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Merged
robjmcgibbon merged 1 commit into from
Oct 2, 2026
Merged

Update COLIBRE scripts #238

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16 changes: 11 additions & 5 deletions parameter_files/COLIBRE_HYBRID.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# Values in this section are substituted into the other sections
Parameters:
sim_dir: /cosma8/data/dp004/jlvc76/COLIBRE/ScienceRuns
output_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap_aug_04
scratch_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap_aug_04
output_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap
scratch_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap

# Location of the Swift snapshots:
Snapshots:
Expand All @@ -12,10 +12,10 @@ Snapshots:
# Which halo finder we're using, and base name for halo finder output files
HaloFinder:
type: HBTplus
filename: "/snap8/scratch/dp004/dc-mcgi1/COLIBRE/sort_hbt/{sim_name}/HBT-HERONS/OrderedSubSnap_{snap_nr:03d}.hdf5"
fof_filename: "{sim_dir}/{sim_name}/fof/fof_output_{snap_nr:04d}/fof_output_{snap_nr:04d}.{file_nr}.hdf5"
fof_radius_filename: "{sim_dir}/{sim_name}/fof_radii/fof_output_{snap_nr:04d}/fof_output_{snap_nr:04d}.{file_nr}.hdf5"
filename: "{sim_dir}/{sim_name}/HBT-HERONS/{snap_nr:03d}/SubSnap_{snap_nr:03d}"
fof_filename: "{sim_dir}/{sim_name}/fof/fof_output_{snap_nr:04d}.hdf5"
read_potential_energies: true
index_by_track_id: true

GroupMembership:
# Where to write the group membership files
Expand Down Expand Up @@ -257,6 +257,12 @@ ApertureProperties:
StellarInertiaTensorReducedLuminosityWeighted: false
StellarInertiaTensorReducedNoniterative: false
StellarInertiaTensorReducedNoniterativeLuminosityWeighted: false
ShrinkingSphereCentre: false
StellarAsymmetry: false
StellarAsymmetry48: false
StellarAsymmetry192: false
StellarAsymmetryShrink: false
StellarAsymmetrySubsample: false
variations:
exclusive_100_pc:
inclusive: false
Expand Down
16 changes: 11 additions & 5 deletions parameter_files/COLIBRE_THERMAL.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# Values in this section are substituted into the other sections
Parameters:
sim_dir: /cosma8/data/dp004/jlvc76/COLIBRE/ScienceRuns
output_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap_aug_04
scratch_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap_aug_04
output_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap
scratch_dir: /snap8/scratch/dp004/dc-mcgi1/COLIBRE/soap

# Location of the Swift snapshots:
Snapshots:
Expand All @@ -12,10 +12,10 @@ Snapshots:
# Which halo finder we're using, and base name for halo finder output files
HaloFinder:
type: HBTplus
filename: "/snap8/scratch/dp004/dc-mcgi1/COLIBRE/sort_hbt/{sim_name}/HBT-HERONS/OrderedSubSnap_{snap_nr:03d}.hdf5"
fof_filename: "{sim_dir}/{sim_name}/fof/fof_output_{snap_nr:04d}/fof_output_{snap_nr:04d}.{file_nr}.hdf5"
fof_radius_filename: "{sim_dir}/{sim_name}/fof_radii/fof_output_{snap_nr:04d}/fof_output_{snap_nr:04d}.{file_nr}.hdf5"
filename: "{sim_dir}/{sim_name}/HBT-HERONS/{snap_nr:03d}/SubSnap_{snap_nr:03d}"
fof_filename: "{sim_dir}/{sim_name}/fof/fof_output_{snap_nr:04d}.hdf5"
read_potential_energies: true
index_by_track_id: true

GroupMembership:
# Where to write the group membership files
Expand Down Expand Up @@ -257,6 +257,12 @@ ApertureProperties:
StellarInertiaTensorReducedLuminosityWeighted: false
StellarInertiaTensorReducedNoniterative: false
StellarInertiaTensorReducedNoniterativeLuminosityWeighted: false
ShrinkingSphereCentre: false
StellarAsymmetry: false
StellarAsymmetry48: false
StellarAsymmetry192: false
StellarAsymmetryShrink: false
StellarAsymmetrySubsample: false
variations:
exclusive_100_pc:
inclusive: false
Expand Down
3 changes: 2 additions & 1 deletion scripts/COLIBRE/compress_group_membership.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
#
#SBATCH --ntasks=128
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/compress_membership.%a.%A.out
#SBATCH -o ./logs/%x/compress_membership.%a.%A.out
#SBATCH -p cosma8
#SBATCH -A dp004
#SBATCH --exclusive
Expand Down Expand Up @@ -60,6 +60,7 @@ outbase="${output_dir}/${sim}/SOAP-HBT/"
# Create the output folder if it does not exist
outdir="${outbase}/membership_${snapnum}"
mkdir -p "${outdir}"
lfs setstripe --stripe-count=-1 --stripe-size=32M "${outdir}"

# Uncompressed membership file basename
input_filename="${inbase}/membership_${snapnum}/membership_${snapnum}"
Expand Down
4 changes: 2 additions & 2 deletions scripts/COLIBRE/compress_halo_properties.sh
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Expand Up @@ -11,7 +11,7 @@
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/compress_properties.%a.%A.out
#SBATCH -o ./logs/%x/compress_properties.%a.%A.out
#SBATCH -p cosma8
#SBATCH -A dp004
#SBATCH --exclusive
Expand Down Expand Up @@ -41,7 +41,7 @@ sim="${SLURM_JOB_NAME}"
input_filename="${input_dir}/${sim}/SOAP_uncompressed/halo_properties_${snapnum}.hdf5"

# Location and name of the output SOAP catalogue
outbase="${output_dir}/${sim}/SOAP-ExSitu"
outbase="${output_dir}/${sim}/SOAP-HBT"
mkdir -p $outbase
output_filename="${outbase}/halo_properties_${snapnum}.hdf5"

Expand Down
2 changes: 1 addition & 1 deletion scripts/COLIBRE/group_membership_hybrid.sh
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Expand Up @@ -13,7 +13,7 @@
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/colibre_membership.%a.%A.out
#SBATCH -o ./logs/%x/colibre_membership.%a.%A.out
#SBATCH -J group_membership_colibre
#SBATCH -p cosma8
#SBATCH -A dp004
Expand Down
2 changes: 1 addition & 1 deletion scripts/COLIBRE/group_membership_thermal.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/colibre_membership.%a.%A.out
#SBATCH -o ./logs/%x/colibre_membership.%a.%A.out
#SBATCH -J group_membership_colibre
#SBATCH -p cosma8
#SBATCH -A dp004
Expand Down
2 changes: 1 addition & 1 deletion scripts/COLIBRE/halo_properties_hybrid.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/colibre_properties_%a.%A.out
#SBATCH -o ./logs/%x/colibre_properties_%a.%A.out
#SBATCH -J halo_properties_colibre
#SBATCH -p cosma8
#SBATCH -A dp004
Expand Down
2 changes: 1 addition & 1 deletion scripts/COLIBRE/halo_properties_thermal.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH -o ./logs/colibre_properties_%a.%A.out
#SBATCH -o ./logs/%x/colibre_properties_%a.%A.out
#SBATCH -J halo_properties_colibre
#SBATCH -p cosma8
#SBATCH -A dp004
Expand Down
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