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Added Agora, expanded monofonic tests
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11 changed files with 545 additions and 1 deletions
21
agora/README.md
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agora/README.md
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# AGORA
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Resimulating the AGORA box (https://arxiv.org/abs/1308.2669) with 1024^3 particles. See also: https://cosmicweb.astro.univie.ac.at/simulation/AGORA_512 for IC setup and snapshot times (though they are here as well).
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## ICs
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Created with musIC-panphasia,
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- MusIC-panphasia: [54a88338aaa4afc5e4ba2b07b633372994d3b5d4](https://github.com/glatterf42/music-panphasia/tree/54a88338aaa4afc5e4ba2b07b633372994d3b5d4)
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- no compile-time parameters
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- `agora_1024.conf`
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## Swift code at the VSC
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- version: [94e73ee944d84782601c87e490b7fb96420bb68f](https://gitlab.cosma.dur.ac.uk/swift/swiftsim/-/tree/94e73ee944d84782601c87e490b7fb96420bb68f)
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- configure: `./configure --with-gsl=$(gsl-config --prefix) --enable-fof --with-metis=/opt/sw/spack-0.12.1/opt/spack/linux-centos7-x86_64/gcc-9.1.0/metis-5.1.0-gvmpssik7izg6ds4gdioiyq7ajvcxnvh --enable-compiler-warnings=yes --with-numa --with-tbbmalloc --enable-mpi-mesh-gravity`
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- execute: `mpirun -np 8 /gpfs/data/fs71636/fglatter/swiftsim/examples/swift_mpi --cosmology --self-gravity --fof --limiter --threads=24 --pin /gpfs/data/fs71636/fglatter/swiftsim/examples/agora/1024/agora_1024.yml`
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- output times: snap_times_agora1024.txt
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- example job script: agora_job.sh
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37
agora/agora_1024.conf
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agora/agora_1024.conf
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[setup]
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boxlength = 60.0
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zstart = 100
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levelmin = 7
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levelmin_TF = 7
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levelmax = 7
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padding = 16 # try reduce it at your own risk
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overlap = 4
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align_top = no
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baryons = no # switch on for baryon runs
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use_2LPT = no
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use_LLA = no # AMR codes might want to enable this
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[cosmology]
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Omega_m = 0.272
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Omega_L = 0.728
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Omega_b = 0.0455
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H0 = 70.2
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sigma_8 = 0.807
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nspec = 0.961
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transfer = eisenstein
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[random]
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cubesize = 256
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seed[8] = 95064
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seed[9] = 31415
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seed[10] = 27183
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[poisson]
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fft_fine = yes
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accuracy = 1e-6
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grad_order = 6
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laplace_order = 6
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[output]
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format = swift
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filename = agora_128.hdf5
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agora/agora_1024.yml
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agora/agora_1024.yml
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# Define some meta data about the simulation.
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MetaData:
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run_name: agora_1024
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# Define the system of units to use internally.
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InternalUnitSystem:
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UnitMass_in_cgs: 1.98848e43 # 10^10 M_sun in grams
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UnitLength_in_cgs: 3.08567758e24 # 1 Mpc in centimeters
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UnitVelocity_in_cgs: 1e5 # 1 km/s in centimeters per second
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UnitCurrent_in_cgs: 1 # 1 Ampere
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UnitTemp_in_cgs: 1 # 1 Kelvin
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# Values of some physical constants
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#PhysicalConstants:
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# G: 6.67408e-8 # (Optional) Overwrite the value of Newton's constant used internally by the code.
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# Cosmological parameters # update according to monofonic output
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Cosmology:
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h: 0.702 # Reduced Hubble constant
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a_begin: 0.0099009901 # Initial scale-factor of the simulation, z = 100
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a_end: 1.0 # Final scale factor of the simulation, z = 0
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Omega_cdm: 2.72e-01 # 0.2610089 # CDM density parameter, new: Omega_m = _cdm + _b (w/o neutrinos)
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Omega_lambda: 0.728 # Dark-energy density parameter
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Omega_b: 0.0 # 0.0488911 # Baryon density parameter
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# Parameters for the self-gravity scheme
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Gravity:
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mesh_side_length: 2048# Number of cells along each axis for the periodic gravity mesh (must be even).
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eta: 0.025 # Constant dimensionless multiplier for time integration.
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MAC: adaptive # Choice of mulitpole acceptance criterion: 'adaptive' OR 'geometric'.
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epsilon_fmm: 0.001 # Tolerance parameter for the adaptive multipole acceptance criterion.
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theta_cr: 0.7 # Opening angle for the purely gemoetric criterion.
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# use_tree_below_softening: 0 # (Optional) Can the gravity code use the multipole interactions below the softening scale?
