private void computeTransitionMatrices(
Beagle beagle, int[][] probabilityIndices, double[][] edgeLengths, int[] counts) {
Timer timer;
if (MEASURE_RUN_TIME) {
timer = new Timer();
timer.start();
}
if (DEBUG) {
System.out.print("Computing matrices:");
}
for (int i = 0; i < eigenCount; i++) {
if (DEBUG) {
for (int j = 0; j < counts[i]; j++) {
// System.out.print(" " + probabilityIndices[i][j]);
System.out.print(" " + probabilityIndices[i][j] + " (" + edgeLengths[i][j] + ")");
}
}
if (counts[i] > 0) {
beagle.updateTransitionMatrices(
eigenBufferHelper.getOffsetIndex(i),
probabilityIndices[i],
null, // firstDerivativeIndices
null, // secondDerivativeIndices
edgeLengths[i],
counts[i]);
}
}
if (DEBUG) {
System.out.println();
}
if (MEASURE_RUN_TIME) {
timer.stop();
double timeInSeconds = timer.toSeconds();
updateTime += timeInSeconds;
}
} // END: computeTransitionMatrices
private void convolveMatrices(Beagle beagle, List<Deque<Integer>> convolutionList) {
Timer timer;
if (MEASURE_RUN_TIME) {
timer = new Timer();
timer.start();
}
while (convolutionList.size() > 0) {
int[] firstConvolutionBuffers = new int[nodeCount];
int[] secondConvolutionBuffers = new int[nodeCount];
int[] resultConvolutionBuffers = new int[nodeCount];
int operationsCount = 0;
List<Deque<Integer>> empty = new ArrayList<Deque<Integer>>();
for (Deque<Integer> convolve : convolutionList) {
if (convolve.size() > 3) {
firstConvolutionBuffers[operationsCount] = convolve.pop();
secondConvolutionBuffers[operationsCount] = convolve.pop();
int buffer;
boolean done;
do {
done = true;
buffer = popAvailableBuffer();
if (buffer < 0) {
// no buffers available
// throw new RuntimeException("All out of buffers");
// we have run out of buffers, process what we have and continue...
if (DEBUG) {
System.out.println("Ran out of buffers for convolving - computing current list.");
System.out.print("Convolving " + operationsCount + " matrices:");
for (int i = 0; i < operationsCount; i++) {
System.out.print(
" "
+ firstConvolutionBuffers[i]
+ "*"
+ secondConvolutionBuffers[i]
+ "->"
+ resultConvolutionBuffers[i]);
}
System.out.println();
}
if (operationsCount > 0) {
convolveAndRelease(
beagle,
firstConvolutionBuffers,
secondConvolutionBuffers,
resultConvolutionBuffers,
operationsCount);
// copy the uncompleted operation back down to the beginning of the operations list
firstConvolutionBuffers[0] = firstConvolutionBuffers[operationsCount];
secondConvolutionBuffers[0] = secondConvolutionBuffers[operationsCount];
// reset the operation count
operationsCount = 0;
done = false;
// there should be enough spare buffers to get a resultConvolutionBuffer for this
// operation now
} else {
// only one partially setup operation so there would be none to free up
// in this case we will use the reserve buffer
resultConvolutionBuffers[operationsCount] = getReserveBuffer();
convolveAndRelease(
beagle,
firstConvolutionBuffers,
secondConvolutionBuffers,
resultConvolutionBuffers,
1);
convolve.push(getReserveBuffer());
done = true; // break out of the do loop
}
}
} while (!done);
if (buffer >= 0) {
// if the buffer is still negative then the loop above will have used the reserve buffer
// to complete the convolution.
resultConvolutionBuffers[operationsCount] = buffer;
convolve.push(buffer);
operationsCount++;
}
} else if (convolve.size() == 3) {
firstConvolutionBuffers[operationsCount] = convolve.pop();
secondConvolutionBuffers[operationsCount] = convolve.pop();
resultConvolutionBuffers[operationsCount] = convolve.pop();
operationsCount++;
} else {
throw new RuntimeException("Unexpected convolve list size");
}
if (convolve.size() == 0) {
empty.add(convolve);
}
}
if (DEBUG) {
System.out.print("Convolving " + operationsCount + " matrices:");
for (int i = 0; i < operationsCount; i++) {
System.out.print(
" "
+ firstConvolutionBuffers[i]
+ "*"
+ secondConvolutionBuffers[i]
+ "->"
+ resultConvolutionBuffers[i]);
}
System.out.println();
}
convolveAndRelease(
beagle,
firstConvolutionBuffers,
secondConvolutionBuffers,
resultConvolutionBuffers,
operationsCount);
convolutionList.removeAll(empty);
}
if (MEASURE_RUN_TIME) {
timer.stop();
double timeInSeconds = timer.toSeconds();
convolveTime += timeInSeconds;
}
} // END: convolveTransitionMatrices