mirror of
https://github.com/DifferentiableUniverseInitiative/JaxPM.git
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remove script folder
This commit is contained in:
Wassim KABALAN
parent
e9529d35f8
commit
4da4c66472
4 changed files with 0 additions and 656 deletions
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import os
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from distributed_utils import initialize_distributed, is_on_cluster
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os.environ["EQX_ON_ERROR"] = "nan" # avoid an allgather caused by diffrax
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initialize_distributed()
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import jax
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size = jax.device_count()
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import jax.numpy as jnp
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import jax_cosmo as jc
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import numpy as np
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from diffrax import (ConstantStepSize, Dopri5, LeapfrogMidpoint, ODETerm,
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SaveAt, diffeqsolve)
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from jax.experimental import mesh_utils
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from jax.experimental.multihost_utils import process_allgather
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from jax.sharding import Mesh, NamedSharding
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from jax.sharding import PartitionSpec as P
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from jaxpm.kernels import interpolate_power_spectrum
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from jaxpm.painting import cic_paint_dx
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from jaxpm.pm import linear_field, lpt, make_ode_fn
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size = 256
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mesh_shape = [size] * 3
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box_size = [float(size)] * 3
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snapshots = jnp.linspace(0.1, 1., 4)
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halo_size = 32
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pdims = (1, 1)
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mesh = None
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sharding = None
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if jax.device_count() > 1:
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pdims = (2, 2)
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devices = mesh_utils.create_device_mesh(pdims)
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mesh = Mesh(devices.T, axis_names=('x', 'y'))
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sharding = NamedSharding(mesh, P('x', 'y'))
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@jax.jit
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def run_simulation(omega_c, sigma8):
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# Create a small function to generate the matter power spectrum
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k = jnp.logspace(-4, 1, 128)
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pk = jc.power.linear_matter_power(
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jc.Planck15(Omega_c=omega_c, sigma8=sigma8), k)
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pk_fn = lambda x: interpolate_power_spectrum(x, k, pk, sharding)
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# Create initial conditions
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initial_conditions = linear_field(mesh_shape,
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box_size,
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pk_fn,
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sharding=sharding,
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seed=jax.random.PRNGKey(0))
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cosmo = jc.Planck15(Omega_c=omega_c, sigma8=sigma8)
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# Initial displacement
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dx, p, _ = lpt(cosmo,
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initial_conditions,
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0.1,
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halo_size=halo_size,
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sharding=sharding)
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# return initial_conditions, cic_paint_dx(dx,
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# halo_size=halo_size,
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# sharding=sharding), None, None
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# Evolve the simulation forward
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ode_fn = make_ode_fn(mesh_shape, halo_size=halo_size, sharding=sharding)
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term = ODETerm(
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lambda t, state, args: jnp.stack(ode_fn(state, t, args), axis=0))
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solver = LeapfrogMidpoint()
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stepsize_controller = ConstantStepSize()
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res = diffeqsolve(term,
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solver,
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t0=0.1,
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t1=1.,
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dt0=0.01,
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y0=jnp.stack([dx, p], axis=0),
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args=cosmo,
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saveat=SaveAt(ts=snapshots),
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stepsize_controller=stepsize_controller)
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# Return the simulation volume at requested
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states = res.ys
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field = cic_paint_dx(dx, halo_size=halo_size, sharding=sharding)
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final_fields = [
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cic_paint_dx(state[0], halo_size=halo_size, sharding=sharding)
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for state in states
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]
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return initial_conditions, field, final_fields, res.stats
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# Run the simulation
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distributed_str = "distributed" if mesh is not None else "single device"
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print(f"running {distributed_str} simulation")
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init, field, final_fields, stats = run_simulation(0.32, 0.8)
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# # Print the statistics
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print(stats)
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print(f"done now saving")
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if is_on_cluster():
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rank = jax.process_index()
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# # save the final state
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np.save(f'initial_conditions_{rank}.npy', init.addressable_data(0))
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np.save(f'field_{rank}.npy', field.addressable_data(0))
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if final_fields is not None:
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for i, final_field in enumerate(final_fields):
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np.save(f'final_field_{i}_{rank}.npy',
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final_field.addressable_data(0))
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else:
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gathered_init = process_allgather(init, tiled=True)
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gathered_field = process_allgather(field, tiled=True)
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np.save(f'initial_conditions.npy', gathered_init)
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np.save(f'field.npy', gathered_field)
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if final_fields is not None:
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for i, final_field in enumerate(final_fields):
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gathered_final_field = process_allgather(final_field, tiled=True)
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np.save(f'final_field_{i}.npy', gathered_final_field)
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print(f"Finished!!")
