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Hadrons: disk-based container
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Hadrons/DiskVector.hpp
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293
Hadrons/DiskVector.hpp
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/*************************************************************************************
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Grid physics library, www.github.com/paboyle/Grid
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Source file: Hadrons/DiskVector.hpp
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Copyright (C) 2015-2018
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Author: Antonin Portelli <antonin.portelli@me.com>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License along
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with this program; if not, write to the Free Software Foundation, Inc.,
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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See the full license in the file "LICENSE" in the top level distribution directory
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*************************************************************************************/
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/* END LEGAL */
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#ifndef Hadrons_DiskVector_hpp_
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#define Hadrons_DiskVector_hpp_
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#include <Hadrons/Global.hpp>
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#include <queue>
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#include <sys/stat.h>
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#include <ftw.h>
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#include <unistd.h>
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BEGIN_HADRONS_NAMESPACE
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/******************************************************************************
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* Abstract base class *
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******************************************************************************/
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template <typename T>
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class DiskVectorBase
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{
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public:
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typedef T ObjectType;
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// helper for read/write vector access
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class RwAccessHelper
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{
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public:
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RwAccessHelper(DiskVectorBase<T> &master, const unsigned int i)
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: master_(master), cmaster_(master), i_(i) {}
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// operator=: somebody is trying to store a vector element
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// write to disk and cache
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T &operator=(const T &obj) const
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{
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master_.cacheInsert(i_, obj);
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master_.save(master_.filename(i_), obj);
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return master_.cachePtr_->at(i_);
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}
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// implicit cast to const object reference and redirection
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// to the const operator[] for read-only operations
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operator const T&() const
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{
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return cmaster_[i_];
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}
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private:
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DiskVectorBase<T> &master_;
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const DiskVectorBase<T> &cmaster_;
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const unsigned int i_;
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};
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public:
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DiskVectorBase(const std::string dirname, const unsigned int size = 0,
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const unsigned int cacheSize = 1, const bool clean = true);
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virtual ~DiskVectorBase(void);
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const T & operator[](const unsigned int i) const;
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RwAccessHelper operator[](const unsigned int i);
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private:
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virtual void load(T &obj, const std::string filename) const = 0;
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virtual void save(const std::string filename, const T &obj) const = 0;
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virtual std::string filename(const unsigned int i) const;
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void evict(void) const;
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void fetch(const unsigned int i) const;
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void cacheInsert(const unsigned int i, const T &obj) const;
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void clean(void);
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private:
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std::string dirname_;
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unsigned int size_, cacheSize_;
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bool clean_;
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// using pointers to allow modifications when class is const
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// semantic: const means data unmodified, but cache modification allowed
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std::unique_ptr<std::map<unsigned int, T>> cachePtr_;
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std::unique_ptr<std::queue<unsigned int>> loadsPtr_;
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};
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/******************************************************************************
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* Specialisation for serialisable classes *
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******************************************************************************/
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template <typename T, typename Reader, typename Writer>
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class SerializableDiskVector: public DiskVectorBase<T>
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{
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public:
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using DiskVectorBase<T>::DiskVectorBase;
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private:
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virtual void load(T &obj, const std::string filename) const
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{
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Reader reader(filename);
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read(reader, basename(filename), obj);
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}
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virtual void save(const std::string filename, const T &obj) const
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{
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Writer writer(filename);
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write(writer, basename(filename), obj);
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}
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};
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/******************************************************************************
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* DiskVectorBase implementation *
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******************************************************************************/
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#ifdef DV_DEBUG
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#define DV_DEBUG_MSG(stream) LOG(Debug) << "diskvector " << this << ": " << stream << std::endl
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#endif
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template <typename T>
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DiskVectorBase<T>::DiskVectorBase(const std::string dirname,
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const unsigned int size,
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const unsigned int cacheSize,
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const bool clean)
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: dirname_(dirname), size_(size), cacheSize_(cacheSize), clean_(clean)
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, cachePtr_(new std::map<unsigned int, T>())
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, loadsPtr_(new std::queue<unsigned int>())
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{
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struct stat s;
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if(stat(dirname.c_str(), &s) == 0)
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{
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HADRONS_ERROR(Io, "directory '" + dirname + "' already exists")
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}
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mkdir(dirname);
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}
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template <typename T>
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DiskVectorBase<T>::~DiskVectorBase(void)
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{
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if (clean_)
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{
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clean();
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}
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}
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template <typename T>
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const T & DiskVectorBase<T>::operator[](const unsigned int i) const
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{
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auto &cache = *cachePtr_;
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DV_DEBUG_MSG("accessing " << i << " (RO)");
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if (i >= size_)
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{
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HADRONS_ERROR(Size, "index out of range");
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}
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if (cache.find(i) == cache.end())
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{
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// cache miss
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DV_DEBUG_MSG("cache miss");
