Current Progress: After final design presentation

examples/enhane_xor.py

@@ -18,6 +18,7 @@ def evaluate(problem, func):
         fitnesses.append(f)
     return np.array(fitnesses)
 
+
 # @using_cprofile
 # @partial(using_cprofile, root_abs_path='/mnt/e/neatax/', replace_pattern="/mnt/e/neat-jax/")
 def main():
@@ -36,7 +37,8 @@ def main():
     total_it = pipeline.generation
     mean_time_per_it = (total_time - compile_time) / total_it
     evaluate_time = pipeline.evaluate_time
-    print(f"total time: {total_time:.2f}s, compile time: {compile_time:.2f}s, real_time: {total_time - compile_time:.2f}s, evaluate time: {evaluate_time:.2f}s")
+    print(
+        f"total time: {total_time:.2f}s, compile time: {compile_time:.2f}s, real_time: {total_time - compile_time:.2f}s, evaluate time: {evaluate_time:.2f}s")
     print(f"total it: {total_it}, mean time per it: {mean_time_per_it:.2f}s")
 
 

examples/final_design_experiement.py

@@ -43,7 +43,7 @@ def main():
         else:
             res = "success"
 
-        with open("log", "wb") as f:
+        with open("log", "ab") as f:
             f.write(f"{res}, total time: {total_time:.2f}s, evaluate time: {evaluate_time:.2f}s, total_it: {total_it}\n".encode("utf-8"))
             f.write(str(pipeline.generation_time_list).encode("utf-8"))
 

examples/final_design_experiment2.py

@@ -0,0 +1,52 @@
+
+import numpy as np
+import jax
+from utils import Configer
+from algorithms.neat import Pipeline
+from time_utils import using_cprofile
+from algorithms.neat.function_factory import FunctionFactory
+from problems import EnhanceLogic
+import time
+
+
+def evaluate(problem, func):
+    outs = func(problem.inputs)
+    outs = jax.device_get(outs)
+    fitnesses = -np.mean((problem.outputs - outs) ** 2, axis=(1, 2))
+    return fitnesses
+
+
+def main():
+    config = Configer.load_config()
+    problem = EnhanceLogic("xor", n=3)
+    problem.refactor_config(config)
+
+    evaluate_func = lambda func: evaluate(problem, func)
+
+    for p in [100, 200, 500, 1000, 2000, 5000, 10000, 20000]:
+        config.neat.population.pop_size = p
+        tic = time.time()
+        function_factory = FunctionFactory(config)
+        print(f"running: {p}")
+
+        pipeline = Pipeline(config, function_factory, seed=2)
+        pipeline.auto_run(evaluate_func)
+
+        total_time = time.time() - tic
+        evaluate_time = pipeline.evaluate_time
+        total_it = pipeline.generation
+        print(f"total time: {total_time:.2f}s, evaluate time: {evaluate_time:.2f}s, total_it: {total_it}")
+
+        with open("2060_log2", "ab") as f:
+            f.write \
+                (f"{p}, total time: {total_time:.2f}s, compile time: {function_factory.compile_time:.2f}s, total_it: {total_it}\n".encode
+                    ("utf-8"))
+            f.write(f"{str(pipeline.generation_time_list)}\n".encode("utf-8"))
+
+    compile_time = function_factory.compile_time
+
+    print("total_compile_time:", compile_time)
+
+
+if __name__ == '__main__':
+    main()

examples/jax_playground.py

@@ -1,50 +1,57 @@
 import jax
 import jax.numpy as jnp
 from jax import jit, vmap
-from time_utils import using_cprofile
 from time import time
-#
 import numpy as np
+
+
 @jit
-def fx(x):
+def jax_mutate(seed, x):
-    return jnp.arange(x, x + 10)
+    noise = jax.random.normal(seed, x.shape) * 0.1
-#
+    return x + noise
-#
-# # @jit
-# def fy(z):
-#     z1, z2 = z, z + 1
-#     vmap_fx = vmap(fx)
-#     return vmap_fx(z1, z2)
-#
-# @jit
-# def test_while(num, init_val):
-#     def cond_fun(carry):
-#         i, cumsum = carry
-#         return i < num
-#
-#     def body_fun(carry):
-#         i, cumsum = carry
-#         cumsum += i
-#         return i + 1, cumsum
-#
-#     return jax.lax.while_loop(cond_fun, body_fun, (0, init_val))
 
 
+def numpy_mutate(x):
+    noise = np.random.normal(size=x.shape) * 0.1
+    return x + noise
 
 
-# @using_cprofile
+def jax_mutate_population(seed, pop_x):
+    seeds = jax.random.split(seed, len(pop_x))
+    func = vmap(jax_mutate, in_axes=(0, 0))
+    return func(seeds, pop_x)
+
+
+def numpy_mutate_population(pop_x):
+    return np.stack([numpy_mutate(x) for x in pop_x])
+
+def numpy_mutate_population_vmap(pop_x):
+    noise = np.random.normal(size=pop_x.shape) * 0.1
+    return pop_x + noise
+
 def main():
-    print(fx(1))
+    seed = jax.random.PRNGKey(0)
+    i = 10
+    while i < 200000:
+        pop_x = jnp.ones((i, 100, 100))
+        jax_pop_func = jit(jax_mutate_population).lower(seed, pop_x).compile()
 
