udpate ages with ARM NEON

jb/src/sir_numpy.py

@@ -75,7 +75,7 @@ def add_expansion_slots( columns, num_slots=settings.expansion_slots ):
     num_slots = int(num_slots)
     print( f"Adding {num_slots} expansion slots for future babies." )
     new_ids = [ x for x in range( num_slots ) ]
-    new_nodes = np.ones( num_slots, dtype=np.uint32 )*-1
+    new_nodes = np.ones( num_slots, dtype=np.int32 )*-1
     new_ages = np.ones( num_slots, dtype=np.float32 )*-1
     new_infected = np.zeros( num_slots, dtype=bool )
 

jb/src/test_ua.py

@@ -0,0 +1,21 @@
+import ctypes
+
+import numpy as np
+
+# Requires openmp installed via homebrew
+# Use .so for suffix rather then .dylib even though we are on macOS
+# g++ -shared -fPIC -O3 -flto -fpermissive -I/opt/homebrew/Cellar/libomp/18.1.6/include -std=c++11 -Xpreprocessor -fopenmp -L/opt/homebrew/Cellar/libomp/18.1.6/lib -lomp -o update_ages.so update_ages.cpp
+
+update_ages_lib = ctypes.CDLL("./update_ages.so")
+update_ages_lib.update_ages.argtypes = [
+    ctypes.c_size_t,  # start_idx
+    ctypes.c_size_t,  # stop_idx
+    np.ctypeslib.ndpointer(dtype=np.float32, flags="C_CONTIGUOUS"),
+]
+
+ages = np.random.randint(-4, 28, 1024).astype(np.float32)
+bges = np.array(ages)
+
+update_ages_lib.update_ages(0, len(ages), bges)
+print(ages[0:16])
+print(bges[0:16])

jb/src/update_ages.cpp

@@ -15,9 +15,16 @@
 #include <math.h>
 #include <pthread.h>
 #include <omp.h>
+
+#ifdef __AVX2__
 #include <immintrin.h>
+#endif
+
+#ifdef __ARM_NEON
+#include <arm_neon.h>
+#endif
+
 
-#define SIMD_WIDTH 8     // AVX2 processes 8 integers at a time
 unsigned recovered_counter = 0;
 
 extern "C" {
@@ -51,6 +58,7 @@ void update_ages_vanilla(unsigned long int start_idx, unsigned long int stop_idx
     }
 }
 
+#ifdef __AVX2__
 // avxv2
 void update_ages(unsigned long int start_idx, unsigned long int stop_idx, float *ages) {
     #pragma omp parallel for
@@ -71,6 +79,26 @@ void update_ages(unsigned long int start_idx, unsigned long int stop_idx, float
         _mm256_storeu_ps(&ages[i], ages_vec);
     }
 }
+#endif
+
+#ifdef __ARM_NEON
+// ARM NEON version of update_ages() function
+void update_ages(size_t start_idx, size_t stop_idx, float *ages) {
+
+    const float32x4_t one_day_vec = vdupq_n_f32(one_day);   // Create a vector with the constant value of one_day
+    const float32x4_t zero_vec = vdupq_n_f32(0.0f);         // Create a vector with the constant value of zero
+
+    // Iterate over the indices in the specified range, processing 4 elements at a time
+    for (size_t i = start_idx; i < stop_idx; i += 4) {
+
+        float32x4_t current = vld1q_f32(&ages[i]);                  // Load the age values into a vector// Load 4 age values into a vector
+        uint32x4_t mask     = vcgtq_f32(current, zero_vec);         // Create a mask vector to identify the ages that are greater than zero
+        float32x4_t updated = vaddq_f32(current, one_day_vec);      // Add one_day_vec to ages
+        float32x4_t write   = vbslq_f32(mask, updated, current);    // Use the mask to select the updated age values or the original age values
+        vst1q_f32(&ages[i], write);                                 // Store the updated age values back into the array
+    }
+}
+#endif
 
 /*
  * Progress all infections. Collect the indexes of those who recover. 
@@ -227,12 +255,12 @@ void handle_new_infections_mp(
     int * num_eligible_agents_array
 ) {
     //printf( "handle_new_infections_mp: start_idx=%ld, end_idx=%ld.\n", start_idx, end_idx );
-    std::unordered_map<int, std::vector<int>> node2sus;
+    std::unordered_map<int, std::vector<int> > node2sus;
 
 #pragma omp parallel
     {
         // Thread-local buffers to collect susceptible indices by node
-        std::unordered_map<int, std::vector<int>> local_node2sus;
+        std::unordered_map<int, std::vector<int> > local_node2sus;
 
 #pragma omp for nowait
         for (unsigned long int i = start_idx; i <= end_idx; ++i) {