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# allow_truncation_in_MAC: 0 # (Optional) Can the Multipole acceptance criterion use the truncated force estimator?
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comoving_DM_softening: 0.026041666666666668 # Comoving Plummer-equivalent softening length for DM particles (in internal units).
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max_physical_DM_softening: 0.026041666666666668 # Maximal Plummer-equivalent softening length in physical coordinates for DM particles (in internal units). #should work b/c Lbox is given in Mpc=internal unit
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rebuild_frequency: 0.01 # (Optional) Frequency of the gravity-tree rebuild in units of the number of g-particles (this is the default value).
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a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
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r_cut_max: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
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r_cut_min: 0.1 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
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softening_ratio_background: 0.05 # typical value for zoom simulations, according to docs
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# FOF group finding parameters
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FOF:
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basename: fof_output # Filename for the FOF outputs (Unused when FoF is only run to seed BHs).
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scale_factor_first: 0.91 # Scale-factor of first FoF black hole seeding calls (needed for cosmological runs).
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delta_time: 1.005 # Time between consecutive FoF black hole seeding calls.
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min_group_size: 256 # The minimum no. of particles required for a group.
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linking_length_ratio: 0.2 # Linking length in units of the main inter-particle separation.
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seed_black_holes_enabled: 0 # Enable (1) or disable (0) seeding of black holes in FoF groups
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dump_catalogue_when_seeding: 0 # Enable (1) or disable (0) dumping a group catalogue when runnning FOF for seeding purposes.
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absolute_linking_length: -1. # (Optional) Absolute linking length (in internal units). When not set to -1, this will overwrite the linking length computed from 'linking_length_ratio'.
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group_id_default: 2147483647 # (Optional) Sets the group ID of particles in groups below the minimum size. Defaults to 2^31 - 1 if unspecified. Has to be positive.
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group_id_offset: 1 # (Optional) Sets the offset of group ID labeling. Defaults to 1 if unspecified.
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# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
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TimeIntegration:
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dt_min: 1e-6 # The minimal time-step size of the simulation (in internal units).
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dt_max: 0.025 # The maximal time-step size of the simulation (in internal units).
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# Parameters governing the snapshots
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Snapshots:
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basename: output # Common part of the name of output files.
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# subdir: dir # (Optional) Sub-directory in which to write the snapshots. Defaults to "" (i.e. the directory where SWIFT is run).
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scale_factor_first: 0.1 # (Optional) Scale-factor of the first snapshot if cosmological time-integration.
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delta_time: 0.01 # Time difference between consecutive outputs (in internal units)
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# invoke_stf: 0 # (Optional) Call VELOCIraptor every time a snapshot is written irrespective of the VELOCIraptor output strategy.
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invoke_fof: 1 # (Optional) Call FOF every time a snapshot is written
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# compression: 0 # (Optional) Set the level of GZIP compression of the HDF5 datasets [0-9]. 0 does no compression. The lossless compression is applied to *all* the fields.
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# distributed: 0 # (Optional) When running over MPI, should each rank write a partial snapshot or do we want a single file? 1 implies one file per MPI rank.
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# UnitMass_in_cgs: 1 # (Optional) Unit system for the outputs (Grams)
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# UnitLength_in_cgs: 1 # (Optional) Unit system for the outputs (Centimeters)
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# UnitVelocity_in_cgs: 1 # (Optional) Unit system for the outputs (Centimeters per second)
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# UnitCurrent_in_cgs: 1 # (Optional) Unit system for the outputs (Amperes)
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# UnitTemp_in_cgs: 1 # (Optional) Unit system for the outputs (Kelvin)
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output_list_on: 1 # (Optional) Enable the output list
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output_list: /gpfs/data/fs71636/fglatter/swiftsim/examples/agora/snap_times.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
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# select_output_on: 0 # (Optional) Enable the output selection behaviour
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# select_output: selectoutput.yml # (Optional) File containing information to select outputs with (see documentation in the "Output Selection" section)
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# Parameters governing the conserved quantities statistics
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Statistics:
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delta_time: 1.1 # Time between statistics output
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scale_factor_first: 0.1 # (Optional) Scale-factor of the first statistics dump if cosmological time-integration.
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energy_file_name: statistics # (Optional) File name for statistics output
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timestep_file_name: timesteps # (Optional) File name for timing information output. Note: No underscores "_" allowed in file name
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output_list_on: 1 # (Optional) Enable the output list
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output_list: /gpfs/data/fs71636/fglatter/swiftsim/examples/agora/snap_times.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
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# Parameters related to the initial conditions
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InitialConditions:
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file_name: /gpfs/data/fs71636/fglatter/swiftsim/examples/agora/1024/agora_1024.hdf5 # The file to read
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periodic: 1 # Are we running with periodic ICs?
