diff --git a/.gitignore b/.gitignore index b6e6a4f..c58046d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,10 +1,3 @@ -# Ignore feature_* directory (usually used as git worktree) -feature_*/ - -# Ignore extensions directory -extensions/* -!extensions/__init__.py - # Ignore some symbolic links install @@ -14,17 +7,5 @@ install .vscode/ *.pyc __pycache__/ -pysbmy.egg-info/ -*.h5 -*.rng -*.gadget1 -*.gadget2 -*.gadget3 -log.txt -testpdf.txt -tests/ -params/ -results/ -slurm_logs/ -slurm_scripts/ -work/ +sbmy_control.egg-info/ +*.h5 \ No newline at end of file diff --git a/__init__.py b/__init__.py deleted file mode 100644 index 06d7405..0000000 Binary files a/__init__.py and /dev/null differ diff --git a/analysis/slices.py b/analysis/slices.py deleted file mode 100644 index b3fa8e1..0000000 --- a/analysis/slices.py +++ /dev/null @@ -1,176 +0,0 @@ -import numpy as np - -import sys -sys.path.append('/home/aubin/Simbelmyne/sbmy_control/') -from cosmo_params import register_arguments_cosmo, parse_arguments_cosmo - -fs = 18 -fs_titles = fs -4 - -def plot_imshow_with_reference( data_list, - reference=None, - titles=None, - vmin=None, - vmax=None, - L=None, - cmap='viridis'): - """ - Plot the imshow of a list of 2D arrays with two rows: one for the data itself, - one for the data compared to a reference. Each row will have a common colorbar. - - Parameters: - - data_list: list of 2D arrays to be plotted - - reference: 2D array to be used as reference for comparison - - titles: list of titles for each subplot - - cmap: colormap to be used for plotting - """ - import matplotlib.pyplot as plt - - if titles is None: - titles = [None for f in data_list] - - if L is None: - L = [len(data) for data in data_list] - elif isinstance(L, int) or isinstance(L, float): - L = [L for data in data_list] - - sep = 10 if L[0] < 50 else 20 if L[0] < 200 else 100 - ticks = [np.arange(0, l+1, sep)*len(dat)/l for l, dat in zip(L,data_list)] - tick_labels = [np.arange(0, l+1, sep) for l in L] - - def score(data, reference): - return np.linalg.norm(data-reference)/np.linalg.norm(reference) - - n = len(data_list) - fig, axes = plt.subplots(1 if reference is None else 2, n, figsize=(5 * n, 5 if reference is None else 5*2), dpi=max(500, data_list[0].shape[0]//2)) - - if vmin is None or vmax is None: - vmin = min(np.quantile(data,0.01) for data in data_list) - vmax = max(np.quantile(data,0.99) for data in data_list) - - if reference is not None: - vmin_diff = min(np.quantile((data-reference),0.01) for data in data_list) - vmax_diff = max(np.quantile((data-reference),0.99) for data in data_list) - else: - vmin_diff = vmin - vmax_diff = vmax - - if reference is not None: - # Plot the data itself - for i, data in enumerate(data_list): - im = axes[0, i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax) - axes[0, i].set_title(titles[i], fontsize=fs_titles) - axes[0, i].set_xticks(ticks[i]) - axes[0, i].set_yticks(ticks[i]) - axes[0, i].set_xticklabels(tick_labels[i]) - axes[0, i].set_yticklabels(tick_labels[i]) - axes[0, i].set_xlabel('Mpc/h') - fig.colorbar(im, ax=axes[0, :], orientation='vertical') - - # Plot the data compared to the reference - for i, data in enumerate(data_list): - im = axes[1, i].imshow(data - reference, cmap=cmap, origin='lower', vmin=vmin_diff, vmax=vmax_diff) - axes[1, i].set_title(f'{titles[i]} - Reference', fontsize=fs_titles) - axes[1, i].set_xticks(ticks[i]) - axes[1, i].set_yticks(ticks[i]) - axes[1, i].set_xticklabels(tick_labels[i]) - axes[1, i].set_yticklabels(tick_labels[i]) - axes[1, i].set_xlabel('Mpc/h') - fig.colorbar(im, ax=axes[1, :], orientation='vertical') - - # Add the score on the plots - for i, data in enumerate(data_list): - axes[1, i].text(0.5, 0.9, f"Score: {score(data, reference):.2e}", fontsize=10, transform=axes[1, i].transAxes, color='white') - # plt.tight_layout() - else: - - if len(data_list) == 1: - data_list = data_list[0] - im = axes.imshow(data_list, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax) - axes.set_title(titles[0], fontsize=fs_titles) - axes.set_xticks(ticks[0]) - axes.set_yticks(ticks[0]) - axes.set_xticklabels(tick_labels[0]) - axes.set_yticklabels(tick_labels[0]) - axes.set_xlabel('Mpc/h') - fig.colorbar(im, ax=axes, orientation='vertical') - - else: - for i, data in enumerate(data_list): - im = axes[i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax) - axes[i].set_title(titles[i], fontsize=fs_titles) - axes[i].set_xticks(ticks[i]) - axes[i].set_yticks(ticks[i]) - axes[i].set_xticklabels(tick_labels[i]) - axes[i].set_yticklabels(tick_labels[i]) - axes[i].set_xlabel('Mpc/h') - fig.colorbar(im, ax=axes[:], orientation='vertical') - - return fig, axes - - -if __name__ == "__main__": - from argparse import ArgumentParser - parser = ArgumentParser(description='Comparisons of fields slices.') - - parser.add_argument('-a','--axis', type=int, default=0, help='Axis along which the slices will be taken.') - parser.add_argument('-i','--index', type=int, default=None, help='Index of the slice along the axis.') - parser.add_argument('-d', '--directory', type=str, required=True, help='Directory containing the fields files.') - parser.add_argument('-ref', '--reference', type=str, default=None, help='Reference field file.') - parser.add_argument('-f', '--filenames', type=str, nargs='+', required=True, help='Field files to be plotted.') - parser.add_argument('-o', '--output', type=str, default=None, help='Output plot file name.') - parser.add_argument('-l', '--labels', type=str, nargs='+', default=None, help='Labels for each field.') - parser.add_argument('-c', '--cmap', type=str, default='viridis', help='Colormap to be used for plotting.') - parser.add_argument('-vmin', type=float, default=None, help='Minimum value for the colorbar.') - parser.add_argument('-vmax', type=float, default=None, help='Maximum value for the colorbar.') - parser.add_argument('-t', '--title', type=str, default=None, help='Title for the plot.') - parser.add_argument('-log','--log_scale', action='store_true', help='Use log scale for the data.') - - register_arguments_cosmo(parser) - - args = parser.parse_args() - - from pysbmy.field import read_field - from pysbmy.cosmology import d_plus - - ref_field = read_field(args.directory+args.reference) if args.reference is not None else None - fields = [read_field(args.directory+f) for f in args.filenames] - - if args.index is None: - index = fields[0].N0//2 - else: - index=args.index - - # args.labels=[f"a={f.time:.2f}" for f in fields] - L = [f.L0 for f in fields] - - match args.axis: - case 0 | 'x': - reference = ref_field.data[index,:,:] if ref_field is not None else None - fields = [f.data[index,:,:] for f in fields] - # reference = ref_field.data[index,:,:]/d_plus(1e-3,ref_field.time,parse_arguments_cosmo(args)) - # fields = [f.data[index,:,:]/d_plus(1e-3,f.time,parse_arguments_cosmo(args)) for f in fields] - # reference = ref_field.data[index,:,:]/d_plus(1e-3,0.05,parse_arguments_cosmo(args)) - # fields = [f.data[index,:,:]/d_plus(1e-3,time,parse_arguments_cosmo(args)) for f,time in zip(fields,[0.05, 1.0])] - case 1 | 'y': - reference = ref_field.data[:,index,:] if ref_field is not None else None - fields = [f.data[:,index,:] for f in fields] - case 2 | 'z': - reference = ref_field.data[:,:,index] if ref_field is not None else None - fields = [f.data[:,:,index] for f in fields] - case _: - raise ValueError(f"Wrong axis provided : {args.axis}") - - if args.log_scale: - reference = np.log10(2.+reference) if ref_field is not None else None - fields = [np.log10(2.+f) for f in fields] - - - - fig, axes = plot_imshow_with_reference(fields,reference,args.labels, vmin=args.vmin, vmax=args.vmax,cmap=args.cmap, L=L) - fig.suptitle(args.title) - - if args.output is not None: - fig.savefig(args.output) - else: - fig.savefig(args.directory+'slices.png') \ No newline at end of file diff --git a/ICs.py b/sbmy_control/ICs.py similarity index 87% rename from ICs.py rename to sbmy_control/ICs.py index 188e6c8..daa8cb8 100644 --- a/ICs.py +++ b/sbmy_control/ICs.py @@ -3,9 +3,9 @@ def main_ICs(parsed_args): """ Main function for the initial conditions generator. """ - from args_main import parse_arguments_main - from parameters_card import parse_arguments_card_for_ICs - from low_level import print_starting_module, print_message, print_ending_module + from .args_main import parse_arguments_main + from .parameters_card import parse_arguments_card_for_ICs + from .low_level import print_starting_module, print_message, print_ending_module from os.path import isfile main_dict = parse_arguments_main(parsed_args) @@ -52,10 +52,10 @@ def main_ICs(parsed_args): def ICs_monofonic(parsed_args): - from monofonic import main_monofonic + from .monofonic import main_monofonic from os.path import isfile - from low_level import print_message - from parameters_monofonic import parse_arguments_monofonic + from .low_level import print_message + from .parameters_monofonic import parse_arguments_monofonic monofonic_dict = parse_arguments_monofonic(parsed_args) @@ -67,9 +67,9 @@ def ICs_monofonic(parsed_args): def ICs_sbmy(parsed_args): - from low_level import print_starting_module, print_message + from .low_level import print_starting_module, print_message from os.path import isfile - from parameters_card import parse_arguments_card_for_ICs + from .parameters_card import parse_arguments_card_for_ICs print_starting_module("sbmy IC", verbose=parsed_args.verbose) @@ -99,14 +99,14 @@ def ICs_sbmy(parsed_args): def create_sbmy_power_spectrum_file(parsed_args, card_dict, power_spectrum_file): - from cosmo_params import parse_arguments_cosmo + from .cosmo_params import parse_arguments_cosmo from pysbmy.power import PowerSpectrum cosmo_dict = parse_arguments_cosmo(parsed_args) if parsed_args.verbose < 2: from io import BytesIO - from low_level import stdout_redirector, stderr_redirector + from .low_level import stdout_redirector, stderr_redirector f = BytesIO() g = BytesIO() with stdout_redirector(f): @@ -138,7 +138,7 @@ def create_sbmy_power_spectrum_file(parsed_args, card_dict, power_spectrum_file) def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file): import numpy as np from gc import collect - from low_level import print_message + from .low_level import print_message from pysbmy.field import BaseField print_message(f"Seed: {parsed_args.seed}", 3, "sbmy IC", verbose=parsed_args.verbose) @@ -161,7 +161,7 @@ def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file if parsed_args.verbose < 2: from io import BytesIO - from low_level import stdout_redirector, stderr_redirector + from .low_level import stdout_redirector, stderr_redirector f = BytesIO() g = BytesIO() with stdout_redirector(f): @@ -175,11 +175,11 @@ def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file if __name__ == "__main__": from argparse import ArgumentParser - from args_main import register_arguments_main - from parameters_card import register_arguments_card_for_ICs - from cosmo_params import register_arguments_cosmo - from parameters_monofonic import register_arguments_monofonic - from slurm_submission import register_arguments_slurm + from .args_main import register_arguments_main + from .parameters_card import register_arguments_card_for_ICs + from .cosmo_params import register_arguments_cosmo + from .parameters_monofonic import register_arguments_monofonic + from .slurm_submission import register_arguments_slurm parser = ArgumentParser(description="Generate initial conditions for a Simbelmyne simulation.") # TODO: reduce the volume of arguments @@ -190,4 +190,4 @@ if __name__ == "__main__": register_arguments_cosmo(parser) parsed_args = parser.parse_args() - main_ICs(parsed_args) \ No newline at end of file + main_ICs(parsed_args) diff --git a/analysis/__init__.py b/sbmy_control/__init__.py similarity index 100% rename from analysis/__init__.py rename to sbmy_control/__init__.py diff --git a/sbmy_control/analysis/__init__.py b/sbmy_control/analysis/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/sbmy_control/analysis/colormaps.py b/sbmy_control/analysis/colormaps.py new file mode 100644 index 0000000..54ddf3a --- /dev/null +++ b/sbmy_control/analysis/colormaps.py @@ -0,0 +1,36 @@ + + +def register_colormaps(colormaps): + + # Register cmasher + try: + import cmasher as cma + for name, cmap in cma.cm.cmap_d.items(): + try: + colormaps.register(name=name, cmap=cmap) + except ValueError: + pass + except ImportError: + pass + + # Register cmocean + try: + import cmocean as cmo + for name, cmap in cmo.cm.cmap_d.items(): + try: + colormaps.register(name=name, cmap=cmap) + except ValueError: + pass + except ImportError: + pass + + # Register cmcrameri + try: + import cmcrameri as cmc + for name, cmap in cmc.cm.cmaps.items(): + try: + colormaps.register(name=name, cmap=cmap) + except ValueError: + pass + except ImportError: + pass diff --git a/analysis/power_spectrum.py b/sbmy_control/analysis/power_spectrum.py similarity index 84% rename from analysis/power_spectrum.py rename to sbmy_control/analysis/power_spectrum.py index 64dacb5..7a92370 100644 --- a/analysis/power_spectrum.py +++ b/sbmy_control/analysis/power_spectrum.py @@ -1,10 +1,29 @@ import numpy as np +import os kmin = 1e-1 kmax = 2e0 Nk = 50 AliasingCorr=False +def crop_field(field, Ncrop): + + if Ncrop is None or Ncrop == 0: + return + + elif Ncrop > 0: + field.data = field.data[Ncrop:-Ncrop, Ncrop:-Ncrop, Ncrop:-Ncrop] + d0 = field.L0/field.N0 + d1 = field.L1/field.N1 + d2 = field.L2/field.N2 + field.N0 -= 2*Ncrop + field.N1 -= 2*Ncrop + field.N2 -= 2*Ncrop + field.L0 = field.N0*d0 + field.L1 = field.N1*d1 + field.L2 = field.N2*d2 + + def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None): from pysbmy.power import PowerSpectrum from pysbmy.fft import FourierGrid @@ -15,10 +34,10 @@ def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None): field.L0, field.L1, field.L2, - field.N0, - field.N1, - field.N2, - k_modes=np.concat([PowerSpectrum(field.L0,field.L1,field.L2,field.N0,field.N1,field.N2,).FourierGrid.k_modes[:10],np.logspace( + int(field.N0), + int(field.N1), + int(field.N2), + k_modes=np.concat([PowerSpectrum(field.L0,field.L1,field.L2,int(field.N0),int(field.N1),int(field.N2),).FourierGrid.k_modes[:10],np.logspace( np.log10(kmin), np.log10(kmax), Nk, @@ -43,10 +62,10 @@ def get_cross_correlations(field_A, field_B, kmin=kmin, kmax=kmax, Nk=Nk, G=None field_A.L0, field_A.L1, field_A.L2, - field_A.N0, - field_A.N1, - field_A.N2, - k_modes=np.concat([PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,field_A.N0,field_A.N1,field_A.N2,).FourierGrid.k_modes[:10],np.logspace( + int(field_A.N0), + int(field_A.N1), + int(field_A.N2), + k_modes=np.concat([PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,int(field_A.N0),int(field_A.N1),int(field_A.N2),).FourierGrid.k_modes[:10],np.logspace( np.log10(kmin), np.log10(kmax), Nk, @@ -91,7 +110,8 @@ def plot_power_spectra(filenames, figsize=(8,4), dpi=300, ax=None, - fig=None,): + fig=None, + Ncrop=None,): import matplotlib.pyplot as plt from pysbmy.field import read_field @@ -110,6 +130,7 @@ def plot_power_spectra(filenames, for i, filename in enumerate(filenames): field = read_field(filename) + crop_field(field, Ncrop) _, G, k, _ = add_power_spectrum_to_plot(ax=ax, field=field, Pk_ref=Pk_ref, @@ -128,7 +149,7 @@ def plot_power_spectra(filenames, ax.set_ylim(ylims) if yticks is not None: ax.set_yticks(yticks) - ax.set_xlabel(r'$k$ [$h/\mathrm{Mpc}$]', labelpad=-10) + ax.set_xlabel(r'$k$ [$h/\mathrm{Mpc}$]', labelpad=-0) if Pk_ref is not None: ax.set_ylabel(r'$P(k)/P_\mathrm{ref}(k)$') @@ -163,7 +184,9 @@ def plot_cross_correlations(filenames_A, figsize=(8,4), dpi=300, ax=None, - fig=None,): + fig=None, + Ncrop=None, + ): import matplotlib.pyplot as plt from pysbmy.field import read_field @@ -181,9 +204,11 @@ def plot_cross_correlations(filenames_A, markers = [None for f in filenames_A] field_B = read_field(filename_B) + crop_field(field_B, Ncrop) for i, filename_A in enumerate(filenames_A): field_A = read_field(filename_A) + crop_field(field_A, Ncrop) _, G, k, _ = add_cross_correlations_to_plot(ax=ax, field_A=field_A, field_B=field_B, @@ -202,7 +227,7 @@ def plot_cross_correlations(filenames_A, ax.set_ylim(ylims) if yticks is not None: ax.set_yticks(yticks) - ax.set_xlabel(r'$k$ [$h/\mathrm{Mpc}$]', labelpad=-10) + ax.set_xlabel(r'$k$ [$h/\mathrm{Mpc}$]', labelpad=-0) ax.set_ylabel('$R(k)$') if bound1 is not None: @@ -238,13 +263,15 @@ def get_ylims_and_yticks(ylims): return ylims, yticks -if __name__ == "__main__": + + +def console_main(): from argparse import ArgumentParser parser = ArgumentParser(description='Plot power spectra of fields') parser.add_argument('-ps', '--power_spectrum', action='store_true', help='Plot power spectra.') parser.add_argument('-cc', '--cross_correlation', action='store_true', help='Plot cross correlations.') - parser.add_argument('-d', '--directory', type=str, required=True, help='Directory containing the fields files.') + parser.add_argument('-d', '--directory', type=str, default='./', help='Directory containing the fields files.') parser.add_argument('-ref', '--reference', type=str, default=None, help='Reference field file.') parser.add_argument('-f', '--filenames', type=str, nargs='+', required=True, help='Field files to be plotted.') parser.add_argument('-o', '--output', type=str, default=None, help='Output plot file name.') @@ -255,16 +282,23 @@ if __name__ == "__main__": parser.add_argument('-t','--title', type=str, default=None, help='Title of the plot.') parser.add_argument('-yrp', '--ylim_power', type=float, nargs=2, default=[0.9,1.1], help='Y-axis limits.') parser.add_argument('-yrc', '--ylim_corr', type=float, nargs=2, default=[0.99,1.001], help='Y-axis limits.') + parser.add_argument('--crop', type=int, default=None, help='Remove the outter N pixels of the fields.') args = parser.parse_args() if not args.power_spectrum and not args.cross_correlation: print('You must choose between power_spectrum and cross_correlation.') exit() + + for _k,f in enumerate(args.filenames): + if not os.path.exists(args.directory+f): + raise FileNotFoundError(f"File {args.directory+f} does not exist.") if args.reference is not None: from pysbmy.field import read_field - G, _, Pk_ref = get_power_spectrum(read_field(args.directory+args.reference), kmin=kmin, kmax=kmax, Nk=Nk) + F_ref = read_field(args.directory+args.reference) + crop_field(F_ref, args.crop) + G, _, Pk_ref = get_power_spectrum(F_ref, kmin=kmin, kmax=kmax, Nk=Nk) else: Pk_ref = None G = None @@ -279,6 +313,7 @@ if __name__ == "__main__": if args.power_spectrum and args.cross_correlation: import matplotlib.pyplot as plt fig, axes = plt.subplots(2, 1, figsize=(8,8)) + fig.subplots_adjust(hspace=0.3) plot_power_spectra(filenames=filenames, labels=args.labels, colors=args.colors, @@ -294,7 +329,9 @@ if __name__ == "__main__": kmax=kmax, Nk=Nk, ax=axes[0], - fig=fig) + fig=fig, + Ncrop=args.crop, + ) plot_cross_correlations(filenames_A=filenames, filename_B=args.directory+args.reference, @@ -311,7 +348,9 @@ if __name__ == "__main__": kmax=kmax, Nk=Nk, ax=axes[1], - fig=fig) + fig=fig, + Ncrop=args.crop, + ) axes[1].legend(loc='lower left') axes[0].set_title("Power Spectrum") @@ -334,7 +373,9 @@ if __name__ == "__main__": bound2=0.02, kmin=kmin, kmax=kmax, - Nk=Nk) + Nk=Nk, + Ncrop=args.crop, + ) ax.legend() if args.title is not None: ax.set_title(args.title) @@ -353,7 +394,9 @@ if __name__ == "__main__": bound2=0.002, kmin=kmin, kmax=kmax, - Nk=Nk) + Nk=Nk, + Ncrop=args.crop, + ) ax.legend(loc='lower left') if args.title is not None: ax.set_title(args.title) @@ -362,5 +405,8 @@ if __name__ == "__main__": fig.savefig(args.output) else: fig.savefig(args.directory+'power_spectrum.png') - + +if __name__ == "__main__": + console_main() + \ No newline at end of file diff --git a/sbmy_control/analysis/slices.py b/sbmy_control/analysis/slices.py new file mode 100755 index 0000000..98cbfe9 --- /dev/null +++ b/sbmy_control/analysis/slices.py @@ -0,0 +1,228 @@ +import numpy as np + +import sys +import os + +fs = 18 +fs_titles = fs - 4 + +def add_ax_ticks(ax, ticks, tick_labels): + from matplotlib import ticker + ax.set_xticks(ticks) + ax.set_yticks(ticks) + ax.set_xticklabels([int(t) for t in tick_labels]) + ax.set_yticklabels([int(t) for t in tick_labels]) + ax.set_xlabel('Mpc/h') + # ax.xaxis.set_major_formatter(ticker.FormatStrFormatter('%d')) # Does not work + # ax.yaxis.set_major_formatter(ticker.FormatStrFormatter('%d')) + + + +def plot_imshow_with_reference( data_list, + reference=None, + titles=None, + vmin=None, + vmax=None, + L=None, + cmap='viridis', + cmap_diff='PuOr', + ref_label="Reference"): + """ + Plot the imshow of a list of 2D arrays with two rows: one for the data itself, + one for the data compared to a reference. Each row will have a common colorbar. + + Parameters: + - data_list: list of 2D arrays to be plotted + - reference: 2D array to be used as reference for comparison + - titles: list of titles for each subplot + - cmap: colormap to be used for plotting + """ + import matplotlib.pyplot as plt + + from sbmy_control.analysis.colormaps import register_colormaps + register_colormaps(plt.colormaps) + + if titles is None: + titles = [None for f in data_list] + + if L is None: + L = [len(data) for data in data_list] + elif isinstance(L, int) or isinstance(L, float): + L = [L for data in data_list] + + sep = 10 if L[0] < 50 else 20 if L[0] < 100 else 50 if L[0]<250 else 100 if L[0] < 500 else 200 if L[0] < 1000 else 500 if L[0] < 2500 else 1000 + ticks = [np.arange(0, l+1, sep)*len(dat)/l for l, dat in zip(L,data_list)] + tick_labels = [np.arange(0, l+1, sep) for l in L] + + def score(data, reference): + return np.linalg.norm(data-reference)/np.linalg.norm(reference) + + n = len(data_list) + fig, axes = plt.subplots(1 if reference is None else 2, n, figsize=(5 * n, 5 if reference is None else 5*2), dpi=max(500, data_list[0].shape[0]//2), squeeze = False) + + if vmin is None or vmax is None: + vmin = min(np.quantile(data,0.01) for data in data_list) + vmax = max(np.quantile(data,0.99) for data in data_list) + + if reference is not None: + vmin_diff = min(np.quantile((data-reference),0.01) for data in data_list) + vmax_diff = max(np.quantile((data-reference),0.99) for data in data_list) + vmin_diff = min(vmin_diff, -vmax_diff) + vmax_diff = -vmin_diff + else: + vmin_diff = vmin + vmax_diff = vmax + + # Plot the data itself + for i, data in enumerate(data_list): + im = axes[0, i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax) + axes[0, i].set_title(titles[i], fontsize=fs_titles) + add_ax_ticks(axes[0, i], ticks[i], tick_labels[i]) + fig.colorbar(im, ax=axes[0, :], orientation='vertical') + + if reference is not None: + # Plot the data compared to the reference + for i, data in enumerate(data_list): + im = axes[1, i].imshow(data - reference, cmap=cmap_diff, origin='lower', vmin=vmin_diff, vmax=vmax_diff) + axes[1, i].set_title(f'{titles[i]} - {ref_label}', fontsize=fs_titles) + add_ax_ticks(axes[1, i], ticks[i], tick_labels[i]) + fig.colorbar(im, ax=axes[1, :], orientation='vertical') + + # Add the score on the plots + for i, data in enumerate(data_list): + axes[1, i].text(0.5, 0.9, f"RMS: {score(data, reference):.2e}", fontsize=10, transform=axes[1, i].transAxes, color='black') + # plt.tight_layout() + + return fig, axes + + + +def plot_imshow_diff(data_list, + reference, + titles, + vmin=None, + vmax=None, + L=None, + cmap='viridis', + ref_label="Reference"): + + import matplotlib.pyplot as plt + + from sbmy_control.analysis.colormapss import register_colormaps + register_colormaps(plt.colormaps) + + if reference is None: + raise ValueError("Reference field is None") + + if titles is None: + titles = [None for f in data_list] + + if L is None: + L = [len(data) for data in data_list] + elif isinstance(L, int) or isinstance(L, float): + L = [L for data in data_list] + + sep = 10 if L[0] < 50 else 20 if L[0] < 100 else 50 if L[0]<250 else 100 if L[0] < 500 else 200 if L[0] < 1000 else 500 if L[0] < 2500 else 1000 + ticks = [np.arange(0, l+1, sep)*len(dat)/l for l, dat in zip(L,data_list)] + tick_labels = [np.arange(0, l+1, sep) for l in L] + + def score(data, reference): + return np.linalg.norm(data-reference)/np.linalg.norm(reference) + + n = len(data_list) + fig, axes = plt.subplots(1, n, figsize=(5 * n, 5), dpi=max(500, data_list[0].shape[0]//2), squeeze = False) + + if vmin is None or vmax is None: + vmin = min(np.quantile(data-reference,0.01) for data in data_list) + vmax = max(np.quantile(data-reference,0.99) for data in data_list) + vmin = min(vmin, -vmax) + vmax = -vmin + + # Plot the data compared to the reference + for i, data in enumerate(data_list): + im = axes[0, i].imshow(data - reference, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax) + axes[0, i].set_title(f'{titles[i]} - {ref_label}', fontsize=fs_titles) + add_ax_ticks(axes[0, i], ticks[i], tick_labels[i]) + fig.colorbar(im, ax=axes[0, :], orientation='vertical') + + return fig, axes + + +def console_main(): + from argparse import ArgumentParser + parser = ArgumentParser(description='Comparisons of fields slices.') + + parser.add_argument('-a','--axis', type=int, default=0, help='Axis along which the slices will be taken.') + parser.add_argument('-i','--index', type=int, default=None, help='Index of the slice along the axis.') + parser.add_argument('-d', '--directory', type=str, default='./', help='Directory containing the fields files.') + parser.add_argument('-ref', '--reference', type=str, default=None, help='Reference field file.') + parser.add_argument('-f', '--filenames', type=str, nargs='+', required=True, help='Field files to be plotted.') + parser.add_argument('-o', '--output', type=str, default=None, help='Output plot file name.') + parser.add_argument('-l', '--labels', type=str, nargs='+', default=None, help='Labels for each field.') + parser.add_argument('-c', '--cmap', type=str, default='viridis', help='Colormap to be used for plotting.') + parser.add_argument('-vmin', type=float, default=None, help='Minimum value for the colorbar.') + parser.add_argument('-vmax', type=float, default=None, help='Maximum value for the colorbar.') + parser.add_argument('-t', '--title', type=str, default=None, help='Title for the plot.') + parser.add_argument('-log','--log_scale', action='store_true', help='Use log scale for the data.') + parser.add_argument('--diff', action='store_true', help='Plot only the difference with the reference field.') + parser.add_argument('--ref_label', type=str, default='Reference', help='Label for the reference field.') + parser.add_argument('--cmap_diff', type=str, default='PuOr', help='Colormap to be used for the difference plot.') + + args = parser.parse_args() + + from pysbmy.field import read_field + + ref_label = args.ref_label + ref_field = read_field(args.directory+args.reference) if args.reference is not None else None + fields = [] + for k,f in enumerate(args.filenames): + if not os.path.exists(args.directory+f): + raise FileNotFoundError(f"File {args.directory+f} does not exist.") + if args.reference is not None and f == args.reference: + fields.append(ref_field) # Simply copy the reference field instead of reading it again + if args.labels is not None: + ref_label = args.labels[k] # Use the label of the field as the reference label + else: + fields.append(read_field(args.directory+f)) + + if args.index is None: + index = fields[0].N0//2 + else: + index=args.index + + # args.labels=[f"a={f.time:.2f}" for f in fields] + L = [f.L0 for f in fields] + + match args.axis: + case 0 | 'x': + reference = ref_field.data[index,:,:] if ref_field is not None else None + fields = [f.data[index,:,:] for f in fields] + case 1 | 'y': + reference = ref_field.data[:,index,:] if ref_field is not None else None + fields = [f.data[:,index,:] for f in fields] + case 2 | 'z': + reference = ref_field.data[:,:,index] if ref_field is not None else None + fields = [f.data[:,:,index] for f in fields] + case _: + raise ValueError(f"Wrong axis provided : {args.axis}") + + if args.log_scale: + reference = np.log10(2.+reference) if ref_field is not None else None + fields = [np.log10(2.+f) for f in fields] + + + if args.diff: + fig, axes = plot_imshow_diff(fields,reference,args.labels, vmin=args.vmin, vmax=args.vmax,cmap=args.cmap_diff, L=L, ref_label=ref_label) + else: + fig, axes = plot_imshow_with_reference(fields,reference,args.labels, vmin=args.vmin, vmax=args.vmax,cmap=args.cmap, L=L, ref_label=ref_label, cmap_diff=args.cmap_diff) + fig.suptitle(args.title) + + if args.output is not None: + fig.savefig(args.output,bbox_inches='tight') + else: + fig.savefig(args.directory+'slices.jpg',bbox_inches='tight') + + + +if __name__ == "__main__": + console_main() diff --git a/args_main.py b/sbmy_control/args_main.py similarity index 100% rename from args_main.py rename to sbmy_control/args_main.py diff --git a/cosmo_params.py b/sbmy_control/cosmo_params.py similarity index 100% rename from cosmo_params.py rename to sbmy_control/cosmo_params.py diff --git a/low_level.py b/sbmy_control/low_level.py similarity index 98% rename from low_level.py rename to sbmy_control/low_level.py index 8d56a98..26054bf 100644 --- a/low_level.py +++ b/sbmy_control/low_level.py @@ -225,6 +225,8 @@ def get_progress_from_logfile(filename): pass elif "Fatal" in line or "Error" in line: return -1, -1 + elif "Everything done successfully, exiting." in line: + current_operation = total_operations return current_operation, total_operations @@ -237,7 +239,6 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs k=0 limit=600 update_interval=0.2 - sleep(2) # Wait for the process to be launched, and for the previous log file to be overwritten if necessary. wait_until_file_exists(filename, verbose=verbose, limit=limit) current_operation, total_operations = get_progress_from_logfile(filename) previous_operation = 0 @@ -266,4 +267,4 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs if k*update_interval >= limit: print_message(f"Progress bar timed out after {limit} seconds.", 3, "low level", verbose=verbose) - return \ No newline at end of file + return diff --git a/main.py b/sbmy_control/main.py similarity index 84% rename from main.py rename to sbmy_control/main.py index 357f93a..350c97d 100644 --- a/main.py +++ b/sbmy_control/main.py @@ -1,9 +1,9 @@ def main(parsed_args): - from low_level import print_starting_module, print_message, print_ending_module, wait_until_file_exists + from .low_level import print_starting_module, print_message, print_ending_module, wait_until_file_exists from os.path import isfile - from args_main import parse_arguments_main + from .args_main import parse_arguments_main print_starting_module("control", verbose=parsed_args.verbose) main_dict = parse_arguments_main(parsed_args) @@ -12,22 +12,22 @@ def main(parsed_args): case "ICs" | "InitialConditions" | "InitialConditionsGenerator" | "ICsGenerator" | "ICsGen" | "ini": print_message("Running