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Merge branch 'branch_1_6_1' into 'master'
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Branch 1 6 1

See merge request gromos/gromosXX!145
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@oostenbrink
oostenbrink committed Apr 3, 2024
2 parents 2f977b0 + a2f0738 commit 3383f4b
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Showing 2 changed files with 86 additions and 51 deletions.
68 changes: 34 additions & 34 deletions md++/src/util/timing.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,8 @@ double util::now()
* Constructor
*/
util::Algorithm_Timer::Algorithm_Timer(const std::string & name) {
DEBUG(5, "Construct main-timer: " + m_maintimer_name);
m_maintimer_name = name;
DEBUG(5, "Construct main-timer: " + m_name);
m_name = name;

/*
* Evaluate number of available threads
Expand All @@ -88,19 +88,20 @@ util::Algorithm_Timer::Algorithm_Timer(const std::string & name) {
}
#endif
m_max_thread_num = tracked_thread_count;
DEBUG(10, "Maximum tracked threads in main-timer " + m_maintimer_name + " : " + std::to_string(m_max_thread_num));
DEBUG(10, "Maximum tracked threads in main-timer " + m_name + " : " + std::to_string(m_max_thread_num));
}

/**
* initializes a (sub) timer
*/
void util::Algorithm_Timer::initialize(const std::string & name) {
DEBUG(5, "Initializes sub-timer " + name + " of main-timer " + m_maintimer_name + ".");
DEBUG(5, "Initializes sub-timer " + name + " of main-timer " + m_name + ".");

Subtimer_Class subtimer_obj(m_max_thread_num);
m_subtimers.emplace(std::make_pair(name, subtimer_obj));
subtimer_in_use.clear();

std::pair<Subtimer_Container::iterator, bool>
ret = m_subtimers.emplace(name, Subtimer(m_max_thread_num));
// assert the insertion took place
assert(ret.second && "re-initialization of sub-timer is not allowed");
subtimer_in_use.clear();
}

/**
Expand All @@ -119,7 +120,8 @@ void util::Algorithm_Timer::start(const simulation::Simulation & sim) {
* Create detailed timing output. Set "@print timings_report" as md++ input parameter
*/
m_detailed_report = false;
if (sim.param().print.timings_report) { //If "@print timings_report" is set as md++ parameter
//If "@print timings_report" is set as md++ parameter
if (sim.param().print.timings_report) {

//Write detailed report for timesteps 900 to 904 (if pairlist skipstep = 5)
const uint first_report_step = (180 * sim.param().pairlist.skip_step);
Expand Down Expand Up @@ -264,45 +266,43 @@ void util::Algorithm_Timer::stop_subtimer(const std::string & name) {
io::messages.add("Usage of both OpenMP and MPI not yet implemented in util/timing.cc. Timings might be wrong!","Timing",io::message::notice);
#endif
#endif

/*
* Check if an timer has been stopped without beeing in the subtimer map.
* This should never happen!!
* It would mean, that the subtimer was not yet initialized and we have a serious race condition
*/
//#pragma omp critical (timing_system)
{
if (m_subtimers.count(name) == 0){

#pragma omp critical (timing_system)
{ /*
* Check if the timer has been stopped without beeing in the subtimer map.
* This should never happen!!
* It would mean, that the subtimer was not yet initialized and we have a serious race condition
*
* calling .count() without lock is thread-unsafe
* existence of 'name' means initialized subtimer, however
* adding another subtimer simultaneously by another thread
* may lead to rehashing, that temporarily invalidates
* the .count() call
*/
if (m_subtimers.count(name) == 0) {
{
//io::messages.add("Sub-timer " + name + " was stopped that has not been initialized before!","Timing",io::message::notice);
//DEBUG(5, "Sub-timer " + name + " was stopped that has not been initialized before!");
throw std::runtime_error("Sub-timer " + name + " was stopped that has not been initialized before! (Simulation step: " + std::to_string(m_step_index) + ")\n");
}
}
}

#pragma omp critical (timing_system)
{
m_subtimers.at(name).end_time.at(thread_id) = util::now();

if (thread_id == m_subtimers.at(name).master_thread){
m_subtimers.at(name).total_walltime += (m_subtimers.at(name).end_time.at(thread_id) - m_subtimers.at(name).start_time.at(thread_id));
}
m_subtimers.at(name).total_cputime += (m_subtimers.at(name).end_time.at(thread_id) - m_subtimers.at(name).start_time.at(thread_id));
}

