merge: Address several regressions in simulator

This pull request addresses several regressions that have been introduced in the past few pull requests.

- Fix queue resizing logic
- Change clock resolution from milliseconds to nanoseconds in `OtelClockAdapter`
- Compute energy usage in absence of convergence
- Fix duplicate classpath entries
- Fix release workflow

**Breaking API Changes**

- `OtelClockAdapter` now exports time in nanoseconds as the method contract describes.

4 files changed, 31 insertions, 5 deletions

diff --git a/opendc-simulator/opendc-simulator-compute/src/main/kotlin/org/opendc/simulator/compute/SimBareMetalMachine.kt b/opendc-simulator/opendc-simulator-compute/src/main/kotlin/org/opendc/simulator/compute/SimBareMetalMachine.kt
index 9140d31b..5df03d45 100644
--- a/opendc-simulator/opendc-simulator-compute/src/main/kotlin/org/opendc/simulator/compute/SimBareMetalMachine.kt
+++ b/opendc-simulator/opendc-simulator-compute/src/main/kotlin/org/opendc/simulator/compute/SimBareMetalMachine.kt
@@ -60,8 +60,12 @@ public class SimBareMetalMachine(
      * The total energy usage of the machine (without PSU loss) in Joules.
      */
     public val energyUsage: Double
-        get() = _energyUsage
+        get() {
+            computeEnergyUsage(engine.clock.millis())
+            return _energyUsage
+        }
     private var _energyUsage = 0.0
+    private var _energyLastComputation = 0L
 
     /**
      * The processing units of the machine.
@@ -86,13 +90,25 @@ public class SimBareMetalMachine(
         val duration = max(0, now - lastConverge)
         if (duration > 0) {
             // Compute the power and energy usage of the machine
-            _energyUsage += _powerUsage * (duration / 1000.0)
+            computeEnergyUsage(now)
             _powerUsage = powerDriverLogic.computePower()
         }
     }
 
     init {
         psu.connect(powerDriverLogic)
+        _powerUsage = powerDriverLogic.computePower()
+    }
+
+    /**
+     * Helper method to compute total energy usage.
+     */
+    private fun computeEnergyUsage(now: Long) {
+        val duration = max(0, now - _energyLastComputation)
+        _energyLastComputation = now
+
+        // Compute the energy usage of the machine
+        _energyUsage += _powerUsage * (duration / 1000.0)
     }
 
     /**
diff --git a/opendc-simulator/opendc-simulator-flow/build.gradle.kts b/opendc-simulator/opendc-simulator-flow/build.gradle.kts
index 05e21c3c..f5b67851 100644
--- a/opendc-simulator/opendc-simulator-flow/build.gradle.kts
+++ b/opendc-simulator/opendc-simulator-flow/build.gradle.kts
@@ -36,4 +36,6 @@ dependencies {
 
     testImplementation(projects.opendcSimulator.opendcSimulatorCore)
     testImplementation(libs.slf4j.simple)
+
+    jmhImplementation(projects.opendcSimulator.opendcSimulatorCore)
 }
diff --git a/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowDeque.kt b/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowDeque.kt
index c6cba4b7..94232954 100644
--- a/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowDeque.kt
+++ b/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowDeque.kt
@@ -25,7 +25,10 @@ package org.opendc.simulator.flow.internal
 import java.util.*
 
 /**
- * A specialized [ArrayDeque] for [FlowConsumerContextImpl] implementations.
+ * A specialized [ArrayDeque] that tracks the [FlowConsumerContextImpl] instances that have updated in an interpreter
+ * cycle.
+ *
+ * By using a specialized class, we reduce the overhead caused by type-erasure.
  */
 internal class FlowDeque(initialCapacity: Int = 256) {
     /**
@@ -106,7 +109,7 @@ internal class FlowDeque(initialCapacity: Int = 256) {
 
         val a = arrayOfNulls<FlowConsumerContextImpl>(newCapacity)
 
-        _elements.copyInto(a, 0, p, r)
+        _elements.copyInto(a, 0, p, n)
         _elements.copyInto(a, r, 0, p)
 
         _elements = a
diff --git a/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowTimerQueue.kt b/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowTimerQueue.kt
index 22a390e6..47061a91 100644
--- a/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowTimerQueue.kt
+++ b/opendc-simulator/opendc-simulator-flow/src/main/kotlin/org/opendc/simulator/flow/internal/FlowTimerQueue.kt
@@ -24,6 +24,9 @@ package org.opendc.simulator.flow.internal
 
 /**
  * Specialized priority queue for flow timers.
+ *
+ * By using a specialized priority queue, we reduce the overhead caused by the default priority queue implementation
+ * being generic.
  */
 internal class FlowTimerQueue(initialCapacity: Int = 256) {
     /**
@@ -46,9 +49,11 @@ internal class FlowTimerQueue(initialCapacity: Int = 256) {
      */
     fun add(ctx: FlowConsumerContextImpl, deadline: Long) {
         val i = size
-        val deadlines = _deadlines
+        var deadlines = _deadlines
         if (i >= deadlines.size) {
             grow()
+            // Re-fetch the resized array
+            deadlines = _deadlines
         }
 
         siftUp(deadlines, _pending, i, ctx, deadline)