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Added Agora, expanded monofonic tests

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# AGORA
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).
## ICs
Created with musIC-panphasia,
- MusIC-panphasia: [54a88338aaa4afc5e4ba2b07b633372994d3b5d4](https://github.com/glatterf42/music-panphasia/tree/54a88338aaa4afc5e4ba2b07b633372994d3b5d4)
- no compile-time parameters
- `agora_1024.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 --with-numa --with-tbbmalloc --enable-mpi-mesh-gravity`
- 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`
- output times: snap_times_agora1024.txt
- example job script: agora_job.sh

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[setup]
boxlength = 60.0
zstart = 100
levelmin = 7
levelmin_TF = 7
levelmax = 7
padding = 16 # try reduce it at your own risk
overlap = 4
align_top = no
baryons = no # switch on for baryon runs
use_2LPT = no
use_LLA = no # AMR codes might want to enable this
[cosmology]
Omega_m = 0.272
Omega_L = 0.728
Omega_b = 0.0455
H0 = 70.2
sigma_8 = 0.807
nspec = 0.961
transfer = eisenstein
[random]
cubesize = 256
seed[8] = 95064
seed[9] = 31415
seed[10] = 27183
[poisson]
fft_fine = yes
accuracy = 1e-6
grad_order = 6
laplace_order = 6
[output]
format = swift
filename = agora_128.hdf5

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# Define some meta data about the simulation.
MetaData:
run_name: agora_1024
# 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: 0.702 # Reduced Hubble constant
a_begin: 0.0099009901 # Initial scale-factor of the simulation, z = 100
a_end: 1.0 # Final scale factor of the simulation, z = 0
Omega_cdm: 2.72e-01 # 0.2610089 # CDM density parameter, new: Omega_m = _cdm + _b (w/o neutrinos)
Omega_lambda: 0.728 # Dark-energy density parameter
Omega_b: 0.0 # 0.0488911 # Baryon density parameter
# Parameters for the self-gravity scheme
Gravity:
mesh_side_length: 2048# 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: 0.026041666666666668 # Comoving Plummer-equivalent softening length for DM particles (in internal units).
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
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).
softening_ratio_background: 0.05 # typical value for zoom simulations, according to docs
# 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/examples/agora/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/examples/agora/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/examples/agora/1024/agora_1024.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.
#StructureFinding:
# config_file_name: vrconfig_auriga6_halo7_8_9.cfg
# basename: haloes
# output_list_on: 1
# output_list: /home/ben/sims/swiftsim/examples/zoom_tests/snap_times.txt
# 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

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#!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=a01611430@unet.univie.ac.at
#SBATCH --time=10:10:00
#SBATCH --nodes=4 #equal to -N x
#SBATCH --ntasks-per-node=2
#SBATCH --exclusive
#SBATCH --job-name AG1024
#SBATCH -o agora_1024.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
module load intel-tbb/2019.4-gcc-9.1.0-sjg5kuu
module load numactl/2.0.12-gcc-9.1.0-vqkmtbi
cd $DATA/swiftsim/examples/agora
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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# Redshift
12.00
11.67
11.34
11.03
10.72
10.42
10.13
9.84
9.57
9.30
9.03
8.78
8.53
8.28
8.05
7.81
7.59
7.37
7.15
6.95
6.74
6.54
6.35
6.16
5.98
5.80
5.63
5.46
5.29
5.13
4.98
4.82
4.67
4.53
4.39
4.25
4.12
3.98
3.86
3.73
3.61
3.49
3.38
3.27
3.16
3.05
2.95
2.85
2.75
2.65
2.56
2.47
2.38
2.29
2.21
2.13
2.05
1.97
1.89
1.82
1.75
1.68
1.61
1.54
1.48
1.41
1.35
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

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## ICs
- MusIC-panphasia: [54a88338aaa4afc5e4ba2b07b633372994d3b5d4](https://github.com/glatterf42/music-panphasia/tree/54a88338aaa4afc5e4ba2b07b633372994d3b5d4)
- no compile-time parameters
- `auriga_6_ics.conf`

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# 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

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# Scale Factor
0.166666
0.333333
0.5
0.666666
1.0

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[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

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# 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

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#!/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