minor changes, removed unused imports and comments, doc

sybila · May 24, 2017 · 275d41e · 275d41e
1 parent 1a1cb13
commit 275d41e
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Showing 7 changed files with 40 additions and 168 deletions.
diff --git a/experiments/SIR/outbreak5.formula.xml b/experiments/SIR/outbreak5.formula.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <formula xmlns="http://www.sybila.org/parasim/stl-formula">
 <future>
-<interval>
-<lower type="closed">1.0</lower>
-<upper type="closed">5.0</upper>
-</interval>
-<predicate>
-<variable multiplier="1.0">I</variable>
-<greater/>
-<value>5.0</value>
-</predicate>
+    <interval>
+        <lower type="closed">1.0</lower>
+        <upper type="closed">5.0</upper>
+    </interval>
+    <predicate>
+        <variable multiplier="1.0">I</variable>
+        <greater/>
+        <value>5.0</value>
+    </predicate>
 </future>
 </formula>
diff --git a/...tion-impl/src/main/java/org/sybila/parasim/computation/simulation/SimulatorRegistrar.java b/...tion-impl/src/main/java/org/sybila/parasim/computation/simulation/SimulatorRegistrar.java
@@ -19,16 +19,13 @@
  */
 package org.sybila.parasim.computation.simulation;
 
-import dk.ange.octave.OctaveEngine;
-import dk.ange.octave.OctaveEngineFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sybila.parasim.computation.lifecycle.api.annotations.ComputationInstanceScope;
 import org.sybila.parasim.computation.simulation.api.AdaptiveStepSimulator;
 import org.sybila.parasim.computation.simulation.cpu.SimpleAdaptiveStepSimulator;
 import org.sybila.parasim.computation.simulation.octave.LsodeEngineFactory;
 import org.sybila.parasim.computation.simulation.octave.OctaveSimulationEngineFactory;
-import org.sybila.parasim.computation.simulation.simulationcore.SimCoreSimulationEngineFactory;
 import org.sybila.parasim.core.annotation.Provide;
 import org.sybila.parasim.core.api.configuration.ExtensionDescriptor;
 import org.sybila.parasim.core.api.configuration.ExtensionDescriptorMapper;

diff --git a/...on-impl/src/main/java/org/sybila/parasim/computation/simulation/cpu/SimulationEngine.java b/...on-impl/src/main/java/org/sybila/parasim/computation/simulation/cpu/SimulationEngine.java
@@ -29,14 +29,18 @@
  */
 public interface SimulationEngine {
 
+    /**
+     * Closes SimulationEngine. This method is called after the simulation of the whole space is performed.
+     * Enables to close external software e.g. GNU Octave
+     */
     void close();
 
     /**
-     * Performs simulation of a differential equation system from given point in time to timelimit
-     * @param point where to start simulation, contains start time
+     * Performs simulation of a differential equation system from given point.
+     * @param point initial point where to start simulation, contains start time and values of state variables and parameters
      * @param odeSystem differential equation system
      * @param timeLimit end time of simulation
-     * @param configuration relative error, absolute error and time step configuration
+     * @param configuration contains relative error, absolute error and time step configuration
      * @return computed trajectory
      */
     Trajectory simulate(Point point, OdeSystem odeSystem, double timeLimit, PrecisionConfiguration configuration);

diff --git a/.../src/main/java/org/sybila/parasim/computation/simulation/cpu/SimulationEngineFactory.java b/.../src/main/java/org/sybila/parasim/computation/simulation/cpu/SimulationEngineFactory.java
@@ -28,8 +28,17 @@ public interface SimulationEngineFactory<E extends SimulationEngine>{
 
     boolean isAvailable();
 
+    /**
+     * To get simulation engine for the thread which this method is called from.
+     * New SimulationeEngine instance is constructed, if none exists according to THREAD_SIMULATION_ENGINE_MAP.
+     * @param stepLimit max number of simulation steps of the simulation engine
+     * @return SimulationEngine
+     */
     E simulationEngine(long stepLimit);
 
+    /**
+     * Hash map that allows closing of all SimulationEngine instances after the simulation of the whole space finishes
+     */
     ConcurrentHashMap<Thread,SimulationEngine> THREAD_SIMULATION_ENGINE_MAP = new ConcurrentHashMap<>();
 
 }
diff --git a/...pl/src/main/java/org/sybila/parasim/computation/simulation/octave/LsodeEngineFactory.java b/...pl/src/main/java/org/sybila/parasim/computation/simulation/octave/LsodeEngineFactory.java
@@ -23,10 +23,8 @@
 import dk.ange.octave.OctaveEngineFactory;
 import dk.ange.octave.type.OctaveDouble;
 import java.util.Arrays;
-import java.util.function.Function;
 
 import org.sybila.parasim.computation.simulation.api.PrecisionConfiguration;
-import org.sybila.parasim.computation.simulation.cpu.SimulationEngine;
 import org.sybila.parasim.computation.simulation.cpu.SimulationEngineFactory;
 import org.sybila.parasim.model.ode.OctaveOdeSystem;
 import org.sybila.parasim.model.trajectory.Point;
@@ -47,15 +45,15 @@ public LsodeEngineFactory(IntegrationMethod integrationMethod) {
     public boolean isAvailable() {
         try {
             new OctaveEngineFactory().getScriptEngine();
-//            octave.close(); //closing octave after opening? but this method seems to work not
+//            octave.close(); //should close octave after opening? -- luckily this method is not called anywhere (old one)
             return true;
         } catch (Exception ignored) {
             return false;
         }
     }
 