initial conditions generator.", 1, "control", verbose=parsed_args.verbose) - from ICs import main_ICs + from .ICs import main_ICs main_ICs(parsed_args) print_message("Initial conditions generator finished.", 1, "control", verbose=parsed_args.verbose) case "TS" | "timestepping": print_message("Running timestepping generator.", 1, "control", verbose=parsed_args.verbose) - from timestepping import main_timestepping + from .timestepping import main_timestepping main_timestepping(parsed_args) print_message("Timestepping generator finished.", 1, "control", verbose=parsed_args.verbose) case "PM" | "LPT" | "tCOLA" | "simbelmyne" | "sbmy": print_message(f"Running Simbelmyne in mode {main_dict["mode"]}.", 1, "control", verbose=parsed_args.verbose) - from simbelmyne import main_simbelmyne - from parameters_card import parse_arguments_card + from .simbelmyne import main_simbelmyne + from .parameters_card import parse_arguments_card from os.path import isfile card_dict = parse_arguments_card(parsed_args) @@ -47,8 +47,8 @@ def main(parsed_args): case "pre_sCOLA": print_message("Running pre-sCOLA.", 1, "control", verbose=parsed_args.verbose) - from scola import main_pre_scola - from parameters_card import parse_arguments_card + from .scola import main_pre_scola + from .parameters_card import parse_arguments_card card_dict = parse_arguments_card(parsed_args) @@ -60,8 +60,8 @@ def main(parsed_args): case "post_sCOLA": print_message("Running post-sCOLA.", 1, "control", verbose=parsed_args.verbose) - from scola import main_post_scola - from parameters_card import parse_arguments_card + from .scola import main_post_scola + from .parameters_card import parse_arguments_card card_dict = parse_arguments_card(parsed_args) @@ -73,8 +73,8 @@ def main(parsed_args): case "sCOLA": print_message("Running sCOLA.", 1, "control", verbose=parsed_args.verbose) - from scola import main_scola - from parameters_card import parse_arguments_card + from .scola import main_scola + from .parameters_card import parse_arguments_card card_dict = parse_arguments_card(parsed_args) @@ -86,12 +86,12 @@ def main(parsed_args): case "alltCOLA" | "allPM": print_message(f"Running ICs and Simbelmyne in mode {main_dict["mode"]}.", 1, "control", verbose=parsed_args.verbose) - from parameters_card import parse_arguments_card, main_parameter_card - from timestepping import main_timestepping - from ICs import main_ICs - from simbelmyne import main_simbelmyne + from .parameters_card import parse_arguments_card, main_parameter_card + from .timestepping import main_timestepping + from .ICs import main_ICs + from .simbelmyne import main_simbelmyne from os.path import isfile - from low_level import wait_until_file_exists + from .low_level import wait_until_file_exists card_dict = main_parameter_card(parsed_args) @@ -101,7 +101,7 @@ def main(parsed_args): ## Check consistency of ICs_gen and ICs if main_dict["ICs_gen"] == "monofonic": - from parameters_monofonic import parse_arguments_monofonic + from .parameters_monofonic import parse_arguments_monofonic monofonic_dict = parse_arguments_monofonic(parsed_args) if monofonic_dict["output"]+"DM_delta.h5" != card_dict["ICs"]: raise ValueError(f"ICs {card_dict['ICs']} does not match monofonic output {monofonic_dict['output']+'DM_delta.h5'}") @@ -133,10 +133,17 @@ def main(parsed_args): case "allsCOLA": print_message(f"Running ICs, pre_sCOLA, sCOLA and post_sCOLA.", 1, "control", verbose=parsed_args.verbose) +<<<<<<< HEAD:main.py from parameters_card import parse_arguments_card, main_parameter_card from timestepping import main_timestepping from ICs import main_ICs from scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles +======= + from .parameters_card import parse_arguments_card, main_parameter_card + from .timestepping import main_timestepping + from .ICs import main_ICs + from .scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles +>>>>>>> main:sbmy_control/main.py card_dict = main_parameter_card(parsed_args) @@ -146,7 +153,7 @@ def main(parsed_args): ## Check consistency of ICs_gen and OutputLPTPotential if main_dict["ICs_gen"] == "monofonic": - from parameters_monofonic import parse_arguments_monofonic + from .parameters_monofonic import parse_arguments_monofonic monofonic_dict = parse_arguments_monofonic(parsed_args) if monofonic_dict["output"]+"DM_phi.h5" != card_dict["OutputLPTPotential1"]: raise ValueError(f"OutputLPTPotential1 {card_dict['OutputLPTPotential1']} does not match monofonic output {monofonic_dict['output']+'DM_phi.h5'}") @@ -179,7 +186,7 @@ def main(parsed_args): main_scola(parsed_args) if parsed_args.execution == "slurm" and not have_all_tiles(parsed_args): from tqdm import tqdm - from low_level import progress_bar_from_logfile + from .low_level import progress_bar_from_logfile for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)): progress_bar_from_logfile(main_dict["logdir"]+main_dict["simname"]+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False) print_message("sCOLA finished.", 1, "control", verbose=parsed_args.verbose) @@ -220,15 +227,15 @@ def check_consistency(card_dict, mode): raise ValueError(f"ModulePMCOLA is not 1: ModulePMCOLA={card_dict["ModulePMCOLA"]}") -if __name__ == "__main__": +def console_main(): from argparse import ArgumentParser - from args_main import register_arguments_main - from timestepping import register_arguments_timestepping, main_timestepping - from parameters_card import register_arguments_card, main_parameter_card - from cosmo_params import register_arguments_cosmo - from parameters_monofonic import register_arguments_monofonic - from slurm_submission import register_arguments_slurm - from low_level import wait_until_file_exists + from .args_main import register_arguments_main + from .timestepping import register_arguments_timestepping, main_timestepping + from .parameters_card import register_arguments_card, main_parameter_card + from .cosmo_params import register_arguments_cosmo + from .parameters_monofonic import register_arguments_monofonic + from .slurm_submission import register_arguments_slurm + from .low_level import wait_until_file_exists parser = ArgumentParser(description="Run sCOLA.") register_arguments_main(parser) @@ -238,4 +245,9 @@ if __name__ == "__main__": register_arguments_card(parser) register_arguments_cosmo(parser) parsed_args = parser.parse_args() - main(parsed_args) \ No newline at end of file + main(parsed_args) + + +if __name__ == "__main__": + console_main() + \ No newline at end of file diff --git a/monofonic.py b/sbmy_control/monofonic.py similarity index 83% rename from monofonic.py rename to sbmy_control/monofonic.py index 4fe11ee..134b55b 100644 --- a/monofonic.py +++ b/sbmy_control/monofonic.py @@ -2,8 +2,8 @@ path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC" def main_monofonic(parsed_args): - from parameters_monofonic import main_parameters_monofonic - from low_level import print_starting_module, print_message, print_ending_module + from .parameters_monofonic import main_parameters_monofonic + from .low_level import print_starting_module, print_message, print_ending_module from os.path import isfile import subprocess @@ -27,8 +27,8 @@ def main_monofonic(parsed_args): print_message("Monofonic finished.", 1, "monofonic", verbose=parsed_args.verbose) elif parsed_args.execution == "slurm": - from slurm_submission import create_slurm_script, parse_arguments_slurm - from args_main import parse_arguments_main + from .slurm_submission import create_slurm_script, parse_arguments_slurm + from .args_main import parse_arguments_main print_message("Running monofonic in slurm mode.", 1, "monofonic", verbose=parsed_args.verbose) slurm_dict=parse_arguments_slurm(parsed_args) main_dict=parse_arguments_main(parsed_args) @@ -67,11 +67,11 @@ def main_monofonic(parsed_args): if __name__ == "__main__": from argparse import ArgumentParser - from parameters_monofonic import register_arguments_monofonic - from args_main import register_arguments_main - from parameters_card import register_arguments_card_for_ICs - from cosmo_params import register_arguments_cosmo - from slurm_submission import register_arguments_slurm + from .parameters_monofonic import register_arguments_monofonic + from .args_main import register_arguments_main + from .parameters_card import register_arguments_card_for_ICs + from .cosmo_params import register_arguments_cosmo + from .slurm_submission import register_arguments_slurm parser = ArgumentParser(description="Run monofonIC initial conditions generator for a Simbelmyne simulation.") # TODO: reduce the volume of arguments @@ -82,4 +82,4 @@ if __name__ == "__main__": register_arguments_cosmo(parser) parsed_args = parser.parse_args() - main_monofonic(parsed_args) \ No newline at end of file + main_monofonic(parsed_args) diff --git a/parameters_card.py b/sbmy_control/parameters_card.py similarity index 91% rename from parameters_card.py rename to sbmy_control/parameters_card.py index 082c297..7381759 100644 --- a/parameters_card.py +++ b/sbmy_control/parameters_card.py @@ -47,6 +47,7 @@ def register_arguments_card(parser:ArgumentParser): parser.add_argument("--OutputFCsDensity", type=str, default=None, help="Output FCs density file.") parser.add_argument("--OutputFCsSnapshot", type=str, default=None, help="Output FCs snapshot file.") parser.add_argument("--OutputRngStateLPT", type=str, default=None, help="Output RNG state file.") +<<<<<<< HEAD:parameters_card.py ## Tests with phiBCs and density parser.add_argument("--WriteGravPot", type=bool, default=False, help="Write gravitational potential.") parser.add_argument("--OutputGravitationalPotentialBase", type=str, default=None, help="Output gravitational potential base.") @@ -56,6 +57,12 @@ def register_arguments_card(parser:ArgumentParser): parser.add_argument("--MeshDensity", type=int, default=None, help="Mesh for density.") parser.add_argument("--LoadPhiBCs", type=bool, default=False, help="Load phiBCs.") parser.add_argument("--InputPhiBCsBase", type=str, default=None, help="Input phiBCs file base.") +======= + parser.add_argument("--WriteReferenceFrame", type=bool, default=False, help="Write reference frame (COCA).") + parser.add_argument("--OutputMomentaBase", type=str, default=None, help="Output momenta base (COCA).") + parser.add_argument("--ReadReferenceFrame", type=bool, default=False, help="Read