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cleanup_h_factors: 0 # (Optional) Clean up the h-factors used in the ICs (e.g. in Gadget files).
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cleanup_velocity_factors: 0 # (Optional) Clean up the scale-factors used in the definition of the velocity variable in the ICs (e.g. in Gadget files).
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cleanup_smoothing_lengths: 0 # (Optional) Clean the values of the smoothing lengths that are read in to remove stupid values. Set to 1 to activate.
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smoothing_length_scaling: 1. # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
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replicate: 1 # (Optional) Replicate all particles along each axis a given integer number of times. Default 1.
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remap_ids: 0 # (Optional) Remap all the particle IDs to the range [1, NumPart].
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metadata_group_name: ICs_parameters # (Optional) Copy this HDF5 group from the initial conditions file to all snapshots, if found
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# Parameters controlling restarts
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Restarts:
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enable: 1 # (Optional) whether to enable dumping restarts at fixed intervals.
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save: 0 # (Optional) whether to save copies of the previous set of restart files (named .prev)
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# onexit: 0 # (Optional) whether to dump restarts on exit (*needs enable*)
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subdir: restart # (Optional) name of subdirectory for restart files.
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basename: restart # (Optional) prefix used in naming restart files.
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delta_hours: 2.0 # (Optional) decimal hours between dumps of restart files.
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stop_steps: 100 # (Optional) how many steps to process before checking if the <subdir>/stop file exists. When present the application will attempt to exit early, dumping restart files first.
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max_run_time: 24.0 # (optional) Maximal wall-clock time in hours. The application will exit when this limit is reached.
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# resubmit_on_exit: 0 # (Optional) whether to run a command when exiting after the time limit has been reached.
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# resubmit_command: ./resub.sh # (Optional) Command to run when time limit is reached. Compulsory if resubmit_on_exit is switched on. Note potentially unsafe.
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#StructureFinding:
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# config_file_name: vrconfig_auriga6_halo7_8_9.cfg
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# basename: haloes
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# output_list_on: 1
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# output_list: /home/ben/sims/swiftsim/examples/zoom_tests/snap_times.txt
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# Parameters governing domain decomposition
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# DomainDecomposition:
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# initial_type: memory # (Optional) The initial decomposition strategy: "grid",
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# # "region", "memory", or "vectorized".
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# initial_grid: [10,10,10] # (Optional) Grid sizes if the "grid" strategy is chosen.
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#
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# synchronous: 0 # (Optional) Use synchronous MPI requests to redistribute, uses less system memory, but slower.
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# repartition_type: fullcosts # (Optional) The re-decomposition strategy, one of:
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# # "none", "fullcosts", "edgecosts", "memory" or
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# # "timecosts".
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# trigger: 0.05 # (Optional) Fractional (<1) CPU time difference between MPI ranks required to trigger a
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# # new decomposition, or number of steps (>1) between decompositions
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# minfrac: 0.9 # (Optional) Fractional of all particles that should be updated in previous step when
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# # using CPU time trigger
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# usemetis: 0 # Use serial METIS when ParMETIS is also available.
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# adaptive: 1 # Use adaptive repartition when ParMETIS is available, otherwise simple refinement.
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# itr: 100 # When adaptive defines the ratio of inter node communication time to data redistribution time, in the range 0.00001 to 10000000.0.
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# # Lower values give less data movement during redistributions, at the cost of global balance which may require more communication.
