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

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This commit is contained in:
Ed Bennett 2017-01-27 22:12:11 +00:00
commit c946d3bf3f
58 changed files with 1333 additions and 213 deletions
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8
.gitignore vendored
View File

@ -9,6 +9,7 @@
################
*~
*#
*.sublime-*
# Precompiled Headers #
#######################
@ -104,3 +105,10 @@ lib/fftw/*
##################
m4/lt*
m4/libtool.m4
# Buck files #
##############
.buck*
buck-out
BUCK
make-bin-BUCK.sh

19
configure.ac
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@ -99,6 +99,13 @@ case ${ac_MKL} in
AC_DEFINE([USE_MKL], [1], [Define to 1 if you use the Intel MKL]);;
esac
############### HDF5
AC_ARG_WITH([hdf5],
[AS_HELP_STRING([--with-hdf5=prefix],
[try this for a non-standard install prefix of the HDF5 library])],
[AM_CXXFLAGS="-I$with_hdf5/include $AM_CXXFLAGS"]
[AM_LDFLAGS="-L$with_hdf5/lib $AM_LDFLAGS"])
############### first-touch
AC_ARG_ENABLE([numa],
[AC_HELP_STRING([--enable-numa=yes|no|prefix], [enable first touch numa opt])],
@ -145,6 +152,12 @@ AC_SEARCH_LIBS([fftw_execute], [fftw3],
[AC_DEFINE([HAVE_FFTW], [1], [Define to 1 if you have the `FFTW' library])]
[have_fftw=true])
AC_SEARCH_LIBS([H5Fopen], [hdf5_cpp],
[AC_DEFINE([HAVE_HDF5], [1], [Define to 1 if you have the `HDF5' library])]
[have_hdf5=true]
[LIBS="${LIBS} -lhdf5"], [], [-lhdf5])
AM_CONDITIONAL(BUILD_HDF5, [ test "${have_hdf5}X" == "trueX" ])
CXXFLAGS=$CXXFLAGS_CPY
LDFLAGS=$LDFLAGS_CPY
@ -306,7 +319,7 @@ AM_CONDITIONAL(BUILD_COMMS_MPI3L, [ test "${comms_type}X" == "mpi3lX" ] )
AM_CONDITIONAL(BUILD_COMMS_NONE, [ test "${comms_type}X" == "noneX" ])
############### RNG selection
AC_ARG_ENABLE([rng],[AC_HELP_STRING([--enable-rng=ranlux48|mt19937],\
AC_ARG_ENABLE([rng],[AC_HELP_STRING([--enable-rng=ranlux48|mt19937|sitmo],\
[Select Random Number Generator to be used])],\
[ac_RNG=${enable_rng}],[ac_RNG=ranlux48])
@ -317,6 +330,9 @@ case ${ac_RNG} in
mt19937)
AC_DEFINE([RNG_MT19937],[1],[RNG_MT19937] )
;;
sitmo)
AC_DEFINE([RNG_SITMO],[1],[RNG_SITMO] )
;;
*)
AC_MSG_ERROR([${ac_RNG} unsupported --enable-rng option]);
;;
@ -410,6 +426,7 @@ RNG choice : ${ac_RNG}
GMP : `if test "x$have_gmp" = xtrue; then echo yes; else echo no; fi`
LAPACK : ${ac_LAPACK}
FFTW : `if test "x$have_fftw" = xtrue; then echo yes; else echo no; fi`
HDF5 : `if test "x$have_hdf5" = xtrue; then echo yes; else echo no; fi`
build DOXYGEN documentation : `if test "$DX_FLAG_doc" = '1'; then echo yes; else echo no; fi`
----- BUILD FLAGS -------------------------------------
CXXFLAGS:

43
extras/Hadrons/Application.cc
View File

@ -42,7 +42,6 @@ using namespace Hadrons;
******************************************************************************/
// constructors ////////////////////////////////////////////////////////////////
Application::Application(void)
: env_(Environment::getInstance())
{
LOG(Message) << "Modules available:" << std::endl;
auto list = ModuleFactory::getInstance().getBuilderList();
@ -74,11 +73,17 @@ Application::Application(const std::string parameterFileName)
parameterFileName_ = parameterFileName;
}
// environment shortcut ////////////////////////////////////////////////////////
Environment & Application::env(void) const
{
return Environment::getInstance();
}
// access //////////////////////////////////////////////////////////////////////
void Application::setPar(const Application::GlobalPar &par)
{
par_ = par;
env_.setSeed(strToVec<int>(par_.seed));
env().setSeed(strToVec<int>(par_.seed));
}
const Application::GlobalPar & Application::getPar(void)
@ -89,7 +94,7 @@ const Application::GlobalPar & Application::getPar(void)
// execute /////////////////////////////////////////////////////////////////////
void Application::run(void)
{
if (!parameterFileName_.empty() and (env_.getNModule() == 0))
if (!parameterFileName_.empty() and (env().getNModule() == 0))
{
parseParameterFile(parameterFileName_);
}
@ -124,7 +129,7 @@ void Application::parseParameterFile(const std::string parameterFileName)
do
{
read(reader, "id", id);
env_.createModule(id.name, id.type, reader);
env().createModule(id.name, id.type, reader);
} while (reader.nextElement("module"));
pop(reader);
pop(reader);
@ -134,7 +139,7 @@ void Application::saveParameterFile(const std::string parameterFileName)
{
XmlWriter writer(parameterFileName);
ObjectId id;
const unsigned int nMod = env_.getNModule();
const unsigned int nMod = env().getNModule();
LOG(Message) << "Saving application to '" << parameterFileName << "'..." << std::endl;
write(writer, "parameters", getPar());
@ -142,10 +147,10 @@ void Application::saveParameterFile(const std::string parameterFileName)
for (unsigned int i = 0; i < nMod; ++i)
{
push(writer, "module");
id.name = env_.getModuleName(i);
id.type = env_.getModule(i)->getRegisteredName();
id.name = env().getModuleName(i);
id.type = env().getModule(i)->getRegisteredName();
write(writer, "id", id);
env_.getModule(i)->saveParameters(writer, "options");
env().getModule(i)->saveParameters(writer, "options");
pop(writer);
}
pop(writer);
@ -164,10 +169,10 @@ auto memPeak = [this](const std::vector<unsigned int> &program)\
\
msg = HadronsLogMessage.isActive();\
HadronsLogMessage.Active(false);\
env_.dryRun(true);\
memPeak = env_.executeProgram(program);\
env_.dryRun(false);\
env_.freeAll();\
env().dryRun(true);\
memPeak = env().executeProgram(program);\
env().dryRun(false);\
env().freeAll();\
HadronsLogMessage.Active(true);\
\
return memPeak;\
@ -179,7 +184,7 @@ void Application::schedule(void)
// build module dependency graph
LOG(Message) << "Building module graph..." << std::endl;
auto graph = env_.makeModuleGraph();
auto graph = env().makeModuleGraph();
auto con = graph.getConnectedComponents();
// constrained topological sort using a genetic algorithm
@ -256,7 +261,7 @@ void Application::saveSchedule(const std::string filename)
<< std::endl;
for (auto address: program_)
{
program.push_back(env_.getModuleName(address));
program.push_back(env().getModuleName(address));
}
write(writer, "schedule", program);
}
@ -274,7 +279,7 @@ void Application::loadSchedule(const std::string filename)
program_.clear();
for (auto &name: program)
{
program_.push_back(env_.getModuleAddress(name));
program_.push_back(env().getModuleAddress(name));
}
scheduled_ = true;
memPeak_ = memPeak(program_);
@ -291,7 +296,7 @@ void Application::printSchedule(void)
for (unsigned int i = 0; i < program_.size(); ++i)
{
LOG(Message) << std::setw(4) << i + 1 << ": "
<< env_.getModuleName(program_[i]) << std::endl;
<< env().getModuleName(program_[i]) << std::endl;
}
}
@ -304,9 +309,9 @@ void Application::configLoop(void)
{
LOG(Message) << BIG_SEP << " Starting measurement for trajectory " << t
<< " " << BIG_SEP << std::endl;
env_.setTrajectory(t);
env_.executeProgram(program_);
env_.freeAll();
env().setTrajectory(t);
env().executeProgram(program_);
}
LOG(Message) << BIG_SEP << " End of measurement " << BIG_SEP << std::endl;
env().freeAll();
}