reference frame (COCA).") + parser.add_argument("--InputMomentaBase", type=str, default=None, help="Read momenta base (COCA).") +>>>>>>> main:sbmy_control/parameters_card.py def register_arguments_card_for_ICs(parser:ArgumentParser): @@ -82,8 +89,8 @@ def parse_arguments_card(parsed_args): """ Parse the arguments for the parameter card. """ - from args_main import parse_arguments_main - from cosmo_params import parse_arguments_cosmo + from .args_main import parse_arguments_main + from .cosmo_params import parse_arguments_cosmo cosmo_dict=parse_arguments_cosmo(parsed_args) card_dict=dict( @@ -121,6 +128,10 @@ def parse_arguments_card(parsed_args): GenerateLightcone=parsed_args.GenerateLightcone, OutputAlsoFCs=parsed_args.OutputAlsoFCs, Observer=parsed_args.Observer, + WriteReferenceFrame=parsed_args.WriteReferenceFrame, + OutputMomentaBase=parsed_args.OutputMomentaBase, + ReadReferenceFrame=parsed_args.ReadReferenceFrame, + InputMomentaBase=parsed_args.InputMomentaBase, N_tiles=parsed_args.N_tiles, Np_buffer=parsed_args.Np_buffer, Np_lpt_buffer=parsed_args.Np_lpt_buffer, @@ -222,6 +233,7 @@ def parse_arguments_card(parsed_args): card_dict["OutputFCsSnapshot"] = main_dict["resultdir"]+"final_particles_"+main_dict["simname"]+".gadget3" if card_dict["OutputRngStateLPT"] is None: card_dict["OutputRngStateLPT"] = main_dict["workdir"]+"rng_state.h5" +<<<<<<< HEAD:parameters_card.py ## Tests with phiBCs and density if card_dict["OutputGravitationalPotentialBase"] is None: card_dict["OutputGravitationalPotentialBase"] = main_dict["workdir"]+"gravpot_"+main_dict["simname"] @@ -233,6 +245,12 @@ def parse_arguments_card(parsed_args): card_dict["MeshDensity"] = card_dict["N_PM_mesh"] if card_dict["InputPhiBCsBase"] is None: card_dict["InputPhiBCsBase"] = main_dict["workdir"]+"gravpot_tCOLA" +======= + if card_dict["OutputMomentaBase"] is None: + card_dict["OutputMomentaBase"] = main_dict["workdir"]+"momenta_"+main_dict["simname"]+"_" + if card_dict["InputMomentaBase"] is None: + card_dict["InputMomentaBase"] = main_dict["workdir"]+"momenta_"+main_dict["simname"]+"_" +>>>>>>> main:sbmy_control/parameters_card.py return card_dict @@ -242,7 +260,7 @@ def parse_arguments_card_for_ICs(parsed_args): """ Parse the arguments for the parameter card for ICs. """ - from args_main import parse_arguments_main + from .args_main import parse_arguments_main main_dict = parse_arguments_main(parsed_args) card_dict = dict( @@ -282,7 +300,7 @@ def parse_arguments_card_for_timestepping(parsed_args): """ Parse the arguments for the parameter card for timestepping. """ - from args_main import parse_arguments_main + from .args_main import parse_arguments_main main_dict = parse_arguments_main(parsed_args) card_dict = dict( @@ -351,6 +369,7 @@ def create_parameter_card_dict( OutputFCsDensity:str = 'fcs_density.h5', OutputFCsSnapshot:str = 'fcs_particles.gadget3', +<<<<<<< HEAD:parameters_card.py ## Tests with phiBCs and density WriteGravPot:bool = True, OutputGravitationalPotentialBase:str = 'gravitational_potential.h5', @@ -360,6 +379,13 @@ def create_parameter_card_dict( MeshDensity:int = 128, LoadPhiBCs:bool = False, InputPhiBCsBase:str = 'gravitational_potential.h5', +======= + ## COCA parameters + WriteReferenceFrame:bool = False, + OutputMomentaBase:str = 'momenta_', + ReadReferenceFrame:bool = False, + InputMomentaBase:str = 'momenta_', +>>>>>>> main:sbmy_control/parameters_card.py ## Cosmological parameters h:float = 0.6732, @@ -415,6 +441,10 @@ def create_parameter_card_dict( Observer2=Observer[2], OutputFCsDensity=OutputFCsDensity, OutputFCsSnapshot=OutputFCsSnapshot, + WriteReferenceFrame=int(WriteReferenceFrame), + OutputMomentaBase=OutputMomentaBase, + ReadReferenceFrame=int(ReadReferenceFrame), + InputMomentaBase=InputMomentaBase, NumberOfTilesPerDimension=N_tiles, NumberOfParticlesInBuffer=Np_buffer, NumberOfParticlesInLPTBuffer=Np_lpt_buffer, @@ -452,7 +482,7 @@ def write_parameter_card(parameter_card_dict:dict, filename:str, verbose:int = 1 if verbose < 2: from io import BytesIO - from low_level import stdout_redirector, stderr_redirector + from .low_level import stdout_redirector, stderr_redirector f = BytesIO() g = BytesIO() @@ -471,7 +501,7 @@ def main_parameter_card(parsed_args): """ Main function for the parameter card. """ - from low_level import print_message, print_starting_module, print_ending_module + from .low_level import print_message, print_starting_module, print_ending_module print_starting_module("card", verbose=parsed_args.verbose) print_message("Parsing arguments for the parameter card.", 1, "card", verbose=parsed_args.verbose) card_dict = parse_arguments_card(parsed_args) @@ -487,8 +517,8 @@ def main_parameter_card(parsed_args): return card_dict if __name__ == "__main__": - from args_main import register_arguments_main - from cosmo_params import register_arguments_cosmo + from .args_main import register_arguments_main + from .cosmo_params import register_arguments_cosmo parser = ArgumentParser(description="Create sbmy parameter card.") register_arguments_main(parser) @@ -496,4 +526,4 @@ if __name__ == "__main__": register_arguments_cosmo(parser) parsed_args = parser.parse_args() - main_parameter_card(parsed_args) \ No newline at end of file + main_parameter_card(parsed_args) diff --git a/parameters_monofonic.py b/sbmy_control/parameters_monofonic.py similarity index 92% rename from parameters_monofonic.py rename to sbmy_control/parameters_monofonic.py index ead1055..e4a2169 100644 --- a/parameters_monofonic.py +++ b/sbmy_control/parameters_monofonic.py @@ -16,9 +16,9 @@ def parse_arguments_monofonic(parsed_args): """ Parse the arguments for the monofonIC parameters. """ - from args_main import parse_arguments_main - from parameters_card import parse_arguments_card_for_ICs - from cosmo_params import parse_arguments_cosmo + from .args_main import parse_arguments_main + from .parameters_card import parse_arguments_card_for_ICs + from .cosmo_params import parse_arguments_cosmo main_dict = parse_arguments_main(parsed_args) card_dict = parse_arguments_card_for_ICs(parsed_args) @@ -71,7 +71,7 @@ def get_config_from_dict(monofonic_dict): config["setup"] = { "GridRes": monofonic_dict["gridres"], "BoxLength": monofonic_dict["boxlength"], - "zstart": 999.0, + "zstart": 99.0, "LPTorder": 2, "DoBaryons": False, "DoBaryonVrel": False, @@ -131,7 +131,7 @@ def get_config_from_dict(monofonic_dict): def main_parameters_monofonic(parsed_args): - from low_level import print_message + from .low_level import print_message print_message("Parsing arguments for the config file.", 1, "monofonic", verbose=parsed_args.verbose) monofonic_dict = parse_arguments_monofonic(parsed_args) @@ -144,9 +144,9 @@ def main_parameters_monofonic(parsed_args): if __name__ == "__main__": - from args_main import register_arguments_main - from parameters_card import register_arguments_card_for_ICs - from cosmo_params import register_arguments_cosmo + from .args_main import register_arguments_main + from .parameters_card import register_arguments_card_for_ICs + from .cosmo_params import register_arguments_cosmo parser = ArgumentParser(description="Create monofonIC configuration file.") register_arguments_main(parser) @@ -155,4 +155,4 @@ if __name__ == "__main__": register_arguments_cosmo(parser) parsed_args = parser.parse_args() - main_parameters_monofonic(parsed_args) \ No newline at end of file + main_parameters_monofonic(parsed_args) diff --git a/progress_bar.py b/sbmy_control/progress_bar.py similarity index 88% rename from progress_bar.py rename to sbmy_control/progress_bar.py index 5155b20..b61fa8b 100644 --- a/progress_bar.py +++ b/sbmy_control/progress_bar.py @@ -1,7 +1,7 @@ if __name__ == "__main__": from argparse import ArgumentParser from tqdm import tqdm - from low_level import progress_bar_from_logfile + from .low_level import progress_bar_from_logfile parser = ArgumentParser(description="Progress bar from log files.") parser.add_argument("-l","--logdir", type=str, help="Log directory.") @@ -12,4 +12,4 @@ if __name__ == "__main__": parsed_args = parser.parse_args() for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)): - progress_bar_from_logfile(parsed_args.logdir+parsed_args.simname+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False) \ No newline at end of file + progress_bar_from_logfile(parsed_args.logdir+parsed_args.simname+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False) diff --git a/scola.py b/sbmy_control/scola.py similarity index 85% rename from scola.py rename to sbmy_control/scola.py index ff341ab..5f646f1 100644 --- a/scola.py +++ b/sbmy_control/scola.py @@ -1,6 +1,8 @@ + + def main_scola(parsed_args): - from args_main import parse_arguments_main - from low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile, wait_until_file_exists + from .args_main import parse_arguments_main + from .low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile, wait_until_file_exists from os.path import isfile import subprocess @@ -19,7 +21,7 @@ def main_scola(parsed_args): return if parsed_args.execution == "local": - from parameters_card import parse_arguments_card + from .parameters_card import parse_arguments_card from tqdm import tqdm card_dict = parse_arguments_card(parsed_args) print_message("Running sCOLA in local mode.", 1, "scola", verbose=parsed_args.verbose) @@ -50,14 +52,16 @@ def main_scola(parsed_args): print_message("sCOLA finished.", 1, "scola", verbose=parsed_args.verbose) elif parsed_args.execution == "slurm": - from slurm_submission import create_slurm_script, parse_arguments_slurm - from args_main import parse_arguments_main + from .slurm_submission import create_slurm_script, parse_arguments_slurm, limit_slurm_arrays + from .args_main import parse_arguments_main + from .parameters_card import parse_arguments_card import os print_message("Running scola in slurm mode.", 1, "scola", verbose=parsed_args.verbose) slurm_dict=parse_arguments_slurm(parsed_args) main_dict=parse_arguments_main(parsed_args) + card_dict=parse_arguments_card(parsed_args) - if have_no_tiles(parsed_args) or parsed_args.force: + if (have_no_tiles(parsed_args) or parsed_args.force) and card_dict["N_tiles"]**3 < limit_slurm_arrays : ## Submit all boxes print_message("Submitting all boxes.", 2, "scola", verbose=parsed_args.verbose) slurm_script = slurm_dict["scripts"]+"scola_"+main_dict["simname"]+".sh" @@ -93,6 +97,7 @@ def main_scola(parsed_args): else: ## Submit missing boxes + from time import sleep missing_tiles_arrays = get_missing_tiles_arrays(parsed_args) print_message(f"Submitting missing boxes: {missing_tiles_arrays}.", 2, "scola", verbose=parsed_args.verbose) @@ -127,6 +132,7 @@ def main_scola(parsed_args): subprocess.run(command_args) print_message("sCOLA job submitted.", 2, "scola", verbose=parsed_args.verbose) + sleep((missing_tiles[1]-missing_tiles[0])*1.0) # Sleep for a bit to avoid overloading the scheduler os.remove(slurm_script) # Remove the script after submission (because it is specific to the missing tiles) @@ -142,15 +148,15 @@ def main_pre_scola(parsed_args): If they already exist, it does nothing. If all tiles exist, raises error. """ from os.path import isfile - from low_level import print_starting_module, print_message, print_ending_module - from parameters_card import parse_arguments_card + from .low_level import print_starting_module, print_message, print_ending_module + from .parameters_card import parse_arguments_card print_starting_module("pre-scola", verbose=parsed_args.verbose) card_dict = parse_arguments_card(parsed_args) if not isfile(card_dict["OutputLPTPotential1"]) or not isfile(card_dict["OutputLPTPotential2"]) or parsed_args.force: if not have_all_tiles(parsed_args): print_message("Running pre-scola.", 1, "pre-scola", verbose=parsed_args.verbose) - from simbelmyne import main_simbelmyne + from .simbelmyne import main_simbelmyne main_simbelmyne(parsed_args) else: raise NotImplementedError("All tiles exists, so calling simbelmyne would generate the final output instead of the LPT potentials.") @@ -166,8 +172,8 @@ def main_post_scola(parsed_args): If the output already exists, it does nothing. If tiles are missing, print the missing tiles. """ from os.path import isfile - from low_level import print_starting_module, print_message, print_ending_module - from parameters_card import parse_arguments_card + from .low_level import print_starting_module, print_message, print_ending_module + from .parameters_card import parse_arguments_card print_starting_module("post-scola", verbose=parsed_args.verbose) card_dict = parse_arguments_card(parsed_args) @@ -180,7 +186,7 @@ def main_post_scola(parsed_args): if (card_dict["WriteFinalDensity"] and not isfile(card_dict["OutputFinalDensity"])) or (card_dict["WriteFinalSnapshot"] and not isfile(card_dict["OutputFinalSnapshot"])) or parsed_args.force: if have_all_tiles(parsed_args): print_message("Running post-scola.", 1, "post-scola", verbose=parsed_args.verbose) - from simbelmyne import main_simbelmyne + from .simbelmyne import main_simbelmyne main_simbelmyne(parsed_args) else: missing_tiles_arrays = get_missing_tiles_arrays(parsed_args) @@ -197,7 +203,7 @@ def main_post_scola(parsed_args): def have_all_tiles(parsed_args): from os.path import isfile - from parameters_card import parse_arguments_card + from .parameters_card import parse_arguments_card card_dict = parse_arguments_card(parsed_args) nboxes_tot = int(parsed_args.N_tiles**3) @@ -210,7 +216,7 @@ def have_all_tiles(parsed_args): def have_no_tiles(parsed_args): from os.path import isfile - from parameters_card import parse_arguments_card + from .parameters_card import parse_arguments_card card_dict = parse_arguments_card(parsed_args) nboxes_tot = int(parsed_args.N_tiles**3) @@ -223,17 +229,24 @@ def have_no_tiles(parsed_args): def get_missing_tiles_arrays(parsed_args): from os.path import isfile - from parameters_card import parse_arguments_card + from .parameters_card import parse_arguments_card + from .slurm_submission import limit_slurm_arrays card_dict = parse_arguments_card(parsed_args) nboxes_tot = int(parsed_args.N_tiles**3) missing_tiles_arrays = [] in_sequence_of_missing = False + len_sequence_of_missing = 0 for b in range(1,nboxes_tot+1): if not isfile(card_dict["OutputTilesBase"]+str(b)+".h5"): + len_sequence_of_missing += 1 if not in_sequence_of_missing: missing_tiles_arrays.append([b]) in_sequence_of_missing = True + len_sequence_of_missing = 1 + if b%limit_slurm_arrays==limit_slurm_arrays-1: + missing_tiles_arrays[-1].append(b) + in_sequence_of_missing = False elif in_sequence_of_missing: missing_tiles_arrays[-1].append(b-1) in_sequence_of_missing = False @@ -247,13 +260,13 @@ def get_missing_tiles_arrays(parsed_args): if __name__ == "__main__": from argparse import ArgumentParser - from args_main import register_arguments_main - from timestepping import register_arguments_timestepping, main_timestepping - from parameters_card import register_arguments_card, main_parameter_card - from cosmo_params import register_arguments_cosmo - from parameters_monofonic import register_arguments_monofonic - from slurm_submission import register_arguments_slurm - from low_level import wait_until_file_exists + from .args_main import register_arguments_main + from .timestepping import register_arguments_timestepping, main_timestepping + from .parameters_card import register_arguments_card, main_parameter_card + from .cosmo_params import register_arguments_cosmo + from .parameters_monofonic import register_arguments_monofonic + from .slurm_submission import register_arguments_slurm + from .low_level import wait_until_file_exists parser = ArgumentParser(description="Run sCOLA.") register_arguments_main(parser) @@ -274,4 +287,4 @@ if __name__ == "__main__": if parsed_args.execution == "slurm": for b in range(1,nboxes_tot+1): wait_until_file_exists(f"{card_dict['OutputTilesBase']}{b}.h5", verbose=parsed_args.verbose, limit=5*60) - main_post_scola(parsed_args) \ No newline at end of file + main_post_scola(parsed_args) diff --git a/sbmy_control/scripts/__init__.py b/sbmy_control/scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/sbmy_control/scripts/convert_snapshot_to_density.py b/sbmy_control/scripts/convert_snapshot_to_density.py new file mode 100644 index 0000000..dadefed --- /dev/null +++ b/sbmy_control/scripts/convert_snapshot_to_density.py @@ -0,0 +1,82 @@ +from pysbmy.density import get_density_pm_snapshot +from pysbmy.snapshot import read_snapshot +import argparse + + +def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0, 0.0, 0.0)): + """ + Convert a snapshot to a density field. + + Parameters + ---------- + snapshot_path : str + Path to the snapshot file. + output_path : str + Path to the output density file. + N : int + Size of the density field grid (N x N x N). + corner : tuple of float + Corner of the box (x, y, z). + """ + # Read the snapshot + print("Reading snapshot...") + snap = read_snapshot(snapshot_path) + + if N is None: + N = snap.Np0 + + # Calculate density + print("Calculating density...") + F = get_density_pm_snapshot(snap, N, N, N, corner[0], corner[1], corner[2]) + + # Write density to file + print("Writing density...") + F.write(output_path) + print("Density written to", output_path) + print("Done.") + + +def console_main(): + parser = argparse.ArgumentParser(description="Convert snapshot to density.") + parser.add_argument( + "-S", + "--snapshot", + type=str, + required=True, + help="Path to the snapshot file.", + ) + parser.add_argument( + "-o", + "--output", + type=str, + required=True, + help="Path to the output density file.", + ) + parser.add_argument( + "-N", + "--N", + type=int, + default=None, + help="Size of the density field grid (N x N x N).", + ) + parser.add_argument( + "-c", + "--corner", + type=float, + nargs=3, + default=[0.0, 0.0, 0.0], + help="Corner of the box (x, y, z).", + ) + + args = parser.parse_args() + + convert_snapshot_to_density( + snapshot_path=args.snapshot, + output_path=args.output, + N=args.N, + corner=args.corner, + ) + + +if __name__ == "__main__": + console_main() \ No newline at end of file diff --git a/sbmy_control/scripts/field_to_field.py b/sbmy_control/scripts/field_to_field.py new file mode 100644 index 0000000..c9137e2 --- /dev/null +++ b/sbmy_control/scripts/field_to_field.py @@ -0,0 +1,134 @@ +from pysbmy.density import mesh_to_mesh +from pysbmy.field import Field, read_field +import numpy as np +import os + + +def field_to_field( + input_file:str, + output_file:str, + output_size:int|tuple[int,int,int]|list[int], + output_L:float|tuple[float,float,float]|list[float], + output_dpm:float|tuple[float,float,float]|list[float], + output_corner:tuple[float,float,float]|list[float], + boundary_conditions:int, + ): + + + ### Make sure all inputs are valid + if output_L is not None and output_dpm is not None: + raise ValueError("Either output_L or output_dpm can be specified, not both.") + + if isinstance(output_size, int): + output_size = (output_size, output_size, output_size) # N0, N1, N2 + elif len(output_size) == 1: + output_size = (output_size[0], output_size[0], output_size[0]) + + if output_L is not None: + if isinstance(output_L, float): + output_L = (output_L, output_L, output_L) + elif len(output_L) == 1: + output_L = (output_L[0], output_L[0], output_L[0]) + + if output_dpm is None: + if output_L is None: + output_dpm = (-1, -1, -1) + else: + output_dpm = (output_L[0] / output_size[0], output_L[1] / output_size[1], output_L[2] / output_size[2]) + elif isinstance(output_dpm, float): + output_dpm = (output_dpm, output_dpm, output_dpm) # d0, d1, d2 + elif len(output_dpm) == 1: + output_dpm = (output_dpm[0], output_dpm[0], output_dpm[0]) + + if not os.path.exists(input_file): + raise FileNotFoundError(f"Input file {input_file} does not exist.") + + + + # Read the input field + print(f"Reading input field from {input_file}") + input_field = read_field(input_file) + + if input_field.rank != 1 or input_field.data.ndim != 3: + raise NotImplementedError("Only 3D scalar fields are supported for now.") + + L0 = input_field.L0 + L1 = input_field.L1 + L2 = input_field.L2 + N0 = input_field.N0 + N1 = input_field.N1 + N2 = input_field.N2 + corner0 = input_field.corner0 + corner1 = input_field.corner1 + corner2 = input_field.corner2 + + d0_in = L0 / N0 + d1_in = L1 / N1 + d2_in = L2 / N2 + + d0_out = output_dpm[0] if output_dpm[0] > 0 else d0_in + d1_out = output_dpm[1] if output_dpm[1] > 0 else d1_in + d2_out = output_dpm[2] if output_dpm[2] > 0 else d2_in + + offset_out_x = (output_corner[0] - corner0) + offset_out_y = (output_corner[1] - corner1) + offset_out_z = (output_corner[2] - corner2) + + print("-----------------------------------------") + print(f"Input field size: {N0} x {N1} x {N2}") + print(f"Output field size: {output_size[0]} x {output_size[1]} x {output_size[2]}") + print(f"Input field dpm: {d0_in:.3f} x {d1_in:.3f} x {d2_in:.3f}") + print(f"Output field dpm: {d0_out:.3f} x {d1_out:.3f} x {d2_out:.3f}") + print(f"Input field corner: ({corner0:.1f}, {corner1:.1f}, {corner2:.1f})") + print(f"Output field corner: ({output_corner[0]:.1f}, {output_corner[1]:.1f}, {output_corner[2]:.1f})") + print(f"Boundary conditions: {'periodic' if boundary_conditions == 1 else 'non-periodic'}") + print("-----------------------------------------") + + input_grid = input_field.data + + output_grid = np.zeros(output_size, dtype=input_grid.dtype) + + + # Mesh to mesh interpolation + print("Interpolating field...") + mesh_to_mesh(input_grid, output_grid, d0_in, d1_in, d2_in, d0_out, d1_out, d2_out, offset_out_x, offset_out_y, offset_out_z, boundary_conditions) + + # Create the output field + output_field = Field( + L0=output_size[0] * d0_out, + L1=output_size[1] * d1_out, + L2=output_size[2] * d2_out, + corner0=output_corner[0], + corner1=output_corner[1], + corner2=output_corner[2], + rank=input_field.rank, + N0=output_size[0], + N1=output_size[1], + N2=output_size[2], + time=input_field.time, + data=output_grid + ) + + # Write the output field + print(f"Writing output field to {output_file}") + output_field.write(output_file) + print("Done.") + + +def console_main(): + import argparse + parser = argparse.ArgumentParser(description="Convert a field from one size to another.") + parser.add_argument("-i","--input_file", type=str, help="Input field file") + parser.add_argument("-o","--output_file", type=str, help="Output field file") + parser.add_argument("-N","--output_size", type=int, nargs="+", help="Output field size (N0, N1, N2)") + parser.add_argument("-L","--output_L", type=float, nargs="+", default=None, help="Output field size (L0, L1, L2)") + parser.add_argument("-dpm","--output_dpm", type=float, nargs="+", default=None, help="Output field dpm (d0, d1, d2)") + parser.add_argument("-corner","--output_corner", type=float, nargs=3, default=(0.,0.,0.), help="Output field corner (corner0, corner1, corner2)") + parser.add_argument("-BC","--boundary_conditions", type=int, default=1, help="Boundary conditions (1: periodic, 3: non-periodic)") + args = parser.parse_args() + + field_to_field(args.input_file, args.output_file, args.output_size, args.output_L, args.output_dpm, args.output_corner, args.boundary_conditions) + + +if __name__ == "__main__": + console_main() \ No newline at end of file diff --git a/sbmy_control/scripts/gather_tiles.py b/sbmy_control/scripts/gather_tiles.py new file mode 100644 index 0000000..13d3eda --- /dev/null +++ b/sbmy_control/scripts/gather_tiles.py @@ -0,0 +1,128 @@ +import numpy as np +from pysbmy.snapshot import read_tile +from pysbmy.field import Field +from pysbmy.density import get_density_pm, density_to_delta +from pysbmy import c_float_t +import tqdm +import argparse + +def get_indices(tile, N_TILES0, N_TILES1, N_TILES2): + """Get the indices of the tile in a 3D grid.""" + i = (tile // (N_TILES1 * N_TILES2))%N_TILES0 + j = ((tile - N_TILES1 * N_TILES2 * i) // N_TILES2)%N_TILES1 + k = (tile - N_TILES2 * j - N_TILES1 * N_TILES2 * i)%N_TILES2 + return i, j, k + + +def tile_to_density_with_buffer(T, N, d, buffer): + """ + Convert a tile to density with a buffer. + """ + # Create a buffer for the density + A = np.zeros((N+2*buffer, N+2*buffer, N+2*buffer), dtype=np.float32) + + # Get the density of the tile + A = get_density_pm(T.pos-T.corner_position.astype(c_float_t)+d*buffer, A, d) + return A + + +def add_density_tile(A,A_tile,corner_indices): + N = A.shape[0] + Np = A_tile.shape[0] + i0, j0, k0 = corner_indices + + # Create index arrays for the tile + i_idx = (np.arange(Np) + i0) % N + j_idx = (np.arange(Np) + j0) % N + k_idx = (np.arange(Np) + k0) % N + + # Use np.ix_ to get all combinations of indices + A[np.ix_(i_idx, j_idx, k_idx)] += A_tile + + +def gather_density(A, folder, tile_base, Np_tile, dpm, buffer, N_TILES): + """ + Gather the density from the tiles. + """ + for tile in tqdm.tqdm(range(N_TILES**3), desc="Density of tiles", unit="tiles"): + T=read_tile(folder+tile_base+str(tile+1)+".h5", int(Np_tile**3)) + # Get the corner position of the tile + corner_position = T.corner_position + # Get the corner indices of the tile + i,j,k = get_indices(tile, N_TILES, N_TILES, N_TILES) + corner_grid_indices = (i*Np_tile-buffer, j*Np_tile-buffer, k*Np_tile-buffer) + # Get the density of the tile with a buffer + A_tile = tile_to_density_with_buffer(T, Np_tile, dpm, buffer) + # Add the density of the tile to the grid + add_density_tile(A, A_tile, corner_grid_indices) + + + +def gather_tiles(folder, tile_base, L, Np, N_TILES, buffer): + """ + Gather sCOLA tiles into a single density field. + + Parameters + ---------- + folder : str + Folder containing the tiles. + tile_base : str + Base name of the tiles. + L : float + Size of the box in Mpc/h. + Np : int + Number of cells per dimension for the full box. + N_TILES : int + Number of tiles per dimension. + buffer : int + Buffer size for the density field of tiles. + """ + Np_tile = Np//N_TILES + dpm = L/Np_tile + + print("Memory allocation for the grid...") + A=np.zeros((Np,Np,Np), dtype=np.float32) + + print("Starting to read the tiles...") + gather_density(A, folder, tile_base, Np_tile, dpm, buffer, N_TILES) + + print("Finished reading the tiles.") + A=density_to_delta(A,-1) + + print("Converting to field...") + F=Field(L,L,L, 0.,0.,0., 1, Np,Np,Np, 1., A) + + print("Saving field...") + F.write(folder+"../results/final_density_sCOLA.h5") + print("Density field saved to", folder+"../results/final_density_sCOLA.h5") + print("Done.") + + + +def console_main(): + parser = argparse.ArgumentParser(description="Gather density from tiles.") + parser.add_argument("-d","--folder", type=str, default="./", help="Folder containing the tiles") + parser.add_argument("--tile_base", type=str, default="sCOLA_tile", help="Base name of the tiles") + parser.add_argument("-L","--L", type=int, default=1920, help="Size of the box in Mpc/h") + parser.add_argument("-Np","--Np", type=int, default=80, help="Number of cells per dimension for the full box") + parser.add_argument("-Nt","--N_tiles", type=int, default=4, help="Number of tiles per dimension.") + parser.add_argument("--buffer", type=int, default=40, help="Buffer size for the density field of tiles") + args = parser.parse_args() + + L = args.L + Np = args.Np + N_TILES = args.N_tiles + buffer = args.buffer + + folder = args.folder + tile_base = args.tile_base + + Np_tile = Np//N_TILES + dpm = L/Np_tile + + gather_tiles(folder, tile_base, L, Np, N_TILES, buffer) + + + +if __name__ == "__main__": + console_main() \ No newline at end of file diff --git a/sbmy_control/scripts/scola_submit.py b/sbmy_control/scripts/scola_submit.py new file mode 100644 index 0000000..e68e56f --- /dev/null +++ b/sbmy_control/scripts/scola_submit.py @@ -0,0 +1,502 @@ +import tqdm +import argparse +import numpy as np +import os +import subprocess +import time + + +def create_scola_slurm_script(slurmfile, box): + """ + Create a slurm script for sCOLA. + Parameters + ---------- + slurmfile : str + Path to the slurm script file. + box : str + Box number to be replaced in the slurm script. + """ + # Read the slurm file + with open(slurmfile, "r") as f: + slurm_script = f.read() + + # Replace the placeholders in the slurm script + slurm_script = slurm_script.replace("BOX", box) + + # Write the modified slurm script to a new file + with open(slurmfile+f".{box}", "w") as f: + f.write(slurm_script) + + +def submit_slurm_job(slurmfile): + """ + Submit a slurm job using the sbatch command. + Parameters + ---------- + slurmfile : str + Path to the slurm script file. + Returns + ------- + str + Job ID of the submitted job. None if the submission failed. + """ + # Submit the job + result = subprocess.run(["sbatch", slurmfile], capture_output=True, text=True) + + # Check if the submission was successful + if result.returncode != 0: + print(f"Error submitting job: {result.stderr}") + return None + + # Get the job ID from the output + job_id = result.stdout.split()[-1] + + return job_id + + +def convert_time_to_seconds(time_str): + """ + Convert a time string of the format D-HH:MM:SS or HH:MM:SS or MM:SS to seconds. + """ + time_parts = time_str.split("-") + if len(time_parts) == 2: + days = int(time_parts[0]) + time_str = time_parts[1] + else: + days = 0 + + time_parts = time_str.split(":") + if len(time_parts) == 3: + hours, minutes, seconds = map(int, time_parts) + elif len(time_parts) == 2: + hours, minutes = map(int, time_parts) + seconds = 0 + else: + raise ValueError("Invalid time format") + + total_seconds = days * 86400 + hours * 3600 + minutes * 60 + seconds + return total_seconds + + +def convert_seconds_to_time(seconds): + """ + Convert seconds to a time string of the format D-HH:MM:SS. + """ + seconds = int(seconds) + if seconds < 0: + return "N/A" + days = seconds // 86400 + seconds %= 86400 + hours = seconds // 3600 + seconds %= 3600 + minutes = seconds // 60 + seconds %= 60 + + if days > 0: + return f"{days}-{hours:02}:{minutes:02}:{seconds:02}" + if hours > 0: + return f"{hours:02}:{minutes:02}:{seconds:02}" + return f"{minutes:02}:{seconds:02}" + + +def check_job_status(job_id): + """ + Check the status of a job using the squeue command. + Returns the job status and running time. + Parameters + ---------- + job_id : str + Job ID of the job to check. + Returns + ------- + str + Job status. Possible values are 'R' (running), 'PD' (pending), 'X' (failed), 'CP' (completed). + int + Running time in seconds. -1 if the job is not found. + """ + # Check the job status + result = subprocess.run(["squeue", "-j", str(job_id)], capture_output=True, text=True) + + # Check if the job is still running + if result.returncode == 1: + return "X", -1 + + if len(result.stdout.split("\n")[1].split()) == 0: + return "X", -1 + + status = result.stdout.split("\n")[1].split()[4] + job_time = convert_time_to_seconds(result.stdout.split("\n")[1].split()[5]) + + return status, job_time + + +def get_job_id(jobname): + """ + Get the job ID from the job name using the squeue command. + """ + # Check the job status + result = subprocess.run(["squeue", "-n", jobname], capture_output=True, text=True) + + # Check if the job is still running + if result.returncode == 1: + return None + if len(result.stdout.split("\n")[1].split()) == 0: + return None + + # Get the job ID + job_id = result.stdout.split("\n")[1].split()[0] + + return job_id + + +def resubmit_job(slurmdir,slurmfile,job_ids_array,box,resubmit_count,error_count,MAX_RESUBMIT=10,MAX_ERRORS=10): + """ + Resubmit a job if it has failed. + Parameters + ---------- + slurmdir : str + Directory where the slurm scripts are saved. + slurmfile : str + Slurm script file. + job_ids_array : array + Array of job IDs for all previously submitted jobs. Indexed by box-1 number. + box : int + Box number of the job to resubmit. + resubmit_count : int + Number of resubmissions so far. + error_count : int + Number of errors so far. + MAX_RESUBMIT : int + Maximum number of resubmissions allowed. + MAX_ERRORS : int + Maximum number of errors allowed. + + Returns + ------- + int + Updated resubmit count. + int + Updated error count. + """ + + # Resubmit the job + job_id = submit_slurm_job(slurmdir+slurmfile+"."