/*
* Disable subtimer_in_use flag after stopping subtimer
*/
#ifndef NDEBUG
#pragma omp critical (timing_system)
{
std::string jobname = name + std::to_string(thread_id);
if (name != "total" && subtimer_in_use == jobname){
subtimer_in_use.clear();
}
}
std::string jobname = name + std::to_string(thread_id);
if (name != "total" && subtimer_in_use == jobname){
subtimer_in_use.clear();
}
#endif
}
}


Expand All @@ -312,7 +312,7 @@ void util::Algorithm_Timer::stop_subtimer(const std::string & name) {
double util::Algorithm_Timer::get_total(const std::string & name) {

if (m_subtimers.count(name) == 0){
throw std::runtime_error(std::string("Timer ") + m_maintimer_name + ": " + name +
throw std::runtime_error(std::string("Timer ") + m_name + ": " + name +
" timer does not exist.");
}

Expand All @@ -334,7 +334,7 @@ void util::Algorithm_Timer::print_report(std::ostream & os) {
os << "DETAILED_TIMING" << std::endl;
for(auto& subtimer : m_subtimers) {
//Print start time
os << m_maintimer_name;
os << m_name;
os << ";" << subtimer.first;
os << ";start";
os << std::fixed << std::setprecision(6);
Expand Down Expand Up @@ -372,7 +372,7 @@ void util::Algorithm_Timer::print(std::ostream &os) {
const double total = get_total();

os.precision(3);
os << std::left << std::setw(10) << " " << std::left << std::setw(30) << m_maintimer_name
os << std::left << std::setw(10) << " " << std::left << std::setw(30) << m_name
<< std::setw(14) << std::right << total;

if (m_subtimers.size() > 1){
Expand All @@ -381,7 +381,7 @@ void util::Algorithm_Timer::print(std::ostream &os) {
os << std::endl;
}

std::unordered_map<std::string, Subtimer_Class>::const_iterator
Subtimer_Container::const_iterator
it = m_subtimers.begin(),
to = m_subtimers.end();

Expand Down
69 changes: 52 additions & 17 deletions md++/src/util/timing.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -82,15 +82,28 @@ namespace util
/**
* accessor to name
*/
std::string & get_maintimer_name() {
return m_maintimer_name;
void name(const std::string & name) {
m_name = name;
}
/**
* accessor to name
*/
std::string & name() {
return m_name;
}
/**
* const accessor to name
*/
const std::string & name() const {
return m_name;
}


protected:
/**
* name of the maintimer timer
*/
std::string m_maintimer_name;
std::string m_name;
/**
* maximum number of threads tracked by timer
*/
Expand All @@ -107,28 +120,50 @@ namespace util
/**
* sub-timer class
*/
class Subtimer_Class {
class Subtimer {
public:
uint master_thread = std::numeric_limits<uint>::max();
uint highest_used_thread = 0;
/**
* vector of start times - one per thread
*/
std::vector<double> start_time;
/**
* vector of end times - one per thread
*/
std::vector<double> end_time;
double total_walltime = 0.0; //total runtime for subtimer
double total_cputime = 0.0;
bool double_counted_time = false; //set true if the subtime was once started while another subtimer was still running
/**
* total walltime for subtimer
*/
double total_walltime = 0.0;
/**
* total cputime for subtimer
*/
double total_cputime = 0.0;
/**
* ID of the master thread
*/
uint master_thread = std::numeric_limits<uint>::max();
/**
* highest ID of the used thread
*/
uint highest_used_thread = 0;
/**
* true if the subtimer was started while another subtimer was still running
*/
bool double_counted_time = false;

//Constructor (no arguments)
Subtimer_Class(){
start_time = std::vector<double>(1, 0.0);
end_time = std::vector<double>(1, 0.0);
}
//Constructor
Subtimer_Class(const uint thread_count){
/**
* Constructor
*/
Subtimer(const uint thread_count = 1){
start_time = std::vector<double>(thread_count, 0.0);
end_time = std::vector<double>(thread_count, 0.0);
}
};
std::unordered_map<std::string, Subtimer_Class> m_subtimers;
typedef std::unordered_map<std::string, Subtimer> Subtimer_Container;
/**
* a map of subtimers, one subtimer per algorithm name
*/
Subtimer_Container m_subtimers;
/**
* store which subtimer is actually in use (debug only)
*/
Expand Down

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