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Grid/Hadrons/DiskVector.hpp

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/*************************************************************************************
Grid physics library, www.github.com/paboyle/Grid
Source file: Hadrons/DiskVector.hpp
Copyright (C) 2015-2019
Author: Antonin Portelli <antonin.portelli@me.com>
This program 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 2 of the License, or
(at your option) any later version.
This program 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; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#ifndef Hadrons_DiskVector_hpp_
#define Hadrons_DiskVector_hpp_
#include <Hadrons/Global.hpp>
#include <Hadrons/A2AMatrix.hpp>
#include <deque>
#include <sys/stat.h>
#include <ftw.h>
#include <unistd.h>
#ifdef DV_DEBUG
#define DV_DEBUG_MSG(dv, stream) LOG(Debug) << "diskvector " << (dv) << ": " << stream << std::endl
#else
#define DV_DEBUG_MSG(dv, stream)
#endif
BEGIN_HADRONS_NAMESPACE
/******************************************************************************
* Abstract base class *
******************************************************************************/
template <typename T>
class DiskVectorBase
{
public:
typedef T ObjectType;
// helper for read/write vector access
class RwAccessHelper
{
public:
RwAccessHelper(DiskVectorBase<T> &master, const unsigned int i)
: master_(master), cmaster_(master), i_(i) {}
// operator=: somebody is trying to store a vector element
// write to cache and tag as modified
T &operator=(const T &obj) const
{
auto &cache = *master_.cachePtr_;
auto &modified = *master_.modifiedPtr_;
auto &index = *master_.indexPtr_;
DV_DEBUG_MSG(&master_, "writing to " << i_);
master_.cacheInsert(i_, obj);
modified[index.at(i_)] = true;
return cache[index.at(i_)];
}
// implicit cast to const object reference and redirection
// to the const operator[] for read-only operations
operator const T&() const
{
return cmaster_[i_];
}
private:
DiskVectorBase<T> &master_;
const DiskVectorBase<T> &cmaster_;
const unsigned int i_;
};
public:
DiskVectorBase(const std::string dirname, const unsigned int size = 0,
const unsigned int cacheSize = 1, const bool clean = true,
GridBase *grid = nullptr);
DiskVectorBase(DiskVectorBase<T> &&v) = default;
virtual ~DiskVectorBase(void);
const T & operator[](const unsigned int i) const;
RwAccessHelper operator[](const unsigned int i);
double hitRatio(void) const;
void resetStat(void);
void setSize(unsigned int size_);
unsigned int getSize() const;
unsigned int dvSize;
void setGrid(GridBase *grid_);
GridBase *getGrid() const;
GridBase *dvGrid;
private:
virtual void load(T &obj, const std::string filename) const = 0;
virtual void save(const std::string filename, const T &obj) const = 0;
virtual std::string filename(const unsigned int i) const;
void evict(void) const;
void fetch(const unsigned int i) const;
void cacheInsert(const unsigned int i, const T &obj) const;
void clean(void);
private:
std::string dirname_;
unsigned int size_, cacheSize_;
double access_{0.}, hit_{0.};
bool clean_;
GridBase *grid_;
// using pointers to allow modifications when class is const
// semantic: const means data unmodified, but cache modification allowed
std::unique_ptr<std::vector<T>> cachePtr_;
std::unique_ptr<std::vector<bool>> modifiedPtr_;
std::unique_ptr<std::map<unsigned int, unsigned int>> indexPtr_;
std::unique_ptr<std::stack<unsigned int>> freePtr_;
std::unique_ptr<std::deque<unsigned int>> loadsPtr_;
};
/******************************************************************************
* Specialisation for serialisable classes *
******************************************************************************/
template <typename T, typename Reader, typename Writer>
class SerializableDiskVector: public DiskVectorBase<T>
{
public:
using DiskVectorBase<T>::DiskVectorBase;
private:
virtual void load(T &obj, const std::string filename) const
{
Reader reader(filename);
read(reader, basename(filename), obj);
}
virtual void save(const std::string filename, const T &obj) const
{
Writer writer(filename);
