parallel tempering feedback optimization

python/loadl

@@ -28,7 +28,7 @@ if jobdir != '':
     os.chdir(jobdir)
 
 try:
-    job = jobfile.JobFile('./'+os.path.basename(args.jobfile))
+    job = jobfile.JobFile(os.path.basename(args.jobfile))
 except jobfile.JobFileGenError as e:
     print('Error: {}'.format(e))
     sys.exit(1)

python/loadleveller/jobfile.py

@@ -10,7 +10,9 @@ class JobFileGenError(Exception):
 
 class JobFile:
     def __init__(self, filename):
-        result = subprocess.run([filename], stdout=subprocess.PIPE)
+        env = dict(os.environ)
+        env['PATH'] += ':.'
+        result = subprocess.run([filename], stdout=subprocess.PIPE, env=env)
 
         self.raw_jobfile = result.stdout.decode('utf-8')
         if result.returncode != 0:

python/loadleveller/taskmaker.py

@@ -6,24 +6,28 @@ import numpy
 def _expand_path(path):
     return os.path.abspath(os.path.expandvars(os.path.expanduser(path)))
 
+def JobConfig(filename):
+    with open(_expand_path(filename), 'r') as f:
+        return yaml.safe_load(f)
+
 class TaskMaker:
     def __init__(self, name, jobconfig):
-        self._tm_name = os.path.splitext(name)[0]
+        self._tm_name = name
         self._tm_tasks = []
-        with open(_expand_path(jobconfig), 'r') as f:
-            self._tm_jobconfig = yaml.safe_load(f)
+        if type(jobconfig) == dict:
+            self._tm_jobconfig = jobconfig
+        elif type(jobconfig) == str:
+            self._tm_jobconfig = JobConfig(jobconfig)
 
         self._tm_jobconfig['mc_binary'] = _expand_path(self._tm_jobconfig['mc_binary'])
 
-        
     def task(self, **additional_parameters):
         self._tm_tasks.append({**self.__dict__, **additional_parameters})
 
     def write(self):
         filenames = []
         jobfile_dict = { 'jobname': self._tm_name, 'jobconfig': self._tm_jobconfig, 'tasks': {}}
-        
-        
+
         for i, t in enumerate(self._tm_tasks):
             task_name = f'task{i+1:04d}'
             task_dict = {}

src/dump.cpp → src/iodump.cpp

-#include "dump.h"
+#include "iodump.h"
 #include <iostream>
 #include <sstream>
 #include <sys/file.h>

