void add_configuration_to_yaml(YAML_Doc& doc, int numprocs)
{
doc.get("Global Run Parameters")->add("number of processors", numprocs);
doc.add("Platform","");
doc.get("Platform")->add("hostname",MINIFE_HOSTNAME);
doc.get("Platform")->add("kernel name",MINIFE_KERNEL_NAME);
doc.get("Platform")->add("kernel release",MINIFE_KERNEL_RELEASE);
doc.get("Platform")->add("processor",MINIFE_PROCESSOR);
doc.add("Build","");
doc.get("Build")->add("CXX",MINIFE_CXX);
#if MINIFE_INFO != 0
doc.get("Build")->add("compiler version",MINIFE_CXX_VERSION);
#endif
doc.get("Build")->add("CXXFLAGS",MINIFE_CXXFLAGS);
std::string using_mpi("no");
#ifdef HAVE_MPI
using_mpi = "yes";
#endif
doc.get("Build")->add("using MPI",using_mpi);
}
void add_timestring_to_yaml(YAML_Doc& doc)
{
std::time_t rawtime;
struct tm * timeinfo;
std::time(&rawtime);
timeinfo = std::localtime(&rawtime);
std::ostringstream osstr;
osstr.fill('0');
osstr << timeinfo->tm_year+1900 << "-";
osstr.width(2); osstr << timeinfo->tm_mon+1 << "-";
osstr.width(2); osstr << timeinfo->tm_mday << ", ";
osstr.width(2); osstr << timeinfo->tm_hour << "-";
osstr.width(2); osstr << timeinfo->tm_min << "-";
osstr.width(2); osstr << timeinfo->tm_sec;
std::string timestring = osstr.str();
doc.add("Run Date/Time",timestring);
}
void add_params_to_yaml(YAML_Doc& doc, miniFE::Parameters& params)
{
doc.add("Global Run Parameters","");
doc.get("Global Run Parameters")->add("dimensions","");
doc.get("Global Run Parameters")->get("dimensions")->add("nx",params.nx);
doc.get("Global Run Parameters")->get("dimensions")->add("ny",params.ny);
doc.get("Global Run Parameters")->get("dimensions")->add("nz",params.nz);
doc.get("Global Run Parameters")->add("load_imbalance", params.load_imbalance);
if (params.mv_overlap_comm_comp == 1) {
std::string val("1 (yes)");
doc.get("Global Run Parameters")->add("mv_overlap_comm_comp", val);
}
else {
std::string val("0 (no)");
doc.get("Global Run Parameters")->add("mv_overlap_comm_comp", val);
}
}
void add_params_to_yaml(YAML_Doc& doc, miniFE::Parameters& params)
{
doc.add("Global Run Parameters","");
doc.get("Global Run Parameters")->add("dimensions","");
doc.get("Global Run Parameters")->get("dimensions")->add("nx",params.nx);
doc.get("Global Run Parameters")->get("dimensions")->add("ny",params.ny);
doc.get("Global Run Parameters")->get("dimensions")->add("nz",params.nz);
doc.get("Global Run Parameters")->add("load_imbalance", params.load_imbalance);
if (params.mv_overlap_comm_comp == 1) {
std::string val("1 (yes)");
doc.get("Global Run Parameters")->add("mv_overlap_comm_comp", val);
}
else {
std::string val("0 (no)");
doc.get("Global Run Parameters")->add("mv_overlap_comm_comp", val);
}
#ifdef _OPENMP
doc.get("Global Run Parameters")->add("OpenMP Max Threads:", omp_get_max_threads());
#endif
}
void
compute_imbalance(const int global_box[][2],
const int local_box[][2],
float& largest_imbalance,
float& std_dev,
YAML_Doc& doc,
bool record_in_doc)
{
int numprocs = 1, myproc = 0;
#ifdef HAVE_MPI
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &myproc);
#endif
GlobalOrdinal local_nrows = get_num_ids<GlobalOrdinal>(local_box);
GlobalOrdinal min_nrows = 0, max_nrows = 0, global_nrows = 0;
int min_proc = myproc, max_proc = myproc;
get_global_min_max(local_nrows, global_nrows, min_nrows, min_proc,
max_nrows, max_proc);
float avg_nrows = global_nrows;
avg_nrows /= numprocs;
//largest_imbalance will be the difference between the min (or max)
//rows-per-processor and avg_nrows, represented as a percentage:
largest_imbalance = percentage_difference<float>(min_nrows, avg_nrows);
float tmp = percentage_difference<float>(max_nrows, avg_nrows);
if (tmp > largest_imbalance) largest_imbalance = tmp;
std_dev = compute_std_dev_as_percentage<float>(local_nrows, avg_nrows);
if (myproc == 0 && record_in_doc) {
doc.add("Rows-per-proc Load Imbalance","");
doc.get("Rows-per-proc Load Imbalance")->add("Largest (from avg, %)",largest_imbalance);
doc.get("Rows-per-proc Load Imbalance")->add("Std Dev (%)",std_dev);
}
}
int
driver(const Box& global_box, Box& my_box,
Parameters& params, YAML_Doc& ydoc)
{
int global_nx = global_box[0][1];
int global_ny = global_box[1][1];
int global_nz = global_box[2][1];
int numprocs = 1, myproc = 0;
#ifdef HAVE_MPI
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &myproc);
#endif
if (params.load_imbalance > 0) {
add_imbalance<GlobalOrdinal>(global_box, my_box, params.load_imbalance, ydoc);
}
float largest_imbalance = 0, std_dev = 0;
compute_imbalance<GlobalOrdinal>(global_box, my_box, largest_imbalance,
std_dev, ydoc, true);
//Create a representation of the mesh:
//Note that 'simple_mesh_description' is a virtual or conceptual
//mesh that doesn't actually store mesh data.