write(writer, basename(filename), obj);
}
};
/******************************************************************************
* Specialisation for Eigen matrices *
******************************************************************************/
template <typename T>
using EigenDiskVectorMat = A2AMatrix<T>;
template <typename T>
class EigenDiskVector: public DiskVectorBase<EigenDiskVectorMat<T>>
{
public:
using DiskVectorBase<EigenDiskVectorMat<T>>::DiskVectorBase;
typedef EigenDiskVectorMat<T> Matrix;
public:
T operator()(const unsigned int i, const Eigen::Index j,
const Eigen::Index k) const
{
return (*this)[i](j, k);
}
std::vector<int> dimensions() const
{
std::vector<int> dims(3);
dims[0] = (*this).getSize();
dims[1] = (*this)[0].rows();
dims[2] = (*this)[0].cols();
return dims;
}
private:
virtual void load(EigenDiskVectorMat<T> &obj, const std::string filename) const
{
GridBase *loadGrid;
loadGrid = (*this).getGrid();
if (!(loadGrid) || loadGrid->IsBoss())
{
std::ifstream f(filename, std::ios::binary);
uint32_t crc, check;
Eigen::Index nRow, nCol;
size_t matSize;
double tRead, tHash;
f.read(reinterpret_cast<char *>(&crc), sizeof(crc));
f.read(reinterpret_cast<char *>(&nRow), sizeof(nRow));
f.read(reinterpret_cast<char *>(&nCol), sizeof(nCol));
obj.resize(nRow, nCol);
matSize = nRow*nCol*sizeof(T);
tRead = -usecond();
f.read(reinterpret_cast<char *>(obj.data()), matSize);
tRead += usecond();
tHash = -usecond();
#ifdef USE_IPP
check = GridChecksum::crc32c(obj.data(), matSize);
#else
check = GridChecksum::crc32(obj.data(), matSize);
#endif
tHash += usecond();
DV_DEBUG_MSG(this, "Eigen read " << tRead/1.0e6 << " sec " << matSize/tRead*1.0e6/1024/1024 << " MB/s");
DV_DEBUG_MSG(this, "Eigen crc32 " << std::hex << check << std::dec
<< " " << tHash/1.0e6 << " sec " << matSize/tHash*1.0e6/1024/1024 << " MB/s");
if (crc != check)
{
HADRONS_ERROR(Io, "checksum failed")
}
}
int broadcastSize;
broadcastSize = sizeof(T)*obj.size();
if (loadGrid)
{
loadGrid->Broadcast(loadGrid->BossRank(), obj.data(), broadcastSize);
loadGrid->Barrier();
}
}
virtual void save(const std::string filename, const EigenDiskVectorMat<T> &obj) const
{
GridBase *saveGrid;
saveGrid = (*this).getGrid();
if (!(saveGrid) || saveGrid->IsBoss())
{
std::ofstream f(filename, std::ios::binary);
uint32_t crc;
Eigen::Index nRow, nCol;
size_t matSize;
double tWrite, tHash;
nRow = obj.rows();
nCol = obj.cols();
matSize = nRow*nCol*sizeof(T);
tHash = -usecond();
#ifdef USE_IPP
crc = GridChecksum::crc32c(obj.data(), matSize);
#else
crc = GridChecksum::crc32(obj.data(), matSize);
#endif
tHash += usecond();
f.write(reinterpret_cast<char *>(&crc), sizeof(crc));
f.write(reinterpret_cast<char *>(&nRow), sizeof(nRow));
f.write(reinterpret_cast<char *>(&nCol), sizeof(nCol));
tWrite = -usecond();
f.write(reinterpret_cast<const char *>(obj.data()), matSize);
tWrite += usecond();
DV_DEBUG_MSG(this, "Eigen write " << tWrite/1.0e6 << " sec " << matSize/tWrite*1.0e6/1024/1024 << " MB/s");
DV_DEBUG_MSG(this, "Eigen crc32 " << std::hex << crc << std::dec
<< " " << tHash/1.0e6 << " sec " << matSize/tHash*1.0e6/1024/1024 << " MB/s");
}
if (saveGrid) saveGrid->Barrier();
}
};
/******************************************************************************
* DiskVectorBase implementation *
******************************************************************************/
template <typename T>
DiskVectorBase<T>::DiskVectorBase(const std::string dirname,
const unsigned int size,
const unsigned int cacheSize,
const bool clean,
GridBase *grid)
: dirname_(dirname), size_(size), cacheSize_(cacheSize), clean_(clean), grid_(grid)
, cachePtr_(new std::vector<T>(size))
, modifiedPtr_(new std::vector<bool>(size, false))
, indexPtr_(new std::map<unsigned int, unsigned int>())
, freePtr_(new std::stack<unsigned int>)
, loadsPtr_(new std::deque<unsigned int>())
{
struct stat s;
if (!(grid_) || grid_->IsBoss())
{
if(stat(dirname.c_str(), &s) == 0)
{
HADRONS_ERROR(Io, "directory '" + dirname + "' already exists")
}
mkdir(dirname);
}
if (grid_) grid_->Barrier();
for (unsigned int i = 0; i < cacheSize_; ++i)
{