8
extras/Hadrons/Application.hpp
View File

@ -98,11 +98,13 @@ public:
void printSchedule(void);
// loop on configurations
void configLoop(void);
private:
// environment shortcut
Environment & env(void) const;
private:
long unsigned int locVol_;
std::string parameterFileName_{""};
GlobalPar par_;
Environment &env_;
std::vector<unsigned int> program_;
Environment::Size memPeak_;
bool scheduled_{false};
@ -115,14 +117,14 @@ private:
template <typename M>
void Application::createModule(const std::string name)
{
env_.createModule<M>(name);
env().createModule<M>(name);
}
template <typename M>
void Application::createModule(const std::string name,
const typename M::Par &par)
{
env_.createModule<M>(name, par);
env().createModule<M>(name, par);
}
END_HADRONS_NAMESPACE

43
extras/Hadrons/Environment.cc
View File

@ -41,8 +41,9 @@ using namespace Hadrons;
// constructor /////////////////////////////////////////////////////////////////
Environment::Environment(void)
{
nd_ = GridDefaultLatt().size();
grid4d_.reset(SpaceTimeGrid::makeFourDimGrid(
GridDefaultLatt(), GridDefaultSimd(Nd, vComplex::Nsimd()),
GridDefaultLatt(), GridDefaultSimd(nd_, vComplex::Nsimd()),
GridDefaultMpi()));
gridRb4d_.reset(SpaceTimeGrid::makeFourDimRedBlackGrid(grid4d_.get()));
auto loc = getGrid()->LocalDimensions();
@ -126,6 +127,11 @@ GridRedBlackCartesian * Environment::getRbGrid(const unsigned int Ls) const
}
}
unsigned int Environment::getNd(void) const
{
return nd_;
}
// random number generator /////////////////////////////////////////////////////
void Environment::setSeed(const std::vector<int> &seed)
{
@ -409,6 +415,8 @@ Environment::Size Environment::executeProgram(const std::vector<std::string> &p)
// general memory management ///////////////////////////////////////////////////
void Environment::addObject(const std::string name, const int moduleAddress)
{
if (!hasObject(name))
{
ObjInfo info;
@ -417,6 +425,11 @@ void Environment::addObject(const std::string name, const int moduleAddress)
object_.push_back(std::move(info));
objectAddress_[name] = static_cast<unsigned int>(object_.size() - 1);
}
else
{
HADRON_ERROR("object '" + name + "' already exists");
}
}
void Environment::registerObject(const unsigned int address,
const unsigned int size, const unsigned int Ls)
@ -444,6 +457,10 @@ void Environment::registerObject(const unsigned int address,
void Environment::registerObject(const std::string name,
const unsigned int size, const unsigned int Ls)
{
if (!hasObject(name))
{
addObject(name);
}
registerObject(getObjectAddress(name), size, Ls);
}
@ -573,6 +590,30 @@ bool Environment::hasRegisteredObject(const std::string name) const
}
}
bool Environment::hasCreatedObject(const unsigned int address) const
{
if (hasObject(address))
{
return (object_[address].data != nullptr);
}
else
{
return false;
}
}
bool Environment::hasCreatedObject(const std::string name) const
{
if (hasObject(name))
{
return hasCreatedObject(getObjectAddress(name));
}
else
{
return false;
}
}
bool Environment::isObject5d(const unsigned int address) const
{
return (getObjectLs(address) > 1);

6
extras/Hadrons/Environment.hpp
View File

@ -106,6 +106,7 @@ public:
void createGrid(const unsigned int Ls);
GridCartesian * getGrid(const unsigned int Ls = 1) const;
GridRedBlackCartesian * getRbGrid(const unsigned int Ls = 1) const;
unsigned int getNd(void) const;
// random number generator
void setSeed(const std::vector<int> &seed);
GridParallelRNG * get4dRng(void) const;
@ -137,7 +138,7 @@ public:
Size executeProgram(const std::vector<std::string> &p);
// general memory management
void addObject(const std::string name,
const int moduleAddress);
const int moduleAddress = -1);
void registerObject(const unsigned int address,
const unsigned int size,
const unsigned int Ls = 1);
@ -176,6 +177,8 @@ public:
bool hasObject(const std::string name) const;
bool hasRegisteredObject(const unsigned int address) const;
bool hasRegisteredObject(const std::string name) const;
bool hasCreatedObject(const unsigned int address) const;
bool hasCreatedObject(const std::string name) const;
bool isObject5d(const unsigned int address) const;
bool isObject5d(const std::string name) const;
Environment::Size getTotalSize(void) const;
@ -198,6 +201,7 @@ private:
std::map<unsigned int, GridPt> grid5d_;
GridRbPt gridRb4d_;
std::map<unsigned int, GridRbPt> gridRb5d_;
unsigned int nd_;
// random number generator
RngPt rng4d_;
// module and related maps

12
extras/Hadrons/GeneticScheduler.hpp
View File

@ -134,7 +134,7 @@ void GeneticScheduler<T>::nextGeneration(void)
LOG(Debug) << "Starting population:\n" << *this << std::endl;
// random mutations
PARALLEL_FOR_LOOP
//PARALLEL_FOR_LOOP
for (unsigned int i = 0; i < par_.popSize; ++i)
{
doMutation();
@ -142,7 +142,7 @@ void GeneticScheduler<T>::nextGeneration(void)
LOG(Debug) << "After mutations:\n" << *this << std::endl;
// mating
PARALLEL_FOR_LOOP
//PARALLEL_FOR_LOOP
for (unsigned int i = 0; i < par_.popSize/2; ++i)
{
doCrossover();
@ -166,7 +166,7 @@ void GeneticScheduler<T>::initPopulation(void)
{
auto p = graph_.topoSort(gen_);
population_.emplace(func_(p), p);
population_.insert(std::make_pair(func_(p), p));
}
}
@ -180,8 +180,8 @@ void GeneticScheduler<T>::doCrossover(void)
crossover(c1, c2, p1, p2);
PARALLEL_CRITICAL
{
population_.emplace(func_(c1), c1);
population_.emplace(func_(c2), c2);
population_.insert(std::make_pair(func_(c1), c1));
population_.insert(std::make_pair(func_(c2), c2));
}
}
@ -200,7 +200,7 @@ void GeneticScheduler<T>::doMutation(void)
mutation(m, it->second);
PARALLEL_CRITICAL
{
population_.emplace(func_(m), m);
population_.insert(std::make_pair(func_(m), m));
}
}
}

2
extras/Hadrons/Modules/MSource/SeqGamma.hpp
View File

@ -147,7 +147,7 @@ void TSeqGamma<FImpl>::execute(void)
g = makeGammaProd(par().gamma);
p = strToVec<Real>(par().mom);
ph = zero;
for(unsigned int mu = 0; mu < Nd; mu++)
for(unsigned int mu = 0; mu < env().getNd(); mu++)
{
LatticeCoordinate(coor, mu);
ph = ph + p[mu]*coor;

2
lib/Grid.h
View File

@ -59,13 +59,13 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
///////////////////
// Grid headers
///////////////////
#include <Grid/serialisation/Serialisation.h>
#include "Config.h"
#include <Grid/Timer.h>
#include <Grid/PerfCount.h>
#include <Grid/Log.h>
#include <Grid/AlignedAllocator.h>
#include <Grid/Simd.h>
#include <Grid/serialisation/Serialisation.h>
#include <Grid/Threads.h>
#include <Grid/Lexicographic.h>
#include <Grid/Init.h>

