Performance improvements

src/main/java/org/mitre/synthea/engine/ExpressedConditionRecord.java

@@ -3,10 +3,10 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
 
 import org.mitre.synthea.engine.ExpressedSymptom.SymptomInfo;
 import org.mitre.synthea.engine.ExpressedSymptom.SymptomSource;
@@ -140,8 +140,8 @@ public class ModuleConditions implements Cloneable, Serializable {
      */
     public ModuleConditions(String source) {
       this.source = source;
-      onsetConditions = new ConcurrentHashMap<String, OnsetCondition>();
-      state2conditionMapping = new ConcurrentHashMap<String, String>();
+      onsetConditions = new HashMap<String, OnsetCondition>();
+      state2conditionMapping = new HashMap<String, String>();
     }
 
     /**
@@ -231,7 +231,7 @@ public ConditionWithSymptoms(String name, Long onsetTime, Long endTime) {
       this.conditionName = name;
       this.onsetTime = onsetTime;
       this.endTime = endTime;
-      this.symptoms = new ConcurrentHashMap<String, List<Integer>>();
+      this.symptoms = new HashMap<String, List<Integer>>();
     }
 
     /**
@@ -295,7 +295,7 @@ public Map<String, List<Integer>> getSymptoms() {
 
   public ExpressedConditionRecord(Person person) {
     this.person = person;
-    sources = new ConcurrentHashMap<String, ModuleConditions>();
+    sources = new HashMap<String, ModuleConditions>();
   }
 
   /**
@@ -384,7 +384,7 @@ public void onConditionEnd(String module, String condition, long time) {
   public Map<Long, List<ConditionWithSymptoms>> getConditionSymptoms() {
     Map<String, ExpressedSymptom> symptoms = person.getExpressedSymptoms();
     Map<Long, List<ConditionWithSymptoms>> result;
-    result = new ConcurrentHashMap<Long, List<ConditionWithSymptoms>>();    
+    result = new HashMap<Long, List<ConditionWithSymptoms>>();    
     for (String module : sources.keySet()) {
       ModuleConditions moduleConditions = sources.get(module);
       for (String condition : moduleConditions.getOnsetConditions().keySet()) {

src/main/java/org/mitre/synthea/engine/ExpressedSymptom.java

@@ -1,8 +1,8 @@
 package org.mitre.synthea.engine;
 
 import java.io.Serializable;
+import java.util.HashMap;
 import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
 
 public class ExpressedSymptom implements Cloneable, Serializable {
 
@@ -64,7 +64,7 @@ public class SymptomSource implements Cloneable, Serializable {
      */
     public SymptomSource(String source) {
       this.source = source;
-      timeInfos = new ConcurrentHashMap<Long, ExpressedSymptom.SymptomInfo>();
+      timeInfos = new HashMap<Long, ExpressedSymptom.SymptomInfo>();
       resolved = false;
       lastUpdateTime = null;
     }
@@ -114,8 +114,9 @@ public void addInfo(String cause, long time, int value, Boolean addressed) {
      * Get the current value of the symptom.
      */
     public Integer getCurrentValue() {
-      if (timeInfos.containsKey(lastUpdateTime)) {
-        return timeInfos.get(lastUpdateTime).getValue();
+	  final SymptomInfo timeInfo = timeInfos.get(lastUpdateTime);
+      if (timeInfo != null) {
+        return timeInfo.getValue();
       }
       return null;
     }
@@ -134,7 +135,7 @@ public Map<Long, SymptomInfo> getTimeInfos() {
 
   public ExpressedSymptom(String name) {
     this.name = name;  
-    sources = new ConcurrentHashMap<String, SymptomSource>();
+    sources = new HashMap<String, SymptomSource>();
   }
 
   /**
@@ -165,12 +166,13 @@ public void onSet(String module, String cause, long time, int value, Boolean add
    */
   public int getSymptom() {
     int max = 0;
-    for (String module : sources.keySet()) {
-      Integer value = sources.get(module).getCurrentValue();
-      Boolean isResolved = sources.get(module).isResolved();
-      if (value != null && value.intValue() > max && !isResolved) {
-        max = value.intValue();
-      }
+    for (SymptomSource module : sources.values()) {
+      if(!module.isResolved()) {
+        Integer value = module.getCurrentValue();
+        if (value != null && value.intValue() > max) {
+          max = value.intValue();
+        }
+	  }
     }
     return max;
   }

src/main/java/org/mitre/synthea/engine/Logic.java

@@ -300,7 +300,12 @@ private abstract static class GroupedCondition extends Logic {
   public static class And extends GroupedCondition {
     @Override
     public boolean test(Person person, long time) {
-      return conditions.stream().allMatch(c -> c.test(person, time));
+	  for(Logic condition: conditions) {
+		  if (!condition.test(person, time))
+			  return false;
+	  }
+
+	  return true;
     }
   }
 

src/main/java/org/mitre/synthea/engine/Module.java

@@ -34,6 +34,7 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Predicate;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
 import org.mitre.synthea.helpers.Config;
 import org.mitre.synthea.helpers.Utilities;
@@ -301,7 +302,7 @@ public Module(JsonObject definition, boolean submodule) throws Exception {
       states.put(entry.getKey(), state);
     }
   }
-
+  
   /**
    * Clone this module. Never provide the original.
    */
@@ -311,10 +312,12 @@ public Module clone() {
     clone.submodule = this.submodule;
     clone.remarks = this.remarks;
     if (this.states != null) {
-      clone.states = new ConcurrentHashMap<String, State>();
-      for (String key : this.states.keySet()) {
-        clone.states.put(key, this.states.get(key).clone());
-      }
+	  clone.states = this.states.entrySet().stream()
+			  .collect(Collectors.toMap(
+					  e -> e.getKey(),
+					  e -> e.getValue().clone(),
+					  (oldValue, newValue) -> newValue,
+					  ConcurrentHashMap::new));
     }
     return clone;
   }
@@ -423,11 +426,13 @@ public Collection<String> getStateNames() {
    */
   public static class ModuleSupplier implements Supplier<Module> {
 
