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Merge branch 'develop' of github.com:paboyle/Grid into develop

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This commit is contained in:
Antonin Portelli 2018-10-17 20:28:20 +01:00
commit 2b4e253473
4 changed files with 135 additions and 24 deletions
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6
Grid/lattice/Lattice_rng.h
View File

@ -392,14 +392,10 @@ namespace Grid {
void SeedUniqueString(const std::string &s){
std::vector<int> seeds;
std::stringstream sha;
seeds = GridChecksum::sha256_seeds(s);
for(int i=0;i<seeds.size();i++) {
sha << std::hex << seeds[i];
}
std::cout << GridLogMessage << "Intialising parallel RNG with unique string '"
<< s << "'" << std::endl;
std::cout << GridLogMessage << "Seed SHA256: " << sha.str() << std::endl;
std::cout << GridLogMessage << "Seed SHA256: " << GridChecksum::sha256_string(seeds) << std::endl;
SeedFixedIntegers(seeds);
}
void SeedFixedIntegers(const std::vector<int> &seeds){

16
Grid/util/Sha.h
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@ -38,7 +38,21 @@ public:
{
return ::crc32(0L,(unsigned char *)data,bytes);
}
static inline std::vector<unsigned char> sha256(void *data,size_t bytes)
template <typename T>
static inline std::string sha256_string(const std::vector<T> &hash)
{
std::stringstream sha;
std::string s;
for(unsigned int i = 0; i < hash.size(); i++)
{
sha << std::hex << static_cast<unsigned int>(hash[i]);
}
s = sha.str();
return s;
}
static inline std::vector<unsigned char> sha256(const void *data,size_t bytes)
{
std::vector<unsigned char> hash(SHA256_DIGEST_LENGTH);
SHA256_CTX sha256;