src/jobinfo.cpp

+#include "jobinfo.h"
+#include <ctime>
+#include <iomanip>
+#include <iostream>
+#include <fstream>
+#include <regex>
+#include <dirent.h>
+#include "merger.h"
+
+namespace loadl {
+
+// parses the duration '[[hours:]minutes:]seconds' into seconds
+// replace as soon as there is an alternative
+static int parse_duration(const std::string &str) {
+	size_t idx;
+
+	try {
+		int i1 = std::stoi(str, &idx, 10);
+		if(idx == str.size()) {
+			return i1;
+		} else if(str[idx] == ':') {
+			std::string str1 = str.substr(idx + 1);
+			int i2 = std::stoi(str1, &idx, 10);
+
+			if(idx == str1.size()) {
+				return 60 * i1 + i2;
+			} else if(str[idx] == ':') {
+				std::string str2 = str1.substr(idx + 1);
+				int i3 = std::stoi(str2, &idx, 10);
+				if(idx != str2.size()) {
+					throw std::runtime_error{"minutes"};
+				}
+
+				return 60 * 60 * i1 + 60 * i2 + i3;
+			} else {
+				throw std::runtime_error{"hours"};
+			}
+		} else {
+			throw std::runtime_error{"seconds"};
+		}
+	} catch(std::exception &e) {
+		throw std::runtime_error{fmt::format(
+		    "'{}' does not fit time format [[hours:]minutes:]seconds: {}", str, e.what())};
+	}
+}
+
+std::string jobinfo::jobdir() const {
+	return jobname + ".data";
+}
+
+std::string jobinfo::taskdir(int task_id) const {
+	return fmt::format("{}/{}", jobdir(), task_names.at(task_id));
+}
+
+std::string jobinfo::rundir(int task_id, int run_id) const {
+	return fmt::format("{}/run{:04d}", taskdir(task_id), run_id);
+}
+
+jobinfo::jobinfo(const std::string &jobfile_name) : jobfile{jobfile_name} {
+	for(auto node : jobfile["tasks"]) {
+		std::string task_name = node.first;
+		task_names.push_back(task_name);
+	}
+	std::sort(task_names.begin(), task_names.end());
+
+	jobname = jobfile.get<std::string>("jobname");
+
+	std::string datadir = jobdir();
+	int rc = mkdir(datadir.c_str(), 0755);
+	if(rc != 0 && errno != EEXIST) {
+		throw std::runtime_error{
+		    fmt::format("creation of output directory '{}' failed: {}", datadir, strerror(errno))};
+	}
+
+	// perhaps a bit controversally, jobinfo tries to create the task directories. TODO: single file
+	// output.
+	for(size_t i = 0; i < task_names.size(); i++) {
+		int rc = mkdir(taskdir(i).c_str(), 0755);
+		if(rc != 0 && errno != EEXIST) {
+			throw std::runtime_error{fmt::format("creation of output directory '{}' failed: {}",
+			                                     taskdir(i), strerror(errno))};
+		}
+	}
+
+	parser jobconfig{jobfile["jobconfig"]};
+
+	walltime = parse_duration(jobconfig.get<std::string>("mc_walltime"));
+	checkpoint_time = parse_duration(jobconfig.get<std::string>("mc_checkpoint_time"));
+}
+
+// This function lists files that could be run files being in the taskdir
+// and having the right file_ending.
+// The regex has to be matched with the output of the rundir function.
+std::vector<std::string> jobinfo::list_run_files(const std::string &taskdir,
+                                                 const std::string &file_ending) {
+	std::regex run_filename{"run\\d{4,}\\." + file_ending};
+	std::vector<std::string> results;
+	DIR *dir = opendir(taskdir.c_str());
+	if(dir == nullptr) {
+		throw std::ios_base::failure(
+		    fmt::format("could not open directory '{}': {}", taskdir, strerror(errno)));
+	}
+	struct dirent *result;
+	while((result = readdir(dir)) != nullptr) {
+		std::string fname{result->d_name};
+		if(std::regex_search(fname, run_filename)) {
+			results.emplace_back(fmt::format("{}/{}", taskdir, fname));
+		}
+	}
+	closedir(dir);
+
+	return results;
+}
+
+int jobinfo::read_dump_progress(int task_id) const {
+	int sweeps = 0;
+	try {
+		for(auto &dump_name : list_run_files(taskdir(task_id), "dump\\.h5")) {
+			int dump_sweeps = 0;
+			iodump d = iodump::open_readonly(dump_name);
+			d.get_root().read("sweeps", dump_sweeps);
+			sweeps += dump_sweeps;
+		}
+	} catch(std::ios_base::failure &e) {
+		// might happen if the taskdir does not exist
+	}
+
+	return sweeps;
+}
+
+void jobinfo::concatenate_results() {
+	std::ofstream cat_results{fmt::format("{}.results.yml", jobname)};
+	for(size_t i = 0; i < task_names.size(); i++) {
+		std::ifstream res_file{taskdir(i) + "/results.yml"};
+		res_file.seekg(0, res_file.end);
+		size_t size = res_file.tellg();
+		res_file.seekg(0, res_file.beg);
+
+		std::vector<char> buf(size + 1, 0);
+		res_file.read(buf.data(), size);
+		cat_results << buf.data() << "\n";
+	}
+}
+
+void jobinfo::merge_task(int task_id, const std::vector<evalable> &evalables) {
+	std::vector<std::string> meas_files = list_run_files(taskdir(task_id), "meas\\.h5");
+	results results = merge(meas_files, evalables);
+
+	std::string result_filename = fmt::format("{}/results.yml", taskdir(task_id));
+	const std::string &task_name = task_names.at(task_id);
+	results.write_yaml(result_filename, taskdir(task_id), jobfile["tasks"][task_name].get_yaml());
+}
+
+void jobinfo::log(const std::string &message) {
+	std::time_t t = std::time(nullptr);
+	std::cout << std::put_time(std::localtime(&t), "%F %T: ") << message << "\n";
+}
+
+}

