galform-execution 0.2.0__tar.gz → 0.2.2__tar.gz

{galform_execution-0.2.0 → galform_execution-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: galform_execution
-Version: 0.2.0
+Version: 0.2.2
 Summary: GALFORM execution helper utilities
 Author: Oscar Hickman
 License: MIT

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/__init__.py

@@ -2,4 +2,4 @@
 galform_execution: Python-based utility to manage GALFORM N-body simulation submissions to SLURM.
 """
 
-__version__ = "0.1.6"
+__version__ = "0.2.2"

galform_execution-0.2.2/galform_execution/config/simulations/colibre_family.json

@@ -0,0 +1,43 @@
+{
+  "COLIBRE-L100m6": {
+    "aquarius_particle_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/particle_lists/particle_list_127",
+    "aquarius_tree_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/tree_127",
+    "h0": 0.681,
+    "iz0": 127,
+    "iz_list": [
+      127,
+      102,
+      92
+    ],
+    "lambda0": 0.693922,
+    "lbox": 68.1,
+    "mpart": 1569616.5,
+    "nbody_trees_dir": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees",
+    "nvol_range": "1-64",
+    "omega0": 0.306078,
+    "omegab": 0.0486,
+    "pk_file": "Power_Spec/pk_FLAMINGO_DMO_FIDUCIAL.dat",
+    "sigma8": 0.807,
+    "snapshot_file": "COLIBRE-L100m6.txt",
+    "volume": 4934.706890625
+  },
+  "COLIBRE-L400m7": {
+    "_note": "GALFORM-format aquarius trees not yet built from COLIBRE DMO. dhalo trees at /cosma7/data/dp004/jch/COLIBRE/L400_m7/DMO/dhalo_trees/ (not yet in GALFORM aquarius format). Update tree paths and iz0/iz_list/nvol_range before submitting.",
+    "aquarius_particle_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/particle_lists/particle_list_TBD",
+    "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/treedir_TBD/tree_TBD",
+    "h0": 0.681,
+    "iz0": null,
+    "iz_list": [],
+    "lambda0": 0.693922,
+    "lbox": 272.4,
+    "mpart": 12556932.0,
+    "nbody_trees_dir": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7",
+    "nvol_range": "1-64",
+    "omega0": 0.306078,
+    "omegab": 0.0486,
+    "pk_file": "Power_Spec/pk_COLIBRE_norm.dat",
+    "sigma8": 0.807,
+    "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/redshift_list.txt",
+    "volume": null
+  }
+}

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/config/simulations/eagle_family.json

@@ -8,8 +8,8 @@
       200
     ],
     "lambda0": 0.693,
-    "lbox": null,
-    "mpart": null,
+    "lbox": 67.77,
+    "mpart": 7795580.0,
     "nbody_trees_dir": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504",
     "nvol_range": "1-128",
     "omega0": 0.307,
@@ -28,8 +28,8 @@
       101
     ],
     "lambda0": 0.693,
-    "lbox": null,
-    "mpart": null,
+    "lbox": 67.77,
+    "mpart": 7795580.0,
     "nbody_trees_dir": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums100",
     "nvol_range": "1-128",
     "omega0": 0.307,
@@ -48,8 +48,8 @@
       67
     ],
     "lambda0": 0.693,
-    "lbox": null,
-    "mpart": null,
+    "lbox": 67.77,
+    "mpart": 7795580.0,
     "nbody_trees_dir": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums62",
     "nvol_range": "1-128",
     "omega0": 0.307,

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/config/simulations/flamingo_family.json

@@ -4,10 +4,15 @@
     "aquarius_tree_file": "/cosma8/data/dp004/jch/FLAMINGO/HBT/L1000N1800/DMO_FIDUCIAL/trees/tree_077",
     "h0": 0.681,
     "iz0": 77,
-    "iz_list": [77, 67, 57, 37],
+    "iz_list": [
+      77,
+      67,
+      57,
+      37
+    ],
     "lambda0": 0.693922,
     "lbox": 681.0,
-    "mpart": 4599600000.0,
+    "mpart": 4578145711.0,
     "nbody_trees_dir": "/cosma8/data/dp004/jch/FLAMINGO/HBT/L1000N1800/DMO_FIDUCIAL/trees",
     "nvol_range": "1-64",
     "omega0": 0.306078,
@@ -15,6 +20,6 @@
     "pk_file": "Power_Spec/pk_FLAMINGO_DMO_FIDUCIAL.dat",
     "sigma8": 0.807,
     "snapshot_file": "FLAMINGO-L1000N1800.txt",
-    "volume": 315821241.0
+    "volume": 4934706.890625
   }
 }