121
Hadrons/DiskVector.hpp
View File

@ -34,6 +34,12 @@ See the full license in the file "LICENSE" in the top level distribution directo
#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
/******************************************************************************
@ -56,9 +62,7 @@ public:
// write to disk and cache
T &operator=(const T &obj) const
{
#ifdef DV_DEBUG
LOG(Debug) << "diskvector " << &master_ << ": writing to " << i_ << std::endl;
#endif
DV_DEBUG_MSG(&master_, "writing to " << i_);
master_.cacheInsert(i_, obj);
master_.save(master_.filename(i_), obj);
@ -82,6 +86,8 @@ public:
virtual ~DiskVectorBase(void);
const T & operator[](const unsigned int i) const;
RwAccessHelper operator[](const unsigned int i);
double hitRatio(void) const;
void resetStat(void);
private:
virtual void load(T &obj, const std::string filename) const = 0;
virtual void save(const std::string filename, const T &obj) const = 0;
@ -93,6 +99,7 @@ private:
private:
std::string dirname_;
unsigned int size_, cacheSize_;
double access_{0.}, hit_{0.};
bool clean_;
// using pointers to allow modifications when class is const
// semantic: const means data unmodified, but cache modification allowed
@ -115,6 +122,7 @@ private:
read(reader, basename(filename), obj);
}
virtual void save(const std::string filename, const T &obj) const
{
Writer writer(filename);
@ -123,13 +131,76 @@ private:
}
};
/******************************************************************************
* Specialisation for Eigen matrices *
******************************************************************************/
template <typename T>
using EigenDiskVectorMat = Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic>;
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);
}
private:
virtual void load(EigenDiskVectorMat<T> &obj, const std::string filename) const
{
std::ifstream f(filename, std::ios::binary);
std::vector<unsigned char> hash(SHA256_DIGEST_LENGTH);
Eigen::Index nRow, nCol;
size_t matSize;
double t;
f.read(reinterpret_cast<char *>(hash.data()), hash.size()*sizeof(unsigned char));
f.read(reinterpret_cast<char *>(&nRow), sizeof(Eigen::Index));
f.read(reinterpret_cast<char *>(&nCol), sizeof(Eigen::Index));
obj.resize(nRow, nCol);
matSize = nRow*nCol*sizeof(T);
t = -usecond();
f.read(reinterpret_cast<char *>(obj.data()), matSize);
t += usecond();
DV_DEBUG_MSG(this, "Eigen read " << matSize/t*1.0e6/1024/1024 << " MB/s");
auto check = GridChecksum::sha256(obj.data(), matSize);
DV_DEBUG_MSG(this, "Eigen sha256 " << GridChecksum::sha256_string(check));
if (hash != check)
{
HADRONS_ERROR(Io, "checksum failed")
}
}
virtual void save(const std::string filename, const EigenDiskVectorMat<T> &obj) const
{
std::ofstream f(filename, std::ios::binary);
std::vector<unsigned char> hash(SHA256_DIGEST_LENGTH);
Eigen::Index nRow, nCol;
size_t matSize;
double t;
nRow = obj.rows();
nCol = obj.cols();
matSize = nRow*nCol*sizeof(T);
hash = GridChecksum::sha256(obj.data(), matSize);
DV_DEBUG_MSG(this, "Eigen sha256 " << GridChecksum::sha256_string(hash));
f.write(reinterpret_cast<char *>(hash.data()), hash.size()*sizeof(unsigned char));
f.write(reinterpret_cast<char *>(&nRow), sizeof(Eigen::Index));
f.write(reinterpret_cast<char *>(&nCol), sizeof(Eigen::Index));
t = -usecond();
f.write(reinterpret_cast<const char *>(obj.data()), matSize);
t += usecond();
DV_DEBUG_MSG(this, "Eigen write " << matSize/t*1.0e6/1024/1024 << " MB/s");
}
};
/******************************************************************************
* DiskVectorBase implementation *
******************************************************************************/
#ifdef DV_DEBUG
#define DV_DEBUG_MSG(stream) LOG(Debug) << "diskvector " << this << ": " << stream << std::endl
#endif
template <typename T>
DiskVectorBase<T>::DiskVectorBase(const std::string dirname,
const unsigned int size,
@ -160,28 +231,29 @@ DiskVectorBase<T>::~DiskVectorBase(void)
template <typename T>
const T & DiskVectorBase<T>::operator[](const unsigned int i) const
{
auto &cache = *cachePtr_;
auto &loads = *loadsPtr_;
auto &cache = *cachePtr_;
auto &loads = *loadsPtr_;
DV_DEBUG_MSG("accessing " << i << " (RO)");
DV_DEBUG_MSG(this, "accessing " << i << " (RO)");
if (i >= size_)
{
HADRONS_ERROR(Size, "index out of range");
}
const_cast<double &>(access_)++;
if (cache.find(i) == cache.end())
{
// cache miss
DV_DEBUG_MSG("cache miss");
DV_DEBUG_MSG(this, "cache miss");
fetch(i);
}
else
{
DV_DEBUG_MSG("cache hit");
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);
}
@ -193,7 +265,7 @@ const T & DiskVectorBase<T>::operator[](const unsigned int i) const
{
msg += std::to_string(p) + " ";
}
DV_DEBUG_MSG("in cache: " << msg);
DV_DEBUG_MSG(this, "in cache: " << msg);
#endif
return cache.at(i);
@ -202,7 +274,7 @@ const T & DiskVectorBase<T>::operator[](const unsigned int i) const
template <typename T>
typename DiskVectorBase<T>::RwAccessHelper DiskVectorBase<T>::operator[](const unsigned int i)
{
DV_DEBUG_MSG("accessing " << i << " (RW)");
DV_DEBUG_MSG(this, "accessing " << i << " (RW)");
if (i >= size_)
{
@ -212,6 +284,19 @@ typename DiskVectorBase<T>::RwAccessHelper DiskVectorBase<T>::operator[](const u
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
{
@ -226,7 +311,7 @@ void DiskVectorBase<T>::evict(void) const
if (cache.size() >= cacheSize_)
{
DV_DEBUG_MSG("evicting " << loads.front());
DV_DEBUG_MSG(this, "evicting " << loads.front());
cache.erase(loads.front());
loads.pop_front();
}
@ -239,7 +324,7 @@ void DiskVectorBase<T>::fetch(const unsigned int i) const
auto &loads = *loadsPtr_;
struct stat s;
DV_DEBUG_MSG("loading " << i << " from disk");
DV_DEBUG_MSG(this, "loading " << i << " from disk");
evict();
if(stat(filename(i).c_str(), &s) != 0)
@ -267,7 +352,7 @@ void DiskVectorBase<T>::cacheInsert(const unsigned int i, const T &obj) const
{
msg += std::to_string(p) + " ";
}
DV_DEBUG_MSG("in cache: " << msg);
DV_DEBUG_MSG(this, "in cache: " << msg);
#endif
}

16
tests/hadrons/Test_diskvector.cc
View File

@ -91,6 +91,22 @@ int main(int argc, char *argv[])
v13r = v[13];
LOG(Message) << "v[13] correct? "
<< ((v13r == v13w) ? "yes" : "no" ) << std::endl;
LOG(Message) << "hit ratio " << v.hitRatio() << std::endl;
EigenDiskVector<ComplexD> w("eigendiskvector_test", 1000, 4);
EigenDiskVector<ComplexD>::Matrix m,n;
w[2] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
m = w[2];
w[3] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
w[4] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
w[5] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
w[6] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
w[7] = EigenDiskVectorMat<ComplexD>::Random(2000, 2000);
n = w[2];
LOG(Message) << "w[2] correct? "
<< ((m == n) ? "yes" : "no" ) << std::endl;
LOG(Message) << "hit ratio " << w.hitRatio() << std::endl;
Grid_finalize();