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Adding initial MPI support

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This commit is contained in:
Noah L. Schrick 2022-12-04 15:12:12 -06:00
parent b15ad49b2c
commit 9e24817a14
81 changed files with 14016 additions and 6 deletions
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Code/CMakeLists.txt Normal file
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cmake_minimum_required(VERSION 3.0)
project(par_gwas)
# Common compiler options among built types
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--allow-multiple-definition")
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
# Specific compiler options for Debug or Release builds
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0 -ggdb -Wall -fopenmp -pedantic")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -g -Wall -fopenmp -pedantic -O1")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O1 -fopenmp")
find_package(OpenMP REQUIRED)
find_package(MPI REQUIRED)
find_package(Boost REQUIRED mpi)
find_package(Palisade REQUIRED PATHS ${CMAKE_CURRENT_SOURCE_DIR}/../Duality_Technologies/PALISADE/)
set( CMAKE_CXX_FLAGS ${PALISADE_CXX_FLAGS} )
set( CMAKE_EXE_LINKER_FLAGS ${PALISADE_EXE_LINKER_FLAGS} )
include_directories( ${PALISADE_INCLUDE} )
include_directories( ${PALISADE_INCLUDE}/core )
include_directories( ${PALISADE_INCLUDE}/pke )
include_directories(${Boost_INCLUDE_DIR})
include_directories("${CMAKE_SOURCE_DIR}/Duality_Technologies/GWAS/")
#include_directories("${CMAKE_SOURCE_DIR}/PLINK/libplinkio/")
#include_directories("${CMAKE_SOURCE_DIR}/PLINK/libplinkio/install/include/plinkio/")
#include_directories("${CMAKE_SOURCE_DIR}/PLINK/libplinkio/libs/cmockery/")
#include_directories("${CMAKE_SOURCE_DIR}/PLINK/libplinkio/libs/libcsv/inc/")
link_directories( ${PALISADE_LIBDIR} )
# Enable thread-level parallelization if OpenMP is found.
if(OpenMP_CXX_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
if(MPI_CXX_FOUND)
INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH})
LIST(APPEND SCR_EXTERNAL_LIBS ${MPI_CXX_LIBRARIES})
#set(CMAKE_CXX_COMPILER "mpic++")
endif()
file(GLOB gwas_src "${CMAKE_SOURCE_DIR}/Duality_Technologies/GWAS/demo-chi2.cpp" "${CMAKE_SOURCE_DIR}/Duality_Technologies/GWAS/demo-chi2.h")
#add_library(gwas "${CMAKE_SOURCE_DIR}/Duality_Technologies/GWAS/demo-chi2.cpp")
#file(GLOB libplink_src "${CMAKE_SOURCE_DIR}/PLINK/libplinkio/src/*.c" "${CMAKE_SOURCE_DIR}/PLINK/libplinkio/src/*.cpp")
#file(GLOB plinkio_src "${CMAKE_SOURCE_DIR}/PLINK/libplinkio/src/plinkio/*.c" "${CMAKE_SOURCE_DIR}/PLINK/libplinkio/src/plinkio/*.cpp")
add_executable(par_gwas "${CMAKE_SOURCE_DIR}/src/main.cpp" ${gwas_src})
target_link_libraries(par_gwas Boost::mpi ${MPI_CXX_LIBRARIES}) #libplinkio)
# ${gwas_src}) #${libplink_src}) #${plinkio_src})

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Code/Schrick-Noah_CS-6643_Research-Project.cpp
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#include <boost/mpi.hpp>
#include <boost/mpi/environment.hpp>
#include <plinkio/plinkio.h>
#include <Rcpp.h>

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Code/Schrick-Noah_CS-6643_Research-Project.h
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#include <boost/mpi.hpp>
#include <boost/mpi/environment.hpp>
//#include <plinkio.h>
#include <avail_mem.h>
#include <demo_chi2.h>
namespace mpi = boost::mpi;
namespace mt = mpi::threading;
int main(int argc, char *argv[]) {
mt::level mt_level = mt::multiple;
boost::mpi::environment env(argc, argv, mt_level);
mt ::level provided = env.thread_level();
mpi::communicator world;
if (world.rank() == 0){
std::cout << "Asked the MPI environment to be created with threading level: "\
<< mt_level << std::endl;
std::cout << "MPI Environment was created with threading level: " << provided \
<< std::endl;
}
char hammer_host[256];
gethostname(hammer_host, 256);
std::cout << "\nHello from process " << world.rank() << " of " << world.size()
<< " running on " << hammer_host << std::endl;
int sample_size = 0;
std::string data_file;
std::string pval_file;
std::string runtime_res;
std::string data_path;
int num_vars = 0;
int opt;
while ((opt = getopt(argc, argv, "d:f:s:p:r:v:")) != -1) {
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case 'd':
data_file = optarg;
break;
case 'f':
data_path = optarg;
break;
case 's':
sample_size = atoi(optarg);
break;
case 'p':
pval_file = optarg;
case 'r':
runtime_res = optarg;
case 'v':
num_vars = atoi(optarg);
break;
}
}
std::vector<string> headersS;
std::vector<double> yData;
std::vector<std::vector<double>> sData;
std::string full_path = "../" + data_file;
size_t N = 1;
size_t M = 1;
size_t from = 0;
ReadSNPFile(headersS,sData,yData,full_path, N, M, from);
auto tot_sys_mem = getTotalSystemMemory();
auto mem_test = ((yData.size() * (sizeof(double_t)) + (sData.size() * (sData.back().size() * sizeof(double_t)))))/tot_sys_mem;
//Leave 20% buffer
int batch_size = 0.8/mem_test;
int rem = sample_size % world.size();
int node_samples = sample_size/world.size();
int node_start = world.rank()*node_samples + rem;
//int node_stop = node_start+(node_samples-1);
if (world.rank() < rem){
node_start = world.rank() * (node_samples+1);
//int node_stop = node_start + node_samples;
}
for (int i = 0; i < ceil(node_samples/batch_size); i++)
{
int curr_batch = node_samples - (batch_size*i);
int batch_gen = batch_size;
if (curr_batch > batch_size){
batch_gen = curr_batch;
}
int file_start = node_start + (batch_size*i);
RunChi2(data_path, data_file, pval_file, runtime_res, std::to_string(batch_gen), std::to_string(num_vars), file_start);
}
}

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