Merge pull request #503 from JulienDoerner/Interrupt

Handling of interruptions

.github/workflows/test_examples.yml

@@ -67,6 +67,8 @@ jobs:
                 [ "$file" = "MHD_modelsipynb.py" ] || 
                 [ "$file" = "density_grid_samplingipynb.py" ] ||
                 [ "$file" = "lensing_crv4ipynb.py" ] ||
+                [ "$file" = "interrupt_candidateVectoripynb.py" ] ||
+                [ "$file" = "interrupt_sourceipynb.py" ] ||
                 [ "$file" = "lensing_mapsv4ipynb.py" ]; then
                 echo "skip file $file"
             else 

doc/index.rst

@@ -31,6 +31,7 @@ Contents
    pages/acceleration.rst
    pages/extending_crpropa.rst
    pages/example_notebooks/propagation_comparison/Propagation_Comparison_CK_BP.ipynb
+   pages/interrupting-simulations.rst
    pages/AdditionalResources.rst
 
 

doc/pages/interrupting-simulations.rst

@@ -0,0 +1,22 @@
+Interrupting simulations on runtime
+------------------------------------------------
+
+CRPropa simulations can be interrupted on runtime with the `SIGTERM` or `SIGINT` signals. 
+If the user defines an output for the interruption (called `InterruptAction`) all candidates which are currently in the simulation will be passed to this output. 
+In the error stream the user will see a message denoting the number of candidates which have not been started yet. 
+If the simulation was run with a `candidateVector` as source, the indices of the candidates which have not been started yet will be printed or written to the file.
+For a simulation with a source interface, a restart with the missing number of candidates will be sufficient to continue the simulation.
+
+.. toctree:: 
+   :caption: Using a candidateVector as source
+   :maxdepth: 1
+
+   example_notebooks/interrupting_simulations/interrupt_candidateVector.ipynb
+
+.. toctree:: 
+   :caption: Using a source interface
+   :maxdepth: 1
+
+   example_notebooks/interrupting_simulations/interrupt_source.ipynb
+
+

include/crpropa/ModuleList.h

@@ -4,6 +4,7 @@
 #include "crpropa/Candidate.h"
 #include "crpropa/Module.h"
 #include "crpropa/Source.h"
+#include "crpropa/module/Output.h"
 
 #include <list>
 #include <sstream>
@@ -47,9 +48,15 @@ class ModuleList: public Module {
 	iterator end();
 	const_iterator end() const;
 
+	void setInterruptAction(Output* action);
+	void dumpCandidate(Candidate* cand) const;
+
 private:
 	module_list_t modules;
 	bool showProgress;
+	Output* interruptAction;
+	bool haveInterruptAction = false;
+	std::vector<int> notFinished; // list with not finished numbers of candidates
 };
 
 /**

include/crpropa/module/Output.h

@@ -52,16 +52,18 @@ namespace crpropa {
  They can be easily customised by enabling/disabling specific columns.
  */
 class Output: public Module {
-protected:
-	double lengthScale, energyScale;
-	std::bitset<64> fields;
-
+public: 
 	struct Property
 	{
 		std::string name;
 		std::string comment;
 		Variant defaultValue;
 	};
+
+protected:
+	double lengthScale, energyScale;
+	std::bitset<64> fields;
+
 	std::vector<Property> properties;
 
 	bool oneDimensional;
@@ -163,6 +165,18 @@ class Output: public Module {
 	size_t size() const;
 
 	void process(Candidate *) const;
+
+	/**	
+	 * write the indices of not started candidates into the output file. 
+	 * Used for interrupting the simulation
+	 * @param indices list of not started indices
+	 */
+	virtual void dumpIndexList(std::vector<int> indices) {
+		std::cout << "indices:\t"; 
+		for (int i = 0; i < indices.size(); i++) 
+			std::cout << indices[i] << ", ";
+		std::cout << "\n";
+	};
 };
 
 /** @}*/

include/crpropa/module/TextOutput.h

@@ -71,6 +71,8 @@ class TextOutput: public Output {
 	 */
 	static void load(const std::string &filename, ParticleCollector *collector);
 	std::string getDescription() const;
+
+	void dumpIndexList(std::vector<int> indicies);
 };
 /** @}*/
 

python/2_headers.i

@@ -279,6 +279,11 @@
 %feature("director") crpropa::AbstractCondition;
 %include "crpropa/Module.h"
 
+%template(OutputRefPtr) crpropa::ref_ptr<Output>;
+%feature("director") crpropa::Output;
+%ignore crpropa::Output::dumpIndexList(std::vector<int>);
+%include "crpropa/module/Output.h"
+
 %implicitconv crpropa::ref_ptr<crpropa::MagneticField>;
 %template(MagneticFieldRefPtr) crpropa::ref_ptr<crpropa::MagneticField>;
 %feature("director") crpropa::MagneticField;
@@ -394,8 +399,6 @@
   }
 }
 