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@ -1,144 +0,0 @@
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import os
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from math import prod
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setup_done = False
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on_cluster = False
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def is_on_cluster():
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global on_cluster
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return on_cluster
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def initialize_distributed():
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global setup_done
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global on_cluster
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if not setup_done:
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if "SLURM_JOB_ID" in os.environ:
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on_cluster = True
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print("Running on cluster")
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import jax
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jax.distributed.initialize()
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setup_done = True
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on_cluster = True
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else:
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print("Running locally")
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setup_done = True
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on_cluster = False
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os.environ["JAX_PLATFORM_NAME"] = "cpu"
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os.environ[
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"XLA_FLAGS"] = "--xla_force_host_platform_device_count=4"
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import jax
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def compare_sharding(sharding1, sharding2):
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from jaxdecomp._src.spmd_ops import get_pdims_from_sharding
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pdims1 = get_pdims_from_sharding(sharding1)
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pdims2 = get_pdims_from_sharding(sharding2)
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pdims1 = pdims1 + (1, ) * (3 - len(pdims1))
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pdims2 = pdims2 + (1, ) * (3 - len(pdims2))
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return pdims1 == pdims2
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def replace_none_or_zero(value):
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# Replace None or 0 with 1
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return 0 if value is None else value
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def process_slices(slices_tuple):
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start_product = 1
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stop_product = 1
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for s in slices_tuple:
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# Multiply the start and stop values, replacing None/0 with 1
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start_product *= replace_none_or_zero(s.start)
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stop_product *= replace_none_or_zero(s.stop)
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# Return the sum of the two products
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return int(start_product + stop_product)
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def device_arange(pdims):
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import jax
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from jax import numpy as jnp
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from jax.experimental import mesh_utils
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from jax.sharding import Mesh, NamedSharding
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from jax.sharding import PartitionSpec as P
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devices = mesh_utils.create_device_mesh(pdims)
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mesh = Mesh(devices.T, axis_names=('z', 'y'))
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sharding = NamedSharding(mesh, P('z', 'y'))
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def generate_aranged(x):
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x_start = replace_none_or_zero(x[0].start)
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y_start = replace_none_or_zero(x[1].start)
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a = jnp.array([[x_start + y_start * pdims[0]]])
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print(f"index is {x} and value is {a}")
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return a
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aranged = jax.make_array_from_callback(mesh.devices.shape,
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sharding,
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data_callback=generate_aranged)
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return aranged
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def create_ones_spmd_array(global_shape, pdims):
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import jax
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from jax.experimental import mesh_utils
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from jax.sharding import Mesh, NamedSharding
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from jax.sharding import PartitionSpec as P
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size = jax.device_count()
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assert (len(global_shape) == 3)
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assert (len(pdims) == 2)
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assert (
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prod(pdims) == size
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), "The product of pdims must be equal to the number of MPI processes"
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local_shape = (global_shape[0] // pdims[1], global_shape[1] // pdims[0],
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global_shape[2])
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# Remap to the global array from the local slice
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devices = mesh_utils.create_device_mesh(pdims)
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mesh = Mesh(devices.T, axis_names=('z', 'y'))
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sharding = NamedSharding(mesh, P('z', 'y'))
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global_array = jax.make_array_from_callback(
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global_shape,
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sharding,
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data_callback=lambda _: jax.numpy.ones(local_shape))
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return global_array, mesh
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# Helper function to create a 3D array and remap it to the global array