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# use_fixed_costs: 0 # If 1 then use any compiled in fixed costs for
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# # task weights in first repartition, if 0 only use task timings, if > 1 only use
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# # fixed costs, unless none are available
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24
agora/agora_job.sh
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24
agora/agora_job.sh
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#!/bin/bash
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#SBATCH --mail-type=ALL
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#SBATCH --mail-user=a01611430@unet.univie.ac.at
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#SBATCH --time=10:10:00
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#SBATCH --nodes=4 #equal to -N x
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#SBATCH --ntasks-per-node=2
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#SBATCH --exclusive
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#SBATCH --job-name AG1024
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#SBATCH -o agora_1024.out
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module load gcc/9.1.0-gcc-4.8.5-mj7s6dg
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module load openmpi/3.1.4-gcc-9.1.0-fdssbx5
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module load gsl/2.5-gcc-9.1.0-ucmpak4
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module load fftw/3.3.8-gcc-9.1.0-2kyouz7
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module load libtool/2.4.6-gcc-9.1.0-vkpnfol
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module load hdf5/1.10.5-gcc-9.1.0-rolgskh
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module load metis/5.1.0-gcc-9.1.0-gvmpssi
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module load python/3.9.4-gcc-9.1.0-l7amfu6
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module load intel-tbb/2019.4-gcc-9.1.0-sjg5kuu
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module load numactl/2.0.12-gcc-9.1.0-vqkmtbi
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cd $DATA/swiftsim/examples/agora
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mpirun -np 8 /gpfs/data/fs71636/fglatter/swiftsim/examples/swift_mpi --cosmology --self-gravity --fof --limiter --threads=24 --pin /gpfs/data/fs71636/fglatter/swiftsim/examples/agora/1024/agora_1024.yml
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101
agora/snap_times_agora1024.txt
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101
agora/snap_times_agora1024.txt
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# Redshift
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12.00
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11.67
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11.34
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11.03
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|
10.72
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|
10.42
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|
10.13
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|
9.84
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|
9.57
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|
9.30
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|
9.03
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|
8.78
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|
8.53
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|
8.28
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||||||
|
8.05
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||||||
|
7.81
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||||||
|
7.59
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||||||
|
7.37
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||||||
|
7.15
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||||||
|
6.95
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||||||
|
6.74
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||||||
|
6.54
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||||||
|
6.35
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||||||
|
6.16
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|
5.98
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||||||
|
5.80
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||||||
|
5.63
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||||||
|
5.46
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||||||
|
5.29
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|
5.13
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||||||
|
4.98
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||||||
|
4.82
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||||||
|
4.67
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||||||
|
4.53
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||||||
|
4.39
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||||||
|
4.25
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|
4.12
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|
3.98
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||||||
|
3.86
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||||||
|
3.73
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||||||
|
3.61
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||||||
|
3.49
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||||||
|
3.38
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||||||
|
3.27
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||||||
|
3.16
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||||||
|
3.05
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||||||
|
2.95
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||||||
|
2.85
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||||||
|
2.75
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||||||
|
2.65
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||||||
|
2.56
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||||||
|
2.47
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|
2.38
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||||||
|
2.29
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||||||
|
2.21
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||||||
|
2.13
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||||||
|
2.05
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||||||
|
1.97
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||||||
|
1.89
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||||||
|
1.82
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||||||
|
1.75
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||||||
|
1.68
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||||||
|
1.61
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||||||
|
1.54
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||||||
|
1.48
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||||||
|
1.41
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|
1.35
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||||||
|
1.29
|
||||||
|
1.23
|
||||||
|
1.18
|
||||||
|
1.12
|
||||||
|
1.07
|
||||||
|
1.01
|
||||||
|
0.96
|
||||||
|
0.91
|
||||||
|
0.86
|
||||||
|
0.81
|
||||||
|
0.77
|
||||||
|
0.72
|
||||||
|
0.68
|
||||||
|
0.64
|
||||||
|
0.59
|
||||||
|
0.55
|
||||||
|
0.51
|
||||||
|
0.47
|
||||||
|
0.44
|
||||||
|
0.40
|
||||||
|
0.36
|
||||||
|
0.33
|
||||||
|
0.30
|
||||||
|
0.26
|
||||||
|
0.23
|
||||||
|
0.20
|
||||||
|
0.17
|
||||||
|
0.14
|
||||||
|
0.11
|
||||||
|
0.08
|
||||||
|
0.05
|
||||||
|
0.03
|
||||||
|
0.00
|
|
@ -5,7 +5,6 @@ Trying to create a zoom-in simulation of a specific halo from https://virgodb.du
|
||||||
|
|
||||||
## ICs
|
## ICs
|
||||||
|
|
||||||
|
|
||||||
- MusIC-panphasia: [54a88338aaa4afc5e4ba2b07b633372994d3b5d4](https://github.com/glatterf42/music-panphasia/tree/54a88338aaa4afc5e4ba2b07b633372994d3b5d4)
|
- MusIC-panphasia: [54a88338aaa4afc5e4ba2b07b633372994d3b5d4](https://github.com/glatterf42/music-panphasia/tree/54a88338aaa4afc5e4ba2b07b633372994d3b5d4)
|
||||||
- no compile-time parameters
|
- no compile-time parameters
|
||||||
- `auriga_6_ics.conf`
|
- `auriga_6_ics.conf`
|
||||||
|
|
|
@ -1,3 +1,22 @@
|
||||||
# MonofonIC Tests
|
# MonofonIC Tests
|
||||||
|
|
||||||
|
The monofonIC code is available at https://bitbucket.org/ohahn/monofonic/src/master/ . However, for our tests, we use the experimental version (only available through admission from Oliver Hahn, ohahn) from https://bitbucket.org/ohahn/monofonic-experimental/src/master/ . The branch newrandom is the one holding all desired code.
