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Updating Kokkos lib

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15556 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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stamoor
2016-09-06 23:06:32 +00:00
parent 1ad033ec0c
commit 39be4185c4
502 changed files with 157510 additions and 0 deletions
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17
lib/kokkos/example/global_2_local_ids/CMakeLists.txt Normal file
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INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
SET(SOURCES "")
SET(SOURCES
G2L_Main.cpp
)
TRIBITS_ADD_EXECUTABLE(
global_2_local_ids
SOURCES ${SOURCES}
COMM serial mpi
)

266
lib/kokkos/example/global_2_local_ids/G2L.hpp Normal file
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//@HEADER
// ************************************************************************
//
// Kokkos v. 2.0
// Copyright (2014) Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov)
//
// ************************************************************************
//@HEADER
#ifndef KOKKOS_GLOBAL_TO_LOCAL_IDS_HPP
#define KOKKOS_GLOBAL_TO_LOCAL_IDS_HPP
#include <Kokkos_Core.hpp>
#include <Kokkos_UnorderedMap.hpp>
#include <vector>
#include <algorithm>
#include <iomanip>
#include <impl/Kokkos_Timer.hpp>
// This test will simulate global ids
namespace G2L {
static const unsigned begin_id_size = 256u;
static const unsigned end_id_size = 1u << 25;
static const unsigned id_step = 2u;
//use to help generate global ids
union helper
{
uint32_t word;
uint8_t byte[4];
};
//generate a unique global id from the local id
template <typename Device>
struct generate_ids
{
typedef Device execution_space;
typedef typename execution_space::size_type size_type;
typedef Kokkos::View<uint32_t*,execution_space> local_id_view;
local_id_view local_2_global;
generate_ids( local_id_view & ids)
: local_2_global(ids)
{
Kokkos::parallel_for(local_2_global.size(), *this);
}
KOKKOS_INLINE_FUNCTION
void operator()(size_type i) const
{
helper x = {static_cast<uint32_t>(i)};
// shuffle the bytes of i to create a unique, semi-random global_id
x.word = ~x.word;
uint8_t tmp = x.byte[3];
x.byte[3] = x.byte[1];
x.byte[1] = tmp;
tmp = x.byte[2];
x.byte[2] = x.byte[0];
x.byte[0] = tmp;
local_2_global[i] = x.word;
}
};
// fill a map of global_id -> local_id
template <typename Device>
struct fill_map
{
typedef Device execution_space;
typedef typename execution_space::size_type size_type;
typedef Kokkos::View<const uint32_t*,execution_space, Kokkos::MemoryRandomAccess> local_id_view;
typedef Kokkos::UnorderedMap<uint32_t,size_type,execution_space> global_id_view;
global_id_view global_2_local;
local_id_view local_2_global;
fill_map( global_id_view gIds, local_id_view lIds)
: global_2_local(gIds) , local_2_global(lIds)
{
Kokkos::parallel_for(local_2_global.size(), *this);
}
KOKKOS_INLINE_FUNCTION
void operator()(size_type i) const
{
global_2_local.insert( local_2_global[i], i);
}
};
// check that the global id is found and that it maps to the local id
template <typename Device>
struct find_test
{
typedef Device execution_space;
typedef typename execution_space::size_type size_type;
typedef Kokkos::View<const uint32_t*,execution_space, Kokkos::MemoryRandomAccess> local_id_view;
typedef Kokkos::UnorderedMap<const uint32_t, const size_type,execution_space> global_id_view;
global_id_view global_2_local;
