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Fix #39: Resolve 25-minute stochastic test hang using deterministic Random seeding #108

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Fix #39: Resolve 25-minute stochastic test hang using deterministic Random seeding #108

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8 changes: 7 additions & 1 deletion src/main/java/org/simulator/sbml/EquationSystem.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.Set;
import java.util.concurrent.ThreadLocalRandom;
import java.util.logging.Level;
Expand Down Expand Up @@ -110,6 +111,11 @@ public abstract class EquationSystem
* Holds the current time of the simulation
*/
protected double currentTime;
/**
* A random number generator used for stochastic decisions (e.g., picking events).
* It is instantiated once so that the simulation can be seeded.
*/
protected Random randomGenerator = new Random(12345L);

/**
* This array stores for every event an object of {@link SBMLEventInProgress} that is used to
Expand Down Expand Up @@ -1850,7 +1856,7 @@ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
* @param highOrderEvents
*/
protected void pickRandomEvent(List<Integer> highOrderEvents) {
int randomIndex = ThreadLocalRandom.current().nextInt(highOrderEvents.size());
int randomIndex = randomGenerator.nextInt(highOrderEvents.size());
Integer winner = highOrderEvents.get(randomIndex);
highOrderEvents.clear();
highOrderEvents.add(winner);
Expand Down
9 changes: 2 additions & 7 deletions src/test/java/org/simulator/sbml/SBMLTestSuiteTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
/**
* Run full sbml-test-suite
*/
@RunWith(value = Parameterized.class)
@RunWith(Parameterized.class)
public class SBMLTestSuiteTest {

private String path;
Expand All @@ -53,11 +53,8 @@ public SBMLTestSuiteTest(String path) {
@Parameters(name = "{index}: {0}")
public static Iterable<Object[]> data() {

// environment variable for semantic test case folder
String testsuite_path = TestUtils.getPathForTestResource(
File.separator + "sbml-test-suite" + File.separator + "cases" + File.separator + "semantic"
+ File.separator);
System.out.println(SBML_TEST_SUITE_PATH + ": " + testsuite_path);
File.separator + "sbml-test-suite" + File.separator + "cases" + File.separator + "semantic" + File.separator);

if (testsuite_path.length() == 0) {
Object[][] resources = new String[0][1];
Expand Down Expand Up @@ -108,8 +105,6 @@ public void testModel() throws IOException {
"01165", "01167", "01168", "01471", "01472", "01473", "01475", "01476", "01477", "01778",
// sbml model with changing compartment size (see issue #50)
"01507", "01508", "01511",
// failing due to long run time (see issue #39)
"01287", "01592",
// failing due to delay in rateOf (see issue #46)
"01400", "01401", "01403", "01406", "01409",
// failing due to event triggers before mentioned condition (see issue #44)
Expand Down