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Added the new initial root heuristics as command line arguments.
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@computations
computations committed Nov 11, 2020
1 parent d927bcb commit 2718030
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Showing 5 changed files with 123 additions and 47 deletions.
4 changes: 3 additions & 1 deletion src/checkpoint.cpp
View file
Expand Up @@ -2,11 +2,11 @@
#include "debug.h"
#include "util.hpp"
#include <fcntl.h>
#include <functional>
#include <stdexcept>
#include <sys/stat.h>
#include <unistd.h>
#include <vector>
#include <functional>

template <> size_t write(int fd, const std::string &str) {
size_t string_size = str.size();
Expand Down Expand Up @@ -70,6 +70,7 @@ template <> size_t write(int fd, const cli_options_t &options) {
total_written += write(fd, options.echo);
total_written += write(fd, options.invariant_sites);
total_written += write(fd, options.early_stop);
total_written += write(fd, options.initial_root_strategy);
debug_print(
EMIT_LEVEL_DEBUG, "Wrote %lu bytes for cli_options", total_written);
return total_written;
Expand Down Expand Up @@ -101,6 +102,7 @@ template <> size_t read(int fd, cli_options_t &options) {
total_read += read(fd, options.echo);
total_read += read(fd, options.invariant_sites);
total_read += read(fd, options.early_stop);
total_read += read(fd, options.initial_root_strategy);
debug_print(EMIT_LEVEL_DEBUG, "Read %lu bytes for cli_options", total_read);
return total_read;
}
Expand Down
91 changes: 56 additions & 35 deletions src/main.cpp
View file
Expand Up @@ -7,12 +7,12 @@ extern "C" {
#include <chrono>
#include <cmath>
#include <fstream>
#include <functional>
#include <getopt.h>
#include <iomanip>
#include <iostream>
#include <omp.h>
#include <sstream>
#include <functional>
#ifdef MPI_BUILD
#include <mpi.h>
#endif
Expand Down Expand Up @@ -118,6 +118,14 @@ static void print_usage() {
<< " Tolerance for the BFGS steps. Default is 1e-7\n"
<< " --factor [NUMBER]\n"
<< " Factor for the BFGS steps. Default is 1e2\n"
<< " --initial-root-strategy {random, midpoint, modified-mad}\n"
<< " The strategy to pick the initial branches for rooting.\n"
<< " Random is the default, and simply picks the branches at\n"
<< " random. Midpoint uses the midpoint and similar branches to\n"
<< " start. Modified MAD will use a modified version of mad to\n"
<< " pick the starting branches. This can actually drive the\n"
<< " so care should be taken when selecting this option.\n"
<< " Default is random\n"
<< " --threads [NUMBER]\n"
<< " Number of threads to use\n"
<< " --silent\n"
Expand All @@ -137,33 +145,34 @@ static void print_usage() {

