vmin2; + vmax = vmax2; + ++dt; + return optional(); + } + } + + SVI flush(Real quantum) { + // Compute new support vector: the point sv that is closest to x1 + // while maintaining the derivate bounds vmin/vmax + Real sv; + if (x1 - x0 < vmin * dt) { sv = x0 + vmin * dt; } + else if (x1 - x0 > vmax * dt) { sv = x0 + vmax * dt; } + else { sv = x1; } + + // create integer support vector (the data struct to VLI-compress) + SVI svi; + assert(dt > 0); + svi.dt = dt - 1; + svi.v = signed2unsigned(quantize(sv - x0, quantum)); + + // start new segment from sv, not from x1 + qx0 = quantize(sv, quantum); + x0 = quant2real(qx0, quantum); + + return svi; + } +}; + +// state of the compressor +template +struct CompressorState { + // Input config + TId numTraj; + Real error, bound, quantum; + + // Output config + int chunkSize; // maximal number of support vectors (SVI) + + // Store the order in which support vectors are expected and in + // which we know them respectively. Only the later might store more + // than one support vector for a trajectory + priority_queue::container_type, std::greater> expectedSegment; + map knownSegment; + Time curTime; + + TrajState *trajState; + + // Current chunk of support vectors to be written + int curSV; + SplitSVIBuffer buf; + + // function which is called with the compressedSV + function sink; + + /// the functions of the compressor in order + + // 0. init compressor + CompressorState(TId numTraj, Real error, Real bound, Real quantum, + int chunkSize, EncodingPtr encoder, + function sink) + : numTraj(numTraj), + error(error), + bound(bound), + quantum(quantum), + chunkSize(chunkSize), + curTime(0), + trajState(new TrajState[numTraj]), + curSV(0), + buf(encoder, chunkSize), + sink(sink) + {} + + // 1. add another frame of trajectory data + void addFrame(Real *trajVal) { + if (curTime) { addLaterFrame(trajVal); } + else { addFirstFrame(trajVal); } + } + + // Use the first frame for late initialization of TrajState and + // expected segment queue. + void addFirstFrame(Real *trajVal) { + // Instead of compressed support vectors, initial value (x) is + // stored uncompressed with the minimal number of bits given bound + // and quantum (+1 for sign) + uint bit_count = 2 + ceil(log2(bound / quantum)); + dynamic_bitset iv(bit_count * numTraj); + for (int traj=0; traj> i) & 1; + } + + // write data to stream + // TODO: use buffer of interal representation of dynamic_bitset + ChunkSize sz; + sz.raw = bit_count * numTraj; + sz.compressed = (sz.raw + 7) / 8; + uint8_t *raw_iv = new uint8_t[sz.compressed]; + to_block_range(iv, raw_iv); + sink((char*) raw_iv, sz); + delete[] raw_iv; + + // Add all expected segments + curTime = 1; + for (int traj=0; trajdt + 1); + stp.id = traj; + knownSegment.insert(make_pair(stp, *maybePoint)); + + // Test if we know the next required support vector. Add it to + // the raw chunk if so. Push the chunk once it is full. + while (expectedSegment.size() && (expectedSegment.top() == knownSegment.begin()->first)) { + auto segIter = knownSegment.begin(); + auto expectedTraj = expectedSegment.top().id; + + // add new expected segemnt + STP newSeg; + newSeg.time = segIter->first.time + segIter->second.dt + 1; + newSeg.id = expectedTraj; + expectedSegment.push(newSeg); + + // write out known segment + buf.set(curSV++, segIter->second); + knownSegment.erase(segIter); + expectedSegment.pop(); + + // write out chunk once full + if (curSV >= chunkSize) + pushChunk(); + } + } + } + + assert(curTime++ < maxTime); + } + + // X. compress chunk, push it to sink, reset it + void pushChunk() { + uint32_t *cbuf; + ChunkSize sz; + sz.raw = curSV * 2 * 4; // two 4-byte int per support vector + if (curSV) { + tie(cbuf, sz.compressed) = buf.encode(curSV); + sz.compressed *= sizeof(uint32_t); + }else{ + sz.compressed = 0; + } + sink((char*) cbuf, sz); + curSV = 0; + } + + void finish() { + // The data structure must have been initialized. + assert(curTime); + // We only have full trajectory (x and v) if at least two frames + // have been seen. Only