format

benchmarks/bench_pm.py

@@ -10,13 +10,14 @@ size = jax.process_count()
 
 import argparse
 import time
-from hpc_plotter.timer import Timer
+
 import jax.numpy as jnp
 import jax_cosmo as jc
 import numpy as np
 from cupy.cuda.nvtx import RangePop, RangePush
 from diffrax import (ConstantStepSize, Dopri5, LeapfrogMidpoint, ODETerm,
                      PIDController, SaveAt, Tsit5, diffeqsolve)
+from hpc_plotter.timer import Timer
 from jax.experimental import mesh_utils
 from jax.experimental.multihost_utils import sync_global_devices
 from jax.sharding import Mesh, NamedSharding
@@ -27,7 +28,6 @@ from jaxpm.painting import cic_paint_dx
 from jaxpm.pm import linear_field, lpt, make_ode_fn
 
 
-
 def run_simulation(mesh_shape,
                    box_size,
                    halo_size,
@@ -94,12 +94,18 @@ def run_simulation(mesh_shape,
         # Warm start
         chrono_fun = Timer()
         RangePush("warmup")
-        final_field, stats = chrono_fun.chrono_jit(simulate, 0.32, 0.8 , ndarray_arg = 0)
+        final_field, stats = chrono_fun.chrono_jit(simulate,
+                                                   0.32,
+                                                   0.8,
+                                                   ndarray_arg=0)
         RangePop()
         sync_global_devices("warmup")
         for i in range(iterations):
             RangePush(f"sim iter {i}")
-            final_field, stats = chrono_fun.chrono_fun(simulate, 0.32, 0.8 , ndarray_arg = 0)
+            final_field, stats = chrono_fun.chrono_fun(simulate,
+                                                       0.32,
+                                                       0.8,
+                                                       ndarray_arg=0)
             RangePop()
         return final_field, stats, chrono_fun
 
@@ -134,11 +140,13 @@ if __name__ == "__main__":
                         type=str,
                         help='Processor dimensions',
                         default=None)
-    parser.add_argument('-pr',
+    parser.add_argument(
+        '-pr',
         '--precision',
         type=str,
         help='Precision',
-                        choices=["float32", "float64"],)
+        choices=["float32", "float64"],
+    )
     parser.add_argument('-hs',
                         '--halo_size',
                         type=int,
@@ -185,11 +193,11 @@ if __name__ == "__main__":
 
     print(f"solver choice: {solver_choice}")
     match solver_choice:
-        case "Dopri5" | "dopri5"| "d5":
+        case "Dopri5" | "dopri5" | "d5":
             solver_choice = "Dopri5"
-        case "Tsit5"| "tsit5"| "t5":
+        case "Tsit5" | "tsit5" | "t5":
             solver_choice = "Tsit5"
-        case "LeapfrogMidpoint"| "leapfrogmidpoint"| "lfm":
+        case "LeapfrogMidpoint" | "leapfrogmidpoint" | "lfm":
             solver_choice = "LeapfrogMidpoint"
         case "lpt":
             solver_choice = "lpt"
@@ -209,9 +217,13 @@ if __name__ == "__main__":
 
     mesh_shape = [mesh_size] * 3
 
-    final_field , stats, chrono_fun = run_simulation(mesh_shape, box_size, halo_size, solver_choice, iterations, pdims)
+    final_field, stats, chrono_fun = run_simulation(mesh_shape, box_size,
+                                                    halo_size, solver_choice,
+                                                    iterations, pdims)
 
-    print(f"shape of final_field {final_field.shape} and sharding spec {final_field.sharding} and local shape {final_field.addressable_data(0).shape}")
+    print(
+        f"shape of final_field {final_field.shape} and sharding spec {final_field.sharding} and local shape {final_field.addressable_data(0).shape}"
+    )
 
     metadata = {
         'rank': rank,
@@ -236,7 +248,7 @@ if __name__ == "__main__":
     with open(f'{field_folder}/jaxpm.log', 'w') as f:
         f.write(f"Args: {args}\n")
         f.write(f"JIT time: {chrono_fun.jit_time:.4f} ms\n")
-        for i , time in enumerate(chrono_fun.times):
+        for i, time in enumerate(chrono_fun.times):
             f.write(f"Time {i}: {time:.4f} ms\n")
         f.write(f"Stats: {stats}\n")
     if args.save_fields:

benchmarks/bench_pmwd.py

@@ -3,34 +3,41 @@ import os
 # Change JAX GPU memory preallocation fraction
 os.environ['XLA_PYTHON_CLIENT_MEM_FRACTION'] = '.95'
 