cli_options_t parse_options(int argv, char **argc) {
static struct option long_opts[] = {
{"msa", required_argument, 0, 0}, /* 0 */
{"tree", required_argument, 0, 0}, /* 1 */
{"model", required_argument, 0, 0}, /* 2 */
{"seed", required_argument, 0, 0}, /* 3 */
{"verbose", no_argument, 0, 0}, /* 4 */
{"silent", no_argument, 0, 0}, /* 5 */
{"min-roots", required_argument, 0, 0}, /* 6 */
{"root-ratio", required_argument, 0, 0}, /* 7 */
{"atol", required_argument, 0, 0}, /* 8 */
{"brtol", required_argument, 0, 0}, /* 9 */
{"bfgstol", required_argument, 0, 0}, /* 10 */
{"factor", required_argument, 0, 0}, /* 11 */
{"partition", required_argument, 0, 0}, /* 12 */
{"prefix", required_argument, 0, 0}, /* 13 */
{"exhaustive", no_argument, 0, 0}, /* 14 */
{"early-stop", no_argument, 0, 0}, /* 15 */
{"no-early-stop", no_argument, 0, 0}, /* 16 */
{"rate-cats", required_argument, 0, 0}, /* 17 */
{"rate-cats-type", required_argument, 0, 0}, /* 18 */
{"invariant-sites", no_argument, 0, 0}, /* 19 */
{"threads", required_argument, 0, 0}, /* 20 */
{"version", no_argument, 0, 0}, /* 21 */
{"debug", no_argument, 0, 0}, /* 22 */
{"mpi-debug", no_argument, 0, 0}, /* 23 */
{"clean", no_argument, 0, 0}, /* 24 */
{"echo", no_argument, 0, 0}, /* 25 */
{"help", no_argument, 0, 0}, /* 26 */
{"msa", required_argument, 0, 0}, /* 0 */
{"tree", required_argument, 0, 0}, /* 1 */
{"model", required_argument, 0, 0}, /* 2 */
{"seed", required_argument, 0, 0}, /* 3 */
{"verbose", no_argument, 0, 0}, /* 4 */
{"silent", no_argument, 0, 0}, /* 5 */
{"min-roots", required_argument, 0, 0}, /* 6 */
{"root-ratio", required_argument, 0, 0}, /* 7 */
{"atol", required_argument, 0, 0}, /* 8 */
{"brtol", required_argument, 0, 0}, /* 9 */
{"bfgstol", required_argument, 0, 0}, /* 10 */
{"factor", required_argument, 0, 0}, /* 11 */
{"partition", required_argument, 0, 0}, /* 12 */
{"prefix", required_argument, 0, 0}, /* 13 */
{"exhaustive", no_argument, 0, 0}, /* 14 */
{"early-stop", no_argument, 0, 0}, /* 15 */
{"no-early-stop", no_argument, 0, 0}, /* 16 */
{"rate-cats", required_argument, 0, 0}, /* 17 */
{"rate-cats-type", required_argument, 0, 0}, /* 18 */
{"invariant-sites", no_argument, 0, 0}, /* 19 */
{"initial-root-strategy", required_argument, 0, 0}, /* 20 */
{"threads", required_argument, 0, 0}, /* 21 */
{"version", no_argument, 0, 0}, /* 22 */
{"debug", no_argument, 0, 0}, /* 23 */
{"mpi-debug", no_argument, 0, 0}, /* 24 */
{"clean", no_argument, 0, 0}, /* 25 */
{"echo", no_argument, 0, 0}, /* 26 */
{"help", no_argument, 0, 0}, /* 27 */
{0, 0, 0, 0},
};

Expand Down Expand Up @@ -241,25 +250,36 @@ cli_options_t parse_options(int argv, char **argc) {
case 19: // invariant-sites
cli_options.invariant_sites = true;
break;
case 20: // threads
case 20: // initial-root-strategy
if (strcmp(optarg, "random") == 0) {
cli_options.initial_root_strategy = {initial_root_strategy_t::random};
} else if (strcmp(optarg, "midpoint") == 0) {
cli_options.initial_root_strategy = {initial_root_strategy_t::midpoint};
} else if (strcmp(optarg, "modified-mad") == 0) {
cli_options.initial_root_strategy = {
initial_root_strategy_t::modified_mad};
}

break;
case 21: // threads
cli_options.threads = {(size_t)atol(optarg)};
break;
case 21: // version
case 22: // version
print_version();
std::exit(0);
case 22: // debug
case 23: // debug
__VERBOSE__ = EMIT_LEVEL_DEBUG;
break;
case 23: // mpi-debug
case 24: // mpi-debug
__VERBOSE__ = EMIT_LEVEL_MPI_DEBUG;
break;
case 24: // clean
case 25: // clean
cli_options.clean = true;
break;
case 25: // echo
case 26: // echo
cli_options.echo = true;
break;
case 26: // help
case 27: // help
print_usage();
std::exit(0);
break;
Expand Down Expand Up @@ -526,6 +546,7 @@ int wrapped_main(int argv, char **argc) {
cli_options.root_ratio,
static_cast<size_t>(__MPI_RANK__),
static_cast<size_t>(__MPI_NUM_TASKS__),
cli_options.initial_root_strategy,
checkpoint);
#ifdef MPI_VERSION
MPI_Barrier(MPI_COMM_WORLD);
Expand Down
34 changes: 28 additions & 6 deletions src/model.cpp
View file
Expand Up @@ -1816,12 +1816,34 @@ void model_t::assign_indicies_by_rank_search(size_t min_roots,
size_t rank,
size_t num_tasks,
checkpoint_t &checkpoint) {
auto completed_work = checkpoint.completed_indicies();
// auto shuffled_idx = shuffle_root_indicies();
// auto shuffled_idx = suggest_root_indicies_midpoint();
// auto shuffled_idx = suggest_root_indicies_length();
auto shuffled_idx = suggest_root_indicies_modified_mad();
size_t root_count = std::min(
assign_indicies_by_rank_search(min_roots,
root_ratio,
rank,
num_tasks,
initial_root_strategy_t::random,
checkpoint);
}