then we need to flush the unfinished + // trajectories. + if (curTime > 1) { + for (; expectedSegment.size(); expectedSegment.pop()) { + auto es = expectedSegment.top(); + auto fks = knownSegment.begin(); + assert(es.time < curTime); + // If we already have a support vector for the point, use it; + // otherwise we have to create one by flushing it + if ((fks != knownSegment.end()) & (es == fks->first)) { + // Construct the next segment to wait for. Note: + // - An SVI is only known if it terminates before curTime. + // - There may be more than one pending SVI for each + // trajectory. + STP newSeg; + newSeg.time = fks->first.time + fks->second.dt + 1; + newSeg.id = fks->first.id; + assert(newSeg.time < curTime); + expectedSegment.push(newSeg); + + buf.set(curSV++, fks->second); + knownSegment.erase(fks); + }else{ + buf.set(curSV++, trajState[es.id].flush(quantum)); + } + if (curSV >= chunkSize) pushChunk(); + } + } + // Flush non-empty buffers. + if (curSV) pushChunk(); + // Add one empty chunk to signal the end of this stream. + pushChunk(); + } + + ~CompressorState() { + delete[] trajState; + } +}; diff --git a/decompressor.hpp b/decompressor.hpp new file mode 100644 index 0000000..63f3cb4 --- /dev/null +++ b/decompressor.hpp @@ -0,0 +1,174 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include "common.hpp" +#include "num_util.hpp" + +struct DecompTrajState { + Time t0, dt; + int x0, dx; + + template + Real get(Time t1, Real quantum) { + return dt + ? quant2real(x0, quantum) + + Real(t1 - t0) * quant2real(dx, quantum) / dt + : quant2real(x0, quantum); + } +}; + +template +struct DecompressorState { + TId numTraj; + Real quantum; + + DecompTrajState *trajState; + priority_queue::container_type, std::greater> expectedSegment; + Time curTime; + + SplitSVIBuffer buf; + uint64_t chunkSz, chunkCur; + + function chunkSrc; + EncodingPtr decoder; + + // statistic helpers +#ifdef HACKY_STATS + map stat_key_x, stat_dx, stat_dt; +#endif + + DecompressorState(TId numTraj, Real quantum, + uint64_t maxChunkSize, EncodingPtr decoder, + function chunkSrc) + : numTraj(numTraj), + quantum(quantum), + trajState(new DecompTrajState[numTraj]), + curTime(0), + buf(decoder, maxChunkSize), + chunkSz(0), + chunkCur(0), + chunkSrc(chunkSrc), + decoder(decoder) + {} + + bool readFrame(Real *trajDst) { + if (!curTime) + if (!readKeyFrame()) return false; + while ((curTime == expectedSegment.top().time) && (chunkCur < chunkSz)) + readSegment(); + if (expectedSegment.top().time <= curTime) + return false; + // push data to trajDst + if (trajDst) { + for (int i=0; i(curTime, quantum); + } + curTime++; + return true; + } + + bool readKeyFrame() { + // init expected segements + uint8_t *raw_iv = new uint8_t[numTraj * sizeof(Real)]; + ChunkSize sz = chunkSrc((char*) raw_iv); + if (!sz.raw) return false; + uint bit_count = sz.raw / numTraj; + assert(bit_count * numTraj == sz.raw); + dynamic_bitset iv(raw_iv, raw_iv + sz.compressed); + delete[] raw_iv; + + for (int i=0; i(stat)) + cout << get<1>(stat) << " " << i.first << " " << i.second << endl; +#endif + } +}; diff --git a/format.hpp b/format.hpp new file mode 100644 index 0000000..7ec8971 --- /dev/null +++ b/format.hpp @@ -0,0 +1,109 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include +#include + +bool readAll(int fd, char *buf, size_t size) { + size_t cur = 0; + while (cur < size) { + auto ret = read(fd, buf+cur, size-cur); + assert(ret >= 0); // catch FS errors + if (ret ==0) // EOF + return false; + cur += ret; + } + return true; +} + +template +/* read binary format data file, which contains trajectories followed by velocities and ??? */ +bool readHubin(Real* targetBuffer, uint64_t numberOfTrajectories, int sourceFileHandle) { + uint32_t size = numberOfTrajectories * sizeof(Real); + static Real *trash = new Real[2*size]; + + // read payload (coordinates) + return (readAll(sourceFileHandle, (char*) targetBuffer, size) + && read(sourceFileHandle, trash, 2*size)); +} + +template +bool readTSV(Real* targetBuffer, uint64_t