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def create_spmd_array(global_shape, pdims):
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import jax
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from jax.experimental import mesh_utils
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from jax.sharding import Mesh, NamedSharding
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from jax.sharding import PartitionSpec as P
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size = jax.device_count()
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assert (len(global_shape) == 3)
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assert (len(pdims) == 2)
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assert (
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prod(pdims) == size
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), "The product of pdims must be equal to the number of MPI processes"
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local_shape = (global_shape[0] // pdims[1], global_shape[1] // pdims[0],
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global_shape[2])
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# Remap to the global array from the local slicei
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devices = mesh_utils.create_device_mesh(pdims)
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mesh = Mesh(devices.T, axis_names=('z', 'y'))
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sharding = NamedSharding(mesh, P('z', 'y'))
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global_array = jax.make_array_from_callback(
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global_shape,
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sharding,
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data_callback=lambda x: jax.random.normal(
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jax.random.PRNGKey(process_slices(x)), local_shape))
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return global_array, mesh
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File diff suppressed because one or more lines are too long
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@ -1,168 +0,0 @@
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#!/bin/bash
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##########################################
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## SELECT EITHER tkc@a100 OR tkc@v100 ##
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##########################################
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#SBATCH --account tkc@a100
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##########################################
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#SBATCH --job-name=Particle-Mesh # nom du job
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# Il est possible d'utiliser une autre partition que celle par default
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# en activant l'une des 5 directives suivantes :
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##########################################
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## SELECT EITHER a100 or v100-32g ##
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##########################################
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#SBATCH -C a100
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##########################################
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#******************************************
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##########################################
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## SELECT Number of nodes and GPUs per node
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## For A100 ntasks-per-node and gres=gpu should be 8
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## For V100 ntasks-per-node and gres=gpu should be 4
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##########################################
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#SBATCH --nodes=1 # nombre de noeud
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#SBATCH --ntasks-per-node=8 # nombre de tache MPI par noeud (= nombre de GPU par noeud)
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#SBATCH --gres=gpu:8 # nombre de GPU par nœud (max 8 avec gpu_p2, gpu_p5)
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##########################################
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## Le nombre de CPU par tache doit etre adapte en fonction de la partition utilisee. Sachant
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## qu'ici on ne reserve qu'un seul GPU par tache (soit 1/4 ou 1/8 des GPU du noeud suivant
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## la partition), l'ideal est de reserver 1/4 ou 1/8 des CPU du noeud pour chaque tache:
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##########################################
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#SBATCH --cpus-per-task=8 # nombre de CPU par tache pour gpu_p5 (1/8 du noeud 8-GPU)
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##########################################
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# /!\ Attention, "multithread" fait reference a l'hyperthreading dans la terminologie Slurm
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#SBATCH --hint=nomultithread # hyperthreading desactive
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#SBATCH --time=04:00:00 # temps d'execution maximum demande (HH:MM:SS)
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#SBATCH --output=%x_%N_a100.out # nom du fichier de sortie
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#SBATCH --error=%x_%N_a100.out # nom du fichier d'erreur (ici commun avec la sortie)
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#SBATCH --qos=qos_gpu-dev
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#SBATCH --exclusive # ressources dediees
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# Nettoyage des modules charges en interactif et herites par defaut
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num_nodes=$SLURM_JOB_NUM_NODES
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num_gpu_per_node=$SLURM_NTASKS_PER_NODE
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OUTPUT_FOLDER_ARGS=1
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# Calculate the number of GPUs
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nb_gpus=$(( num_nodes * num_gpu_per_node))
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module purge
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# Decommenter la commande module suivante si vous utilisez la partition "gpu_p5"
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# pour avoir acces aux modules compatibles avec cette partition
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if [ $num_gpu_per_node -eq 8 ]; then
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module load cpuarch/amd
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source /gpfsdswork/projects/rech/tkc/commun/venv/a100/bin/activate
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else
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source /gpfsdswork/projects/rech/tkc/commun/venv/v100/bin/activate