+str(box)) + + # Check if the job was submitted successfully + if job_id is None: + print(f"Error resubmitting job for box {box}") + error_count+=1 + # Check if the error count exceeds the maximum + if error_count >= MAX_ERRORS: + raise RuntimeError(f"Error count exceeded {MAX_ERRORS}. Stopping job submission.") + else: + job_ids_array[box-1] = int(job_id) + + resubmit_count += 1 + # Check if the resubmit count exceeds the maximum + if resubmit_count >= MAX_RESUBMIT: + raise RuntimeError(f"Resubmit count exceeded {MAX_RESUBMIT}. Stopping job submission.") + + return resubmit_count, error_count + + + +def check_previous_jobs(workdir,slurmdir,slurmfile,tilefile,sleeptime,job_ids_array,box,resubmit_count,error_count,MAX_RESUBMIT=10,MAX_ERRORS=10): + """ + Get the status of all previously submitted jobs. + For each job, check if it is running, completed, or failed. + If the job is failed, resubmit it. + Parameters + ---------- + workdir : str + Directory where the tiles are saved. + slurmdir : str + Directory where the slurm scripts are saved. + slurmfile : str + Slurm script file. + tilefile : str + Tile file name. + sleeptime : float + Sleep time between each job submission (in s). + job_ids_array : array + Array of job IDs for all previously submitted jobs. Indexed by box-1 number. + box : int + Up to which box the job status is checked. + resubmit_count : int + Number of resubmissions so far. + error_count : int + Number of errors so far. + MAX_RESUBMIT : int + Maximum number of resubmissions allowed. + MAX_ERRORS : int + Maximum number of errors allowed. + + Returns + ------- + dict + Dictionary with the job status categories and their corresponding box numbers. + int + Updated resubmit count. + int + Updated error count. + """ + job_status_categories = {'R':[],'CP':[],'PD':[],'X':[]} + + # Check the status of every previously submitted job + for prev_box in tqdm.tqdm(range(1,box), desc="Checking jobs", unit="boxes", leave=False, position=1): + # Check the job status + status, job_time = check_job_status(job_ids_array[prev_box-1]) + # Add the job status to the dictionary + if status not in job_status_categories: + job_status_categories[status] = [] + # If the status is 'X', check if the tile file was created + if status == 'X': + # Check if the tile file was created + if os.path.exists(workdir+f"{tilefile}{prev_box}.h5"): + job_status_categories['CP'].append(prev_box) # Classify as completed + else: + resubmit_count, error_count = resubmit_job(slurmdir,slurmfile,job_ids_array,prev_box,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS) + job_status_categories[status].append(prev_box) # Classify as failed + # Sleep for a while before resubmitting the next job + time.sleep(sleeptime) + # If the status is not 'X', record the job status + else: + job_status_categories[status].append(prev_box) + + return job_status_categories, resubmit_count, error_count + + + +def cap_number_of_jobs(job_status_categories,job_ids_array, max_jobs, sleep_time): + """ + Cap the number of jobs to a maximum number. + Parameters + ---------- + job_status_categories : dict + Dictionary with the job status categories and their corresponding box numbers. + job_ids_array : array + Array of job IDs for all previously submitted jobs. Indexed by box-1 number. + max_jobs : int + Maximum number of jobs allowed. + sleep_time : float + Sleep time between each job submission (in s). + + Returns + ------- + dict + Updated dictionary with the job status categories and their corresponding box numbers. + """ + discard_categories = ['CP', 'X'] # Completed and Failed + # Check the number of running /pending jobs + job_num = 0 + for status in job_status_categories.keys(): + if status not in discard_categories: + job_num += len(job_status_categories[status]) + + # We wait until the number of jobs is below the maximum + while job_num > max_jobs: + print(f"Number of open jobs: {job_num} > {max_jobs}. Waiting...") + for status in job_status_categories.keys(): + if status not in discard_categories: + for box in job_status_categories[status]: + # Check the new job status + new_status, job_time = check_job_status(job_ids_array[box-1]) + time.sleep(sleep_time) + if new_status in discard_categories: + job_num -= 1 + job_status_categories[new_status].append(box) # WARNING: We do not reclassify 'X' jobs as 'CP' + job_status_categories[status].remove(box) + + return job_status_categories + + +def print_summary_job_status(job_status_categories, box, resubmit_count, error_count): + print("---------------------------------------------------") + # Print summary of job statuses + print(f"Job statuses after box {box}:") + # Print a table with columns for each status and below the % of jobs in that status + row0 = f"{'Status':<14}" + for status in job_status_categories.keys(): + row0 += f"{status:>9} " + print(row0) + row1 = f"{'Percentage':<14}" + for status in job_status_categories.keys(): + row1 += f"{len(job_status_categories[status])/box*100:>9.1f}%" + print(row1) + # Print the rate of resubmissions + print(f"Resubmission rate: {resubmit_count/box*100:.2f}%") + print(f"Error count: {error_count}") + + + +def scola_submit(directory, + slurmdir=None, + workdir=None, + slurmfile="scola_sCOLA.sh", + tilefile="scola_tile", + jobname="sCOLA_", + N_tiles=4, + sleep=1.5, + force=False, + MAX_ERRORS=10, + MAX_RESUBMIT=10, + MAX_JOBS_AT_ONCE=48, + CHECK_EVERY=100): + + if slurmdir is None: + slurmdir = directory + "slurm_scripts/" + if workdir is None: + workdir = directory + "work/" + + + # Check that the slurm file exists + if not os.path.exists(slurmdir+slurmfile): + raise FileNotFoundError(f"Slurm file {slurmdir+slurmfile} does not exist.") + # Check that the work directory exists + if not os.path.exists(workdir): + raise FileNotFoundError(f"Work directory {workdir} does not exist.") + + # If force, remove all pre-existing tile files + if force: + count_removed = 0 + for box in range(1,N_tiles**3+1): + if os.path.exists(workdir+f"{tilefile}{box}.h5"): + os.remove(workdir+f"{tilefile}{box}.h5") + count_removed += 1 + print(f"Removed {count_removed} ({100*count_removed/N_tiles**3:.1f}%) pre-existing tile files.") + + # MAX_ERRORS = 10 + if MAX_RESUBMIT is None: + MAX_RESUBMIT = int(0.1*N_tiles**3) # 10% of the total number of jobs + # MAX_JOBS_AT_ONCE = int(3*128/8) # 3 nodes with 128 cores each, 8 jobs per core + # CHECK_EVERY = 100 + + error_count = 0 + resubmit_count = 0 + counter_for_checks = 0 + + job_ids_array = np.zeros((N_tiles**3,), dtype=int) + + + print("---------------------------------------------------") + print("Starting job submission for sCOLA tiles with the following parameters:") + print(f"Directory: {directory}") + print(f"Slurm file: {slurmdir}{slurmfile}") + print(f"Work directory: {workdir}") + print(f"Number of tiles: {N_tiles**3} tiles") + print(f"Sleep time: {sleep} s") + print(f"Max errors: {MAX_ERRORS} errors") + print(f"Max resubmits: {MAX_RESUBMIT} resubmits") + print(f"Max jobs at once: {MAX_JOBS_AT_ONCE} jobs") + print(f"Check every: {CHECK_EVERY} jobs") + print("---------------------------------------------------") + print(f"ETA: {convert_seconds_to_time(N_tiles**3*sleep*1.2)}") + print("Starting job submission...") + + + + for box in tqdm.tqdm(range(1,N_tiles**3+1), desc="Submitting jobs", unit="boxes"): + + # Check if the tile file already exists + if os.path.exists(workdir+f"{tilefile}{box}.h5"): + continue + + # Check if the slurm job is already running + job_id = get_job_id(f"{jobname}{box}") + if job_id is not None: + job_ids_array[box-1] = int(job_id) + time.sleep(sleep) + continue + + # Create the slurm script for the box + create_scola_slurm_script(slurmdir+slurmfile, str(box)) + + # Submit the job + job_id = submit_slurm_job(slurmdir+slurmfile+"."+str(box)) + + # Check if the job was submitted successfully + if job_id is None: + print(f"Error submitting job for box {box}") + error_count+=1 + else: + job_ids_array[box-1] = int(job_id) + + # Sleep for a while before submitting the next job + time.sleep(sleep) + + counter_for_checks += 1 + + # Check if the error count exceeds the maximum + if error_count >= MAX_ERRORS: + raise RuntimeError(f"Error count exceeded {MAX_ERRORS}. Stopping job submission.") + + # Check the job status every CHECK_EVERY jobs + if counter_for_checks >= CHECK_EVERY: + + counter_for_checks = 0 + + job_status_categories, resubmit_count, error_count = check_previous_jobs(workdir,slurmdir,slurmfile,tilefile,sleep,job_ids_array,box,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS) + print_summary_job_status(job_status_categories, box, resubmit_count, error_count) + job_status_categories = cap_number_of_jobs(job_status_categories,job_ids_array,MAX_JOBS_AT_ONCE,sleep) + + + + print("All jobs submitted. Now checking the status of the jobs.") + + + job_status_categories, resubmit_count, error_count = check_previous_jobs(workdir,slurmdir,slurmfile,tilefile,sleep,job_ids_array,N_tiles**3+1,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS) + print_summary_job_status(job_status_categories, box, resubmit_count, error_count) + # Now wait for all jobs to finish + while len(job_status_categories['CP'])