Mherbold test branch

Examples/configs/data/iron_FS_sampler_test.yaml → Examples/configs/data/loa_FS_sampler_test.yaml

@@ -4,26 +4,31 @@ general:
   slurm args:
     mail-type: fail
     mail-user: herbold.9@osu.edu
-  defaults file: Iron_FS.yaml
+  defaults file: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/loa_fs_v2_no_lyB.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
+  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
-  use existing: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/iron_baseline_test
+  use existing: /global/cfs/cdirs/desi/science/lya/y3-fs/validation-tests/v1-0-0-0/baseline
 correlations:
   computed distortions:
-    general: /pscratch/sd/m/mherbold/tests/bookkeeper/full_shape/iron_baseline_test/correlations/results
+    general: /global/cfs/cdirs/desi/science/lya/y3-fs/validation-tests/v1-0-0-0/baseline/correlations/results
 fits:
+  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
   extra args: 
     vega_main:
       general:
+        control:
+          run_sampler: True
+          sampler: Polychord   # or PocoMC 
         Polychord:
           num_live: 512
           num_repeats: 20
-          path:
           do_clustering: True
           resume: True
           boost_posterior: 3
@@ -37,17 +42,3 @@ fits:
         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
-
-# Note: to calculate polychord and slurm args: 
-  # num_live = 25 * num_params (rounded down to nearest multiple of 64)
-  # nodes = num_live / tasks_per_node
-  # num_repeats = num_params
-
-# e.g. for 16 parameters:
-  # num_repeats=16
-  # num_live=384
-  # tasks_per_node=64
-  # nodes=6

README.md

@@ -22,11 +22,13 @@ cd vega
 pip install -e .
 ```
 
-If using the Vega sampler, install MPI: 
+For running the Vega sampler, install MPI: 
 ```bash
 MPICC="cc -shared" pip install --force-reinstall --no-cache-dir --no-binary=mpi4py mpi4py
 ```
 
+Then install Polychord or PocoMC (Vega instructions here: https://github.com/andreicuceu/vega). 
+
 To get the most up-to-date version of the bookkeper, clone the repo:
 ```bash
 git clone https://github.com/cramirezpe/picca_bookkeeper.git picca_bookkeeper
@@ -115,7 +117,38 @@ To run the sampler, ensure that MPI is properly installed with NERSC specific se
 ```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.)
+
+### You will also need to install Polychord or PocoMC (Polychord instructions here are taken from: https://github.com/andreicuceu/vega): 
+
+1) Clone the Polychord repo (does not require conda environment yet):
+```bash
+git clone https://github.com/PolyChord/PolyChordLite.git
+cd PolyChordLite
+```
+2) In the PolyChordLite folder, locate a file called ``Makefile_gnu``, and change 3 lines:
+ ```bash
+FC = mpifort
+CC = mpicc
+CXX = mpicxx
+```
+to
+ ```bash
+FC = ftn
+CC = CC
+CXX = CC
+```
+3) Then, inside your conda environment, install Polychord:
+```bash
+make veryclean
+make COMPILER_TYPE=gnu
+pip install -e .
+```
+4) You can test by running the following on an interractive node:
+```bash
+srun -n 2 python run_pypolychord.py
+```
+
+Note: for the bookkeeper.yaml 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
@@ -125,6 +158,18 @@ general:
 fits:
   sampler environment: /path/to/conda_environment
 ```
+
+You will also need to specify which sampler (Polychord / PocoMC) you will be using. 
+```bash
+fits:
+  extra args: 
+    vega_main:
+      general:
+        control:
+          run_sampler: True
+          sampler: Polychord   # or PocoMC
+```
+
 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/resources/default_configs/loa_fs_v2_no_lyB.yaml → picca_bookkeeper/resources/default_configs/loa_fs_v2.yaml

@@ -1,3 +1,4 @@
+# the goal is to modify this for full shape analysis
 delta extraction: 
   extra args:
     picca_delta_extraction:
@@ -389,16 +390,16 @@ fits:
           # smooth-scaling: False
 
         ## FS peak/smooth AP: fit phi-alpha, smooth-scaling True
-          cosmo fit func: phi_alpha
-          full-shape: False
-          full-shape-alpha: False
-          smooth-scaling: True
-
-        ## FS AP: fit phi_alpha, smooth-scaling True, FS True
           # cosmo fit func: phi_alpha
-          # full-shape: True
+          # full-shape: False
           # full-shape-alpha: False
           # smooth-scaling: True
+
+        ## FS AP: fit phi_alpha, smooth-scaling True, FS True
+          cosmo fit func: phi_alpha
+          full-shape: True
+          full-shape-alpha: False
+          smooth-scaling: True
 
         ## FS galaxy: fit phi-alpha, all True
           # cosmo fit func: phi_alpha
@@ -439,16 +440,16 @@ fits:
           dnl_arinyo_kp: 5 22 19.47 0.1
 
           # Peak/smooth AP config
-          phi: True
-          alpha: True
-          phi_smooth: True
-          alpha_smooth: True
-
-          # Full-shape AP config
+          # phi: True
           # alpha: True
-          # phi_full: True
+          # phi_smooth: True
           # alpha_smooth: True
 
+          # Full-shape AP config
+          alpha: True
+          phi_full: True
+          alpha_smooth: True
+
           # Galaxy full-shape config
           # phi_full: True
           # alpha_full: True
@@ -503,16 +504,16 @@ fits:
           desi_inst_sys_amp: 1e-4
 
           # Peak/smooth AP config
-          phi: 1.0
-          alpha: 1.0
-          phi_smooth: 1.0
-          alpha_smooth: 1.0
-
-          # Full-shape AP config
+          # phi: 1.0
           # alpha: 1.0
-          # phi_full: 1.0
+          # phi_smooth: 1.0
           # alpha_smooth: 1.0
 
+          # Full-shape AP config
+          alpha: 1.0
+          phi_full: 1.0
+          alpha_smooth: 1.0
+
           # Galaxy full-shape config
           # phi_full: 1.0
           # alpha_full: 1.0