-
-%include "crpropa/module/Output.h"
 %include "crpropa/module/DiffusionSDE.h"
 %include "crpropa/module/TextOutput.h"
 %include "crpropa/module/HDF5Output.h"

src/ModuleList.cpp.in

@@ -8,6 +8,7 @@
 
 #include <algorithm>
 #include <csignal>
+#include <bits/stdc++.h> 
 #ifndef sighandler_t
 typedef void (*sighandler_t)(int);
 #endif
@@ -87,6 +88,10 @@ void ModuleList::run(Candidate* candidate, bool recursive, bool secondariesFirst
 			run(candidate->secondaries[i], recursive, secondariesFirst);
 		}
 	}
+
+	// dump candidae and secondaries if interrupted.
+	if (candidate->isActive() && (g_cancel_signal_flag != 0)) 
+		dumpCandidate(candidate);
 }
 
 void ModuleList::run(ref_ptr<Candidate> candidate, bool recursive, bool secondariesFirst) {
@@ -114,8 +119,11 @@ void ModuleList::run(const candidate_vector_t *candidates, bool recursive, bool
 
 #pragma omp parallel for schedule(OMP_SCHEDULE)
 	for (size_t i = 0; i < count; i++) {
-		if (g_cancel_signal_flag != 0)
+		if (g_cancel_signal_flag != 0) {
+#pragma omp critical(interrupt_write)
+			notFinished.push_back(i);
 			continue;
+		}
 
 		try {
 			run(candidates->operator[](i), recursive);
@@ -132,8 +140,18 @@ void ModuleList::run(const candidate_vector_t *candidates, bool recursive, bool
 	::signal(SIGINT, old_sigint_handler);
 	::signal(SIGTERM, old_sigterm_handler);
 	// Propagate signal to old handler.
-	if (g_cancel_signal_flag > 0)
+	if (g_cancel_signal_flag > 0) {
 		raise(g_cancel_signal_flag);
+		std::cerr << "############################################################################\n";
+		std::cerr << "#	Interrupted CRPropa simulation \n";
+		std::cerr << "# A total of " << notFinished.size() << " candidates have not been started.\n";
+		std::cerr << "# the indices of the vector haven been written to to output file. \n";
+		std::cerr << "############################################################################\n";
+
+		// dump list to output file 
+		std::sort(notFinished.begin(), notFinished.end());
+		interruptAction->dumpIndexList(notFinished);
+	}
 }
 
 void ModuleList::run(SourceInterface *source, size_t count, bool recursive, bool secondariesFirst) {
@@ -156,8 +174,11 @@ void ModuleList::run(SourceInterface *source, size_t count, bool recursive, bool
 
 #pragma omp parallel for schedule(OMP_SCHEDULE)
 	for (size_t i = 0; i < count; i++) {
-		if (g_cancel_signal_flag !=0)
+		if (g_cancel_signal_flag !=0) {
+#pragma omp critical(interrupt_write)
+			notFinished.push_back(i);	
 			continue;
+		}
 
 		ref_ptr<Candidate> candidate;
 
@@ -189,8 +210,13 @@ void ModuleList::run(SourceInterface *source, size_t count, bool recursive, bool
 	::signal(SIGINT, old_signal_handler);
 	::signal(SIGTERM, old_sigterm_handler);
 	// Propagate signal to old handler.
-	if (g_cancel_signal_flag > 0)
+	if (g_cancel_signal_flag > 0) {
 		raise(g_cancel_signal_flag);
+		std::cerr << "############################################################################\n";
+		std::cerr << "# Interrupted CRPropa simulation \n";
+		std::cerr << "# Number of not started candidates from source: " << notFinished.size() << "\n";
+		std::cerr << "############################################################################\n";
+	}
 }
 
 ModuleList::iterator ModuleList::begin() {
@@ -222,6 +248,27 @@ void ModuleList::showModules() const {
 	std::cout << getDescription();
 }
 
+void ModuleList::setInterruptAction(Output* action) {
+	interruptAction = action;
+	haveInterruptAction = true;
+}
+
+void ModuleList::dumpCandidate(Candidate *cand) const {
+	if (!haveInterruptAction) 
+		return;
+
+	if (cand->isActive())
+		interruptAction->process(cand); 
+	else 
+		KISS_LOG_WARNING << "ModuleList::dumpCandidate is called with a non active candidate. This should not happen for the interrupt action. Please check candidate with serial number " 
+		 << cand->getSerialNumber() << std::endl;
+
+	for (int i = 0; i < cand->secondaries.size(); i++) {
+		if (cand->secondaries[i])
+			dumpCandidate(cand->secondaries[i]);
+	}
+}
+
 ModuleListRunner::ModuleListRunner(ModuleList *mlist) : mlist(mlist) {
 }
 

src/module/TextOutput.cpp

@@ -7,6 +7,7 @@
 
 #include "kiss/string.h"
 
+#include <sstream>
 #include <cstdio>
 #include <stdexcept>
 #include <iostream>
@@ -378,4 +379,17 @@ void TextOutput::gzip() {
 #endif
 }
 
+void TextOutput::dumpIndexList(std::vector<int> indices) {
+#pragma omp critical(FileOutput)
+	{
+		std::stringstream ss;
+		ss << "#" << "\t";
+		for (int i = 0; i < indices.size(); i++)
+			ss << indices[i] << "\t";
+
+		const std::string cstr = ss.str();
+		out-> write(cstr.c_str(), cstr.length());
+	}
+}
+
 } // namespace crpropa