src/jobinfo.h

+#pragma once
+
+#include <vector>
+#include <string>
+#include "parser.h"
+#include "iodump.h"
+#include "evalable.h"
+
+namespace loadl {
+
+struct jobinfo {
+	parser jobfile;
+	std::string jobname;
+
+	std::vector<std::string> task_names;
+
+	double checkpoint_time;
+	double walltime;
+
+	jobinfo(const std::string &jobfile_name);
+
+	std::string jobdir() const;
+	std::string rundir(int task_id, int run_id) const;
+	std::string taskdir(int task_id) const;
+
+	static std::vector<std::string> list_run_files(const std::string &taskdir,
+	                                               const std::string &file_ending);
+	int read_dump_progress(int task_id) const;
+	void merge_task(int task_id, const std::vector<evalable> &evalables);
+	void concatenate_results();
+	void log(const std::string &message);
+};
+
+}

src/mc.cpp

@@ -2,7 +2,8 @@
 namespace loadl {
 
 mc::mc(const parser &p) : param{p} {
-	therm_ = param.get<int>("thermalization");
+	therm_ = p.get<int>("thermalization");
+	pt_sweeps_per_global_update_ = p.get<int>("pt_sweeps_per_global_update", -1);
 }
 
 void mc::write_output(const std::string &) {}
@@ -19,12 +20,13 @@ void mc::_init() {
 	// simple profiling support: measure the time spent for sweeps/measurements etc
 	measure.add_observable("_ll_checkpoint_read_time", 1);
 	measure.add_observable("_ll_checkpoint_write_time", 1);
-	measure.add_observable("_ll_measurement_time", 1000);
-	measure.add_observable("_ll_sweep_time", 1000);
+	measure.add_observable("_ll_measurement_time", pt_mode_ ? pt_sweeps_per_global_update_ : 1000);
+	measure.add_observable("_ll_sweep_time", pt_mode_ ? pt_sweeps_per_global_update_ : 1000);
 
-	if(param.get<bool>("pt_statistics", false)) {
-		measure.add_observable("_ll_pt_rank", 1);
-		measure.add_observable("_ll_pt_weight_ratio", 1);
+	if(pt_mode_) {
+		if(param.get<bool>("pt_statistics", false)) {
+			measure.add_observable("_ll_pt_rank", 1);
+		}
 	}
 		
 	if(param.defined("seed")) {
@@ -69,44 +71,54 @@ void mc::_do_update() {
 
 void mc::_pt_update_param(double new_param, const std::string &new_dir) {
 	// take over the bins of the new target dir
-	/*{
+	{
 		iodump dump_file = iodump::open_readonly(new_dir + ".dump.h5");
 		measure.checkpoint_read(dump_file.get_root().open_group("measurements"));
-	}*/
+	}
 
+	auto unclean = measure.is_unclean();
+	if(unclean) {
+		throw std::runtime_error(fmt::format("Unclean observable: {}\nIn parallel tempering mode you have to choose the binsize for all observables so that it is commensurate with pt_sweeps_per_global_update (so that all bins are empty once it happens). If you don’t like this limitation, implement it properly.", *unclean));
+	}
+
+	pt_update_param(new_param);
+}
+
+void mc::pt_measure_statistics() {
 	if(param.get<bool>("pt_statistics", false)) {
 		int rank;
 		MPI_Comm_rank(MPI_COMM_WORLD, &rank);
 		measure.add("_ll_pt_rank", rank);
 	}
-	pt_update_param(new_param);
 }
 
 double mc::_pt_weight_ratio(double new_param) {
 	double wr = pt_weight_ratio(new_param);
-	if(param.get<bool>("pt_statistics", false)) {
-		measure.add("_ll_pt_weight_ratio", wr);
-	}
 	return wr;
 }
 
-void mc::_write(const std::string &dir) {
-	struct timespec tstart, tend;
-	clock_gettime(CLOCK_MONOTONIC_RAW, &tstart);
-
+void mc::measurements_write(const std::string &dir) {
 	// blocks limit scopes of the dump file handles to ensure they are closed at the right time.
 	{
 		iodump meas_file = iodump::open_readwrite(dir + ".meas.h5");
-		measure.samples_write(meas_file.get_root());
+		auto g = meas_file.get_root();
+		measure.samples_write(g);
 	}
+}
+
+void mc::_write(const std::string &dir) {
+	struct timespec tstart, tend;
+	clock_gettime(CLOCK_MONOTONIC_RAW, &tstart);
+
+	measurements_write(dir);
 