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/config/simulations/millennium_family.json

@@ -91,7 +91,7 @@
     "volume": 1953125.0
   },
   "MillGas62.5": {
-    "_note": "Tree files not present on disk — lbox/mpart unverified.",
+    "_note": "Tree files not present on disk — lbox/mpart unverified. Previous volume=1953125.0 was a copy-paste from the 500 Mpc/h MillGas box and wrong for a 62.5 box; set to null.",
     "aquarius_particle_file": "/cosma5/data/jch/Galform/Merger_Trees/MillGas/dm/62.5/new/particle_lists/particle_list_061",
     "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/MillGas/dm/62.5/new/treedir_061/tree_061",
     "h0": 0.704,
@@ -109,7 +109,7 @@
     "pk_file": "Power_Spec/pk_MillGas_norm.dat",
     "sigma8": 0.81,
     "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/MillGas/dm/62.5/new/redshift_list",
-    "volume": 1953125.0
+    "volume": null
   },
   "MilliMil": {
     "aquarius_particle_file": "/cosma5/data/jch/MilliMillennium/trees/particle_lists/particle_list_063",

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/config/simulations/nifty_family.json

@@ -1,5 +1,6 @@
 {
   "nifty62.5": {
+    "_note": "Tree dir /cosma5/data/jch/Galform/Merger_Trees/nifty/ no longer exists on disk. Previous volume=1953125.0 was a copy-paste from the 500 Mpc/h MillGas box and wrong for a 62.5 box; set to null until trees are located.",
     "aquarius_particle_file": "",
     "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/nifty/62.5/treedir_061/tree_061",
     "h0": 0.704,
@@ -17,6 +18,6 @@
     "pk_file": "Power_Spec/pk_MillGas_norm.dat",
     "sigma8": 0.81,
     "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/nifty/62.5/redshift_list",
-    "volume": 1953125.0
+    "volume": null
   }
 }

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution/submit_galform_job.py

@@ -301,6 +301,8 @@ class GalformSubmitter:
         submit_retries: int = 4,
         submit_retry_delay_s: float = 15.0,
         submit_retry_backoff: float = 2.0,
+        mail_user: Optional[str] = None,
+        mail_type: str = "END,FAIL",
     ):
         self.galform_dir = Path(galform_dir)
         self.nbody_sim = nbody_sim
@@ -324,6 +326,8 @@ class GalformSubmitter:
         self.submit_retries = max(1, int(submit_retries))
         self.submit_retry_delay_s = max(0.0, float(submit_retry_delay_s))
         self.submit_retry_backoff = max(1.0, float(submit_retry_backoff))
+        self.mail_user = mail_user
+        self.mail_type = mail_type
         self._snapshot_redshift_cache: Optional[Dict[int, float]] = None
 
         if self.output_redshifts is not None and self.output_iz_list is not None:
@@ -923,6 +927,12 @@ set SAMPLE_GALS_EXE    = ${{build_dir}}/sample_gals
             else self.nvol_count
         )
 
+        mail_lines = (
+            f"#SBATCH --mail-user={self.mail_user}\n#SBATCH --mail-type={self.mail_type}"
+            if self.mail_user
+            else ""
+        )
+
         script = f"""#!/bin/bash
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task={effective_cpus}
@@ -932,6 +942,7 @@ set SAMPLE_GALS_EXE    = ${{build_dir}}/sample_gals
 #SBATCH -p {self.partition}
 #SBATCH -A {self.account}
 #SBATCH -t {self.walltime}
+{mail_lines}
 
 _run_worker() {{
     local task_id=$1
@@ -1103,6 +1114,16 @@ Examples:
     parser.add_argument(
         "--walltime", default="72:00:00", help="Job wall-time (default: 72:00:00)"
     )
+    parser.add_argument(
+        "--mail-user",
+        default=None,
+        help="Email address for SLURM job notifications",
+    )
+    parser.add_argument(
+        "--mail-type",
+        default="END,FAIL",
+        help="SLURM mail event types (default: END,FAIL)",
+    )
     parser.add_argument(
         "--iz-list", type=int, nargs="+", help="Override default snapshot list"
     )
@@ -1271,6 +1292,8 @@ Examples:
             partition=args.partition,
             account=args.account,
             walltime=args.walltime,
+            mail_user=args.mail_user,
+            mail_type=args.mail_type,
             iz_list=args.iz_list,
             nvol_range=args.nvol_range,
             run_flags=run_flags,