#ifdef TIME_IT
if (myproc==0) {
std::cout.width(30);
std::cout << "creating/filling mesh...";
std::cout.flush();
}
#endif
timer_type t_start = mytimer();
timer_type t0 = mytimer();
simple_mesh_description<GlobalOrdinal> mesh(global_box, my_box);
timer_type mesh_fill = mytimer() - t0;
timer_type t_total = mytimer() - t_start;
#ifdef TIME_IT
if (myproc==0) {
std::cout << mesh_fill << "s, total time: " << t_total << std::endl;
}
#endif
//next we will generate the matrix structure.
//Declare matrix object:
#if defined(MINIFE_ELL_MATRIX)
typedef ELLMatrix<Scalar,LocalOrdinal,GlobalOrdinal> MatrixType;
#else
typedef CSRMatrix<Scalar,LocalOrdinal,GlobalOrdinal> MatrixType;
#endif
MatrixType A;
timer_type gen_structure;
RUN_TIMED_FUNCTION("generating matrix structure...",
generate_matrix_structure(mesh, A),
gen_structure, t_total);
GlobalOrdinal local_nrows = A.rows.size();
GlobalOrdinal my_first_row = local_nrows > 0 ? A.rows[0] : -1;
Vector<Scalar,LocalOrdinal,GlobalOrdinal> b(my_first_row, local_nrows);
Vector<Scalar,LocalOrdinal,GlobalOrdinal> x(my_first_row, local_nrows);
//Assemble finite-element sub-matrices and sub-vectors into the global
//linear system:
timer_type fe_assembly;
RUN_TIMED_FUNCTION("assembling FE data...",
assemble_FE_data(mesh, A, b, params),
fe_assembly, t_total);
if (myproc == 0) {
ydoc.add("Matrix structure generation","");
ydoc.get("Matrix structure generation")->add("Mat-struc-gen Time",gen_structure);
ydoc.add("FE assembly","");
ydoc.get("FE assembly")->add("FE assembly Time",fe_assembly);
}
#ifdef MINIFE_DEBUG
write_matrix("A_prebc.mtx", A);
write_vector("b_prebc.vec", b);
#endif
//Now apply dirichlet boundary-conditions
//(Apply the 0-valued surfaces first, then the 1-valued surface last.)
timer_type dirbc_time;
RUN_TIMED_FUNCTION("imposing Dirichlet BC...",
impose_dirichlet(0.0, A, b, global_nx+1, global_ny+1, global_nz+1, mesh.bc_rows_0), dirbc_time, t_total);
RUN_TIMED_FUNCTION("imposing Dirichlet BC...",
impose_dirichlet(1.0, A, b, global_nx+1, global_ny+1, global_nz+1, mesh.bc_rows_1), dirbc_time, t_total);
#ifdef MINIFE_DEBUG
write_matrix("A.mtx", A);
write_vector("b.vec", b);
#endif
//Transform global indices to local, set up communication information:
timer_type make_local_time;
RUN_TIMED_FUNCTION("making matrix indices local...",
make_local_matrix(A),
make_local_time, t_total);
#ifdef MINIFE_DEBUG
write_matrix("A_local.mtx", A);
write_vector("b_local.vec", b);
#endif
size_t global_nnz = compute_matrix_stats(A, myproc, numprocs, ydoc);
//Prepare to perform conjugate gradient solve:
LocalOrdinal max_iters = 200;
LocalOrdinal num_iters = 0;
typedef typename TypeTraits<Scalar>::magnitude_type magnitude;
magnitude rnorm = 0;