|
||||||
|
|
||||||
|
|
||||||
|
## Accessing the different waveforms
|
||||||
|
|
||||||
|
To change the Daubechies wavelet in question, go to line 146 of /src/plugins/random_music2.cc and spell out the desired wavelet there. Only exception: to change to the exact solution (the shannon wavelet), change line 258 to '#if 0'.
|
||||||
|
|
||||||
|
|
||||||
|
## MonofonIC code at the VSC
|
||||||
|
|
||||||
|
- version: [981c093447fe1860297e8cf2337f24f280181ec5](https://bitbucket.org/ohahn/monofonic-experimental/src/981c093447fe1860297e8cf2337f24f280181ec5)
|
||||||
|
- configuration: shannon_512_100.conf
|
||||||
|
|
||||||
|
## Swift code at the VSC
|
||||||
|
|
||||||
|
- version: [94e73ee944d84782601c87e490b7fb96420bb68f](https://gitlab.cosma.dur.ac.uk/swift/swiftsim/-/tree/94e73ee944d84782601c87e490b7fb96420bb68f)
|
||||||
|
- configure: `./configure --with-gsl=$(gsl-config --prefix) --enable-fof --with-metis=/opt/sw/spack-0.12.1/opt/spack/linux-centos7-x86_64/gcc-9.1.0/metis-5.1.0-gvmpssik7izg6ds4gdioiyq7ajvcxnvh --enable-compiler-warnings=yes `
|
||||||
|
- execute: `/gpfs/data/fs71636/fglatter/swiftsim/examples/swift --cosmology --self-gravity --fof --threads=$SLURM_NPROCS /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/output/shannon_512_100/shannon_512_100_param.yml`
|
||||||
|
- output times: monofonic_snap_times.txt
|
||||||
|
- example job file: shannon_job.sh
|
||||||
|
|
6
monofonic_tests/monofonic_snap_times.txt
Normal file
6
monofonic_tests/monofonic_snap_times.txt
Normal file
|
@ -0,0 +1,6 @@
|
||||||
|
# Scale Factor
|
||||||
|
0.166666
|
||||||
|
0.333333
|
||||||
|
0.5
|
||||||
|
0.666666
|
||||||
|
1.0
|
29
monofonic_tests/shannon_512_100.conf
Normal file
29
monofonic_tests/shannon_512_100.conf
Normal file
|
@ -0,0 +1,29 @@
|
||||||
|
[setup]
|
||||||
|
GridRes = 512
|
||||||
|
BoxLength = 67.742
|
||||||
|
zstart = 49.0
|
||||||
|
LPTorder = 2
|
||||||
|
DoBaryons = no
|
||||||
|
DoBaryonVrel = no
|
||||||
|
DoFixing = yes
|
||||||
|
DoInversion = no
|
||||||
|
ParticleLoad = sc
|
||||||
|
|
||||||
|
[cosmology]
|
||||||
|
ParameterSet = Planck2018EE+BAO+SN
|
||||||
|
ZeroRadiation = false
|
||||||
|
transfer = CLASS
|
||||||
|
ztarget = 2.5
|
||||||
|
|
||||||
|
[random]
|
||||||
|
generator = MUSIC2
|
||||||
|
seed = 12345
|
||||||
|
|
||||||
|
[execution]
|
||||||
|
NumThreads = 24
|
||||||
|
|
||||||
|
[output]
|
||||||
|
format = SWIFT
|
||||||
|
filename = ics_shannon_512_100.hdf5
|
||||||
|
UseLongids = true
|
||||||
|
|
136
monofonic_tests/shannon_512_100_param.yml
Normal file
136
monofonic_tests/shannon_512_100_param.yml
Normal file
|
@ -0,0 +1,136 @@
|
||||||
|
|
||||||
|
# Define some meta data about the simulation.
|
||||||
|
MetaData:
|
||||||
|
run_name: mon_test_shannon_512_100
|
||||||
|
|
||||||
|
# Define the system of units to use internally.
|
||||||
|
InternalUnitSystem:
|
||||||
|
UnitMass_in_cgs: 1.98848e43 # 10^10 M_sun in grams
|
||||||
|
UnitLength_in_cgs: 3.08567758e24 # 1 Mpc in centimeters
|
||||||
|
UnitVelocity_in_cgs: 1e5 # 1 km/s in centimeters per second
|
||||||
|
UnitCurrent_in_cgs: 1 # 1 Ampere
|
||||||
|
UnitTemp_in_cgs: 1 # 1 Kelvin
|
||||||
|
|
||||||
|
|
||||||
|
# Values of some physical constants
|
||||||
|
#PhysicalConstants:
