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SPH for CSiBORG1 support (#109)

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* Add edited files

* Update scripts

* Updates

* Little fix

* Little ifx
This commit is contained in:
Richard Stiskalek 2024-02-20 12:24:58 +00:00 committed by GitHub
parent f0ab6fc9b4
commit b88c0703f6
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2 changed files with 68 additions and 30 deletions
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60
scripts_independent/field_sph_gadget.py
View File

@ -16,11 +16,11 @@
Script to construct the density and velocity fields for a simulation snapshot.
The SPH filter is implemented in the cosmotool package.
"""
from argparse import ArgumentParser
from os import remove
from os.path import join, exists
import subprocess
from argparse import ArgumentParser
from datetime import datetime
from os import remove
from os.path import exists, join
import hdf5plugin # noqa
import numpy as np
@ -137,7 +137,7 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
SPH_executable : str
Path to the `simple3DFilter` executable [1].
snapshot_kind : str
Kind of the simulation snapshot. Currently only `gadget4` is supported.
Kind of the simulation snapshot.
Returns
-------
@ -147,12 +147,24 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
----------
[1] https://bitbucket.org/glavaux/cosmotool/src/master/sample/simple3DFilter.cpp # noqa
"""
if snapshot_kind != "gadget4":
raise NotImplementedError("Only GADGET HDF5 snapshots are supported.")
# First get the temporary file path.
if snapshot_kind == "gadget4":
temporary_output_path = join(
scratch_space, generate_unique_id(snapshot_path))
elif snapshot_kind == "ramses":
temporary_output_path = snapshot_path
else:
raise NotImplementedError("Only GADGET HDF5 or preprocessed RAMSES "
"snapshots are supported.")
if not temporary_output_path.endswith(".hdf5"):
raise RuntimeError("Temporary output path must end with `.hdf5`.")
# Print the job information.
print("---------- SPH Density & Velocity Field Job Information ----------")
print(f"Snapshot path: {snapshot_path}")
print(f"Output path: {output_path}")
print(f"Temporary path: {temporary_output_path}")
print(f"Resolution: {resolution}")
print(f"Scratch space: {scratch_space}")
print(f"SPH executable: {SPH_executable}")
@ -160,24 +172,28 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
print("------------------------------------------------------------------")
print(flush=True)
temporary_output_path = join(
scratch_space, generate_unique_id(snapshot_path))
if not temporary_output_path.endswith(".hdf5"):
raise RuntimeError("Temporary output path must end with `.hdf5`.")
print(f"{now()}: preparing snapshot...", flush=True)
boxsize = prepare_gadget(snapshot_path, temporary_output_path)
print(f"{now()}: wrote temporary data to {temporary_output_path}.",
flush=True)
# Prepare or read-off the temporary snapshot file.
if snapshot_kind == "gadget4":
print(f"{now()}: preparing snapshot...", flush=True)
boxsize = prepare_gadget(snapshot_path, temporary_output_path)
print(f"{now()}: wrote temporary data to {temporary_output_path}.",
flush=True)
else:
boxsize = 677.7 # Mpc/h
print(f"{now()}: CAREFUL, forcefully setting the boxsize to {boxsize} Mpc / h.", # noqa
flush=True)
# Run the SPH filter.
run_sph_filter(temporary_output_path, output_path, boxsize, resolution,
SPH_executable)
print(f"{now()}: removing the temporary snapshot file.", flush=True)
try:
remove(temporary_output_path)
except FileNotFoundError:
pass
# Remove the temporary snapshot file if it was created.
if snapshot_kind == "gadget4":
print(f"{now()}: removing the temporary snapshot file.", flush=True)
try:
remove(temporary_output_path)
except FileNotFoundError:
pass
if __name__ == "__main__":
@ -193,7 +209,7 @@ if __name__ == "__main__":
parser.add_argument("--SPH_executable", type=str, required=True,
help="Path to the `simple3DFilter` executable.")
parser.add_argument("--snapshot_kind", type=str, required=True,
choices=["gadget4"],
choices=["gadget4", "ramses"],
help="Kind of the simulation snapshot.")
args = parser.parse_args()

38
scripts_independent/run_field_sph_gadget.py
View File

@ -17,12 +17,27 @@ Script to write the SLURM submission script and submit it to the queue to
calculate the SPH density & velocity field for GADGET.
"""
from os import system
from os.path import join
def write_submit(chain_index, kind, resolution, nthreads):
def write_submit(chain_index, kind, resolution, nthreads, snapshot_kind):
if kind not in ["main", "random", "varysmall"]:
raise RuntimeError(f"Unknown kind `{kind}`.")
basepath = "/cosma8/data/dp016/dc-stis1/"
if snapshot_kind == "gadget4":
snapshot_path = join(basepath, f"csiborg2_{kind}/chain_{chain_index}",
"output/snapshot_099_full.hdf5")
output_path = join(
basepath,
f"csiborg2_{kind}/field/chain_{chain_index}_{resolution}.hdf5")
else:
chain_index = str(chain_index).zfill(5)
snapshot_path = join(basepath, "csiborg1_sph",
f"ramses_{chain_index}.hdf5")
output_path = join(basepath, "csiborg1_sph",
f"sph_ramses_{chain_index}_{resolution}.hdf5")
txt = f"""#!/bin/sh
#SBATCH --ntasks-per-node=1
@ -53,12 +68,12 @@ source /cosma/home/dp016/dc-stis1/csiborgtools/venv_csiborgtools/bin/activate
export OMP_NUM_THREADS={nthreads}
export OMP_NESTED=true
snapshot_path="/cosma8/data/dp016/dc-stis1/csiborg2_{kind}/chain_{chain_index}/output/snapshot_099_full.hdf5"
output_path="/cosma8/data/dp016/dc-stis1/csiborg2_{kind}/field/chain_{chain_index}_{resolution}.hdf5"
snapshot_path={snapshot_path}
output_path={output_path}
resolution={resolution}
scratch_space="/snap8/scratch/dp016/dc-stis1/"
SPH_executable="/cosma8/data/dp016/dc-stis1/cosmotool/bld2/sample/simple3DFilter"
snapshot_kind="gadget4"
snapshot_kind={snapshot_kind}
python3 field_sph_gadget.py --snapshot_path $snapshot_path --output_path $output_path --resolution $resolution --scratch_space $scratch_space --SPH_executable $SPH_executable --snapshot_kind $snapshot_kind
"""
@ -72,18 +87,25 @@ python3 field_sph_gadget.py --snapshot_path $snapshot_path --output_path $output
if __name__ == "__main__":
snapshot_kind = "gadget4"
# kind = "main"
# chains = [15617, 15717, 15817, 15917, 16017, 16117, 16217, 16317, 16417, 16517, 16617, 16717, 16817, 16917, 17017, 17117, 17217, 17317, 17417]
# kind = "varysmall"
# chains = ["16417_001", "16417_025", "16417_050", "16417_075", "16417_100", "16417_125", "16417_150", "16417_175", "16417_200", "16417_225", "16417_250", "16417_275", "16417_300", "16417_325", "16417_350", "16417_375", "16417_400", "16417_425", "16417_450", "16417_475"]
kind = "random"
chains = [1, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475]
# kind = "random"
# chains = [1, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475]
# CSiBORG1 RAMSES
snapshot_kind = "ramses"
kind = "main"
chains = [7444]
resolution = 1024
nthreads = 32
for chain_index in chains:
fname = write_submit(chain_index, kind, resolution, nthreads)
fname = write_submit(chain_index, kind, resolution, nthreads,
snapshot_kind)
system(f"sbatch {fname}")