2
lib/Init.cc
View File

@ -41,7 +41,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
#include <signal.h>
#include <iostream>
#include <iterator>
#include <Grid.h>
#include <Grid/Grid.h>
#include <algorithm>
#include <iterator>
#include <cstdlib>

2
lib/Log.cc
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@ -29,7 +29,7 @@ See the full license in the file "LICENSE" in the top level distribution
directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
#include <cxxabi.h>

12
lib/Makefile.am
View File

@ -1,4 +1,5 @@
extra_sources=
extra_headers=
if BUILD_COMMS_MPI
extra_sources+=communicator/Communicator_mpi.cc
extra_sources+=communicator/Communicator_base.cc
@ -24,6 +25,12 @@ if BUILD_COMMS_NONE
extra_sources+=communicator/Communicator_base.cc
endif
if BUILD_HDF5
extra_sources+=serialisation/Hdf5IO.cc
extra_headers+=serialisation/Hdf5IO.h
extra_headers+=serialisation/Hdf5Type.h
endif
#
# Libraries
#
@ -32,6 +39,9 @@ include Eigen.inc
lib_LIBRARIES = libGrid.a
libGrid_a_SOURCES = $(CCFILES) $(extra_sources)
CCFILES += $(extra_sources)
HFILES += $(extra_headers)
libGrid_a_SOURCES = $(CCFILES)
libGrid_adir = $(pkgincludedir)
nobase_dist_pkginclude_HEADERS = $(HFILES) $(eigen_files) Config.h

4
lib/PerfCount.cc
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@ -26,8 +26,8 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <PerfCount.h>
#include <Grid/Grid.h>
#include <Grid/PerfCount.h>
namespace Grid {

6
lib/Stat.cc
View File

@ -1,6 +1,6 @@
#include <Grid.h>
#include <PerfCount.h>
#include <Stat.h>
#include <Grid/Grid.h>
#include <Grid/PerfCount.h>
#include <Grid/Stat.h>
namespace Grid {

2
lib/algorithms/approx/MultiShiftFunction.cc
View File

@ -25,7 +25,7 @@ Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
double MultiShiftFunction::approx(double x)

2
lib/algorithms/approx/Remez.cc
View File

@ -20,7 +20,7 @@
#include<iomanip>
#include<cassert>
#include<algorithms/approx/Remez.h>
#include<Grid/algorithms/approx/Remez.h>
// Constructor
AlgRemez::AlgRemez(double lower, double upper, long precision)

2
lib/algorithms/iterative/Matrix.h
View File

@ -36,7 +36,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
#include <iomanip>
#include <complex>
#include <typeinfo>
#include <Grid.h>
#include <Grid/Grid.h>
/** Sign function **/

2
lib/communicator/Communicator_base.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
namespace Grid {
///////////////////////////////////////////////////////////////

2
lib/communicator/Communicator_mpi.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
#include <mpi.h>
namespace Grid {

2
lib/communicator/Communicator_mpi3.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
#include <mpi.h>
namespace Grid {

2
lib/communicator/Communicator_none.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
namespace Grid {
///////////////////////////////////////////////////////////////////////////////////////////////////

2
lib/communicator/Communicator_shmem.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
#include <mpp/shmem.h>
namespace Grid {

7
lib/lattice/Lattice_rng.h
View File

@ -30,6 +30,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
#define GRID_LATTICE_RNG_H
#include <random>
#include <Grid/sitmo_rng/sitmo_prng_engine.hpp>
namespace Grid {
@ -114,10 +115,14 @@ namespace Grid {
typedef uint64_t RngStateType;
typedef std::ranlux48 RngEngine;
static const int RngStateCount = 15;
#else
#elif RNG_MT19937
typedef std::mt19937 RngEngine;
typedef uint32_t RngStateType;
static const int RngStateCount = std::mt19937::state_size;
#elif RNG_SITMO
typedef sitmo::prng_engine RngEngine;
typedef uint64_t RngStateType;
static const int RngStateCount = 4;
#endif
std::vector<RngEngine> _generators;
std::vector<std::uniform_real_distribution<RealD>> _uniform;

1
lib/lattice/Lattice_transfer.h
View File

@ -386,6 +386,7 @@ void InsertSlice(Lattice<vobj> &lowDim,Lattice<vobj> & higherDim,int slice, int
}
// the above should guarantee that the operations are local
// Guido: check the threading here
//PARALLEL_FOR_LOOP
for(int idx=0;idx<lg->lSites();idx++){
std::vector<int> lcoor(nl);

2
lib/pugixml/pugixml.cc
View File

@ -14,7 +14,7 @@
#ifndef SOURCE_PUGIXML_CPP
#define SOURCE_PUGIXML_CPP
#include <pugixml/pugixml.h>
#include <Grid/pugixml/pugixml.h>
#include <stdlib.h>
#include <stdio.h>

2
lib/qcd/action/fermion/CayleyFermion5D.cc
View File

@ -30,7 +30,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
/* END LEGAL */
#include <Grid/Eigen/Dense>
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/CayleyFermion5Dcache.cc
View File

@ -29,7 +29,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/CayleyFermion5Ddense.cc
View File

@ -30,7 +30,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
/* END LEGAL */
#include <Grid/Eigen/Dense>
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/CayleyFermion5Dssp.cc
View File

@ -29,7 +29,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/CayleyFermion5Dvec.cc
View File

@ -30,7 +30,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/ContinuedFractionFermion5D.cc
View File

@ -26,7 +26,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

2
lib/qcd/action/fermion/PartialFractionFermion5D.cc
View File

@ -26,7 +26,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

2
lib/qcd/action/fermion/WilsonFermion.cc
View File

@ -29,7 +29,7 @@ See the full license in the file "LICENSE" in the top level distribution
directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

4
lib/qcd/action/fermion/WilsonFermion5D.cc
View File

@ -29,8 +29,8 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <PerfCount.h>
#include <Grid/Grid.h>
#include <Grid/PerfCount.h>
namespace Grid {
namespace QCD {

2
lib/qcd/action/fermion/WilsonKernels.cc
View File

@ -28,7 +28,7 @@ See the full license in the file "LICENSE" in the top level distribution
directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

2
lib/qcd/action/fermion/WilsonKernelsAsm.cc
View File

@ -30,7 +30,7 @@ Author: Guido Cossu <guido.cossu@ed.ac.uk>
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/action/fermion/WilsonKernelsHand.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
#define REGISTER

2
lib/qcd/action/fermion/WilsonTMFermion.cc
View File

@ -25,7 +25,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

2
lib/qcd/hmc/HMC.cc
View File

@ -27,7 +27,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid{
namespace QCD{

2
lib/qcd/spin/Dirac.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {

2
lib/qcd/utils/SpaceTimeGrid.cc
View File

@ -25,7 +25,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
namespace Grid {
namespace QCD {