|
||||||
|
# G: 6.67408e-8 # (Optional) Overwrite the value of Newton's constant used internally by the code.
|
||||||
|
|
||||||
|
# Cosmological parameters # update according to monofonic output
|
||||||
|
Cosmology:
|
||||||
|
h: 0.67742 # Reduced Hubble constant
|
||||||
|
a_begin: 0.02 # Initial scale-factor of the simulation, z = 49
|
||||||
|
a_end: 1.0 # Final scale factor of the simulation, z = 0
|
||||||
|
Omega_cdm: 0.2610089 # CDM density parameter, new: Omega_m = _cdm + _b (w/o neutrinos)
|
||||||
|
Omega_lambda: 0.690021 # Dark-energy density parameter
|
||||||
|
Omega_b: 0.0488911 # Baryon density parameter
|
||||||
|
|
||||||
|
# Parameters for the self-gravity scheme
|
||||||
|
Gravity:
|
||||||
|
mesh_side_length: 1024# Number of cells along each axis for the periodic gravity mesh (must be even).
|
||||||
|
eta: 0.025 # Constant dimensionless multiplier for time integration.
|
||||||
|
MAC: adaptive # Choice of mulitpole acceptance criterion: 'adaptive' OR 'geometric'.
|
||||||
|
epsilon_fmm: 0.001 # Tolerance parameter for the adaptive multipole acceptance criterion.
|
||||||
|
theta_cr: 0.7 # Opening angle for the purely gemoetric criterion.
|
||||||
|
# use_tree_below_softening: 0 # (Optional) Can the gravity code use the multipole interactions below the softening scale?
|
||||||
|
# allow_truncation_in_MAC: 0 # (Optional) Can the Multipole acceptance criterion use the truncated force estimator?
|
||||||
|
comoving_DM_softening: 0.006510416666666667 # Comoving Plummer-equivalent softening length for DM particles (in internal units).
|
||||||
|
max_physical_DM_softening: 0.006510416666666667 # Maximal Plummer-equivalent softening length in physical coordinates for DM particles (in internal units). #should work b/c Lbox is given in Mpc=internal unit
|
||||||
|
rebuild_frequency: 0.01 # (Optional) Frequency of the gravity-tree rebuild in units of the number of g-particles (this is the default value).
|
||||||
|
a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
|
||||||
|
r_cut_max: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
|
||||||
|
r_cut_min: 0.1 # (Optional) Cut-off in number of top-level cells below which no truncation of FMM forces are performed (this is the default value).
|
||||||
|
|
||||||
|
# FOF group finding parameters
|
||||||
|
FOF:
|
||||||
|
basename: fof_output # Filename for the FOF outputs (Unused when FoF is only run to seed BHs).
|
||||||
|
scale_factor_first: 0.91 # Scale-factor of first FoF black hole seeding calls (needed for cosmological runs).
|
||||||
|
delta_time: 1.005 # Time between consecutive FoF black hole seeding calls.
|
||||||
|
min_group_size: 256 # The minimum no. of particles required for a group.
|
||||||
|
linking_length_ratio: 0.2 # Linking length in units of the main inter-particle separation.
|
||||||
|
seed_black_holes_enabled: 0 # Enable (1) or disable (0) seeding of black holes in FoF groups
|
||||||
|
dump_catalogue_when_seeding: 0 # Enable (1) or disable (0) dumping a group catalogue when runnning FOF for seeding purposes.
|
||||||
|
absolute_linking_length: -1. # (Optional) Absolute linking length (in internal units). When not set to -1, this will overwrite the linking length computed from 'linking_length_ratio'.
|
||||||
|
group_id_default: 2147483647 # (Optional) Sets the group ID of particles in groups below the minimum size. Defaults to 2^31 - 1 if unspecified. Has to be positive.
|
||||||
|
group_id_offset: 1 # (Optional) Sets the offset of group ID labeling. Defaults to 1 if unspecified.
|
||||||
|
|
||||||
|
# Parameters governing the time integration (Set dt_min and dt_max to the same value for a fixed time-step run.)
|
||||||
|
TimeIntegration:
|
||||||
|
dt_min: 1e-6 # The minimal time-step size of the simulation (in internal units).
|
||||||
|
dt_max: 0.025 # The maximal time-step size of the simulation (in internal units).
|
||||||
|
|
||||||
|
# Parameters governing the snapshots
|
||||||
|
Snapshots:
|
||||||
|
basename: output # Common part of the name of output files.
|
||||||
|
# subdir: dir # (Optional) Sub-directory in which to write the snapshots. Defaults to "" (i.e. the directory where SWIFT is run).
|
||||||
|
scale_factor_first: 0.1 # (Optional) Scale-factor of the first snapshot if cosmological time-integration.