freePtr_->push(i);
}
setSize(size_);
setGrid(grid_);
}
template <typename T>
DiskVectorBase<T>::~DiskVectorBase(void)
{
if (clean_)
{
clean();
}
}
template <typename T>
void DiskVectorBase<T>::setSize(unsigned int size_)
{
dvSize = size_;
}
template <typename T>
unsigned int DiskVectorBase<T>::getSize() const
{
return dvSize;
}
template <typename T>
void DiskVectorBase<T>::setGrid(GridBase *grid_)
{
dvGrid = grid_;
}
template <typename T>
GridBase *DiskVectorBase<T>::getGrid() const
{
return dvGrid;
}
template <typename T>
const T & DiskVectorBase<T>::operator[](const unsigned int i) const
{
auto &cache = *cachePtr_;
auto &index = *indexPtr_;
auto &freeInd = *freePtr_;
auto &loads = *loadsPtr_;
DV_DEBUG_MSG(this, "accessing " << i << " (RO)");
if (i >= size_)
{
HADRONS_ERROR(Size, "index out of range");
}
const_cast<double &>(access_)++;
if (index.find(i) == index.end())
{
// cache miss
DV_DEBUG_MSG(this, "cache miss");
fetch(i);
}
else
{
DV_DEBUG_MSG(this, "cache hit");
auto pos = std::find(loads.begin(), loads.end(), i);
const_cast<double &>(hit_)++;
loads.erase(pos);
loads.push_back(i);
}
#ifdef DV_DEBUG
std::string msg;
for (auto &p: loads)
{
msg += std::to_string(p) + " ";
}
DV_DEBUG_MSG(this, "in cache: " << msg);
#endif
if (grid_) grid_->Barrier();
return cache[index.at(i)];
}
template <typename T>
typename DiskVectorBase<T>::RwAccessHelper DiskVectorBase<T>::operator[](const unsigned int i)
{
DV_DEBUG_MSG(this, "accessing " << i << " (RW)");
if (i >= size_)
{
HADRONS_ERROR(Size, "index out of range");
}
return RwAccessHelper(*this, i);
}
template <typename T>
double DiskVectorBase<T>::hitRatio(void) const
{
return hit_/access_;
}
template <typename T>
void DiskVectorBase<T>::resetStat(void)
{
access_ = 0.;
hit_ = 0.;
}
template <typename T>
std::string DiskVectorBase<T>::filename(const unsigned int i) const
{
return dirname_ + "/elem_" + std::to_string(i);
}
template <typename T>
void DiskVectorBase<T>::evict(void) const
{
auto &cache = *cachePtr_;
auto &modified = *modifiedPtr_;
auto &index = *indexPtr_;
auto &freeInd = *freePtr_;
auto &loads = *loadsPtr_;
if (index.size() >= cacheSize_)
{
unsigned int i = loads.front();
DV_DEBUG_MSG(this, "evicting " << i);
if (modified[index.at(i)])
{
DV_DEBUG_MSG(this, "element " << i << " modified, saving to disk");
save(filename(i), cache[index.at(i)]);
}
freeInd.push(index.at(i));
index.erase(i);
loads.pop_front();
}
if (grid_) grid_->Barrier();
}
template <typename T>
void DiskVectorBase<T>::fetch(const unsigned int i) const
{
auto &cache = *cachePtr_;
auto &modified = *modifiedPtr_;
auto &index = *indexPtr_;
auto &freeInd = *freePtr_;
auto &loads = *loadsPtr_;
struct stat s;
DV_DEBUG_MSG(this, "loading " << i << " from disk");
evict();
if(stat(filename(i).c_str(), &s) != 0)
{
HADRONS_ERROR(Io, "disk vector element " + std::to_string(i) + " uninitialised");
}
index[i] = freeInd.top();
freeInd.pop();
load(cache[index.at(i)], filename(i));
loads.push_back(i);
modified[index.at(i)] = false;
}
template <typename T>
void DiskVectorBase<T>::cacheInsert(const unsigned int i, const T &obj) const
{
auto &cache = *cachePtr_;
auto &modified = *modifiedPtr_;
auto &index = *indexPtr_;
auto &freeInd = *freePtr_;
auto &loads = *loadsPtr_;
evict();
index[i] = freeInd.top();
freeInd.pop();
cache[index.at(i)] = obj;
loads.push_back(i);
modified[index.at(i)] = false;
if (grid_) grid_->Barrier();
#ifdef DV_DEBUG
std::string msg;
for (auto &p: loads)
{
msg += std::to_string(p) + " ";
}
DV_DEBUG_MSG(this, "in cache: " << msg);
#endif
}
#ifdef DV_DEBUG
#undef DV_DEBUG_MSG
#endif
template <typename T>
void DiskVectorBase<T>::clean(void)
{
if (!(grid_) || grid_->IsBoss())
{
auto unlink = [](const char *fpath, const struct stat *sb,
int typeflag, struct FTW *ftwbuf) {
int rv = remove(fpath);
if (rv)
{
HADRONS_ERROR(Io, "cannot remove '" + std::string(fpath) + "': " + std::string(std::strerror(errno)));
}
return rv;
};
nftw(dirname_.c_str(), unlink, 64, FTW_DEPTH | FTW_PHYS);
}
if (grid_) grid_->Barrier();
}
END_HADRONS_NAMESPACE
#endif // Hadrons_DiskVector_hpp_
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