197
lib/serialisation/BaseIO.h
View File

@ -32,6 +32,7 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
#include <type_traits>
namespace Grid {
// Vector IO utilities ///////////////////////////////////////////////////////
// helper function to read space-separated values
template <typename T>
std::vector<T> strToVec(const std::string s)
@ -67,6 +68,77 @@ namespace Grid {
return os;
}
// Vector element trait //////////////////////////////////////////////////////
template <typename T>
struct element
{
typedef T type;
static constexpr bool is_number = false;
};
template <typename T>
struct element<std::vector<T>>
{
typedef typename element<T>::type type;
static constexpr bool is_number = std::is_arithmetic<T>::value
or is_complex<T>::value
or element<T>::is_number;
};
// Vector flatening utility class ////////////////////////////////////////////
// Class to flatten a multidimensional std::vector
template <typename V>
class Flatten
{
public:
typedef typename element<V>::type Element;
public:
explicit Flatten(const V &vector);
const V & getVector(void);
const std::vector<Element> & getFlatVector(void);
const std::vector<size_t> & getDim(void);
private:
void accumulate(const Element &e);
template <typename W>
void accumulate(const W &v);
void accumulateDim(const Element &e);
template <typename W>
void accumulateDim(const W &v);
private:
const V &vector_;
std::vector<Element> flatVector_;
std::vector<size_t> dim_;
};
// Class to reconstruct a multidimensional std::vector
template <typename V>
class Reconstruct
{
public:
typedef typename element<V>::type Element;
public:
Reconstruct(const std::vector<Element> &flatVector,
const std::vector<size_t> &dim);
const V & getVector(void);
const std::vector<Element> & getFlatVector(void);
const std::vector<size_t> & getDim(void);
private:
void fill(std::vector<Element> &v);
template <typename W>
void fill(W &v);
void resize(std::vector<Element> &v, const unsigned int dim);
template <typename W>
void resize(W &v, const unsigned int dim);
private:
V vector_;
const std::vector<Element> &flatVector_;
std::vector<size_t> dim_;
size_t ind_{0};
unsigned int dimInd_{0};
};
// Abstract writer/reader classes ////////////////////////////////////////////
// static polymorphism implemented using CRTP idiom
class Serializable;
@ -132,7 +204,128 @@ namespace Grid {
}
};
// Generic writer interface
// Flatten class template implementation /////////////////////////////////////
template <typename V>
void Flatten<V>::accumulate(const Element &e)
{
flatVector_.push_back(e);
}
template <typename V>
template <typename W>
void Flatten<V>::accumulate(const W &v)
{
for (auto &e: v)
{
accumulate(e);
}
}
template <typename V>
void Flatten<V>::accumulateDim(const Element &e) {};
template <typename V>
template <typename W>
void Flatten<V>::accumulateDim(const W &v)
{
dim_.push_back(v.size());
accumulateDim(v[0]);
}
template <typename V>
Flatten<V>::Flatten(const V &vector)
: vector_(vector)
{
accumulate(vector_);
accumulateDim(vector_);
}
template <typename V>
const V & Flatten<V>::getVector(void)
{
return vector_;
}
template <typename V>
const std::vector<typename Flatten<V>::Element> &
Flatten<V>::getFlatVector(void)
{
return flatVector_;
}
template <typename V>
const std::vector<size_t> & Flatten<V>::getDim(void)
{
return dim_;
}
// Reconstruct class template implementation /////////////////////////////////
template <typename V>
void Reconstruct<V>::fill(std::vector<Element> &v)
{
for (auto &e: v)
{
e = flatVector_[ind_++];
}
}
template <typename V>
template <typename W>
void Reconstruct<V>::fill(W &v)
{
for (auto &e: v)
{
fill(e);
}
}
template <typename V>
void Reconstruct<V>::resize(std::vector<Element> &v, const unsigned int dim)
{
v.resize(dim_[dim]);
}
template <typename V>
template <typename W>
void Reconstruct<V>::resize(W &v, const unsigned int dim)
{
v.resize(dim_[dim]);
for (auto &e: v)
{
resize(e, dim + 1);
}
}
template <typename V>
Reconstruct<V>::Reconstruct(const std::vector<Element> &flatVector,
const std::vector<size_t> &dim)
: flatVector_(flatVector)
, dim_(dim)
{
resize(vector_, 0);
fill(vector_);
}
template <typename V>
const V & Reconstruct<V>::getVector(void)
{
return vector_;
}
template <typename V>
const std::vector<typename Reconstruct<V>::Element> &
Reconstruct<V>::getFlatVector(void)
{
return flatVector_;
}
template <typename V>
const std::vector<size_t> & Reconstruct<V>::getDim(void)
{
return dim_;
}
// Generic writer interface //////////////////////////////////////////////////
template <typename T>
inline void push(Writer<T> &w, const std::string &s)
{
@ -217,7 +410,7 @@ namespace Grid {
upcast->writeDefault(s, output);
}
// Reader template implementation ////////////////////////////////////////////
// Reader template implementation
template <typename T>
Reader<T>::Reader(void)
{

2
lib/serialisation/BinaryIO.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
using namespace Grid;
using namespace std;

103
lib/serialisation/Hdf5IO.cc Normal file
View File

@ -0,0 +1,103 @@
#include <Grid/Grid.h>
using namespace Grid;
#ifndef H5_NO_NAMESPACE
using namespace H5NS;
#endif
// Writer implementation ///////////////////////////////////////////////////////
Hdf5Writer::Hdf5Writer(const std::string &fileName)
: fileName_(fileName)
, file_(fileName.c_str(), H5F_ACC_TRUNC)
{
group_ = file_.openGroup("/");
writeSingleAttribute(dataSetThres_, HDF5_GRID_GUARD "dataset_threshold",
Hdf5Type<unsigned int>::type());
}
void Hdf5Writer::push(const std::string &s)
{
group_ = group_.createGroup(s);
path_.push_back(s);
}
void Hdf5Writer::pop(void)
{
path_.pop_back();
if (path_.empty())
{
group_ = file_.openGroup("/");
}
else
{
auto binOp = [](const std::string &a, const std::string &b)->std::string
{
return a + "/" + b;
};
group_ = group_.openGroup(std::accumulate(path_.begin(), path_.end(),
std::string(""), binOp));
}
}
template <>
void Hdf5Writer::writeDefault(const std::string &s, const std::string &x)
{
StrType strType(PredType::C_S1, x.size());
writeSingleAttribute(*(x.data()), s, strType);
}
void Hdf5Writer::writeDefault(const std::string &s, const char *x)
{
std::string sx(x);
writeDefault(s, sx);
}
// Reader implementation ///////////////////////////////////////////////////////
Hdf5Reader::Hdf5Reader(const std::string &fileName)
: fileName_(fileName)
, file_(fileName.c_str(), H5F_ACC_RDONLY)
{
group_ = file_.openGroup("/");
readSingleAttribute(dataSetThres_, HDF5_GRID_GUARD "dataset_threshold",
Hdf5Type<unsigned int>::type());
}
void Hdf5Reader::push(const std::string &s)
{
group_ = group_.openGroup(s);
path_.push_back(s);
}
void Hdf5Reader::pop(void)
{
path_.pop_back();
if (path_.empty())
{
group_ = file_.openGroup("/");
}
else
{
auto binOp = [](const std::string &a, const std::string &b)->std::string
{
return a + "/" + b;
};
group_ = group_.openGroup(std::accumulate(path_.begin(), path_.end(),
std::string(""), binOp));
}
}
template <>
void Hdf5Reader::readDefault(const std::string &s, std::string &x)
{
Attribute attribute;
attribute = group_.openAttribute(s);
StrType strType = attribute.getStrType();
x.resize(strType.getSize());
attribute.read(strType, &(x[0]));
}