|
||||||
|
delta_time: 0.01 # Time difference between consecutive outputs (in internal units)
|
||||||
|
# invoke_stf: 0 # (Optional) Call VELOCIraptor every time a snapshot is written irrespective of the VELOCIraptor output strategy.
|
||||||
|
invoke_fof: 1 # (Optional) Call FOF every time a snapshot is written
|
||||||
|
# compression: 0 # (Optional) Set the level of GZIP compression of the HDF5 datasets [0-9]. 0 does no compression. The lossless compression is applied to *all* the fields.
|
||||||
|
# distributed: 0 # (Optional) When running over MPI, should each rank write a partial snapshot or do we want a single file? 1 implies one file per MPI rank.
|
||||||
|
# UnitMass_in_cgs: 1 # (Optional) Unit system for the outputs (Grams)
|
||||||
|
# UnitLength_in_cgs: 1 # (Optional) Unit system for the outputs (Centimeters)
|
||||||
|
# UnitVelocity_in_cgs: 1 # (Optional) Unit system for the outputs (Centimeters per second)
|
||||||
|
# UnitCurrent_in_cgs: 1 # (Optional) Unit system for the outputs (Amperes)
|
||||||
|
# UnitTemp_in_cgs: 1 # (Optional) Unit system for the outputs (Kelvin)
|
||||||
|
output_list_on: 1 # (Optional) Enable the output list
|
||||||
|
output_list: /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/snap_times.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
|
||||||
|
# select_output_on: 0 # (Optional) Enable the output selection behaviour
|
||||||
|
# select_output: selectoutput.yml # (Optional) File containing information to select outputs with (see documentation in the "Output Selection" section)
|
||||||
|
|
||||||
|
# Parameters governing the conserved quantities statistics
|
||||||
|
Statistics:
|
||||||
|
delta_time: 1.1 # Time between statistics output
|
||||||
|
scale_factor_first: 0.1 # (Optional) Scale-factor of the first statistics dump if cosmological time-integration.
|
||||||
|
energy_file_name: statistics # (Optional) File name for statistics output
|
||||||
|
timestep_file_name: timesteps # (Optional) File name for timing information output. Note: No underscores "_" allowed in file name
|
||||||
|
output_list_on: 1 # (Optional) Enable the output list
|
||||||
|
output_list: /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/snap_times.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
|
||||||
|
|
||||||
|
# Parameters related to the initial conditions
|
||||||
|
InitialConditions:
|
||||||
|
file_name: /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/output/shannon_512_100/ics_shannon_512_100.hdf5 # The file to read
|
||||||
|
periodic: 1 # Are we running with periodic ICs?
|
||||||
|
cleanup_h_factors: 0 # (Optional) Clean up the h-factors used in the ICs (e.g. in Gadget files).
|
||||||
|
cleanup_velocity_factors: 0 # (Optional) Clean up the scale-factors used in the definition of the velocity variable in the ICs (e.g. in Gadget files).
|
||||||
|
cleanup_smoothing_lengths: 0 # (Optional) Clean the values of the smoothing lengths that are read in to remove stupid values. Set to 1 to activate.
|
||||||
|
smoothing_length_scaling: 1. # (Optional) A scaling factor to apply to all smoothing lengths in the ICs.
|
||||||
|
replicate: 1 # (Optional) Replicate all particles along each axis a given integer number of times. Default 1.
|
||||||
|
remap_ids: 0 # (Optional) Remap all the particle IDs to the range [1, NumPart].
|
||||||
|
metadata_group_name: ICs_parameters # (Optional) Copy this HDF5 group from the initial conditions file to all snapshots, if found
|
||||||
|
|
||||||
|
# Parameters controlling restarts
|
||||||
|
Restarts:
|
||||||
|
enable: 1 # (Optional) whether to enable dumping restarts at fixed intervals.
|
||||||
|
save: 0 # (Optional) whether to save copies of the previous set of restart files (named .prev)
|
||||||
|
# onexit: 0 # (Optional) whether to dump restarts on exit (*needs enable*)
|
||||||
|
subdir: restart # (Optional) name of subdirectory for restart files.
|
||||||
|
basename: restart # (Optional) prefix used in naming restart files.
|
||||||
|
delta_hours: 2.0 # (Optional) decimal hours between dumps of restart files.
|
||||||
|
stop_steps: 100 # (Optional) how many steps to process before checking if the <subdir>/stop file exists. When present the application will attempt to exit early, dumping restart files first.
|
||||||
|
max_run_time: 24.0 # (optional) Maximal wall-clock time in hours. The application will exit when this limit is reached.