-import jax
 import argparse
-import numpy as np
+
+import jax
 import matplotlib.pyplot as plt
-from pmwd import (
-    Configuration,
-    Cosmology, SimpleLCDM,
-    boltzmann, linear_power, growth,
-    white_noise, linear_modes,
-    lpt, nbody, scatter
-)
+import numpy as np
+from hpc_plotter.timer import Timer
+from pmwd import (Configuration, Cosmology, SimpleLCDM, boltzmann, growth,
+                  linear_modes, linear_power, lpt, nbody, scatter, white_noise)
 from pmwd.pm_util import fftinv
 from pmwd.spec_util import powspec
 from pmwd.vis_util import simshow
-from hpc_plotter.timer import Timer
+
 
 # Simulation configuration
-def run_pmwd_simulation(ptcl_grid_shape, ptcl_spacing, solver ,  iterations):
+def run_pmwd_simulation(ptcl_grid_shape, ptcl_spacing, solver, iterations):
 
     @jax.jit
     def simulate(omega_m, sigma8):
 
-        
-        conf = Configuration(ptcl_spacing, ptcl_grid_shape=ptcl_grid_shape, mesh_shape=1,lpt_order=1,a_nbody_maxstep=1/91)
+        conf = Configuration(ptcl_spacing,
+                             ptcl_grid_shape=ptcl_grid_shape,
+                             mesh_shape=1,
+                             lpt_order=1,
+                             a_nbody_maxstep=1 / 91)
         print(conf)
-        print(f'Simulating {conf.ptcl_num} particles with a {conf.mesh_shape} mesh for {conf.a_nbody_num} time steps.')
+        print(
+            f'Simulating {conf.ptcl_num} particles with a {conf.mesh_shape} mesh for {conf.a_nbody_num} time steps.'
+        )
 
-        cosmo = Cosmology(conf, A_s_1e9=2.0, n_s=0.96, Omega_m=omega_m, Omega_b=sigma8, h=0.7)
+        cosmo = Cosmology(conf,
+                          A_s_1e9=2.0,
+                          n_s=0.96,
+                          Omega_m=omega_m,
+                          Omega_b=sigma8,
+                          h=0.7)
         print(cosmo)
 
         # Boltzmann calculation
@@ -49,7 +56,8 @@ def run_pmwd_simulation(ptcl_grid_shape, ptcl_spacing, solver ,  iterations):
 
         if solver == "lfm":
             # N-body time integration from LPT initial conditions
-          ptcl, obsvbl = jax.block_until_ready(nbody(ptcl, obsvbl, cosmo, conf))
+            ptcl, obsvbl = jax.block_until_ready(
+                nbody(ptcl, obsvbl, cosmo, conf))
             print("N-body time integration completed.")
 
         # Scatter particles to mesh to get the density field
@@ -62,28 +70,52 @@ def run_pmwd_simulation(ptcl_grid_shape, ptcl_spacing, solver ,  iterations):
     for _ in range(iterations):
         final_field = chrono_timer.chrono_fun(simulate, 0.3, 0.05)
 
-    return final_field , chrono_timer
+    return final_field, chrono_timer
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='PMWD Simulation')
-    parser.add_argument('-m', '--mesh_size', type=int, help='Mesh size', required=True)
-    parser.add_argument('-b', '--box_size', type=float, help='Box size', required=True)
-    parser.add_argument('-i', '--iterations', type=int, help='Number of iterations', default=10)
-    parser.add_argument('-o', '--output_path', type=str, help='Output path', default=".")
-    parser.add_argument('-f', '--save_fields', action='store_true', help='Save fields')
-    parser.add_argument('-s', '--solver', type=str, help='Solver', choices=["lfm" , "lpt"])
-    parser.add_argument('-pr',
+    parser.add_argument('-m',
+                        '--mesh_size',
+                        type=int,
+                        help='Mesh size',
+                        required=True)
+    parser.add_argument('-b',
+                        '--box_size',
+                        type=float,
+                        help='Box size',
+                        required=True)
+    parser.add_argument('-i',
+                        '--iterations',
+                        type=int,
+                        help='Number of iterations',
+                        default=10)
+    parser.add_argument('-o',
+                        '--output_path',
+                        type=str,
+                        help='Output path',
+                        default=".")
+    parser.add_argument('-f',
+                        '--save_fields',
+                        action='store_true',
+                        help='Save fields')
+    parser.add_argument('-s',
+                        '--solver',
+                        type=str,
+                        help='Solver',
+                        choices=["lfm", "lpt"])
+    parser.add_argument(
+        '-pr',
         '--precision',
         type=str,
         help='Precision',
-                          choices=["float32", "float64"],)
-
+        choices=["float32", "float64"],
+    )
 
     args = parser.parse_args()
 
     mesh_shape = [args.mesh_size] * 3
-    ptcl_spacing = args.box_size /args.mesh_size 
+    ptcl_spacing = args.box_size / args.mesh_size
     iterations = args.iterations
     solver = args.solver
     output_path = args.output_path
@@ -92,13 +124,12 @@ if __name__ == "__main__":
     elif args.precision == "float64":
         jax.config.update("jax_enable_x64", True)
 