242
lib/serialisation/Hdf5IO.h Normal file
View File

@ -0,0 +1,242 @@
#ifndef GRID_SERIALISATION_HDF5_H
#define GRID_SERIALISATION_HDF5_H
#include <stack>
#include <string>
#include <vector>
#include <H5Cpp.h>
#include "Hdf5Type.h"
#ifndef H5_NO_NAMESPACE
#define H5NS H5
#endif
// default thresold above which datasets are used instead of attributes
#ifndef HDF5_DEF_DATASET_THRES
#define HDF5_DEF_DATASET_THRES 6u
#endif
// name guard for Grid metadata
#define HDF5_GRID_GUARD "_Grid_"
namespace Grid
{
class Hdf5Writer: public Writer<Hdf5Writer>
{
public:
Hdf5Writer(const std::string &fileName);
virtual ~Hdf5Writer(void) = default;
void push(const std::string &s);
void pop(void);
void writeDefault(const std::string &s, const char *x);
template <typename U>
void writeDefault(const std::string &s, const U &x);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
writeDefault(const std::string &s, const std::vector<U> &x);
template <typename U>
typename std::enable_if<!element<std::vector<U>>::is_number, void>::type
writeDefault(const std::string &s, const std::vector<U> &x);
private:
template <typename U>
void writeSingleAttribute(const U &x, const std::string &name,
const H5NS::DataType &type);
private:
std::string fileName_;
std::vector<std::string> path_;
H5NS::H5File file_;
H5NS::Group group_;
unsigned int dataSetThres_{HDF5_DEF_DATASET_THRES};
};
class Hdf5Reader: public Reader<Hdf5Reader>
{
public:
Hdf5Reader(const std::string &fileName);
virtual ~Hdf5Reader(void) = default;
void push(const std::string &s);
void pop(void);
template <typename U>
void readDefault(const std::string &s, U &output);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
readDefault(const std::string &s, std::vector<U> &x);
template <typename U>
typename std::enable_if<!element<std::vector<U>>::is_number, void>::type
readDefault(const std::string &s, std::vector<U> &x);
private:
template <typename U>
void readSingleAttribute(U &x, const std::string &name,
const H5NS::DataType &type);
private:
std::string fileName_;
std::vector<std::string> path_;
H5NS::H5File file_;
H5NS::Group group_;
unsigned int dataSetThres_;
};
// Writer template implementation ////////////////////////////////////////////
template <typename U>
void Hdf5Writer::writeSingleAttribute(const U &x, const std::string &name,
const H5NS::DataType &type)
{
H5NS::Attribute attribute;
hsize_t attrDim = 1;
H5NS::DataSpace attrSpace(1, &attrDim);
attribute = group_.createAttribute(name, type, attrSpace);
attribute.write(type, &x);
}
template <typename U>
void Hdf5Writer::writeDefault(const std::string &s, const U &x)
{
writeSingleAttribute(x, s, Hdf5Type<U>::type());
}
template <>
void Hdf5Writer::writeDefault(const std::string &s, const std::string &x);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
Hdf5Writer::writeDefault(const std::string &s, const std::vector<U> &x)
{
// alias to element type
typedef typename element<std::vector<U>>::type Element;
// flatten the vector and getting dimensions
Flatten<std::vector<U>> flat(x);
std::vector<hsize_t> dim;
const auto &flatx = flat.getFlatVector();
for (auto &d: flat.getDim())
{
dim.push_back(d);
}
// write to file
H5NS::DataSpace dataSpace(dim.size(), dim.data());
if (flatx.size() > dataSetThres_)
{
H5NS::DataSet dataSet;
dataSet = group_.createDataSet(s, Hdf5Type<Element>::type(), dataSpace);
dataSet.write(flatx.data(), Hdf5Type<Element>::type());
}
else
{
H5NS::Attribute attribute;
attribute = group_.createAttribute(s, Hdf5Type<Element>::type(), dataSpace);
attribute.write(Hdf5Type<Element>::type(), flatx.data());
}
}
template <typename U>
typename std::enable_if<!element<std::vector<U>>::is_number, void>::type
Hdf5Writer::writeDefault(const std::string &s, const std::vector<U> &x)
{
push(s);
writeSingleAttribute(x.size(), HDF5_GRID_GUARD "vector_size",
Hdf5Type<uint64_t>::type());
for (hsize_t i = 0; i < x.size(); ++i)
{
write(s + "_" + std::to_string(i), x[i]);
}
pop();
}
// Reader template implementation ////////////////////////////////////////////
template <typename U>
void Hdf5Reader::readSingleAttribute(U &x, const std::string &name,
const H5NS::DataType &type)
{
H5NS::Attribute attribute;
attribute = group_.openAttribute(name);
attribute.read(type, &x);
}
template <typename U>
void Hdf5Reader::readDefault(const std::string &s, U &output)
{
readSingleAttribute(output, s, Hdf5Type<U>::type());
}
template <>
void Hdf5Reader::readDefault(const std::string &s, std::string &x);
template <typename U>
typename std::enable_if<element<std::vector<U>>::is_number, void>::type
Hdf5Reader::readDefault(const std::string &s, std::vector<U> &x)
{
// alias to element type
typedef typename element<std::vector<U>>::type Element;
// read the dimensions
H5NS::DataSpace dataSpace;
std::vector<hsize_t> hdim;
std::vector<size_t> dim;
hsize_t size = 1;
if (group_.attrExists(s))
{
dataSpace = group_.openAttribute(s).getSpace();
}
else
{
dataSpace = group_.openDataSet(s).getSpace();
}
hdim.resize(dataSpace.getSimpleExtentNdims());
dataSpace.getSimpleExtentDims(hdim.data());
for (auto &d: hdim)
{
dim.push_back(d);
size *= d;
}
// read the flat vector
std::vector<Element> buf(size);
if (size > dataSetThres_)
{
H5NS::DataSet dataSet;
dataSet = group_.openDataSet(s);
dataSet.read(buf.data(), Hdf5Type<Element>::type());
}
else
{
H5NS::Attribute attribute;
attribute = group_.openAttribute(s);
attribute.read(Hdf5Type<Element>::type(), buf.data());
}
// reconstruct the multidimensional vector
Reconstruct<std::vector<U>> r(buf, dim);
x = r.getVector();
}
template <typename U>
typename std::enable_if<!element<std::vector<U>>::is_number, void>::type
Hdf5Reader::readDefault(const std::string &s, std::vector<U> &x)
{
uint64_t size;
push(s);
readSingleAttribute(size, HDF5_GRID_GUARD "vector_size",
Hdf5Type<uint64_t>::type());
x.resize(size);
for (hsize_t i = 0; i < x.size(); ++i)
{
read(s + "_" + std::to_string(i), x[i]);
}
pop();
}
}
#endif

77
lib/serialisation/Hdf5Type.h Normal file
View File

@ -0,0 +1,77 @@
#ifndef GRID_SERIALISATION_HDF5_TYPE_H
#define GRID_SERIALISATION_HDF5_TYPE_H
#include <H5Cpp.h>
#include <complex>
#include <memory>
#ifndef H5_NO_NAMESPACE
#define H5NS H5
#endif
#define HDF5_NATIVE_TYPE(predType, cType)\
template <>\
class Hdf5Type<cType>\
{\
public:\
static inline const H5NS::DataType & type(void)\
{\
return H5NS::PredType::predType;\
}\
static constexpr bool isNative = true;\
};
#define DEFINE_HDF5_NATIVE_TYPES \
HDF5_NATIVE_TYPE(NATIVE_B8, bool);\
HDF5_NATIVE_TYPE(NATIVE_CHAR, char);\
HDF5_NATIVE_TYPE(NATIVE_SCHAR, signed char);\
HDF5_NATIVE_TYPE(NATIVE_UCHAR, unsigned char);\
HDF5_NATIVE_TYPE(NATIVE_SHORT, short);\
HDF5_NATIVE_TYPE(NATIVE_USHORT, unsigned short);\
HDF5_NATIVE_TYPE(NATIVE_INT, int);\
HDF5_NATIVE_TYPE(NATIVE_UINT, unsigned int);\
HDF5_NATIVE_TYPE(NATIVE_LONG, long);\
HDF5_NATIVE_TYPE(NATIVE_ULONG, unsigned long);\
HDF5_NATIVE_TYPE(NATIVE_LLONG, long long);\
HDF5_NATIVE_TYPE(NATIVE_ULLONG, unsigned long long);\
HDF5_NATIVE_TYPE(NATIVE_FLOAT, float);\
HDF5_NATIVE_TYPE(NATIVE_DOUBLE, double);\
HDF5_NATIVE_TYPE(NATIVE_LDOUBLE, long double);
namespace Grid
{
template <typename T> class Hdf5Type
{
public:
static constexpr bool isNative = false;
};
DEFINE_HDF5_NATIVE_TYPES;
template <typename R>
class Hdf5Type<std::complex<R>>
{
public:
static inline const H5NS::DataType & type(void)
{
if (typePtr_ == nullptr)
{
typePtr_.reset(new H5NS::CompType(sizeof(std::complex<R>)));
typePtr_->insertMember("re", 0, Hdf5Type<R>::type());
typePtr_->insertMember("im", sizeof(R), Hdf5Type<R>::type());
}
return *typePtr_;
}
static constexpr bool isNative = false;
private:
static std::unique_ptr<H5NS::CompType> typePtr_;
};
template <typename R>
std::unique_ptr<H5NS::CompType> Hdf5Type<std::complex<R>>::typePtr_ = nullptr;
}
#undef HDF5_NATIVE_TYPE
#endif /* GRID_SERIALISATION_HDF5_TYPE_H */