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fetch(i);
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}
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else
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{
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DV_DEBUG_MSG("cache hit");
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}
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#ifdef DV_DEBUG
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std::string msg;
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for (auto &p: cache)
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{
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msg += std::to_string(p.first) + " ";
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}
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DV_DEBUG_MSG("in cache: " << msg);
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#endif
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return cache.at(i);
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}
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template <typename T>
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typename DiskVectorBase<T>::RwAccessHelper DiskVectorBase<T>::operator[](const unsigned int i)
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{
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DV_DEBUG_MSG("accessing " << i << " (RW)");
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if (i >= size_)
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{
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HADRONS_ERROR(Size, "index out of range");
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}
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RwAccessHelper h(*this, i);
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return h;
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}
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template <typename T>
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std::string DiskVectorBase<T>::filename(const unsigned int i) const
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{
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return dirname_ + "/elem_" + std::to_string(i);
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}
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template <typename T>
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void DiskVectorBase<T>::evict(void) const
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{
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auto &cache = *cachePtr_;
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auto &loads = *loadsPtr_;
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if (cache.size() >= cacheSize_)
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{
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DV_DEBUG_MSG("evicting " << loads.front());
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cache.erase(loads.front());
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loads.pop();
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}
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}
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template <typename T>
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void DiskVectorBase<T>::fetch(const unsigned int i) const
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{
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auto &cache = *cachePtr_;
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auto &loads = *loadsPtr_;
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struct stat s;
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DV_DEBUG_MSG("loading " << i << " from disk");
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evict();
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if(stat(filename(i).c_str(), &s) != 0)
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{
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HADRONS_ERROR(Io, "disk vector element " + std::to_string(i) + " uninitialised");
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}
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load(cache[i], filename(i));
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loads.push(i);
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}
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template <typename T>
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void DiskVectorBase<T>::cacheInsert(const unsigned int i, const T &obj) const
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{
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auto &cache = *cachePtr_;
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auto &loads = *loadsPtr_;
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evict();
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cache[i] = obj;
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loads.push(i);
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#ifdef DV_DEBUG
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std::string msg;
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for (auto &p: cache)
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{
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msg += std::to_string(p.first) + " ";
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}
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DV_DEBUG_MSG("in cache: " << msg);
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#endif
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}
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#ifdef DV_DEBUG
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#undef DV_DEBUG_MSG
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#endif
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template <typename T>
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void DiskVectorBase<T>::clean(void)
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{
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auto unlink = [](const char *fpath, const struct stat *sb,
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int typeflag, struct FTW *ftwbuf)
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{
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int rv = remove(fpath);
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if (rv)
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{
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HADRONS_ERROR(Io, "cannot remove '" + std::string(fpath) + "': "
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+ std::string(std::strerror(errno)));
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}
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return rv;
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};
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nftw(dirname_.c_str(), unlink, 64, FTW_DEPTH | FTW_PHYS);
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}
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END_HADRONS_NAMESPACE
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#endif // Hadrons_DiskVector_hpp_
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@ -18,6 +18,7 @@ nobase_libHadrons_a_HEADERS = \
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A2AMatrix.hpp \
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Application.hpp \
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DilutedNoise.hpp \
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DiskVector.hpp \
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EigenPack.hpp \
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Environment.hpp \
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Exceptions.hpp \
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@ -1,3 +1,3 @@
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AM_LDFLAGS += -L../../extras/Hadrons
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AM_LDFLAGS += -L../../Hadrons
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include Make.inc
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58
tests/hadrons/Test_diskvector.cc
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58
tests/hadrons/Test_diskvector.cc
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#define DV_DEBUG
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#include <Hadrons/DiskVector.hpp>
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using namespace Grid;
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using namespace Grid::QCD;
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using namespace Grid::Hadrons;
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GRID_SERIALIZABLE_ENUM(Enum, undef, red, 1, blue, 2, green, 3);
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class Object: Serializable {
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public:
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GRID_SERIALIZABLE_CLASS_MEMBERS(Object,
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Enum, e,
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SpinColourMatrix, scm);
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};
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#ifdef HAVE_HDF5
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typedef Hdf5Reader TestReader;
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typedef Hdf5Writer TestWriter;
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#else
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typedef BinaryReader TestReader;
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typedef BinaryWriter TestWriter;
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#endif
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int main(int argc, char *argv[])
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{
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Grid_init(&argc, &argv);
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GridSerialRNG rng;
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Object obj, v2w, v2r, v13w, v13r;
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SerializableDiskVector<Object, TestReader, TestWriter> v("diskvector_test", 1000, 2);
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obj.e = Enum::red;
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random(rng, obj.scm);
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v[32] = obj;
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random(rng, obj.scm);
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v[2] = obj;
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v2w = obj;
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random(rng, obj.scm);
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v[6] = obj;
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random(rng, obj.scm);
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v[12] = obj;
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random(rng, obj.scm);
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v[13] = obj;
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v13w = obj;
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v2r = v[2];
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LOG(Message) << "v[2] correct? "
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<< ((v2r == v2w) ? "yes" : "no" ) << std::endl;
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v13r = v[13];
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LOG(Message) << "v[13] correct? "
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<< ((v13r == v13w) ? "yes" : "no" ) << std::endl;
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Grid_finalize();
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return EXIT_SUCCESS;
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}
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