+	private final Object getLock = new Object();
+
     public final boolean core;
     public final boolean submodule;
     public final String path;
 
-    private boolean loaded;
+    private volatile boolean loaded;
     private Callable<Module> loader;
     private Module module;
     private Throwable fault;
@@ -461,17 +466,21 @@ public ModuleSupplier(Module module) {
     }
 
     @Override
-    public synchronized Module get() {
+    public Module get() {
       if (!loaded) {
-        try {
-          module = loader.call();
-        } catch (Throwable e) {
-          e.printStackTrace();
-          fault = e;
-        } finally {
-          loaded = true;
-          loader = null;
-        }
+		synchronized(getLock) {
+          if (!loaded) {
+            try {
+              module = loader.call();
+            } catch (Throwable e) {
+              e.printStackTrace();
+              fault = e;
+            } finally {
+              loaded = true;
+              loader = null;
+            }
+		  }
+		}
       }
       if (fault != null) {
         throw new RuntimeException(fault);

src/main/java/org/mitre/synthea/engine/State.java

@@ -14,6 +14,7 @@
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.math.ode.DerivativeException;
@@ -1724,10 +1725,9 @@ public ObservationGroup clone() {
       // we need to ensure we deep clone the list
       // (otherwise as this gets passed around, the same objects are used for different patients
       // which causes weird and unexpected results)
-      List<Observation> cloneObs = new ArrayList<>(observations.size());
-      for (Observation o : observations) {
-        cloneObs.add(o.clone());
-      }
+      List<Observation> cloneObs = observations.stream()
+			  .map(Observation::clone)
+			  .collect(Collectors.toCollection(ArrayList::new));
       clone.observations = cloneObs;
 
       return clone;

src/main/java/org/mitre/synthea/helpers/Utilities.java

@@ -23,6 +23,16 @@
 import org.mitre.synthea.world.concepts.HealthRecord.Code;
 
 public class Utilities {
+
+  private static final TimeZone UTC_TIME_ZONE = TimeZone.getTimeZone("UTC");
+
+  private static final ThreadLocal<Calendar> threadLocalCalendar = new ThreadLocal<Calendar>(){
+	  @Override
+	  protected Calendar initialValue() {
+		  return Calendar.getInstance(UTC_TIME_ZONE);
+	  }
+  };
+
   /**
    * Convert a quantity of time in a specified units into milliseconds.
    *
@@ -94,7 +104,7 @@ public static long convertCalendarYearsToTime(int years) {
    * Get the year of a Unix timestamp.
    */
   public static int getYear(long time) {
-    Calendar calendar = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
+    Calendar calendar = threadLocalCalendar.get();
     calendar.setTimeInMillis(time);
     return calendar.get(Calendar.YEAR);
   }
@@ -103,7 +113,7 @@ public static int getYear(long time) {
    * Get the month of a Unix timestamp.
    */
   public static int getMonth(long time) {
-    Calendar calendar = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
+    Calendar calendar = threadLocalCalendar.get();
     calendar.setTimeInMillis(time);
     return calendar.get(Calendar.MONTH) + 1;
   }
@@ -133,11 +143,20 @@ public static Object primitive(JsonPrimitive p) {
     return retVal;
   }
 
+  private static double timestepCache = Double.NaN;
+
+  private static double getTimestep() {
+	if(timestepCache == Double.NaN)
+      timestepCache = Double.parseDouble(Config.get("generate.timestep"));
+
+	return timestepCache;
+  }
+
   /**
    * Calculates 1 - (1-risk)^(currTimeStepInMS/originalPeriodInMS).
    */
   public static double convertRiskToTimestep(double risk, double originalPeriodInMS) {
-    double currTimeStepInMS = Double.parseDouble(Config.get("generate.timestep"));
+    double currTimeStepInMS = getTimestep();
 
     return convertRiskToTimestep(risk, originalPeriodInMS, currTimeStepInMS);
   }

src/main/java/org/mitre/synthea/modules/LifecycleModule.java

@@ -602,6 +602,15 @@ private static Map<String, Double> createDrugImpactsMap() {
   private static final double[] RESPIRATION_RATE_NORMAL =
       BiometricsConfig.doubles("respiratory.respiration_rate.normal");
 
+  private static long timestepCache = Long.MIN_VALUE;
+
+  private static long getTimestep() {
+	if(timestepCache == Long.MIN_VALUE)
+      timestepCache = Long.parseLong(Config.get("generate.timestep"));
+
+	return timestepCache;
+  }
+
   /**
    * Calculate this person's vital signs,
    * based on their conditions, medications, body composition, etc.
@@ -743,7 +752,7 @@ private static void calculateVitalSigns(Person person, long time) {
     person.setVitalSign(VitalSign.CARBON_DIOXIDE, person.rand(CO2_RANGE));
     person.setVitalSign(VitalSign.SODIUM, person.rand(SODIUM_RANGE));
 
-    long timestep = Long.parseLong(Config.get("generate.timestep"));
+    long timestep = getTimestep();
     double heartStart = person.rand(HEART_RATE_NORMAL);
     double heartEnd = person.rand(HEART_RATE_NORMAL);
     person.setVitalSign(VitalSign.HEART_RATE,