22
lib/serialisation/MacroMagic.h
View File

@ -109,38 +109,36 @@ THE SOFTWARE.
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#define GRID_MACRO_MEMBER(A,B) A B;
#define GRID_MACRO_COMP_MEMBER(A,B) result = (result and (lhs. B == rhs. B));
#define GRID_MACRO_OS_WRITE_MEMBER(A,B) os<< #A <<" "#B <<" = "<< obj. B <<" ; " <<std::endl;
#define GRID_MACRO_READ_MEMBER(A,B) Grid::read(RD,#B,obj. B);
#define GRID_MACRO_WRITE_MEMBER(A,B) Grid::write(WR,#B,obj. B);
#define GRID_SERIALIZABLE_CLASS_MEMBERS(cname,...)\
\
\
GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_MEMBER,__VA_ARGS__))\
\
\
template <typename T>\
static inline void write(Writer<T> &WR,const std::string &s, const cname &obj){ \
push(WR,s);\
GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_WRITE_MEMBER,__VA_ARGS__)) \
pop(WR);\
}\
\
\
template <typename T>\
static inline void read(Reader<T> &RD,const std::string &s, cname &obj){ \
push(RD,s);\
GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_READ_MEMBER,__VA_ARGS__)) \
pop(RD);\
}\
\
\
friend inline std::ostream & operator << (std::ostream &os, const cname &obj ) { \
os<<"class "<<#cname<<" {"<<std::endl;\
GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_OS_WRITE_MEMBER,__VA_ARGS__)) \
os<<"}"; \
return os;\
};
}\
friend inline bool operator==(const cname &lhs, const cname &rhs) {\
bool result = true;\
GRID_MACRO_EVAL(GRID_MACRO_MAP(GRID_MACRO_COMP_MEMBER,__VA_ARGS__))\
return result;\
}
#define GRID_ENUM_TYPE(obj) std::remove_reference<decltype(obj)>::type
#define GRID_MACRO_ENUMVAL(A,B) A = B,
@ -149,7 +147,7 @@ friend inline std::ostream & operator << (std::ostream &os, const cname &obj ) {
#define GRID_MACRO_ENUMCASEIO(A,B) case GRID_ENUM_TYPE(obj)::A: os << #A; break;
#define GRID_SERIALIZABLE_ENUM(name,undefname,...)\
class name: public Serializable\
class name: public Grid::Serializable\
{\
public:\
enum EnumType\
@ -161,7 +159,7 @@ public:\
name(void): value_(undefname) {};\
name(EnumType value): value_(value) {};\
template <typename T>\
static inline void write(Writer<T> &WR,const std::string &s, const name &obj)\
static inline void write(Grid::Writer<T> &WR,const std::string &s, const name &obj)\
{\
switch (obj.value_)\
{\
@ -171,7 +169,7 @@ public:\
}\
\
template <typename T>\
static inline void read(Reader<T> &RD,const std::string &s, name &obj)\
static inline void read(Grid::Reader<T> &RD,const std::string &s, name &obj)\
{\
std::string buf;\
Grid::read(RD, s, buf);\

3
lib/serialisation/Serialisation.h
View File

@ -36,6 +36,9 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
#include "BinaryIO.h"
#include "TextIO.h"
#include "XmlIO.h"
#ifdef HAVE_HDF5
#include "Hdf5IO.h"
#endif
//////////////////////////////////////////
// Todo:
//////////////////////////////////////////

2
lib/serialisation/TextIO.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
using namespace Grid;
using namespace std;

2
lib/serialisation/XmlIO.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
using namespace Grid;
using namespace std;