|
||||||
|
# resubmit_on_exit: 0 # (Optional) whether to run a command when exiting after the time limit has been reached.
|
||||||
|
# resubmit_command: ./resub.sh # (Optional) Command to run when time limit is reached. Compulsory if resubmit_on_exit is switched on. Note potentially unsafe.
|
||||||
|
|
||||||
|
# Parameters governing domain decomposition
|
||||||
|
# DomainDecomposition:
|
||||||
|
# initial_type: memory # (Optional) The initial decomposition strategy: "grid",
|
||||||
|
# # "region", "memory", or "vectorized".
|
||||||
|
# initial_grid: [10,10,10] # (Optional) Grid sizes if the "grid" strategy is chosen.
|
||||||
|
#
|
||||||
|
# synchronous: 0 # (Optional) Use synchronous MPI requests to redistribute, uses less system memory, but slower.
|
||||||
|
# repartition_type: fullcosts # (Optional) The re-decomposition strategy, one of:
|
||||||
|
# # "none", "fullcosts", "edgecosts", "memory" or
|
||||||
|
# # "timecosts".
|
||||||
|
# trigger: 0.05 # (Optional) Fractional (<1) CPU time difference between MPI ranks required to trigger a
|
||||||
|
# # new decomposition, or number of steps (>1) between decompositions
|
||||||
|
# minfrac: 0.9 # (Optional) Fractional of all particles that should be updated in previous step when
|
||||||
|
# # using CPU time trigger
|
||||||
|
# usemetis: 0 # Use serial METIS when ParMETIS is also available.
|
||||||
|
# adaptive: 1 # Use adaptive repartition when ParMETIS is available, otherwise simple refinement.
|
||||||
|
# itr: 100 # When adaptive defines the ratio of inter node communication time to data redistribution time, in the range 0.00001 to 10000000.0.
|
||||||
|
# # Lower values give less data movement during redistributions, at the cost of global balance which may require more communication.
|
||||||
|
# use_fixed_costs: 0 # If 1 then use any compiled in fixed costs for
|
||||||
|
# # task weights in first repartition, if 0 only use task timings, if > 1 only use
|
||||||
|
# # fixed costs, unless none are available
|
29
monofonic_tests/shannon_job.sh
Normal file
29
monofonic_tests/shannon_job.sh
Normal file
|
@ -0,0 +1,29 @@
|
||||||
|
#!/bin/bash
|
||||||
|
#SBATCH --mail-type=ALL
|
||||||
|
#SBATCH --mail-user=a01611430@unet.univie.ac.at
|
||||||
|
#SBATCH --time=40:00:00
|
||||||
|
#SBATCH --nodes=1 #equal to -N 1
|
||||||
|
#SBATCH --ntasks-per-node=48
|
||||||
|
#SBATCH --exclusive
|
||||||
|
#SBATCH --job-name MON_512
|
||||||
|
#SBATCH -o mon_shannon_512.out
|
||||||
|
|
||||||
|
module load gcc/9.1.0-gcc-4.8.5-mj7s6dg
|
||||||
|
module load openmpi/3.1.4-gcc-9.1.0-fdssbx5
|
||||||
|
module load gsl/2.5-gcc-9.1.0-ucmpak4
|
||||||
|
module load fftw/3.3.8-gcc-9.1.0-2kyouz7
|
||||||
|
module load libtool/2.4.6-gcc-9.1.0-vkpnfol
|
||||||
|
module load hdf5/1.10.5-gcc-9.1.0-rolgskh
|
||||||
|
module load metis/5.1.0-gcc-9.1.0-gvmpssi
|
||||||
|
module load python/3.9.4-gcc-9.1.0-l7amfu6
|
||||||
|
|
||||||
|
source /gpfs/data/fs71636/fglatter/python_files/swift_venv/bin/activate
|
||||||
|
|
||||||
|
cd $DATA/monofonic_exp_shannon/build
|
||||||
|
mpiexec -np 2 ./monofonIC ../swift_shannon_512_100.conf
|
||||||
|
|
||||||
|
python3 /gpfs/data/fs71636/fglatter/python_files/rename_and_move_ics_swift.py 1 $DATA/monofonic_exp_shannon/build /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/output/shannon_512_100 shannon 512 100.0
|
||||||
|
|
||||||
|
cd $DATA/swiftsim/monofonic_tests/output/shannon_512_100
|
||||||
|
/gpfs/data/fs71636/fglatter/swiftsim/examples/swift --cosmology --self-gravity --fof --threads=$SLURM_NPROCS /gpfs/data/fs71636/fglatter/swiftsim/monofonic_tests/output/shannon_512_100/shannon_512_100_param.yml
|
||||||
|
|
Loading…
Reference in a new issue