 	{
 		iodump dump_file = iodump::create(dir + ".dump.h5.tmp");
 		auto g = dump_file.get_root();
 
-		measure.checkpoint_write(g.open_group("measurements"));
 		rng->checkpoint_write(g.open_group("random_number_generator"));
 		checkpoint_write(g.open_group("simulation"));
+		measure.checkpoint_write(g.open_group("measurements"));
 
 		g.write("max_checkpoint_write_time", max_checkpoint_write_time_);
 		g.write("max_sweep_time", max_sweep_time_);
@@ -131,6 +143,7 @@ double mc::safe_exit_interval() {
 	return 2 * (max_checkpoint_write_time_ + max_sweep_time_ + max_meas_time_) + 2;
 }
 
+
 bool mc::_read(const std::string &dir) {
 	if(!file_exists(dir + ".dump.h5")) {
 		return false;
@@ -164,6 +177,11 @@ void mc::_write_output(const std::string &filename) {
 }
 
 bool mc::is_thermalized() {
-	return sweep_ > therm_;
+	int sweep = sweep_;
+	if(pt_mode_ && pt_sweeps_per_global_update_ > 0) {
+		sweep /= pt_sweeps_per_global_update_;
+	}
+		
+	return sweep >= therm_;
 }
 }

src/mc.h

@@ -12,8 +12,9 @@ namespace loadl {
 
 class mc {
 private:
-	int sweep_ = 0;
-	int therm_ = 0;
+	int sweep_{0};
+	int therm_{0};
+	int pt_sweeps_per_global_update_{-1};
 
 	// The following times in seconds are used to estimate a safe exit interval before walltime is
 	// up.
@@ -40,6 +41,8 @@ protected:
 	}
 
 public:
+	bool pt_mode_{};
+
 	double random01();
 	int sweep() const;
 
@@ -52,6 +55,8 @@ public:
 	void _write(const std::string &dir);
 	bool _read(const std::string &dir);
 
+	void measurements_write(const std::string &dir);
+
 	void _write_output(const std::string &filename);
 
 	void _do_update();
@@ -59,10 +64,9 @@ public:
 	void _pt_update_param(double new_param, const std::string &new_dir);
 	double _pt_weight_ratio(double new_param);
 
+	void pt_measure_statistics();
+
 	double safe_exit_interval();
-	
-	// write only measurement data (useful for parallel tempering)
-	void measurement_write(const std::string &dir);
 
 	bool is_thermalized();
 	measurements measure;

src/measurements.cpp

@@ -41,4 +41,13 @@ void measurements::samples_write(const iodump::group &meas_file) {
 		obs.second.measurement_write(g);
 	}
 }
+
+std::optional<std::string> measurements::is_unclean() const {
+	for(const auto &obs : observables_) {
+		if(!obs.second.is_clean()) {
+			return obs.first;
+		}
+	}
+	return std::nullopt;
+}
 }

src/measurements.h

 #pragma once
 
-#include "dump.h"
+#include "iodump.h"
 #include "observable.h"
 #include <map>
 #include <string>
@@ -26,6 +26,10 @@ public:
 	// should be opened in read/write mode.
 	void samples_write(const iodump::group &meas_file);
 
+	// returns nullopt if all observables are clean,
+	// otherwise the name of a non-empty observable 
+	std::optional<std::string> is_unclean() const;
+
 private:
 	std::map<std::string, observable> observables_;
 };

src/merger.cpp

 #include "merger.h"
-#include "dump.h"
+#include "iodump.h"
 #include "evalable.h"
 #include "mc.h"
 #include "measurements.h"

src/meson.build

@@ -14,8 +14,9 @@ configure_file(input : 'config.h.in',
 config_inc = include_directories('.')
 