local_id_view local_2_global;
typedef size_t value_type;
find_test( global_id_view gIds, local_id_view lIds, value_type & num_errors)
: global_2_local(gIds) , local_2_global(lIds)
{
Kokkos::parallel_reduce(local_2_global.size(), *this, num_errors);
}
KOKKOS_INLINE_FUNCTION
void init(value_type & v) const
{ v = 0; }
KOKKOS_INLINE_FUNCTION
void join(volatile value_type & dst, volatile value_type const & src) const
{ dst += src; }
KOKKOS_INLINE_FUNCTION
void operator()(size_type i, value_type & num_errors) const
{
uint32_t index = global_2_local.find( local_2_global[i] );
if ( !global_2_local.valid_at(index)
|| global_2_local.key_at(index) != local_2_global[i]
|| global_2_local.value_at(index) != i)
++num_errors;
}
};
// run test
template <typename Device>
size_t test_global_to_local_ids(unsigned num_ids, unsigned capacity, unsigned num_find_iterations)
{
typedef Device execution_space;
typedef typename execution_space::size_type size_type;
typedef Kokkos::View<uint32_t*,execution_space> local_id_view;
typedef Kokkos::UnorderedMap<uint32_t,size_type,execution_space> global_id_view;
double elasped_time = 0;
Kokkos::Timer timer;
local_id_view local_2_global("local_ids", num_ids);
global_id_view global_2_local(capacity);
int shiftw = 15;
//create
elasped_time = timer.seconds();
std::cout << std::setw(shiftw) << "allocate: " << elasped_time << std::endl;
timer.reset();
// generate unique ids
{
generate_ids<Device> gen(local_2_global);
}
// generate
elasped_time = timer.seconds();
std::cout << std::setw(shiftw) << "generate: " << elasped_time << std::endl;
timer.reset();
{
fill_map<Device> fill(global_2_local, local_2_global);
}
// fill
elasped_time = timer.seconds();
std::cout << std::setw(shiftw) << "fill: " << elasped_time << std::endl;
timer.reset();
size_t num_errors = global_2_local.failed_insert();
if (num_errors == 0u) {
for (unsigned i=0; i<num_find_iterations; ++i)
{
find_test<Device> find(global_2_local, local_2_global,num_errors);
}
// find
elasped_time = timer.seconds();
std::cout << std::setw(shiftw) << "lookup: " << elasped_time << std::endl;
}
else {
std::cout << " !!! Fill Failed !!!" << std::endl;
}
return num_errors;
}
template <typename Device>
size_t run_test(unsigned num_ids, unsigned num_find_iterations)
{
// expect to fail
unsigned capacity = (num_ids*2u)/3u;
std::cout << " 66% of needed capacity (should fail)" << std::endl;
test_global_to_local_ids<Device>(num_ids, capacity, num_find_iterations);
//should not fail
std::cout << " 100% of needed capacity" << std::endl;
capacity = num_ids;
size_t num_errors = test_global_to_local_ids<Device>(num_ids, capacity, num_find_iterations);
//should not fail
std::cout << " 150% of needed capacity" << std::endl;
capacity = (num_ids*3u)/2u;
num_errors += test_global_to_local_ids<Device>(num_ids, capacity, num_find_iterations);
return num_errors;
}
} // namespace G2L
#endif //KOKKOS_GLOBAL_TO_LOCAL_IDS_HPP

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lib/kokkos/example/global_2_local_ids/G2L_Main.cpp Normal file
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/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 2.0
// Copyright (2014) Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact H. Carter Edwards (hcedwar@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#include <Kokkos_Core.hpp>
#include <G2L.hpp>
namespace G2L {
size_t run_serial(unsigned num_ids, unsigned num_find_iterations)
{
#ifdef KOKKOS_HAVE_SERIAL