magnitude tol = std::numeric_limits<magnitude>::epsilon();
timer_type cg_times[NUM_TIMERS];
typedef Vector<Scalar,LocalOrdinal,GlobalOrdinal> VectorType;
t_total = mytimer() - t_start;
bool matvec_with_comm_overlap = params.mv_overlap_comm_comp==1;
int verify_result = 0;
#if MINIFE_KERNELS != 0
if (myproc==0) {
std::cout.width(30);
std::cout << "Starting kernel timing loops ..." << std::endl;
}
max_iters = 500;
x.coefs[0] = 0.9;
if (matvec_with_comm_overlap) {
time_kernels(A, b, x, matvec_overlap<MatrixType,VectorType>(), max_iters, rnorm, cg_times);
}
else {
time_kernels(A, b, x, matvec_std<MatrixType,VectorType>(), max_iters, rnorm, cg_times);
}
num_iters = max_iters;
std::string title("Kernel timings");
#else
if (myproc==0) {
std::cout << "Starting CG solver ... " << std::endl;
}
if (matvec_with_comm_overlap) {
#ifdef MINIFE_CSR_MATRIX
rearrange_matrix_local_external(A);
cg_solve(A, b, x, matvec_overlap<MatrixType,VectorType>(), max_iters, tol,
num_iters, rnorm, cg_times);
#else
std::cout << "ERROR, matvec with overlapping comm/comp only works with CSR matrix."<<std::endl;
#endif
}
else {
cg_solve(A, b, x, matvec_std<MatrixType,VectorType>(), max_iters, tol,
num_iters, rnorm, cg_times);
if (myproc == 0) {
std::cout << "Final Resid Norm: " << rnorm << std::endl;
}
if (params.verify_solution > 0) {
double tolerance = 0.06;
bool verify_whole_domain = false;
#ifdef MINIFE_DEBUG
verify_whole_domain = true;
#endif
if (myproc == 0) {
if (verify_whole_domain) std::cout << "verifying solution..." << std::endl;
else std::cout << "verifying solution at ~ (0.5, 0.5, 0.5) ..." << std::endl;
}
verify_result = verify_solution(mesh, x, tolerance, verify_whole_domain);
}
}
#ifdef MINIFE_DEBUG
write_vector("x.vec", x);
#endif
std::string title("CG solve");
#endif
if (myproc == 0) {
ydoc.get("Global Run Parameters")->add("ScalarType",TypeTraits<Scalar>::name());
ydoc.get("Global Run Parameters")->add("GlobalOrdinalType",TypeTraits<GlobalOrdinal>::name());
ydoc.get("Global Run Parameters")->add("LocalOrdinalType",TypeTraits<LocalOrdinal>::name());
ydoc.add(title,"");
ydoc.get(title)->add("Iterations",num_iters);
ydoc.get(title)->add("Final Resid Norm",rnorm);
GlobalOrdinal global_nrows = global_nx;
global_nrows *= global_ny*global_nz;
//flops-per-mv, flops-per-dot, flops-per-waxpy:
double mv_flops = global_nnz*2.0;
double dot_flops = global_nrows*2.0;
double waxpy_flops = global_nrows*3.0;
#if MINIFE_KERNELS == 0
//if MINIFE_KERNELS == 0 then we did a CG solve, and in that case
//there were num_iters+1 matvecs, num_iters*2 dots, and num_iters*3+2 waxpys.
mv_flops *= (num_iters+1);
dot_flops *= (2*num_iters);
waxpy_flops *= (3*num_iters+2);
#else
//if MINIFE_KERNELS then we did one of each operation per iteration.