numberOfTrjectories, int sourceFileHandle) { + const int bufSz = 65536; + static char *buf = (char*) malloc(bufSz); + static int bufPos = 0, bufMax = 0; + + char numBuf[32], c; + int numPos(0); + int ret; + uint64_t traj(0); + for (;;) { + // refill buffers if empty + if (bufPos == bufMax) { + ret = read(sourceFileHandle, buf, bufSz); + if (ret == 0) return false; // end of stream + if (ret < 0) { + perror("while reading from input stream: "); + exit(EXIT_FAILURE); + } + bufPos = 0; + bufMax = ret; + } + // read one char, interpret it + c = *(buf + bufPos++); + switch (c) { + case '\n': + case '\t': // completed reading number + numBuf[numPos] = 0; + char *endp; + targetBuffer[traj] = strtod((char*) numBuf, &endp); // convert number digits to atcual number + assert(*endp == 0); + numPos = 0; + if (++traj == numberOfTrjectories) return c == '\n'; // after reading values, we should find a line break. otherwise something is weird. + break; + default: // append digit to number + numBuf[numPos] = c; + assert(++numPos < 32); + } + } + return false; +} + +template +function readTest(uint blockSize) { + return [=] (Real* dstBuf, uint64_t numTraj, int) -> bool { + static Real* srcBuf = nullptr; + static int cur = 0; + static int total = 0; + + if (!srcBuf) { + srcBuf = (Real*) malloc(sizeof(Real) * numTraj * blockSize); + assert(srcBuf); + for (size_t i = 0; i. */ + +#include "common.hpp" +#include "compressor.hpp" +#include "decompressor.hpp" +#include "format.hpp" + +const int chunkSize = 1024; + +template +void compressionLoop(function*(void)> compressorFactory, + function reader, + TId numberOfTrajectories, int sourceFileHandle, int blockSize) { + Real *trajectoryData = new Real[numberOfTrajectories]; + int block(blockSize); + CompressorState *compressor(nullptr); + while (reader(trajectoryData, numberOfTrajectories, sourceFileHandle)) { + if (block == blockSize) { + if (compressor) { + compressor->finish(); + delete compressor; + } + compressor = compressorFactory(); + block = 0; + } + compressor->addFrame(trajectoryData); + block++; + } + if (block) + compressor->finish(); + if (compressor) + delete compressor; + cerr << "done at " << __LINE__ << endl; +} + +double *foo = new double; + +template +void decompressionLoop(function*(void)> decompressorFactory, + TId numberOfTrajectories, uint blockSize) { + Real *trajectoryData = new Real[numberOfTrajectories]; + uint frameInBlock; + do { + frameInBlock = 0; + DecompressorState *decompressor = decompressorFactory(); + while (decompressor->readFrame(trajectoryData)) { + frameInBlock++; + for (int i=0; i()->default_value("-"), + "source file name") + ("dst", prog_options::value()->default_value("-"), + "destination file name") + ("format", prog_options::value()->default_value("tsvfloat"), + "file format: hufloat, hudouble, tsvfloat, tsvdouble...") + ("numtraj", prog_options::value(), + "number of trajectories (#particles * #dim)") + ("bound", prog_options::value(), + "maximal (absolute) value of a trajectory") + ("error", prog_options::value(), + "maximal deviation from trajectory (quantization + prediction)") + ("qp-ratio", prog_options::value()->default_value(0.1), + "ratio (0..1) to split the error between quantization and prediction") + ("blocksize", prog_options::value()->default_value(1024), + "frames per block") + ("integer-encoding", prog_options::value()->default_value(14), + "code id used by integer encoding library") + ; + prog_options::variables_map options; // this stores command line options + try { + prog_options::store(prog_options::parse_command_line(argc, argv, cmdOpts), options); + } catch (...) { + cerr << cmdOpts << endl; + exit(EXIT_FAILURE); + } + prog_options::notify(options); + assert(options.count("compress") + options.count("decompress") <= 1); // at least one of the two options is needed! + + auto require = [&](string name) { + if (!options.count(name)) { + cerr << "--" << name << " missing\n\n" << cmdOpts << endl; + exit(EXIT_FAILURE); + } + return options[name]; + }; + + TId numberOfTrajectories = require("numtraj").as(); + + // open I/O handles + int sourceFileHandle = 0; // 0 ≙ std in + { auto name = require("src").as(); + if (name != "-") + assert((sourceFileHandle = open(name.c_str(), O_RDONLY)) >= 0); } + int sinkFileHandle = 1; // 1 ≙ std out + { + auto name = require("dst").as(); + if (name != "-") { + assert((sinkFileHandle = open(name.c_str(), O_WRONLY | O_CREAT | O_TRUNC, S_IRWXU | S_IRGRP | S_IROTH)) >= 0); + } + } + + // Split the error between quantization error (quantum/2) and + // prediction error (error). The total error is error + quantum/2; + double qpr = require("qp-ratio").as(); + assert((qpr >= 0) && (qpr <= 1)); + double error = require("error").as() * (1 - qpr); + double quantum = require("error").as() * qpr * 2; + double bound = require("bound").as(); + int integerEncoder = require("integer-encoding").as(); + + /// execute (de)compression + if (options.count("decompress")) { + auto decompressorFactory = [&]() { + return new DecompressorState (numberOfTrajectories, quantum, chunkSize, integer_encoding::EncodingFactory::create(integerEncoder), [=](char* buf) -> ChunkSize { + ChunkSize chunkSize; + if ((read(sourceFileHandle, &chunkSize, sizeof(chunkSize))) == sizeof(chunkSize)) { + assert(read(sourceFileHandle, buf, chunkSize.compressed) == chunkSize.compressed); + }else{ + chunkSize.compressed = 0, chunkSize.raw = 0; + } + return chunkSize; + }); + }; + decompressionLoop(decompressorFactory, numberOfTrajectories, options["blocksize"].as()); + }else{ + auto compressorFactory = [&]() { + return new CompressorState + (numberOfTrajectories, error, bound, quantum, chunkSize, integer_encoding::EncodingFactory::create(integerEncoder), [&](char* buf, ChunkSize chunkSize) { + assert(write(sinkFileHandle, &chunkSize, sizeof(chunkSize)) == sizeof(chunkSize)); + assert(write(sinkFileHandle, buf, chunkSize.compressed) == chunkSize.compressed); + }); + }; + + function format; + auto fmtString = options["format"].as(); + if (fmtString == "hudouble") { format = readHubin; } + else { assert(false); } + + compressionLoop(compressorFactory, format, numberOfTrajectories, sourceFileHandle, options["blocksize"].as()); + } + + return 0; +} diff --git a/hrtc_wrapper.cpp b/hrtc_wrapper.cpp new file mode 100644 index 0000000..02b9b24 --- /dev/null +++ b/hrtc_wrapper.cpp @@ -0,0 +1,222 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#include "common.hpp" +#include "compressor.hpp" +#include "decompressor.hpp" + + +extern "C" { + #include +} + + template + tng_function_status typed_hrtc_compress(const tng_trajectory_t tng_data, + const int64_t n_frames, + const int64_t n_particles, + char **data, + int64_t *new_len) { + int64_t dimensions; + double bound = 0,error = 0,quantum = 0; + + {// this block: read number of dimensions + read box shape to calculate bound + // this is done here, because tng_data_block_write does not know about + // these things and thus cannot pass it + char type; + union data_values **box_data = 0; + int64_t dummy,current_dimension; + + tng_function_status stat=tng_data_get(tng_data,TNG_TRAJ_BOX_SHAPE,&box_data,&dummy,&dimensions,&type); + assert(stat == TNG_SUCCESS); + assert(dimensions>0); + + double val = 0; // current dimension value in loop + for (current_dimension=0; current_dimension0); + bound = max(val,bound); + } + } + + { // this block: set error and quantum using precision from tng_environment + double precision; + tng_function_status stat = tng_compression_precision_get(tng_data,&precision); + assert(precision!