{galform_execution-0.2.0 → galform_execution-0.2.2}/galform_execution.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: galform_execution
-Version: 0.2.0
+Version: 0.2.2
 Summary: GALFORM execution helper utilities
 Author: Oscar Hickman
 License: MIT

{galform_execution-0.2.0 → galform_execution-0.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "galform_execution"
-version = "0.2.0"
+version = "0.2.2"
 description = "GALFORM execution helper utilities"
 readme = "README.md"
 requires-python = ">=3.8"

{galform_execution-0.2.0 → galform_execution-0.2.2}/tests/test_submit_galform_job.py

@@ -476,6 +476,7 @@ def test_submit_job_retries_transient_error_then_succeeds():
             nvol="101-150",
             submit_retries=3,
             submit_retry_delay_s=0.0,
+            log_path=str(Path(tmpdir) / "logs"),
         )
 
         transient_err = subprocess.CalledProcessError(
@@ -518,6 +519,7 @@ def test_submit_job_fails_immediately_for_non_transient_error():
             nvol="101-150",
             submit_retries=3,
             submit_retry_delay_s=0.0,
+            log_path=str(Path(tmpdir) / "logs"),
         )
 
         fatal_err = subprocess.CalledProcessError(
@@ -556,6 +558,7 @@ def test_submit_job_fails_after_retries_exhausted_for_transient_error():
             nvol="101-150",
             submit_retries=3,
             submit_retry_delay_s=0.0,
+            log_path=str(Path(tmpdir) / "logs"),
         )
 
         transient_err = subprocess.CalledProcessError(
@@ -708,6 +711,52 @@ def test_create_job_script_throttled():
         assert "--array" not in script
 
 
+def test_create_job_script_mail_notifications():
+    """mail_user should add SBATCH mail directives; omitting it should not."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        gdir = _make_galform_dir(tmpdir)
+
+        # With email — default mail_type
+        submitter = GalformSubmitter(
+            galform_dir=gdir,
+            nbody_sim="L800",
+            model="gp14",
+            iz=100,
+            nvol="1-8",
+            mail_user="user@example.com",
+        )
+        script = submitter.create_job_script(iz=100, tcsh_path="/tmp/g.csh")
+        assert "#SBATCH --mail-user=user@example.com" in script
+        assert "#SBATCH --mail-type=END,FAIL" in script
+
+        # Custom mail_type
+        submitter_all = GalformSubmitter(
+            galform_dir=gdir,
+            nbody_sim="L800",
+            model="gp14",
+            iz=100,
+            nvol="1-8",
+            mail_user="user@example.com",
+            mail_type="ALL",
+        )
+        script_all = submitter_all.create_job_script(iz=100, tcsh_path="/tmp/g.csh")
+        assert "#SBATCH --mail-type=ALL" in script_all
+
+        # Without email — directives must be absent
+        submitter_no_mail = GalformSubmitter(
+            galform_dir=gdir,
+            nbody_sim="L800",
+            model="gp14",
+            iz=100,
+            nvol="1-8",
+        )
+        script_no_mail = submitter_no_mail.create_job_script(
+            iz=100, tcsh_path="/tmp/g.csh"
+        )
+        assert "--mail-user" not in script_no_mail
+        assert "--mail-type" not in script_no_mail
+
+
 def test_submit_job_dry_run(capsys):
     """Dry run should print both scripts and not call sbatch."""
     with tempfile.TemporaryDirectory() as tmpdir:

galform_execution-0.2.0/galform_execution/config/simulations/colibre_family.json

@@ -1,20 +0,0 @@
-{
-  "COLIBRE-L100m6": {
-    "aquarius_particle_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/particle_lists/particle_list_127",
-    "aquarius_tree_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/tree_127",
-    "h0": 0.681,
-    "iz0": 127,
-    "iz_list": [127, 102, 92],
-    "lambda0": 0.693922,
-    "lbox": 68.1,
-    "mpart": 7847050.0,
-    "nbody_trees_dir": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees",
-    "nvol_range": "1-64",
-    "omega0": 0.306078,
-    "omegab": 0.0486,
-    "pk_file": "Power_Spec/pk_FLAMINGO_DMO_FIDUCIAL.dat",
-    "sigma8": 0.807,
-    "snapshot_file": "COLIBRE-L100m6.txt",
-    "volume": 315821.241
-  }
-}