void model_t::assign_indicies_by_rank_search(size_t min_roots,
double root_ratio,
size_t rank,
size_t num_tasks,
initial_root_strategy_t init_root,
checkpoint_t &checkpoint) {
auto completed_work = checkpoint.completed_indicies();
std::vector<size_t> shuffled_idx;

if (init_root == initial_root_strategy_t::random) {
shuffled_idx = shuffle_root_indicies();
} else if (init_root == initial_root_strategy_t::midpoint) {
shuffled_idx = suggest_root_indicies_midpoint();
} else if (init_root == initial_root_strategy_t::modified_mad) {
shuffled_idx = suggest_root_indicies_modified_mad();
} else {
throw std::runtime_error{"The initial root strategy was not recognized"};
}

size_t root_count = std::min(
std::max(static_cast<size_t>(_tree.root_count() * root_ratio), min_roots),
_tree.root_count());

Expand Down
14 changes: 10 additions & 4 deletions src/model.hpp
View file
Expand Up @@ -130,10 +130,16 @@ class model_t {
void assign_indicies(size_t beg, size_t end, std::vector<size_t> idx);
void assign_indicies();

void assign_indicies_by_rank_search(size_t min_roots,
double root_ratio,
size_t rank,
size_t num_tasks,
void assign_indicies_by_rank_search(size_t min_roots,
double root_ratio,
size_t rank,
size_t num_tasks,
checkpoint_t &checkpoint);
void assign_indicies_by_rank_search(size_t min_roots,
double root_ratio,
size_t rank,
size_t num_tasks,
initial_root_strategy_t init_root,
checkpoint_t &);
void assign_indicies_by_rank_exhaustive(size_t rank,
size_t num_tasks,
Expand Down
27 changes: 26 additions & 1 deletion src/util.hpp
View file
Expand Up @@ -62,6 +62,27 @@ namespace asc_bias_type {
enum asc_bias_type_e { lewis, fels, stam };
}

struct initial_root_strategy_t {
enum initial_root_strategy_e { random, midpoint, modified_mad };
initial_root_strategy_e strategy;

initial_root_strategy_t(initial_root_strategy_e s) : strategy{s} {}

bool operator==(const initial_root_strategy_t &other) const {
return strategy == other.strategy;
}

bool operator==(const initial_root_strategy_e &other) const {
return strategy == other;
}
};

/*
namespace initial_root_strategy_t {
enum initial_root_strategy_e { random, midpoint, modified_mad };
}
*/

struct asc_bias_opts_t {
asc_bias_type::asc_bias_type_e type;
double fels_weight;
Expand Down Expand Up @@ -158,6 +179,9 @@ struct cli_options_t {
bool clean = false;
initialized_flag_t early_stop;

initial_root_strategy_t initial_root_strategy = {
initial_root_strategy_t::random};

bool operator==(const cli_options_t &other) const {
return msa_filename == other.msa_filename
&& tree_filename == other.tree_filename && prefix == other.prefix
Expand All @@ -173,7 +197,8 @@ struct cli_options_t {
&& br_tolerance == other.br_tolerance && bfgs_tol == other.bfgs_tol
&& states == other.states && exhaustive == other.exhaustive
&& echo == other.echo && invariant_sites == other.invariant_sites
&& early_stop == other.early_stop;
&& early_stop == other.early_stop
&& initial_root_strategy == other.initial_root_strategy;
}
bool operator!=(const cli_options_t &other) const {
return !(*this == other);
Expand Down

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