std::cout << "Serial" << std::endl;
return run_test<Kokkos::Serial>(num_ids,num_find_iterations);
#else
return 0;
#endif // KOKKOS_HAVE_SERIAL
}
size_t run_threads(unsigned num_ids, unsigned num_find_iterations)
{
#ifdef KOKKOS_HAVE_PTHREAD
std::cout << "Threads" << std::endl;
return run_test<Kokkos::Threads>(num_ids,num_find_iterations);
#else
return 0;
#endif
}
size_t run_openmp(unsigned num_ids, unsigned num_find_iterations)
{
#ifdef KOKKOS_HAVE_OPENMP
std::cout << "OpenMP" << std::endl;
return run_test<Kokkos::OpenMP>(num_ids,num_find_iterations);
#else
return 0;
#endif
}
size_t run_cuda(unsigned num_ids, unsigned num_find_iterations)
{
#ifdef KOKKOS_HAVE_CUDA
std::cout << "Cuda" << std::endl;
return run_test<Kokkos::Cuda>(num_ids,num_find_iterations);
#else
return 0;
#endif
}
} // namespace G2L
int main(int argc, char *argv[])
{
unsigned num_ids = 100000;
unsigned num_find_iterations = 1000;
if (argc == 3) {
num_ids = atoi(argv[1]);
num_find_iterations = atoi(argv[2]);
}
else if (argc != 1) {
std::cout << argv[0] << " num_ids num_find_iterations" << std::endl;
return 0;
}
// query the topology of the host
unsigned threads_count = 4 ;
if (Kokkos::hwloc::available()) {
threads_count = Kokkos::hwloc::get_available_numa_count() *
Kokkos::hwloc::get_available_cores_per_numa() *
Kokkos::hwloc::get_available_threads_per_core();
}
std::cout << "Threads: " << threads_count << std::endl;
std::cout << "Number of ids: " << num_ids << std::endl;
std::cout << "Number of find iterations: " << num_find_iterations << std::endl;
size_t num_errors = 0;
num_errors += G2L::run_serial(num_ids,num_find_iterations);
#ifdef KOKKOS_HAVE_CUDA
Kokkos::HostSpace::execution_space::initialize(threads_count);
Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) );
num_errors += G2L::run_cuda(num_ids,num_find_iterations);
Kokkos::Cuda::finalize();
Kokkos::HostSpace::execution_space::finalize();
#endif
#ifdef KOKKOS_HAVE_PTHREAD
Kokkos::Threads::initialize( threads_count );
num_errors += G2L::run_threads(num_ids,num_find_iterations);
Kokkos::Threads::finalize();
#endif
#ifdef KOKKOS_HAVE_OPENMP
Kokkos::OpenMP::initialize( threads_count );
num_errors += G2L::run_openmp(num_ids,num_find_iterations);
Kokkos::OpenMP::finalize();
#endif
return num_errors;
}

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lib/kokkos/example/global_2_local_ids/Makefile Normal file
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KOKKOS_PATH ?= ../..
MAKEFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
SRC_DIR := $(dir $(MAKEFILE_PATH))
SRC = $(wildcard $(SRC_DIR)/*.cpp)
OBJ = $(SRC:$(SRC_DIR)/%.cpp=%.o)
#SRC = $(wildcard *.cpp)
#OBJ = $(SRC:%.cpp=%.o)
default: build
echo "Start Build"
# use installed Makefile.kokkos
include $(KOKKOS_PATH)/Makefile.kokkos
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = $(NVCC_WRAPPER)
CXXFLAGS = -I$(SRC_DIR) -O3
LINK = $(CXX)
LINKFLAGS =
EXE = $(addsuffix .cuda, $(shell basename $(SRC_DIR)))
#KOKKOS_DEVICES = "Cuda,OpenMP"
#KOKKOS_ARCH = "SNB,Kepler35"
else
CXX = g++
CXXFLAGS = -I$(SRC_DIR) -O3
LINK = $(CXX)
LINKFLAGS =
EXE = $(addsuffix .host, $(shell basename $(SRC_DIR)))
#KOKKOS_DEVICES = "OpenMP"
#KOKKOS_ARCH = "SNB"
endif
DEPFLAGS = -M
LIB =
build: $(EXE)
$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean:
rm -f *.a *.o *.cuda *.host
# Compilation rules
%.o:$(SRC_DIR)/%.cpp $(KOKKOS_CPP_DEPENDS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<