=0); + quantum=1/precision; + assert(stat == TNG_SUCCESS); + error = quantum/2; + assert(error>0); + assert(quantum>0); + } + + char* result = nullptr; + size_t result_size=sizeof(double); // for quantum + result=(char*) malloc(result_size); // allocate memory for one double + memcpy(result,&quantum,result_size); // copy double to result data + + int integerEncoder = 5; // pareto optimal / good space-time tradeoff + int numberOfTrajectories=n_particles*dimensions; + + CompressorState compressor(numberOfTrajectories, + error, + bound, + quantum, + 1024 /* chunk size */, + integer_encoding::EncodingFactory::create(integerEncoder), + [&](char* buf, ChunkSize chunkSize) { + auto offset=result_size; + result_size+= sizeof(chunkSize) + chunkSize.compressed; + result = (char*) realloc(result,result_size); +// printf("chunksize: %d (raw) => %d (compressed), offset: %d\n",chunkSize.raw,chunkSize.compressed,offset); + memcpy((void*)(result+offset),(void*)&chunkSize,sizeof(chunkSize)); + offset+=sizeof(chunkSize); + memcpy((void*)(result+offset),(void*)buf,chunkSize.compressed); + }); + + auto traj_data=(T*) *data; + for (int64_t frame_number=0;frame_number + tng_function_status typed_hrtc_uncompress(const tng_trajectory_t tng_data, + char **data) { + + + int64_t dimensions,number_of_frames,number_of_particles; + double bound = 0,error = 0,quantum = 0; + + int integerEncoder = 5; // pareto optimal / good space-time tradeoff + + {// this block: read number of dimensions + number of frames + box shape to calculate bound + char type; + union data_values **box_data = 0; + int64_t current_dimension; + + tng_function_status stat=tng_data_get(tng_data,TNG_TRAJ_BOX_SHAPE,&box_data,&number_of_frames,&dimensions,&type); + assert(stat == TNG_SUCCESS); + assert(dimensions>0); + assert(number_of_frames>0); + + double val = 0; // current dimension value in loop + for (current_dimension=0; current_dimension0); + bound = max(val,bound); + } + } + + { // this block: determine number of particles + tng_function_status stat = tng_num_molecules_get(tng_data, &number_of_particles); + assert(stat == TNG_SUCCESS); + assert(number_of_particles>0); + } + + { // this block: determine number of frames per frameset + tng_function_status stat = tng_num_frames_per_frame_set_get(tng_data, &number_of_frames); + assert(stat == TNG_SUCCESS); + assert(number_of_frames>0); + } + + + int number_of_trajectories=number_of_particles*dimensions; + auto src_buf = *data; + + + { // this block: read quantum from data blob, set error + quantum = *((double*) src_buf); // reading quantum from tip of data blob + src_buf+=sizeof(double); // moving pointer ahead + error = quantum/2; + assert(error>0); + assert(quantum>0); + } + + DecompressorState decompressor(number_of_trajectories, + quantum, + 1024 /* chunk size */, + integer_encoding::EncodingFactory::create(integerEncoder), + [&](char* buf) -> ChunkSize { + ChunkSize chunkSize = *((ChunkSize*) src_buf); + src_buf += sizeof(chunkSize); +// printf("chunksize: %d (compressed) => %d (raw)\n",chunkSize.compressed,chunkSize.raw); +// printf("src_buf: %d\n",src_buf-*data); + memcpy(buf,src_buf,chunkSize.compressed); + src_buf += chunkSize.compressed; + + return chunkSize; + }); + + auto result = (T*) malloc(number_of_frames * number_of_trajectories * sizeof(T)); + auto result_pos = result; + + for (int i=0; i(tng_data,n_frames,n_particles,data,new_len); + case TNG_FLOAT_DATA: + return typed_hrtc_compress(tng_data,n_frames,n_particles,data,new_len); + default: + return TNG_FAILURE; + } + } + + /* decompression */ + tng_function_status hrtc_uncompress(const tng_trajectory_t tng_data, + const char type, + char **data) { + switch (type){ + case TNG_DOUBLE_DATA: + return typed_hrtc_uncompress(tng_data,data); + case TNG_FLOAT_DATA: + return typed_hrtc_uncompress(tng_data,data); + default: + return TNG_FAILURE; + } + } + + void hrtc_version(){ + cout << hrtc_version_string() << "\n"; + } +} diff --git a/integer_encoding_library b/integer_encoding_library new file mode 160000 index 0000000..6473bc2 --- /dev/null +++ b/integer_encoding_library @@ -0,0 +1 @@ +Subproject commit 6473bc232af1160538095daf598d6cb545323e5c diff --git a/num_util.hpp b/num_util.hpp new file mode 100644 index 0000000..ffa808d --- /dev/null +++ b/num_util.hpp @@ -0,0 +1,53 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include +#include +using boost::int_t; +using boost::uint_t; + +#include "common.hpp" + +/// quantization + +template +typename int_t()>::least +quantize(Real v, Real quantum) { + return round(v / quantum); +} + +template +Real quant2real(typename int_t()>::least i, Real quantum) { + return i * quantum; +} + +// Convert a signed integer into an unsigned by storing the sign in +// the least significant bit. This allows to efficiently store small +// negative quantities using the integer_encoding_library (which only +// deals well with small unsigned values). +uint32_t signed2unsigned(int32_t v) { + return (v >= 0) ? ((uint32_t( v ) << 1) | 0) + : ((uint32_t(abs(v)) << 1) | 1); +} + +int32_t unsigned2signed(uint32_t v) { + return (v & 1) ? -(v >> 1) + : (v >> 1); +} diff --git a/perftools.hpp b/perftools.hpp new file mode 100644 index 0000000..ca309b0 --- /dev/null +++ b/perftools.hpp @@ -0,0 +1,43 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#pragma once + +#include +#include + +using namespace std; + +template +void print_throughput(double time, double num, Title &title) { + cerr << title << ": " << time << "\t" << num / time << "/s\n"; +} + +struct Timer { + Timer() { + gettimeofday(&start,NULL); + } + + double diff() { + timeval stop; + gettimeofday(&stop,NULL); + return (stop.tv_sec + stop.tv_usec/1000000.0) - (start.tv_sec + start.tv_usec/1000000.0); + } + + timeval start; +}; diff --git a/test.cpp b/test.cpp new file mode 100644 index 0000000..e20d8b0 --- /dev/null +++ b/test.cpp @@ -0,0 +1,54 @@ +/* Copyright 2014-2016 Jan Huwald, Stephan Richter + + This file is part of HRTC. + + HRTC is free software: you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + HRTC is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public + License for more details. + + You should have received a copy of the GNU General Public License + along with this program (see file LICENSE). If not, see + . */ + +#include +#include + +using namespace std; + +template +Dst bit_convert(Src s) { + static_assert(sizeof(Src) == sizeof(Dst), "bit size mismatch"); + union { + Src s; + Dst d; + } c; + c.s = s; + return c.d; +} + + +#include "num_util.hpp" +#include "perftools.hpp" + +using namespace std; +int main(int argc, char **argv) { + // float x = 10; + // bitset<24> f = get_significant(x); + // bitset<8> e = get_exponent(x); + // cerr << f << " x 2^" << e << endl; + + for (float i=1; i<128; i*=2) { + for (float j=1; j. */ + +include +#include +using namespace std; +#include "num_util.hpp" + +template +ostream& fail(ostream &o, Real r, string msg) { + // BitReal br(r); + + o << "FAILURE " << msg << " for " << r << endl; + // << "\n\tfor " << real_name() << " " << r + // << "\n\tsign: " << br.sign + // << "\n\tsignificant:" << br.significant << " == " << bitset()-1>(br.significant) + // << "\n\texponent:" << br.exponent + // << "\t(min: " << mine << ", max: " << maxe << ")\n"; + return o; +} + + +template +bool test_full() { + typedef typename int_t()>::least Int; + typedef typename uint_t()>::least UInt; + Real error = 0.04; + Real quant = error/2; + + auto r2i = [=](Real r) { return quantize(r, quant); }; + auto i2r = [=](Int i) { return quant2real(i, quant); }; + + // loop over all Real values + union { + Int i; + UInt u; + Real r; + }; + u = 0; + Real r2; + Int q; + do { + if (!(i & ((1 << 20)-1))) { + cerr << "\033[K" << i << "\t/ " << UInt(-1) + << "\t(" << (double(i) / double(UInt(-1)) * 100) << "%)" + << "\r" << flush; + // fail(cerr, r, "NOT YET HAPPENED", maxe, mine); + + } + + // ignore invalid values, infinity and nan + if (!isfinite(r)) goto pass; + if (fabs(r) > 100) goto pass; + + // ignore values that are larger than max exponent + // TODO check if neccessary if (get_exponent(r) > maxe) goto pass; + + q = r2i(r); + + if (q != r2i(i2r(q))) { + fail(cout, r, "requantisation leads to different number") + << "\tquants: " << q << " != " << r2i(i2r(q)) << endl + << "ARG " << i2r(q) << endl; + fail(cout, i2r(q), "..."); + //return false; + } + + r2 = i2r(q); + if (fabs(r-r2) > error) { // TODO: add actual error cond + cerr << endl; + fail(cout, r, "error bound exceed") + << "\tQuantum = " << q << endl; + fail(cout, r2, "..."); + cout << "\tDelta = " <(); +} -- cgit v0.10.1