     @Override
-    public OctaveSimulationEngine simulationEngine(long stepLimit) {//TODO correct retyping?
+    public OctaveSimulationEngine simulationEngine(long stepLimit) {
         return (OctaveSimulationEngine) SimulationEngineFactory.THREAD_SIMULATION_ENGINE_MAP.computeIfAbsent(Thread.currentThread(), thread ->
                 new LsodeEngine(new OctaveEngineFactory().getScriptEngine(), integrationMethod, stepLimit));
     }

diff --git a/...rc/main/java/org/sybila/parasim/computation/simulation/octave/OctaveSimulationEngine.java b/...rc/main/java/org/sybila/parasim/computation/simulation/octave/OctaveSimulationEngine.java
@@ -23,13 +23,10 @@
 import dk.ange.octave.type.OctaveDouble;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.concurrent.atomic.AtomicLong;
-
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sybila.parasim.computation.simulation.api.PrecisionConfiguration;
-import org.sybila.parasim.computation.simulation.cpu.SimpleAdaptiveStepSimulator;
 import org.sybila.parasim.computation.simulation.cpu.SimulationEngine;
 import org.sybila.parasim.model.math.Parameter;
 import org.sybila.parasim.model.math.ParameterValue;
@@ -40,8 +37,6 @@
 import org.sybila.parasim.model.trajectory.Point;
 import org.sybila.parasim.model.trajectory.Trajectory;
 
-import javax.management.ServiceNotFoundException;
-
 /**
  * @author <a href="mailto:xpapous1@fi.muni.cz">Jan Papousek</a>
  */
@@ -63,45 +58,27 @@ public OctaveSimulationEngine(OctaveEngine octave, long stepLimit) {
     /**
      * caching simulation time (can save time if the last simulation lasts the same time as the previous)
      */
-    float[] l_times;
+    private float[] l_times;
     /**
      * start time of last simulation
      */
-    float l_startTime;
+    private float l_startTime;
     /**
      * end of last simulation
      */
-    double l_endTime;
+    private double l_endTime;
     /**
      * time step of last simulation
      */
-    float timeStep;
+    private float timeStep;
 
     @Override
     public void close() {
         getOctave().close();
     }
 
-    private static AtomicLong totalSettingTime;
-    private static AtomicLong totalSimulationTime;
-    private static AtomicLong totalParsingTime;
-
-    private static AtomicLong numOfSimulations;
-
-    static {
-        totalSettingTime = new AtomicLong();
-        totalSettingTime.set(0);
-        totalSimulationTime = new AtomicLong();
-        totalSimulationTime.set(0);
-        totalParsingTime = new AtomicLong();
-        totalParsingTime.set(0);
-        numOfSimulations = new AtomicLong();
-        numOfSimulations.set(0);
-    }
-
     @Override
     public Trajectory simulate(Point point, OdeSystem odeSystem, double timeLimit, PrecisionConfiguration precision) {
-        long settingStartTime = System.nanoTime();
         // load parameter values
         List<ParameterValue> paramValues = loadParameterValues(point, odeSystem);
         // create substituted octave ode system
@@ -111,24 +88,13 @@ public Trajectory simulate(Point point, OdeSystem odeSystem, double timeLimit, P
         if (numOfIterations > getStepLimit()) {
             throw new IllegalStateException("Can't simulate the trajectory because the number of iterations <" + numOfIterations + "> is higher than the given limit <" + getStepLimit() + ">.");
         }
-        long settingTime = System.nanoTime() - settingStartTime;
-
-        long simulationStartTime = System.nanoTime();
         double[] loadedData = rawSimulation(point, octaveOdeSystem, numOfIterations, precision).getData();
-        long simulationTime = System.nanoTime() - simulationStartTime;
-
-
-        long parsingStartTime = System.nanoTime();
         float[] data = new float[loadedData.length];
         for (int dim = 0; dim < octaveOdeSystem.dimension(); dim++) {
             for (int i = 0; i < loadedData.length / octaveOdeSystem.dimension(); i++) {
                 data[dim + i * octaveOdeSystem.dimension()] = (float) loadedData[dim * (loadedData.length / octaveOdeSystem.dimension()) + i];
             }
         }
-        long parsingTime = System.nanoTime() - parsingStartTime;
-
-        long timeStartTime = System.nanoTime();
-
         //if simulation time changed, rewrite cached time array
         if(l_startTime != point.getTime() || l_endTime != timeLimit || timeStep != precision.getTimeStep()){
             l_startTime = point.getTime();
@@ -141,23 +107,6 @@ public Trajectory simulate(Point point, OdeSystem odeSystem, double timeLimit, P
                 l_times[i] = time;
             }
         }
-
-        long timeTime = System.nanoTime() - timeStartTime;
-
-        totalSettingTime.addAndGet(settingTime);
-        totalSimulationTime.addAndGet(simulationTime);
-        totalParsingTime.addAndGet(parsingTime + timeTime);
-        numOfSimulations.addAndGet(1);
-
-        System.out.println("AVERAGE TIME");
-        System.out.printf("Setting time: %.9f ms\n", (totalSettingTime.get()/numOfSimulations.get()) / 1000000000.0);
-        System.out.printf("Simulation time: %.9f ms\n", (totalSimulationTime.get()/numOfSimulations.get()) / 1000000000.0);
-//        System.out.printf("Time time: %.9f ms\n", timeTime / 1000000000.0);
-        System.out.printf("Parsing time: %.9f ms\n", (totalParsingTime.get()/numOfSimulations.get()) / 1000000000.0);
-        System.out.println("Number of simulated trajectories: " + numOfSimulations.get());
-
-
-
         if (paramValues.isEmpty()) {
             return new ArrayTrajectory(data, l_times, point.getDimension());
         } else {