390
lib/sitmo_rng/sitmo_prng_engine.hpp Normal file
View File

@ -0,0 +1,390 @@
// Copyright (c) 2012-2016 M.A. (Thijs) van den Berg, http://sitmo.com/
//
// Use, modification and distribution are subject to the MIT Software License.
//
// The MIT License (MIT)
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
// version history:
// version 1, 6 Sep 2012
// version 2, 10 Dec 2013
// bug fix in the discard() routine, it was discarding to many elements
// added the version() method
// version 3...5, 13 Dec 2013
// fixed type-conversion earning
// fixed potential issues with constructor template matching
// version 6, 4 March 2016
// made min() max() constexpr for C+11 compiler (thanks to James Joseph Balamuta)
#ifndef SITMO_PRNG_ENGINE_HPP
#define SITMO_PRNG_ENGINE_HPP
#include <iostream>
#ifdef __GNUC__
#include <stdint.h> // respecting the C99 standard.
#endif
#ifdef _MSC_VER
typedef unsigned __int64 uint64_t; // Visual Studio 6.0(VC6) and newer..
typedef unsigned __int32 uint32_t;
#endif
// Double mixing function
#define MIX2(x0,x1,rx,z0,z1,rz) \
x0 += x1; \
z0 += z1; \
x1 = (x1 << rx) | (x1 >> (64-rx)); \
z1 = (z1 << rz) | (z1 >> (64-rz)); \
x1 ^= x0; \
z1 ^= z0;
// Double mixing function with key adition
#define MIXK(x0,x1,rx,z0,z1,rz,k0,k1,l0,l1) \
x1 += k1; \
z1 += l1; \
x0 += x1+k0; \
z0 += z1+l0; \
x1 = (x1 << rx) | (x1 >> (64-rx)); \
z1 = (z1 << rz) | (z1 >> (64-rz)); \
x1 ^= x0; \
z1 ^= z0; \
namespace sitmo {
// enable_if for C__98 compilers
template<bool C, typename T = void>
struct sitmo_enable_if { typedef T type; };
template<typename T>
struct sitmo_enable_if<false, T> { };
// SFINAE check for the existence of a "void generate(int*,int*)"member function
template<typename T>
struct has_generate_template
{
typedef char (&Two)[2];;
template<typename F, void (F::*)(int *, int *)> struct helper {};
template<typename C> static char test(helper<C, &C::template generate<int*> >*);
template<typename C> static Two test(...);
static bool const value = sizeof(test<T>(0)) == sizeof(char);
};
class prng_engine
{
public:
// "req" are requirements as stated in the C++ 11 draft n3242=11-0012
//
// req: 26.5.1.3 Uniform random number generator requirements, p.906, table 116, row 1
typedef uint32_t result_type;
// req: 26.5.1.3 Uniform random number generator requirements, p.906, table 116, row 3 & 4
#if __cplusplus <= 199711L
static result_type (min)() { return 0; }
static result_type (max)() { return 0xFFFFFFFF; }
#else
static constexpr result_type (min)() { return 0; }
static constexpr result_type (max)() { return 0xFFFFFFFF; }
#endif
// -------------------------------------------------
// Constructors
// -------------------------------------------------
// req: 26.5.1.4 Random number engine requirements, p.907 table 117, row 1
// Creates an engine with the same initial state as all other
// default-constructed engines of type E.
prng_engine()
{
seed();
}
// req: 26.5.1.4 Random number engine requirements, p.907 table 117, row 2
// Creates an engine that compares equal to x.
prng_engine(const prng_engine& x)
{
for (unsigned short i=0; i<4; ++i) {
_s[i] = x._s[i];
_k[i] = x._k[i];
_o[i] = x._o[i];
}
_o_counter = x._o_counter;
}
// req: 26.5.1.4 Random number engine requirements, p.907 table 117, row 3
// Creates an engine with initial O(size of state) state determined by s.
prng_engine(uint32_t s)
{
seed(s);
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 4
// Creates an engine with an initial state that depends on a sequence
// produced by one call to q.generate.
template<class Seq>
prng_engine(Seq& q, typename sitmo_enable_if< has_generate_template<Seq>::value >::type* = 0 )
{
seed(q);
}
// -------------------------------------------------
// Seeding
// -------------------------------------------------
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 5
void seed()
{
for (unsigned short i=0; i<4; ++i) {
_k[i] = 0;
_s[i] = 0;
}
_o_counter = 0;
_o[0] = 0x09218ebde6c85537;
_o[1] = 0x55941f5266d86105;
_o[2] = 0x4bd25e16282434dc;
_o[3] = 0xee29ec846bd2e40b;
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 6
// s needs to be of return_type, which is uint32_t
void seed(uint32_t s)
{
for (unsigned short i=0; i<4; ++i) {
_k[i] = 0;
_s[i] = 0;
}
_k[0] = s;
_o_counter = 0;
encrypt_counter();
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 7
template<class Seq>
void seed(Seq& q, typename sitmo_enable_if< has_generate_template<Seq>::value >::type* = 0 )
{
typename Seq::result_type w[8];
q.generate(&w[0], &w[8]);
for (unsigned short i=0; i<4; ++i) {
_k[i] = ( static_cast<uint64_t>(w[2*i]) << 32) | w[2*i+1];
_s[i] = 0;
}
_o_counter = 0;
encrypt_counter();
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 8
// Advances e’s state ei to ei+1 = TA(ei) and returns GA(ei).
uint32_t operator()()
{
// can we return a value from the current block?
if (_o_counter < 8) {
unsigned short _o_index = _o_counter >> 1;
_o_counter++;
if (_o_counter&1)
return _o[_o_index] & 0xFFFFFFFF;
else
return _o[_o_index] >> 32;
}
// generate a new block and return the first 32 bits
inc_counter();
encrypt_counter();
_o_counter = 1; // the next call
return _o[0] & 0xFFFFFFFF; // this call
}
// -------------------------------------------------
// misc
// -------------------------------------------------
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 9
// Advances e’s state ei to ei+z by any means equivalent to z
// consecutive calls e().
void discard(uint64_t z)
{
// check if we stay in the current block
if (z < 8 - _o_counter) {
_o_counter += static_cast<unsigned short>(z);
return;
}
// we will have to generate a new block...
z -= (8 - _o_counter); // discard the remainder of the current blok
_o_counter = z % 8; // set the pointer in the correct element in the new block
z -= _o_counter; // update z
z >>= 3; // the number of buffers is elements/8
++z; // and one more because we crossed the buffer line
inc_counter(z);
encrypt_counter();
}
// -------------------------------------------------
// IO
// -------------------------------------------------
template<class CharT, class Traits>
friend std::basic_ostream<CharT,Traits>&
operator<<(std::basic_ostream<CharT,Traits>& os, const prng_engine& s) {
for (unsigned short i=0; i<4; ++i)
os << s._k[i] << ' ' << s._s[i] << ' ' << s._o[i] << ' ';
os << s._o_counter;
return os;
}
template<class CharT, class Traits>
friend std::basic_istream<CharT,Traits>&
operator>>(std::basic_istream<CharT,Traits>& is, prng_engine& s) {
for (unsigned short i=0; i<4; ++i)
is >> s._k[i] >> s._s[i] >> s._o[i];
is >> s._o_counter;
return is;
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 10
// This operator is an equivalence relation. With Sx and Sy as the infinite
// sequences of values that would be generated by repeated future calls to
// x() and y(), respectively, returns true if Sx = Sy; else returns false.
bool operator==(const prng_engine& y)
{
if (_o_counter != y._o_counter) return false;
for (unsigned short i=0; i<4; ++i) {
if (_s[i] != y._s[i]) return false;
if (_k[i] != y._k[i]) return false;
if (_o[i] != y._o[i]) return false;
}
return true;
}
// req: 26.5.1.4 Random number engine requirements, p.908 table 117, row 11
bool operator!=(const prng_engine& y)
{
return !(*this == y);
}
// Extra function to set the key
void set_key(uint64_t k0=0, uint64_t k1=0, uint64_t k2=0, uint64_t k3=0)
{
_k[0] = k0; _k[1] = k1; _k[2] = k2; _k[3] = k3;
encrypt_counter();
}
// set the counter
void set_counter(uint64_t s0=0, uint64_t s1=0, uint64_t s2=0, uint64_t s3=0, unsigned short o_counter=0)
{
_s[0] = s0;
_s[1] = s1;
_s[2] = s2;
_s[3] = s3;
_o_counter = o_counter % 8;
encrypt_counter();
}
// versioning
uint32_t version()
{
return 5;
}
private:
void encrypt_counter()
{
uint64_t b[4];
uint64_t k[5];
for (unsigned short i=0; i<4; ++i) b[i] = _s[i];
for (unsigned short i=0; i<4; ++i) k[i] = _k[i];
k[4] = 0x1BD11BDAA9FC1A22 ^ k[0] ^ k[1] ^ k[2] ^ k[3];
MIXK(b[0], b[1], 14, b[2], b[3], 16, k[0], k[1], k[2], k[3]);
MIX2(b[0], b[3], 52, b[2], b[1], 57);
MIX2(b[0], b[1], 23, b[2], b[3], 40);
MIX2(b[0], b[3], 5, b[2], b[1], 37);
MIXK(b[0], b[1], 25, b[2], b[3], 33, k[1], k[2], k[3], k[4]+1);
MIX2(b[0], b[3], 46, b[2], b[1], 12);
MIX2(b[0], b[1], 58, b[2], b[3], 22);
MIX2(b[0], b[3], 32, b[2], b[1], 32);
MIXK(b[0], b[1], 14, b[2], b[3], 16, k[2], k[3], k[4], k[0]+2);
MIX2(b[0], b[3], 52, b[2], b[1], 57);
MIX2(b[0], b[1], 23, b[2], b[3], 40);
MIX2(b[0], b[3], 5, b[2], b[1], 37);
MIXK(b[0], b[1], 25, b[2], b[3], 33, k[3], k[4], k[0], k[1]+3);
MIX2(b[0], b[3], 46, b[2], b[1], 12);
MIX2(b[0], b[1], 58, b[2], b[3], 22);
MIX2(b[0], b[3], 32, b[2], b[1], 32);
MIXK(b[0], b[1], 14, b[2], b[3], 16, k[4], k[0], k[1], k[2]+4);
MIX2(b[0], b[3], 52, b[2], b[1], 57);
MIX2(b[0], b[1], 23, b[2], b[3], 40);
MIX2(b[0], b[3], 5, b[2], b[1], 37);
for (unsigned int i=0; i<4; ++i) _o[i] = b[i] + k[i];
_o[3] += 5;
}
void inc_counter()
{
++_s[0];
if (_s[0] != 0) return;
++_s[1];
if (_s[1] != 0) return;
++_s[2];
if (_s[2] != 0) return;
++_s[3];
}
void inc_counter(uint64_t z)
{
if (z > 0xFFFFFFFFFFFFFFFF - _s[0]) { // check if we will overflow the first 64 bit int
++_s[1];
if (_s[1] == 0) {
++_s[2];
if (_s[2] == 0) {
++_s[3];
}
}
}
_s[0] += z;
}
private:
uint64_t _k[4]; // key
uint64_t _s[4]; // state (counter)
uint64_t _o[4]; // cipher output 4 * 64 bit = 256 bit output
unsigned short _o_counter; // output chunk counter, the 256 random bits in _o
// are returned in eight 32 bit chunks
};
} // namespace sitmo
#undef MIXK
#undef MIX2
#endif

2
lib/stencil/Lebesgue.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
#include <algorithm>
namespace Grid {

2
lib/stencil/Stencil_common.cc
View File

@ -26,7 +26,7 @@ Author: Peter Boyle <peterboyle@Peters-MacBook-Pro-2.local>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include "Grid.h"
#include <Grid/Grid.h>
namespace Grid {
}