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fi
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# Chargement des modules
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module load nvidia-compilers/23.9 cuda/12.2.0 cudnn/8.9.7.29-cuda openmpi/4.1.5-cuda nccl/2.18.5-1-cuda cmake
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module load nvidia-nsight-systems/2024.1.1.59
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echo "The number of nodes allocated for this job is: $num_nodes"
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echo "The number of GPUs allocated for this job is: $nb_gpus"
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export ENABLE_PERFO_STEP=NVTX
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export MPI4JAX_USE_CUDA_MPI=1
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function profile_python() {
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if [ $# -lt 1 ]; then
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echo "Usage: profile_python <python_script> [arguments for the script]"
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return 1
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fi
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local script_name=$(basename "$1" .py)
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local output_dir="prof_traces/$script_name"
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local report_dir="out_prof/$gpu_name/$nb_gpus/$script_name"
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if [ $OUTPUT_FOLDER_ARGS -eq 1 ]; then
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local args=$(echo "${@:2}" | tr ' ' '_')
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# Remove characters '/' and '-' from folder name
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args=$(echo "$args" | tr -d '/-')
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output_dir="prof_traces/$script_name/$args"
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report_dir="out_prof/$gpu_name/$nb_gpus/$script_name/$args"
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fi
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mkdir -p "$output_dir"
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mkdir -p "$report_dir"
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srun nsys profile -t cuda,nvtx,osrt,mpi -o "$report_dir/report_rank%q{SLURM_PROCID}" python "$@" > "$output_dir/$script_name.out" 2> "$output_dir/$script_name.err" || true
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}
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function run_python() {
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if [ $# -lt 1 ]; then
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echo "Usage: run_python <python_script> [arguments for the script]"
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return 1
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fi
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local script_name=$(basename "$1" .py)
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local output_dir="traces/$script_name"
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if [ $OUTPUT_FOLDER_ARGS -eq 1 ]; then
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local args=$(echo "${@:2}" | tr ' ' '_')
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# Remove characters '/' and '-' from folder name
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args=$(echo "$args" | tr -d '/-')
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output_dir="traces/$script_name/$args"
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fi
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mkdir -p "$output_dir"
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srun python "$@" > "$output_dir/$script_name.out" 2> "$output_dir/$script_name.err" || true
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}
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# Echo des commandes lancees
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set -x
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# Pour la partition "gpu_p5", le code doit etre compile avec les modules compatibles
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# Execution du code avec binding via bind_gpu.sh : 1 GPU par tache
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declare -A pdims_table
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# Define the table
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pdims_table[1]="1x1"
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pdims_table[4]="2x2 1x4"
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pdims_table[8]="2x4 1x8"
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pdims_table[16]="2x8 1x16"
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pdims_table[32]="4x8 1x32"
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pdims_table[64]="4x16 1x64"
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pdims_table[128]="8x16 16x8 4x32 32x4 1x128 128x1 2x64 64x2"
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pdims_table[160]="8x20 20x8 16x10 10x16 5x32 32x5 1x160 160x1 2x80 80x2 4x40 40x4"
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#mpch=(128 256 512 1024 2048 4096)
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grid=(1024 2048 4096)
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pdim="${pdims_table[$nb_gpus]}"
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echo "pdims: $pdim"
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# Check if pdims is not empty
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if [ -z "$pdim" ]; then
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echo "pdims is empty"
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echo "Number of gpus has to be 8, 16, 32, 64, 128 or 160"
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echo "Number of nodes selected: $num_nodes"
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echo "Number of gpus per node: $num_gpu_per_node"
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exit 1
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fi
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# GPU name is a100 if num_gpu_per_node is 8, otherwise it is v100
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if [ $num_gpu_per_node -eq 8 ]; then
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gpu_name="a100"
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else
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gpu_name="v100"
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fi
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out_dir="out/$gpu_name/$nb_gpus"
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echo "Output dir is : $out_dir"
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for g in ${grid[@]}; do
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for p in ${pdim[@]}; do
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# halo is 1/4 of the grid size
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halo_size=$((g / 4))
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slaunch scripts/fastpm_jaxdecomp.py -m $g -b $g -p $p -hs $halo_size -ode diffrax -o $out_dir
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done
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done
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