Mherbold test branch

Examples/configs/data/iron_FS_sampler_test.yaml

@@ -0,0 +1,42 @@
+general:
+  conda environment: /global/homes/m/mherbold/.conda/envs/full_shape_bookkeeper
+  system: slurm_perlmutter
+  slurm args:
+    mail-type: fail
+    mail-user: [email protected]
+  defaults file: Iron_FS.yaml
+data:
+  bookkeeper dir: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/iron_baseline_test
+  healpix data: /global/cfs/cdirs/desi/spectro/redux/iron/healpix/
+  catalog: /global/cfs/cdirs/desicollab/science/lya/y1-kp6/iron-baseline/catalogs/QSO_cat_iron_main_dark_healpix_zlya-altbal_zwarn_cut_20230918.fits
+delta extraction:
+  calib: 1
+  calib region: ciii
+  use existing: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/iron_baseline_test
+correlations:
+  computed distortions:
+    general: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/iron_baseline_test/correlations/results
+fits:
+  extra args: 
+    vega_main:
+      general:
+        Polychord:
+          num_live: 512
+          num_repeats: 20
+          path:
+          do_clustering: True
+          resume: True
+          boost_posterior: 3
+    smooth_covariance:
+      general:
+        block-types: auto cross
+        # note: specify 'auto cross' to just run A region (omit B)
+  slurm args:
+    run_vega_mpi:
+      general:
+        time: "08:00:00"
+        nodes: 6
+        ntasks-per-node: 64
+  sampler environment: /global/homes/m/mherbold/.conda/envs/full_shape_bookkeeper 
+  # need to specify, same as general: conda environment:
+  # default is currently: /global/common/software/desi/users/acuceu/stable_vega/activate_vega.sh

Examples/configs/data/jura_BAO_baseline.yaml

@@ -0,0 +1,19 @@
+general:
+  conda environment: /global/common/software/desi/users/cramireez/conda/envs/picca.marseille
+  system: slurm_perlmutter
+  slurm args:
+    mail-type: fail
+    mail-user: [email protected]
+  defaults file: Jurav1
+data:
+  bookkeeper dir: /global/cfs/cdirs/desicollab/science/lya/y3/jura/validation_tests/baseline
+  healpix data: /dvs_ro/cfs/cdirs/desi/spectro/redux/jura/healpix
+  catalog: /global/cfs/cdirs/desicollab/science/lya/y3/jura/catalogs/QSO_cat_jura_main_dark_healpix_v1_zwarn_cut.fits
+delta extraction:
+  calib: 1
+  calib region: ciii
+  dla: /global/cfs/cdirs/desicollab/science/lya/y3/jura/catalogs/dlacat-20240618-conf05-nhi203-snr3.fits
+  bal: /global/cfs/cdirs/desicollab/science/lya/y3/jura/catalogs/QSO_cat_jura_main_dark_healpix_v1-bal.fits
+  mask file: /global/cfs/cdirs/desicollab/science/lya/y3/jura/deltas/delta-lya-1-0/continuum_fitting_mask.txt
+correlations: {}
+fits: {}

Examples/configs/data/kibo_BAO_baseline.yaml

@@ -0,0 +1,21 @@
+general:
+  conda environment: /global/common/software/desi/users/iprafols/loa_unblind/conda/loa-2-0-2-0
+  system: slurm_perlmutter
+  slurm args:
+    mail-type: fail
+    mail-user: [email protected]
+  defaults file: /global/cfs/cdirs/desi/science/lya/y3/loa/validation_tests/3-0-0-0/configs/loa-3-0-0-0.yaml
+data:
+  bookkeeper dir: /global/cfs/cdirs/desi/science/lya/y3/loa/validation_tests/3-0-0-0/variations_delta/only_qso_targets
+  healpix data: /global/cfs/cdirs/desi/spectro/redux/loa/healpix/
+  catalog: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/QSO_cat_loa_main_dark_healpix_only_qso_targets_v2.fits
+delta extraction:
+  calib: 1
+  calib region: ciii
+  dla: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/loa_gp_and_tmp_or_gp_and_cnn_snr_2_cat_20241217.fits
+  bal: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/QSO_cat_loa_main_dark_healpix_v2-altbal-20241115.fits
+  mask file: /global/cfs/cdirs/desi/science/lya/y3/loa/deltas/delta-lya-3-0/continuum_fitting_mask.txt
+correlations:
+  computed distortions:
+    general: /global/cfs/cdirs/desi/science/lya/y3/loa/validation_tests/3-0-0-0/baseline/correlations/results
+fits: {}

Examples/configs/data/loa_BAO_baseline.yaml

@@ -0,0 +1,19 @@
+general:
+  conda environment: /global/common/software/desi/users/iprafols/loa_unblind/conda/loa-2-0-2-0
+  system: slurm_perlmutter
+  slurm args:
+    mail-type: fail
+    mail-user: [email protected]
+  defaults file: /global/cfs/cdirs/desi/science/lya/y3/loa/validation_tests/3-0-0-0/configs/loa-3-0-0-0.yaml
+data:
+  bookkeeper dir: /global/cfs/cdirs/desi/science/lya/y3/loa/validation_tests/3-0-0-0/baseline
+  healpix data: /global/cfs/cdirs/desi/spectro/redux/loa/healpix/
+  catalog: /global/cfs/cdirs/desi/survey/catalogs/DA2/QSO/loa/QSO_cat_loa_main_dark_healpix_v2.fits
+delta extraction:
+  calib: 1
+  calib region: ciii
+  dla: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/loa_gp_and_tmp_or_gp_and_cnn_snr_2_cat_20241217.fits
+  bal: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/QSO_cat_loa_main_dark_healpix_v2-altbal-20241115.fits
+  mask file: /global/cfs/cdirs/desi/science/lya/y3/loa/deltas/delta-lya-3-0/continuum_fitting_mask.txt
+correlations: {}
+fits: {}