-
     os.makedirs(output_path, exist_ok=True)
 
-    final_field , chrono_fun = run_pmwd_simulation(mesh_shape, ptcl_spacing, solver, iterations)
+    final_field, chrono_fun = run_pmwd_simulation(mesh_shape, ptcl_spacing,
+                                                  solver, iterations)
     print("PMWD simulation completed.")
 
-
     metadata = {
         'rank': 0,
         'function_name': f'PMWD-{solver}',
@@ -118,14 +149,11 @@ if __name__ == "__main__":
         f.write(f"PMWD simulation completed.\n")
         f.write(f"Args : {args}\n")
         f.write(f"JIT time: {chrono_fun.jit_time:.4f} ms\n")
-        for i , time in enumerate(chrono_fun.times):
+        for i, time in enumerate(chrono_fun.times):
             f.write(f"Time {i}: {time:.4f} ms\n")
         if args.save_fields:
             np.save(f"{field_folder}/final_field_0_0.npy", final_field)
             print("Fields saved.")
 
-    
     print(f"saving to {output_path}/pmwd.csv")
     print(f"saving field and logs to {field_folder}/pmwd.log")
-
-

benchmarks/particle_mesh_a100.slurm

@@ -177,7 +177,3 @@ for pr in "${precisions[@]}"; do
         done
     done
 done
-
-
-
-

benchmarks/particle_mesh_v100.slurm

@@ -179,6 +179,3 @@ for pr in "${precisions[@]}"; do
         done
     done
 done
-
-
-

benchmarks/pmwd_a100.slurm

@@ -160,6 +160,3 @@ for pr in "${precisions[@]}"; do
         done
     done
 done
-
-
-

benchmarks/pmwd_v100.slurm

@@ -165,6 +165,3 @@ for pr in "${precisions[@]}"; do
         done
     done
 done
-
-
-

jaxpm/distributed.py

@@ -44,18 +44,21 @@ def autoshmap(f: Callable,
         return f
     else:
         if in_fourrier_space and 1 in mesh.devices.shape:
-            in_specs , out_specs = switch_specs((in_specs , out_specs))
+            in_specs, out_specs = switch_specs((in_specs, out_specs))
         return shard_map(f, mesh, in_specs, out_specs, check_rep, auto)
 
+
 def switch_specs(specs):
     if isinstance(specs, P):
-      new_axes = tuple('y' if ax == 'x' else 'x' if ax == 'y' else ax for ax in specs)
+        new_axes = tuple('y' if ax == 'x' else 'x' if ax == 'y' else ax
+                         for ax in specs)
         return P(*new_axes)
     elif isinstance(specs, tuple):
         return tuple(switch_specs(sub_spec) for sub_spec in specs)
     else:
         raise TypeError("Element must be either a PartitionSpec or a tuple")
 
+
 def fft3d(x):
     if distributed and not (mesh_lib.thread_resources.env.physical_mesh.empty):
         return jaxdecomp.pfft3d(x.astype(jnp.complex64))
@@ -108,12 +111,13 @@ def slice_unpad_impl(x, pad_width):
 
     unpad_slice = [slice(None)] * 3
     if halo_x > 0:
-      unpad_slice[0] = slice(halo_x , -halo_x)
+        unpad_slice[0] = slice(halo_x, -halo_x)
     if halo_y > 0:
-      unpad_slice[1] = slice(halo_y , -halo_y)
+        unpad_slice[1] = slice(halo_y, -halo_y)
 
     return x[tuple(unpad_slice)]
 
+
 def slice_pad(x, pad_width):
     mesh = mesh_lib.thread_resources.env.physical_mesh
     if distributed and not (mesh.empty) and (pad_width[0][0] > 0

jaxpm/kernels.py

@@ -1,3 +1,4 @@
+from enum import Enum
 from functools import partial
 
 import jax.numpy as jnp
@@ -7,7 +8,7 @@ from jax._src import mesh as mesh_lib
 from jax.sharding import PartitionSpec as P
 
 from jaxpm.distributed import autoshmap
-from enum import Enum
+
 
 class PencilType(Enum):
     NO_DECOMP = 0
@@ -15,6 +16,7 @@ class PencilType(Enum):
     SLAB_YZ = 2
     PENCILS = 3
 