5
scripts/filelist
View File

@ -4,9 +4,8 @@ home=`pwd`
# library Make.inc
cd $home/lib
HFILES=`find . -type f -name '*.h' -not -path '*/Old/*' -not -path '*/Eigen/*'`
HFILES="$HFILES"
CCFILES=`find . -type f -name '*.cc' -not -name '*ommunicator*.cc'`
HFILES=`find . -type f -name '*.h' -not -name '*Hdf5*' -not -path '*/Old/*' -not -path '*/Eigen/*'`
CCFILES=`find . -type f -name '*.cc' -not -name '*Communicator*.cc' -not -name '*Hdf5*'`
echo HFILES=$HFILES > Make.inc
echo >> Make.inc
echo CCFILES=$CCFILES >> Make.inc

132
tests/IO/Test_serialisation.cc
View File

@ -28,13 +28,12 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
/* END LEGAL */
#include <Grid/Grid.h>
namespace Grid {
using namespace Grid;
GRID_SERIALIZABLE_ENUM(myenum, undef, red, 1, blue, 2, green, 3);
class myclass: Serializable {
public:
GRID_SERIALIZABLE_CLASS_MEMBERS(myclass,
myenum, e,
std::vector<myenum>, ve,
@ -44,11 +43,14 @@ namespace Grid {
bool , b,
std::vector<double>, array,
std::vector<std::vector<double>>, twodimarray,
std::vector<std::vector<std::vector<Complex>>>, cmplx3darray
);
myclass() {}
myclass(int i)
: array(4,5.1), twodimarray(3,std::vector<double>(2,1.23456)), ve(2, myenum::blue)
: array(4,5.1)
, twodimarray(3,std::vector<double>(5, 1.23456))
, cmplx3darray(3,std::vector<std::vector<Complex>>(5, std::vector<Complex>(7, Complex(1.2, 3.4))))
, ve(2, myenum::blue)
{
e=myenum::red;
x=i;
@ -58,10 +60,6 @@ namespace Grid {
}
};
}
using namespace Grid;
int16_t i16 = 1;
uint16_t u16 = 2;
int32_t i32 = 3;
@ -72,12 +70,34 @@ float f = M_PI;
double d = 2*M_PI;
bool b = false;
template <typename W, typename R, typename O>
void ioTest(const std::string &filename, const O &object, const std::string &name)
{
// writer needs to be destroyed so that writing physically happens
{
W writer(filename);
write(writer, "testobject", object);
}
R reader(filename);
O buf;
bool good;
read(reader, "testobject", buf);
good = (object == buf);
std::cout << name << " IO test: " << (good ? "success" : "failure");
std::cout << std::endl;
if (!good) exit(EXIT_FAILURE);
}
int main(int argc,char **argv)
{
{
std::cout << "==== basic IO" << std::endl;
XmlWriter WR("bother.xml");
// test basic type writing
std::cout << "-- basic writing to 'bother.xml'..." << std::endl;
push(WR,"BasicTypes");
write(WR,std::string("i16"),i16);
write(WR,"u16",u16);
@ -92,66 +112,68 @@ int main(int argc,char **argv)
// test serializable class writing
myclass obj(1234); // non-trivial constructor
std::vector<myclass> vec;
std::cout << "-- serialisable class writing to 'bother.xml'..." << std::endl;
write(WR,"obj",obj);
WR.write("obj2", obj);
std::cout << obj << std::endl;
std::vector<myclass> vec;
vec.push_back(myclass(1234));
vec.push_back(myclass(5678));
vec.push_back(myclass(3838));
write(WR, "objvec", vec);
};
std::cout << "-- serialisable class writing to std::cout:" << std::endl;
std::cout << obj << std::endl;
std::cout << "-- serialisable class comparison:" << std::endl;
std::cout << "vec[0] == obj: " << ((vec[0] == obj) ? "true" : "false") << std::endl;
std::cout << "vec[1] == obj: " << ((vec[1] == obj) ? "true" : "false") << std::endl;
// read tests
myclass copy1, copy2, copy3;
std::vector<myclass> veccopy1, veccopy2, veccopy3;
std::cout << "\n==== IO self-consistency tests" << std::endl;
//// XML
{
XmlReader RD("bother.xml");
read(RD,"obj",copy1);
read(RD,"objvec", veccopy1);
std::cout << "Loaded (XML) -----------------" << std::endl;
std::cout << copy1 << std::endl << veccopy1 << std::endl;
}
ioTest<XmlWriter, XmlReader>("iotest.xml", obj, "XML (object) ");
ioTest<XmlWriter, XmlReader>("iotest.xml", vec, "XML (vector of objects)");
//// binary
{
BinaryWriter BWR("bother.bin");
write(BWR,"discard",copy1 );
write(BWR,"discard",veccopy1 );
}
{
BinaryReader BRD("bother.bin");
read (BRD,"discard",copy2 );
read (BRD,"discard",veccopy2 );
std::cout << "Loaded (bin) -----------------" << std::endl;
std::cout << copy2 << std::endl << veccopy2 << std::endl;
}
ioTest<BinaryWriter, BinaryReader>("iotest.bin", obj, "binary (object) ");
ioTest<BinaryWriter, BinaryReader>("iotest.bin", vec, "binary (vector of objects)");
//// text
{
TextWriter TWR("bother.txt");
write(TWR,"discard",copy1 );
write(TWR,"discard",veccopy1 );
}
{
TextReader TRD("bother.txt");
read (TRD,"discard",copy3 );
read (TRD,"discard",veccopy3 );
std::cout << "Loaded (txt) -----------------" << std::endl;
std::cout << copy3 << std::endl << veccopy3 << std::endl;
}
ioTest<TextWriter, TextReader>("iotest.dat", obj, "text (object) ");
ioTest<TextWriter, TextReader>("iotest.dat", vec, "text (vector of objects)");
//// HDF5
#ifdef HAVE_HDF5
ioTest<Hdf5Writer, Hdf5Reader>("iotest.h5", obj, "HDF5 (object) ");
ioTest<Hdf5Writer, Hdf5Reader>("iotest.h5", vec, "HDF5 (vector of objects)");
#endif
std::vector<int> iv = strToVec<int>("1 2 2 4");
std::vector<std::string> sv = strToVec<std::string>("bli bla blu");
std::cout << "\n==== vector flattening/reconstruction" << std::endl;
typedef std::vector<std::vector<std::vector<double>>> vec3d;
for (auto &e: iv)
vec3d dv, buf;
double d = 0.;
dv.resize(4);
for (auto &v1: dv)
{
std::cout << e << " ";
}
std::cout << std::endl;
for (auto &e: sv)
v1.resize(3);
for (auto &v2: v1)
{
std::cout << e << " ";
v2.resize(5);
for (auto &x: v2)
{
x = d++;
}
std::cout << std::endl;
}
}
std::cout << "original 3D vector:" << std::endl;
std::cout << dv << std::endl;
Flatten<vec3d> flatdv(dv);
std::cout << "\ndimensions:" << std::endl;
std::cout << flatdv.getDim() << std::endl;
std::cout << "\nflattened vector:" << std::endl;
std::cout << flatdv.getFlatVector() << std::endl;
Reconstruct<vec3d> rec(flatdv.getFlatVector(), flatdv.getDim());
std::cout << "\nreconstructed vector:" << std::endl;
std::cout << flatdv.getVector() << std::endl;
}

2
tests/hadrons/Makefile.am
View File

@ -1,3 +1,3 @@
AM_LDFLAGS += -L../../extras/hadrons
AM_LDFLAGS += -L../../extras/Hadrons
include Make.inc

2
tests/qdpxx/Test_qdpxx_loops_staples.cc
View File

@ -25,7 +25,7 @@ Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
double calc_grid_p (Grid::QCD::LatticeGaugeField & lat);
double calc_chroma_p (Grid::QCD::LatticeGaugeField & lat);

2
tests/qdpxx/Test_qdpxx_munprec.cc
View File

@ -26,7 +26,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
See the full license in the file "LICENSE" in the top level distribution directory
*************************************************************************************/
/* END LEGAL */
#include <Grid.h>
#include <Grid/Grid.h>
int Ls=8;
double M5=1.6;