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SPH for CSiBORG1 support (#109)
* Add edited files * Update scripts * Updates * Little fix * Little ifx
This commit is contained in:
Richard Stiskalek
GitHub
parent
f0ab6fc9b4
commit
b88c0703f6
2 changed files with 68 additions and 30 deletions
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@ -16,11 +16,11 @@
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Script to construct the density and velocity fields for a simulation snapshot.
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The SPH filter is implemented in the cosmotool package.
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"""
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from argparse import ArgumentParser
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from os import remove
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from os.path import join, exists
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import subprocess
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from argparse import ArgumentParser
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from datetime import datetime
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from os import remove
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from os.path import exists, join
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import hdf5plugin # noqa
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import numpy as np
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@ -137,7 +137,7 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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SPH_executable : str
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Path to the `simple3DFilter` executable [1].
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snapshot_kind : str
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Kind of the simulation snapshot. Currently only `gadget4` is supported.
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Kind of the simulation snapshot.
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Returns
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-------
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@ -147,12 +147,24 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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----------
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[1] https://bitbucket.org/glavaux/cosmotool/src/master/sample/simple3DFilter.cpp # noqa
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"""
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if snapshot_kind != "gadget4":
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raise NotImplementedError("Only GADGET HDF5 snapshots are supported.")
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# First get the temporary file path.
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if snapshot_kind == "gadget4":
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temporary_output_path = join(
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scratch_space, generate_unique_id(snapshot_path))
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elif snapshot_kind == "ramses":
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temporary_output_path = snapshot_path
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else:
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raise NotImplementedError("Only GADGET HDF5 or preprocessed RAMSES "
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"snapshots are supported.")
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if not temporary_output_path.endswith(".hdf5"):
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raise RuntimeError("Temporary output path must end with `.hdf5`.")
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# Print the job information.
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print("---------- SPH Density & Velocity Field Job Information ----------")
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print(f"Snapshot path: {snapshot_path}")
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print(f"Output path: {output_path}")
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print(f"Temporary path: {temporary_output_path}")
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print(f"Resolution: {resolution}")
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print(f"Scratch space: {scratch_space}")
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print(f"SPH executable: {SPH_executable}")
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@ -160,19 +172,23 @@ def main(snapshot_path, output_path, resolution, scratch_space, SPH_executable,
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print("------------------------------------------------------------------")
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print(flush=True)
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temporary_output_path = join(
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scratch_space, generate_unique_id(snapshot_path))
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if not temporary_output_path.endswith(".hdf5"):
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raise RuntimeError("Temporary output path must end with `.hdf5`.")
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# Prepare or read-off the temporary snapshot file.
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if snapshot_kind == "gadget4":
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print(f"{now()}: preparing snapshot...", flush=True)
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boxsize = prepare_gadget(snapshot_path, temporary_output_path)
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print(f"{now()}: wrote temporary data to {temporary_output_path}.",
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flush=True)
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else:
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boxsize = 677.7 # Mpc/h
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print(f"{now()}: CAREFUL, forcefully setting the boxsize to {boxsize} Mpc / h.", # noqa
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flush=True)
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# Run the SPH filter.
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run_sph_filter(temporary_output_path, output_path, boxsize, resolution,
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SPH_executable)
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# Remove the temporary snapshot file if it was created.
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if snapshot_kind == "gadget4":
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print(f"{now()}: removing the temporary snapshot file.", flush=True)
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try:
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remove(temporary_output_path)
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@ -193,7 +209,7 @@ if __name__ == "__main__":
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parser.add_argument("--SPH_executable", type=str, required=True,
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help="Path to the `simple3DFilter` executable.")
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parser.add_argument("--snapshot_kind", type=str, required=True,
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choices=["gadget4"],
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choices=["gadget4", "ramses"],
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help="Kind of the simulation snapshot.")
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args = parser.parse_args()
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@ -17,12 +17,27 @@ Script to write the SLURM submission script and submit it to the queue to
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calculate the SPH density & velocity field for GADGET.
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"""
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from os import system
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from os.path import join
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def write_submit(chain_index, kind, resolution, nthreads):
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def write_submit(chain_index, kind, resolution, nthreads, snapshot_kind):
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if kind not in ["main", "random", "varysmall"]:
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raise RuntimeError(f"Unknown kind `{kind}`.")
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basepath = "/cosma8/data/dp016/dc-stis1/"
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if snapshot_kind == "gadget4":
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snapshot_path = join(basepath, f"csiborg2_{kind}/chain_{chain_index}",
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"output/snapshot_099_full.hdf5")
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output_path = join(
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basepath,
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f"csiborg2_{kind}/field/chain_{chain_index}_{resolution}.hdf5")
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else:
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chain_index = str(chain_index).zfill(5)
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snapshot_path = join(basepath, "csiborg1_sph",
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f"ramses_{chain_index}.hdf5")
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output_path = join(basepath, "csiborg1_sph",
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f"sph_ramses_{chain_index}_{resolution}.hdf5")
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txt = f"""#!/bin/sh
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#SBATCH --ntasks-per-node=1
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@ -53,12 +68,12 @@ source /cosma/home/dp016/dc-stis1/csiborgtools/venv_csiborgtools/bin/activate
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export OMP_NUM_THREADS={nthreads}
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export OMP_NESTED=true
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snapshot_path="/cosma8/data/dp016/dc-stis1/csiborg2_{kind}/chain_{chain_index}/output/snapshot_099_full.hdf5"
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output_path="/cosma8/data/dp016/dc-stis1/csiborg2_{kind}/field/chain_{chain_index}_{resolution}.hdf5"
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snapshot_path={snapshot_path}
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output_path={output_path}
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resolution={resolution}
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scratch_space="/snap8/scratch/dp016/dc-stis1/"
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SPH_executable="/cosma8/data/dp016/dc-stis1/cosmotool/bld2/sample/simple3DFilter"
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snapshot_kind="gadget4"
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snapshot_kind={snapshot_kind}
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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
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"""
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@ -72,18 +87,25 @@ python3 field_sph_gadget.py --snapshot_path $snapshot_path --output_path $output
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if __name__ == "__main__":
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snapshot_kind = "gadget4"
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# kind = "main"
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# chains = [15617, 15717, 15817, 15917, 16017, 16117, 16217, 16317, 16417, 16517, 16617, 16717, 16817, 16917, 17017, 17117, 17217, 17317, 17417]
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# kind = "varysmall"
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# 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"]
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kind = "random"
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chains = [1, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475]
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# kind = "random"
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# chains = [1, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475]
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# CSiBORG1 RAMSES
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snapshot_kind = "ramses"
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kind = "main"
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chains = [7444]
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resolution = 1024
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nthreads = 32
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for chain_index in chains:
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fname = write_submit(chain_index, kind, resolution, nthreads)
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fname = write_submit(chain_index, kind, resolution, nthreads,
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snapshot_kind)
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system(f"sbatch {fname}")
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