+
 def get_pencil_type():
     mesh = mesh_lib.thread_resources.env.physical_mesh
     if mesh.empty:
@@ -31,6 +33,7 @@ def get_pencil_type():
     else:
         return PencilType.PENCILS
 
+
 def fftk(shape, dtype=np.float32):
     """
     Generate Fourier transform wave numbers for a given mesh.
@@ -46,7 +49,8 @@ def fftk(shape, dtype=np.float32):
 
     @partial(autoshmap,
              in_specs=(P('x'), P('y'), P(None)),
-             out_specs=(P('x'), P(None, 'y'), P(None)),in_fourrier_space=True)
+             out_specs=(P('x'), P(None, 'y'), P(None)),
+             in_fourrier_space=True)
     def get_kvec(ky, kz, kx):
         return (ky.reshape([-1, 1, 1]),
                 kz.reshape([1, -1, 1]),
@@ -73,7 +77,10 @@ def interpolate_power_spectrum(input, k, pk):
 
     pk_fn = lambda x: jc.scipy.interpolate.interp(x.reshape(-1), k, pk
                                                   ).reshape(x.shape)
-    return autoshmap(pk_fn, in_specs=P('x', 'y'), out_specs=P('x', 'y'),in_fourrier_space=True)(input)
+    return autoshmap(pk_fn,
+                     in_specs=P('x', 'y'),
+                     out_specs=P('x', 'y'),
+                     in_fourrier_space=True)(input)
 
 
 def gradient_kernel(kvec, direction, order=1):

jaxpm/painting.py

@@ -173,12 +173,14 @@ def cic_paint_dx(displacements, halo_size=0):
     return mesh
 
 
-def cic_read_dx_impl(mesh ,  halo_size):
+def cic_read_dx_impl(mesh, halo_size):
 
     halo_x, _ = halo_size[0]
     halo_y, _ = halo_size[1]
 
-    original_shape = [dim - 2 * halo[0] for dim , halo in zip(mesh.shape, halo_size)]
+    original_shape = [
+        dim - 2 * halo[0] for dim, halo in zip(mesh.shape, halo_size)
+    ]
     a, b, c = jnp.meshgrid(jnp.arange(original_shape[0]),
                            jnp.arange(original_shape[1]),
                            jnp.arange(original_shape[2]),
@@ -199,7 +201,7 @@ def cic_read_dx(mesh, halo_size=0):
     mesh = halo_exchange(mesh,
                          halo_extents=halo_extents,
                          halo_periods=(True, True, True))
-    displacements = autoshmap(partial(cic_read_dx_impl ,  halo_size=halo_size),
+    displacements = autoshmap(partial(cic_read_dx_impl, halo_size=halo_size),
                               in_specs=(P('x', 'y')),
                               out_specs=P('x', 'y'))(mesh)
 

jaxpm/pm.py

@@ -19,7 +19,8 @@ def pm_forces(positions, mesh_shape=None, delta=None, r_split=0, halo_size=0):
     Computes gravitational forces on particles using a PM scheme
     """
     if mesh_shape is None:
-        assert(delta is not None) , "If mesh_shape is not provided, delta should be provided"
+        assert (delta is not None
+                ), "If mesh_shape is not provided, delta should be provided"
         mesh_shape = delta.shape
     kvec = fftk(mesh_shape)
 
@@ -33,8 +34,8 @@ def pm_forces(positions, mesh_shape=None, delta=None, r_split=0, halo_size=0):
                                                               r_split=r_split)
     # Computes gravitational forces
     forces = jnp.stack([
-        cic_read_dx(ifft3d(gradient_kernel(kvec, i) * pot_k), halo_size=halo_size)
-        for i in range(3)
+        cic_read_dx(ifft3d(gradient_kernel(kvec, i) * pot_k),
+                    halo_size=halo_size) for i in range(3)
     ],
                        axis=-1)
 

scripts/distributed_pm.py

@@ -47,7 +47,6 @@ def run_simulation(omega_c, sigma8):
                                       pk_fn,
                                       seed=jax.random.PRNGKey(0))
 
-
     cosmo = jc.Planck15(Omega_c=omega_c, sigma8=sigma8)
 
     # Initial displacement