mv_flops *= num_iters;
dot_flops *= num_iters;
waxpy_flops *= num_iters;
#endif
double total_flops = mv_flops + dot_flops + waxpy_flops;
double mv_mflops = -1;
if (cg_times[MATVEC] > 1.e-4)
mv_mflops = 1.e-6 * (mv_flops/cg_times[MATVEC]);
double dot_mflops = -1;
if (cg_times[DOT] > 1.e-4)
dot_mflops = 1.e-6 * (dot_flops/cg_times[DOT]);
double waxpy_mflops = -1;
if (cg_times[WAXPY] > 1.e-4)
waxpy_mflops = 1.e-6 * (waxpy_flops/cg_times[WAXPY]);
double total_mflops = -1;
if (cg_times[TOTAL] > 1.e-4)
total_mflops = 1.e-6 * (total_flops/cg_times[TOTAL]);
ydoc.get(title)->add("WAXPY Time",cg_times[WAXPY]);
ydoc.get(title)->add("WAXPY Flops",waxpy_flops);
if (waxpy_mflops >= 0)
ydoc.get(title)->add("WAXPY Mflops",waxpy_mflops);
else
ydoc.get(title)->add("WAXPY Mflops","inf");
ydoc.get(title)->add("DOT Time",cg_times[DOT]);
ydoc.get(title)->add("DOT Flops",dot_flops);
if (dot_mflops >= 0)
ydoc.get(title)->add("DOT Mflops",dot_mflops);
else
ydoc.get(title)->add("DOT Mflops","inf");
ydoc.get(title)->add("MATVEC Time",cg_times[MATVEC]);
ydoc.get(title)->add("MATVEC Flops",mv_flops);
if (mv_mflops >= 0)
ydoc.get(title)->add("MATVEC Mflops",mv_mflops);
else
ydoc.get(title)->add("MATVEC Mflops","inf");
#ifdef MINIFE_FUSED
ydoc.get(title)->add("MATVECDOT Time",cg_times[MATVECDOT]);
ydoc.get(title)->add("MATVECDOT Flops",mv_flops);
if (mv_mflops >= 0)
ydoc.get(title)->add("MATVECDOT Mflops",mv_mflops);
else
ydoc.get(title)->add("MATVECDOT Mflops","inf");
#endif
#if MINIFE_KERNELS == 0
ydoc.get(title)->add("Total","");
ydoc.get(title)->get("Total")->add("Total CG Time",cg_times[TOTAL]);
ydoc.get(title)->get("Total")->add("Total CG Flops",total_flops);
if (total_mflops >= 0)
ydoc.get(title)->get("Total")->add("Total CG Mflops",total_mflops);
else
ydoc.get(title)->get("Total")->add("Total CG Mflops","inf");
ydoc.get(title)->add("Time per iteration",cg_times[TOTAL]/num_iters);
#endif
}
return verify_result;
}
size_t
compute_matrix_stats(const MatrixType& A, int myproc, int numprocs, YAML_Doc& ydoc)
{
typedef typename MatrixType::GlobalOrdinalType GlobalOrdinal;
typedef typename MatrixType::LocalOrdinalType LocalOrdinal;
typedef typename MatrixType::ScalarType Scalar;
GlobalOrdinal min_nrows = 0, max_nrows = 0, global_nrows = 0;
int min_proc = 0, max_proc = 0;
GlobalOrdinal local_nrows = A.rows.size();
get_global_min_max(local_nrows, global_nrows, min_nrows, min_proc,
max_nrows, max_proc);
//Gather stats on global, min/max matrix num-nonzeros:
double local_nnz = A.num_nonzeros();
double dglobal_nnz = 0, dmin_nnz = 0, dmax_nnz = 0;
get_global_min_max(local_nnz, dglobal_nnz, dmin_nnz, min_proc,
dmax_nnz, max_proc);
double avg_nrows = global_nrows;
avg_nrows /= numprocs;
double avg_nnz = dglobal_nnz;
avg_nnz /= numprocs;
double mem_overhead_MB = parallel_memory_overhead_MB(A);
size_t global_nnz = static_cast<size_t>(std::ceil(dglobal_nnz));
size_t min_nnz = static_cast<size_t>(std::ceil(dmin_nnz));
size_t max_nnz = static_cast<size_t>(std::ceil(dmax_nnz));
size_t global_num_rows = global_nrows;
if (myproc == 0) {
ydoc.add("Matrix attributes","");
ydoc.get("Matrix attributes")->add("Global Nrows",global_num_rows);
ydoc.get("Matrix attributes")->add("Global NNZ",global_nnz);
//compute how much memory the matrix occupies:
//num-bytes = sizeof(GlobalOrdinal)*global_nrows for A.rows
// + sizeof(LocalOrdinal)*global_nrows for A.rows_offsets
// + sizeof(GlobalOrdinal)*global_nnz for A.packed_cols
// + sizeof(Scalar)*global_nnz for A.packed_coefs
double invGB = 1.0/(1024*1024*1024);
double memGB = invGB*global_nrows*sizeof(GlobalOrdinal);
memGB += invGB*global_nrows*sizeof(LocalOrdinal);
memGB += invGB*global_nnz*sizeof(GlobalOrdinal);
memGB += invGB*global_nnz*sizeof(Scalar);
ydoc.get("Matrix attributes")->add("Global Memory (GB)",memGB);
ydoc.get("Matrix attributes")->add("Pll Memory Overhead (MB)",mem_overhead_MB);
size_t min_num_rows = min_nrows;
size_t max_num_rows = max_nrows;
ydoc.get("Matrix attributes")->add("Rows per proc MIN",min_num_rows);
ydoc.get("Matrix attributes")->add("Rows per proc MAX",max_num_rows);
ydoc.get("Matrix attributes")->add("Rows per proc AVG",avg_nrows);
ydoc.get("Matrix attributes")->add("NNZ per proc MIN",min_nnz);
ydoc.get("Matrix attributes")->add("NNZ per proc MAX",max_nnz);
ydoc.get("Matrix attributes")->add("NNZ per proc AVG",avg_nnz);
}
return global_nnz;
}