-    # vmap_f = vmap(fx, in_axes=(None, 0))
+        tic = time()
-    # vmap_vmap_f = vmap(vmap_f, in_axes=(0, None))
+        res = jax.device_get(jax_pop_func(seed, pop_x))
-    # a = jnp.array([20,10,30])
+        jax_time = time() - tic
-    # b = jnp.array([6, 5, 4])
-    # res = vmap_vmap_f(a, b)
-    # print(res)
-    # print(jnp.argmin(res, axis=1))
 
+        tic = time()
+        res = numpy_mutate_population(pop_x)
+        numpy_time = time() - tic
 
+        tic = time()
+        res = numpy_mutate_population_vmap(pop_x)
+        numpy_time_vmap = time() - tic
+
+        # print(f'POP_SIZE: {i} | JAX: {jax_time:.4f} | Numpy: {numpy_time:.4f} | Speedup: {numpy_time / jax_time:.4f}')
+        print(f'POP_SIZE: {i} | JAX: {jax_time:.4f} | Numpy: {numpy_time:.4f} | Numpy Vmap: {numpy_time_vmap:.4f}')
+
+        i = int(i * 1.3)
 
 if __name__ == '__main__':
     main()

examples/jitable_speciate_t.py

@@ -1,75 +0,0 @@
-import jax
-import jax.numpy as jnp
-import numpy as np
-from algorithms.neat.function_factory import FunctionFactory
-from algorithms.neat.genome.debug.tools import check_array_valid
-from utils import Configer
-from algorithms.neat.population import speciate
-from algorithms.neat.genome.crossover import crossover
-from algorithms.neat.genome.utils import I_INT
-from time import time
-
-if __name__ == '__main__':
-    config = Configer.load_config()
-    function_factory = FunctionFactory(config, debug=True)
-    initialize_func = function_factory.create_initialize()
-
-    pop_nodes, pop_connections, input_idx, output_idx = initialize_func()
-    mutate_func = function_factory.create_mutate(pop_nodes.shape[1], pop_connections.shape[1])
-    crossover_func = function_factory.create_crossover(pop_nodes.shape[1], pop_connections.shape[1])
-
-    N, C, species_size = function_factory.init_N, function_factory.init_C, 20
-    spe_center_nodes = np.full((species_size, N, 5), np.nan)
-    spe_center_connections = np.full((species_size, C, 4), np.nan)
-    spe_center_nodes[0] = pop_nodes[0]
-    spe_center_connections[0] = pop_connections[0]
-    spe_keys = np.full((species_size,), I_INT)
-    spe_keys[0] = 0
-    new_spe_key = 1
-    key = jax.random.PRNGKey(0)
-    new_node_idx = 100
-
-    while True:
-        start_time = time()
-        key, subkey = jax.random.split(key)
-        mutate_keys = jax.random.split(subkey, len(pop_nodes))
-        new_nodes = np.arange(new_node_idx, new_node_idx + len(pop_nodes))
-        new_node_idx += len(pop_nodes)
-        pop_nodes, pop_connections = mutate_func(mutate_keys, pop_nodes, pop_connections, new_nodes)
-        pop_nodes, pop_connections = jax.device_get([pop_nodes, pop_connections])
-        # for i in range(len(pop_nodes)):
-        #     check_array_valid(pop_nodes[i], pop_connections[i], input_idx, output_idx)
-        idx1 = np.random.permutation(len(pop_nodes))
-        idx2 = np.random.permutation(len(pop_nodes))
-
-        n1, c1 = pop_nodes[idx1], pop_connections[idx1]
-        n2, c2 = pop_nodes[idx2], pop_connections[idx2]
-        crossover_keys = jax.random.split(subkey, len(pop_nodes))
-        pop_nodes, pop_connections = crossover_func(crossover_keys, n1, c1, n2, c2)
-
-
-        # for i in range(len(pop_nodes)):
-        #     check_array_valid(pop_nodes[i], pop_connections[i], input_idx, output_idx)
-
-        #speciate next generation
-
-        idx2specie, spe_center_nodes, spe_center_cons, spe_keys, new_spe_key = speciate(pop_nodes, pop_connections, spe_center_nodes, spe_center_connections,
-                               spe_keys, new_spe_key,
-                               compatibility_threshold=3)
-
-        print(spe_keys, new_spe_key)
-
-        #
-        # idx2specie = np.array(idx2specie)
-        # spe_dict = {}
-        # for i in range(len(idx2specie)):
-        #     spe_idx = idx2specie[i]
-        #     if spe_idx not in spe_dict:
-        #         spe_dict[spe_idx] = 1
-        #     else:
-        #         spe_dict[spe_idx] += 1
-        #
-        # print(spe_dict)
-        # assert np.all(idx2specie != I_INT)
-        print(time() - start_time)
-        # print(idx2specie)

utils/default_config.json

@@ -13,9 +13,9 @@
     "neat": {
         "population": {
             "fitness_criterion": "max",
-            "fitness_threshold": -1e-2,
+            "fitness_threshold": 1e-2,
-            "generation_limit": 500,
+            "generation_limit": 100,
-            "pop_size": 5000,
+            "pop_size": 1000,
             "reset_on_extinction": "False"
         },
         "gene": {