From aa44644ee86f2d397627d20dc589ca2b631a1274 Mon Sep 17 00:00:00 2001 From: robjmcgibbon Date: Fri, 2 Oct 2026 13:06:59 +0100 Subject: [PATCH] Update COLIBRE scripts --- parameter_files/COLIBRE_HYBRID.yml | 16 +++++++++++----- parameter_files/COLIBRE_THERMAL.yml | 16 +++++++++++----- scripts/COLIBRE/compress_group_membership.sh | 3 ++- scripts/COLIBRE/compress_halo_properties.sh | 4 ++-- scripts/COLIBRE/group_membership_hybrid.sh | 2 +- scripts/COLIBRE/group_membership_thermal.sh | 2 +- scripts/COLIBRE/halo_properties_hybrid.sh | 2 +- scripts/COLIBRE/halo_properties_thermal.sh | 2 +- 8 files changed, 30 insertions(+), 17 deletions(-) diff --git a/parameter_files/COLIBRE_HYBRID.yml b/parameter_files/COLIBRE_HYBRID.yml index baaacdac..1b827633 100644 --- a/parameter_files/COLIBRE_HYBRID.yml +++ b/parameter_files/COLIBRE_HYBRID.yml @@ -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: @@ -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 @@ -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 diff --git a/parameter_files/COLIBRE_THERMAL.yml b/parameter_files/COLIBRE_THERMAL.yml index 2a4dc2b2..4303d0b1 100644 --- a/parameter_files/COLIBRE_THERMAL.yml +++ b/parameter_files/COLIBRE_THERMAL.yml @@ -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: @@ -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 @@ -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 diff --git a/scripts/COLIBRE/compress_group_membership.sh b/scripts/COLIBRE/compress_group_membership.sh index 6a3c9eb9..d1033d80 100644 --- a/scripts/COLIBRE/compress_group_membership.sh +++ b/scripts/COLIBRE/compress_group_membership.sh @@ -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 @@ -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_${snapnum}" diff --git a/scripts/COLIBRE/compress_halo_properties.sh b/scripts/COLIBRE/compress_halo_properties.sh index 5acbca36..03910de0 100755 --- a/scripts/COLIBRE/compress_halo_properties.sh +++ b/scripts/COLIBRE/compress_halo_properties.sh @@ -11,7 +11,7 @@ # #SBATCH --nodes=1 #SBATCH --cpus-per-task=1 -#SBATCH -o ./logs/compress_properties.%a.%A.out +#SBATCH -o ./logs/%x/compress_properties.%a.%A.out #SBATCH -p cosma8 #SBATCH -A dp004 #SBATCH --exclusive @@ -41,7 +41,7 @@ sim="${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" diff --git a/scripts/COLIBRE/group_membership_hybrid.sh b/scripts/COLIBRE/group_membership_hybrid.sh index fc97a4ee..c4b88f36 100644 --- a/scripts/COLIBRE/group_membership_hybrid.sh +++ b/scripts/COLIBRE/group_membership_hybrid.sh @@ -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 diff --git a/scripts/COLIBRE/group_membership_thermal.sh b/scripts/COLIBRE/group_membership_thermal.sh index a4efca3d..7b125939 100644 --- a/scripts/COLIBRE/group_membership_thermal.sh +++ b/scripts/COLIBRE/group_membership_thermal.sh @@ -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 diff --git a/scripts/COLIBRE/halo_properties_hybrid.sh b/scripts/COLIBRE/halo_properties_hybrid.sh index c3bc09a3..76cbcf71 100644 --- a/scripts/COLIBRE/halo_properties_hybrid.sh +++ b/scripts/COLIBRE/halo_properties_hybrid.sh @@ -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 diff --git a/scripts/COLIBRE/halo_properties_thermal.sh b/scripts/COLIBRE/halo_properties_thermal.sh index 546b6f07..192ca54f 100644 --- a/scripts/COLIBRE/halo_properties_thermal.sh +++ b/scripts/COLIBRE/halo_properties_thermal.sh @@ -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