Examples/configs/data/loa_FS_baseline.yaml

@@ -0,0 +1,28 @@
+general:
+  conda environment: /global/homes/m/mherbold/.conda/envs/full_shape_bookkeeper
+  system: slurm_perlmutter
+  slurm args:
+    mail-type: fail
+    mail-user: [email protected]
+  defaults file: /global/cfs/cdirs/desi/science/lya/y3-fs/validation-tests/v1-0-0-0/configs/loa_fs_v1.yaml
+
+data:
+  bookkeeper dir: /global/cfs/cdirs/desi/science/lya/y3-fs/validation-tests/v1-0-0-0/baseline
+  healpix data: /global/cfs/cdirs/desi/spectro/redux/loa/healpix/
+  catalog: /global/cfs/cdirs/desi/survey/catalogs/DA2/QSO/loa/QSO_cat_loa_main_dark_healpix_v2.fits
+
+delta extraction:
+  calib: 1
+  calib region: ciii
+  dla: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/loa_gp_and_tmp_or_gp_and_cnn_snr_2_cat_20241217.fits
+  bal: /global/cfs/cdirs/desi/science/lya/y3/loa/catalogs/QSO_cat_loa_main_dark_healpix_v2-altbal-20241115.fits
+  mask file: /global/cfs/cdirs/desi/science/lya/y3/loa/deltas/delta-lya-3-0/continuum_fitting_mask.txt
+
+correlations: {}
+
+fits: 
+  extra args:
+    smooth_covariance:
+      general:
+        block-types: auto cross # us to omit B-region
+

README.md

@@ -10,7 +10,7 @@ Activate new environment, and install a stable version of Picca:
 ```bash
 conda activate evn_name
 
-pip install picca --version=9.13.0
+pip install picca==9.13.0
 ```
 
 Install Vega:
@@ -19,7 +19,12 @@ git clone https://github.com/andreicuceu/vega.git Vega
 
 cd vega
 
-pip install -e
+pip install -e .
+```
+
+If using the Vega sampler, install MPI: 
+```bash
+MPICC="cc -shared" pip install --force-reinstall --no-cache-dir --no-binary=mpi4py mpi4py
 ```
 
 To get the most up-to-date version of the bookkeper, clone the repo:
@@ -104,3 +109,23 @@ To run on mocks, use as a defulat file  ``quickquasars``, ``raw`` or ``True``. T
 ```
 picca_bookkeeper_run_full_analysis \path_to_mock_config.yaml
 ```
+
+## Run the Vega Sampler
+To run the sampler, ensure that MPI is properly installed with NERSC specific settings in your conda environment: 
+```bash
+MPICC="cc -shared" pip install --force-reinstall --no-cache-dir --no-binary=mpi4py mpi4py
+```
+Note: for the bookkeeper config file, you will need to specify your conda environment again. (Otherwise the bookkeeper will default to sourcing a separate Vega installation.)
+```bash
+general:
+  conda environment: /path/to/conda_environment
+
+...
+
+fits:
+  sampler environment: /path/to/conda_environment
+```
+Then to run from the terminal (including arguments like ``--skip-sent`` if skipping deltas, etc.): 
+```bash
+picca_bookkeeper_run_sampler /path_to_config.yaml
+```

picca_bookkeeper/bookkeeper.py

@@ -3055,6 +3055,7 @@ def get_sampler_tasker(
             "job-name": job_name,
             "output": str(self.paths.fits_path / f"logs/{job_name}-%j.out"),
             "error": str(self.paths.fits_path / f"logs/{job_name}-%j.err"),
+            "OMP_NUM_THREADS": 1
         }
 
         slurm_header_args = DictUtils.merge_dicts(

pyproject.toml

@@ -12,16 +12,18 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.dependencies]
 python = ">=3.10"
-astropy = "^6.1.6"
-fitsio = "^1.2.4"
-getdist = "^1.5.4"
+astropy = "^6.1.7"
+fitsio = "^1.2.6"
+getdist = "^1.6.4"
 healpy = "^1.18.0"
-matplotlib = "^3.9.2"
-numpy = ">=1.22,<2.1"
+matplotlib = ">=3.10"
+numpy = "^1.24.4"
 pandas = "^2.2.3"
-scipy = "^1.14.1"
+scipy = "^1.15.3"
 tabulate = "^0.9.0"
-importlib-resources = "^6.4.5"
+importlib-resources = "^6.5.2"
+iminuit = ">=2.31.1"
+gitpython = ">=3.1.44"
 
 [tool.poetry.scripts]
 picca_bookkeeper_run_delta_extraction = "picca_bookkeeper.scripts.run_delta_extraction:main"

tests/test_files/guadalupe_sampler/fits/scripts/run_vega_sampler.sh

@@ -9,6 +9,7 @@
 #SBATCH --job-name vega_sampler
 #SBATCH --output /picca_bookkeeper/tests/test_files/output/results/fits/logs/vega_sampler-%j.out
 #SBATCH --error /picca_bookkeeper/tests/test_files/output/results/fits/logs/vega_sampler-%j.err
+export OMP_NUM_THREADS=1
 
 module load python
 source /global/common/software/desi/users/acuceu/stable_vega/activate_vega.sh