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Hadrons: DiskVector Eigen specialisation with binary I/O and sha256 correctness check
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@ -34,6 +34,12 @@ See the full license in the file "LICENSE" in the top level distribution directo
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#include <ftw.h>
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#include <unistd.h>
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#ifdef DV_DEBUG
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#define DV_DEBUG_MSG(dv, stream) LOG(Debug) << "diskvector " << (dv) << ": " << stream << std::endl
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#else
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#define DV_DEBUG_MSG(dv, stream)
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#endif
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BEGIN_HADRONS_NAMESPACE
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/******************************************************************************
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@ -56,9 +62,7 @@ public:
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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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#ifdef DV_DEBUG
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LOG(Debug) << "diskvector " << &master_ << ": writing to " << i_ << std::endl;
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#endif
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DV_DEBUG_MSG(&master_, "writing to " << i_);
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master_.cacheInsert(i_, obj);
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master_.save(master_.filename(i_), obj);
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@ -82,6 +86,8 @@ public:
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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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double hitRatio(void) const;
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void resetStat(void);
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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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@ -93,6 +99,7 @@ private:
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private:
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std::string dirname_;
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unsigned int size_, cacheSize_;
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double access_{0.}, hit_{0.};
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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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@ -115,6 +122,7 @@ private:
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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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@ -123,13 +131,70 @@ private:
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}
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};
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/******************************************************************************
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* Specialisation for Eigen matrices *
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******************************************************************************/
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template <typename T>
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using EigenDiskVectorMat = Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>;
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template <typename T>
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class EigenDiskVector: public DiskVectorBase<EigenDiskVectorMat<T>>
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{
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public:
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using DiskVectorBase<EigenDiskVectorMat<T>>::DiskVectorBase;
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typedef EigenDiskVectorMat<T> Matrix;
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private:
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virtual void load(EigenDiskVectorMat<T> &obj, const std::string filename) const
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{
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std::ifstream f(filename, std::ios::binary);
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std::vector<unsigned char> hash(SHA256_DIGEST_LENGTH);
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Eigen::Index nRow, nCol;
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size_t matSize;
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double t;
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f.read(reinterpret_cast<char *>(hash.data()), hash.size()*sizeof(unsigned char));
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f.read(reinterpret_cast<char *>(&nRow), sizeof(Eigen::Index));
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f.read(reinterpret_cast<char *>(&nCol), sizeof(Eigen::Index));
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obj.resize(nRow, nCol);
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matSize = nRow*nCol*sizeof(T);
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t = -usecond();
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f.read(reinterpret_cast<char *>(obj.data()), matSize);
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t += usecond();
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DV_DEBUG_MSG(this, "Eigen read " << matSize/t*1.0e6/1024/1024 << " MB/s");
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auto check = GridChecksum::sha256(obj.data(), matSize);
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DV_DEBUG_MSG(this, "Eigen sha256 " << GridChecksum::sha256_string(check));
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if (hash != check)
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{
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HADRONS_ERROR(Io, "checksum failed")
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}
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}
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virtual void save(const std::string filename, const EigenDiskVectorMat<T> &obj) const
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{
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std::ofstream f(filename, std::ios::binary);
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std::vector<unsigned char> hash(SHA256_DIGEST_LENGTH);
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Eigen::Index nRow, nCol;
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size_t matSize;
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double t;
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nRow = obj.rows();
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nCol = obj.cols();
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matSize = nRow*nCol*sizeof(T);
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hash = GridChecksum::sha256(obj.data(), matSize);
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DV_DEBUG_MSG(this, "Eigen sha256 " << GridChecksum::sha256_string(hash));
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f.write(reinterpret_cast<char *>(hash.data()), hash.size()*sizeof(unsigned char));
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f.write(reinterpret_cast<char *>(&nRow), sizeof(Eigen::Index));
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f.write(reinterpret_cast<char *>(&nCol), sizeof(Eigen::Index));
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t = -usecond();
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f.write(reinterpret_cast<const char *>(obj.data()), matSize);
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t += usecond();
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DV_DEBUG_MSG(this, "Eigen write " << matSize/t*1.0e6/1024/1024 << " MB/s");
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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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@ -160,28 +225,29 @@ DiskVectorBase<T>::~DiskVectorBase(void)
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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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auto &loads = *loadsPtr_;
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auto &cache = *cachePtr_;
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auto &loads = *loadsPtr_;
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DV_DEBUG_MSG("accessing " << i << " (RO)");
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DV_DEBUG_MSG(this, "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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const_cast<double &>(access_)++;
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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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DV_DEBUG_MSG(this, "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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DV_DEBUG_MSG(this, "cache hit");
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auto pos = std::find(loads.begin(), loads.end(), i);
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const_cast<double &>(hit_)++;
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loads.erase(pos);
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loads.push_back(i);
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}
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@ -193,7 +259,7 @@ const T & DiskVectorBase<T>::operator[](const unsigned int i) const
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{
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msg += std::to_string(p) + " ";
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}
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DV_DEBUG_MSG("in cache: " << msg);
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DV_DEBUG_MSG(this, "in cache: " << msg);
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#endif
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return cache.at(i);
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@ -202,7 +268,7 @@ const T & DiskVectorBase<T>::operator[](const unsigned int i) const
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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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DV_DEBUG_MSG(this, "accessing " << i << " (RW)");
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if (i >= size_)
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{
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@ -212,6 +278,19 @@ typename DiskVectorBase<T>::RwAccessHelper DiskVectorBase<T>::operator[](const u
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return RwAccessHelper(*this, i);
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}
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template <typename T>
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double DiskVectorBase<T>::hitRatio(void) const
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{
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return hit_/access_;
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}
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template <typename T>
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void DiskVectorBase<T>::resetStat(void)
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{
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access_ = 0.;
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hit_ = 0.;
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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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@ -226,7 +305,7 @@ void DiskVectorBase<T>::evict(void) const
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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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DV_DEBUG_MSG(this, "evicting " << loads.front());
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cache.erase(loads.front());
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loads.pop_front();
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}
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@ -239,7 +318,7 @@ void DiskVectorBase<T>::fetch(const unsigned int i) const
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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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DV_DEBUG_MSG(this, "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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@ -267,7 +346,7 @@ void DiskVectorBase<T>::cacheInsert(const unsigned int i, const T &obj) const
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{
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msg += std::to_string(p) + " ";
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}
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DV_DEBUG_MSG("in cache: " << msg);
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DV_DEBUG_MSG(this, "in cache: " << msg);
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#endif
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}
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@ -91,6 +91,22 @@ int main(int argc, char *argv[])
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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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LOG(Message) << "hit ratio " << v.hitRatio() << std::endl;
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EigenDiskVector<ComplexD> w("eigendiskvector_test", 1000, 4);
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EigenDiskVector<ComplexD>::Matrix m,n;
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w[2] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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m = w[2];
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w[3] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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w[4] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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w[5] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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w[6] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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w[7] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
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n = w[2];
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LOG(Message) << "w[2] correct? "
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<< ((m == n) ? "yes" : "no" ) << std::endl;
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LOG(Message) << "hit ratio " << w.hitRatio() << std::endl;
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Grid_finalize();
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