 loadleveller_sources = files([
-  'dump.cpp',
   'evalable.cpp',
+  'iodump.cpp',
+  'jobinfo.cpp',
   'mc.cpp',
   'measurements.cpp',
   'merger.cpp',
@@ -30,8 +31,9 @@ loadleveller_sources = files([
 ])
 
 loadleveller_headers = files([
-  'dump.h',
   'evalable.h',
+  'iodump.h',
+  'jobinfo.h',
   'loadleveller.h',
   'mc.h',
   'measurements.h',
@@ -58,7 +60,7 @@ libloadleveller = library('loadleveller',
 if should_install
   pkg = import('pkgconfig')
   pkg.generate(libloadleveller,
-    description : 'Framework for distributed (Quantum) Monte Carlo codes',
+    description : 'Framework for distributed (quantum) Monte Carlo codes',
   )
   
   install_headers(loadleveller_headers, subdir : 'loadleveller')

src/observable.cpp

 #include "observable.h"
 #include <fmt/format.h>
-
+#include <iostream>
 namespace loadl {
 
 observable::observable(std::string name, size_t bin_length, size_t vector_length)
@@ -56,4 +56,12 @@ void observable::checkpoint_read(const iodump::group &d) {
 	d.read("samples", samples_);
 	current_bin_ = 0;
 }
+
+bool observable::is_clean() const {
+	if(current_bin_filling_ != 0) {
+		std::cout << current_bin_filling_ << "\n";
+	}
+	return current_bin_ == 0 && current_bin_filling_ == 0;
+}
+
 }

src/observable.h

 #pragma once
 
-#include "dump.h"
+#include "iodump.h"
 #include <cmath>
 #include <map>
 #include <string>
@@ -27,6 +27,9 @@ public:
 
 	void checkpoint_read(const iodump::group &dump_file);
 
+	// true if there are no samples in the bin
+	bool is_clean() const;
+
 private:
 	static const size_t initial_bin_length = 1000;
 

src/random.h

@@ -3,7 +3,7 @@
 #include "config.h"
 
 #include "MersenneTwister.h"
-#include "dump.h"
+#include "iodump.h"
 #include <random>
 #include <sstream>
 #include <typeinfo>

src/runner.cpp

 #include "runner.h"
 #include "merger.h"
+#include "iodump.h"
 #include "runner_pt.h"
-#include <dirent.h>
 #include <fmt/format.h>
-#include <fstream>
-#include <iomanip>
-#include <regex>
-#include <sys/stat.h>
 namespace loadl {
 
 enum {
@@ -25,153 +21,6 @@ enum {
 	A_PROCESS_DATA_NEW_JOB = 4,
 };
 
-// parses the duration '[[hours:]minutes:]seconds' into seconds
-// replace as soon as there is an alternative
-static int parse_duration(const std::string &str) {
-	size_t idx;
-
-	try {
-		int i1 = std::stoi(str, &idx, 10);
-		if(idx == str.size()) {
-			return i1;
-		} else if(str[idx] == ':') {
-			std::string str1 = str.substr(idx + 1);
-			int i2 = std::stoi(str1, &idx, 10);
-
-			if(idx == str1.size()) {
-				return 60 * i1 + i2;
-			} else if(str[idx] == ':') {
-				std::string str2 = str1.substr(idx + 1);
-				int i3 = std::stoi(str2, &idx, 10);
-				if(idx != str2.size()) {
-					throw std::runtime_error{"minutes"};
-				}
-
-				return 60 * 60 * i1 + 60 * i2 + i3;
-			} else {
-				throw std::runtime_error{"hours"};
-			}
-		} else {
-			throw std::runtime_error{"seconds"};
-		}
-	} catch(std::exception &e) {
-		throw std::runtime_error{fmt::format(
-		    "'{}' does not fit time format [[hours:]minutes:]seconds: {}", str, e.what())};
-	}
-}
-
-std::string jobinfo::jobdir() const {
-	return jobname + ".data";
-}
-
-std::string jobinfo::taskdir(int task_id) const {
-	return fmt::format("{}/{}", jobdir(), task_names.at(task_id));
-}
-
-std::string jobinfo::rundir(int task_id, int run_id) const {
-	return fmt::format("{}/run{:04d}", taskdir(task_id), run_id);
-}
-
-jobinfo::jobinfo(const std::string &jobfile_name) : jobfile{jobfile_name} {
-	for(auto node : jobfile["tasks"]) {
-		std::string task_name = node.first;
-		task_names.push_back(task_name);
-	}
-	std::sort(task_names.begin(), task_names.end());
-
-	jobname = jobfile.get<std::string>("jobname");
-
-	std::string datadir = jobdir();
-	int rc = mkdir(datadir.c_str(), 0755);
-	if(rc != 0 && errno != EEXIST) {
-