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Add mmain and other major updates (#44)
* Move paths to a separate file * Add mmain reader * Add a verbosity flag * Fix imports * Fix bug * Rename files * Return ultimate parents * Add script to generate mmain * Remove mmain path * edit path * Add mmain path * Change function name * Rename function * Turn off verbose * Fix list requirement * Edit init match paths * Fix init pathing * Edit paths docs * Edit dumpdir name * Rename path * Fix split paths * Remove unused import * Add comment * Update readme * remove read mmain * Rename haloatalogue * Fix minor bugs * Update nbs * Add create directory option * Move split jobs * Move spliot jobs * Remove splitting * Add import * Edit script * Deeper split folder * Fix paths bug * Rename catalogue * Rename Catalogue * Add new clumpread * Edit paths * add knn paths * Update commenting * Update imports * Add more conversions * Update temp file * Add a note * Add catalogue * Cooment * Update TODO * Update script * add nb * Update * pep8 * edit paths & pep8 * Fix knn auto paths * add paths docs * Add auto and cross knn paths * Add new paths * Simplify tpcf reading * pep8 patch * update readme * Update progress * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * Pep 8 and restructure * add lambda spin * add clump and halo * add checks * Edit halo profile fit * Update gitignore * backup script
This commit is contained in:
Richard Stiskalek
GitHub
parent
e0d3854277
commit
fdb0df8d4c
50 changed files with 2152 additions and 1844 deletions
158
scripts/cluster_crosspk.py
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158
scripts/cluster_crosspk.py
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""
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MPI script to calculate the matter cross power spectrum between CSiBORG
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IC realisations. Units are Mpc/h.
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"""
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from argparse import ArgumentParser
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from datetime import datetime
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from gc import collect
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from itertools import combinations
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from os import remove
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from os.path import join
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import joblib
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import numpy
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import Pk_library as PKL
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from mpi4py import MPI
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try:
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import csiborgtools
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except ModuleNotFoundError:
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import sys
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sys.path.append("../")
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import csiborgtools
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dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
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parser = ArgumentParser()
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parser.add_argument("--grid", type=int)
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parser.add_argument("--halfwidth", type=float, default=0.5)
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args = parser.parse_args()
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# Get MPI things
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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nproc = comm.Get_size()
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MAS = "CIC" # mass asignment scheme
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paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
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box = csiborgtools.read.BoxUnits(paths)
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reader = csiborgtools.read.ParticleReader(paths)
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ics = paths.get_ics(tonew=False)
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nsims = len(ics)
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# File paths
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ftemp = join(dumpdir, "temp_crosspk",
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"out_{}_{}" + "_{}".format(args.halfwidth))
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fout = join(dumpdir, "crosspk",
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"out_{}_{}" + "_{}.p".format(args.halfwidth))
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jobs = csiborgtools.utils.split_jobs(nsims, nproc)[rank]
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for n in jobs:
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print("Rank {}@{}: saving {}th delta.".format(rank, datetime.now(), n))
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nsim = ics[n]
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particles = reader.read_particle(max(paths.get_snapshots(nsim)), nsim,
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["x", "y", "z", "M"], verbose=False)
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# Halfwidth -- particle selection
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if args.halfwidth < 0.5:
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particles = csiborgtools.read.halfwidth_select(
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args.halfwidth, particles)
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length = box.box2mpc(2 * args.halfwidth) * box.h # Mpc/h
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else:
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length = box.box2mpc(1) * box.h # Mpc/h
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# Calculate the overdensity field
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field = csiborgtools.field.DensityField(particles, length, box, MAS)
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delta = field.overdensity_field(args.grid, verbose=False)
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aexp = box._aexp
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# Try to clean up memory
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del field, particles, box, reader
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collect()
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# Dump the results
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with open(ftemp.format(nsim, "delta") + ".npy", "wb") as f:
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numpy.save(f, delta)
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joblib.dump([aexp, length], ftemp.format(nsim, "lengths") + ".p")
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# Try to clean up memory
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del delta
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collect()
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comm.Barrier()
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# Get off-diagonal elements and append the diagoal
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combs = [c for c in combinations(range(nsims), 2)]
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for i in range(nsims):
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combs.append((i, i))
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prev_delta = [-1, None, None, None] # i, delta, aexp, length
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jobs = csiborgtools.utils.split_jobs(len(combs), nproc)[rank]
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for n in jobs:
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i, j = combs[n]
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print("Rank {}@{}: combination {}.".format(rank, datetime.now(), (i, j)))
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# If i same as last time then don't have to load it
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if prev_delta[0] == i:
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delta_i = prev_delta[1]
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aexp_i = prev_delta[2]
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length_i = prev_delta[3]
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else:
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with open(ftemp.format(ics[i], "delta") + ".npy", "rb") as f:
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delta_i = numpy.load(f)
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aexp_i, length_i = joblib.load(ftemp.format(ics[i], "lengths") + ".p")
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# Store in prev_delta
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prev_delta[0] = i
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prev_delta[1] = delta_i
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prev_delta[2] = aexp_i
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prev_delta[3] = length_i
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# Get jth delta
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with open(ftemp.format(ics[j], "delta") + ".npy", "rb") as f:
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delta_j = numpy.load(f)
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aexp_j, length_j = joblib.load(ftemp.format(ics[j], "lengths") + ".p")
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# Verify the difference between the scale factors! Say more than 1%
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daexp = abs((aexp_i - aexp_j) / aexp_i)
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if daexp > 0.01:
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raise ValueError(
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"Boxes {} and {} final snapshot scale factors disagree by "
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"`{}` percent!".format(ics[i], ics[j], daexp * 100))
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# Check how well the boxsizes agree
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dlength = abs((length_i - length_j) / length_i)
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if dlength > 0.001:
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raise ValueError("Boxes {} and {} box sizes disagree by `{}` percent!"
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.format(ics[i], ics[j], dlength * 100))
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# Calculate the cross power spectrum
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Pk = PKL.XPk([delta_i, delta_j], length_i, axis=1, MAS=[MAS, MAS],
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threads=1)
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joblib.dump(Pk, fout.format(ics[i], ics[j]))
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del delta_i, delta_j, Pk
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collect()
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# Clean up the temp files
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comm.Barrier()
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if rank == 0:
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print("Cleaning up the temporary files...")
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for ic in ics:
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remove(ftemp.format(ic, "delta") + ".npy")
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remove(ftemp.format(ic, "lengths") + ".p")
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print("All finished!")
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