Only update bulk flow prior when cosmology changed

borg_velocity/likelihood.py

@@ -189,6 +189,8 @@ class VelocityBORGLikelihood(borg.likelihood.BaseLikelihood):
         self.fwd.setCosmoParams(cpar)
         self.fwd_param.setCosmoParams(cpar)
         
+        self.sigma_bulk = get_sigma_bulk(self.L[0], self.fwd.getCosmoParams())
+        
         
     def generateMBData(self) -> None:
         """
@@ -355,8 +357,7 @@ class VelocityBORGLikelihood(borg.likelihood.BaseLikelihood):
             # self.lkl_ind[i] = temp_lkl_ind.copy()
             
         # Add in bulk flow prior
-        # sigma_bulk = get_sigma_bulk(self.L[0], self.fwd.getCosmoParams())
+        lkl += jnp.sum(0.5 * jnp.log(2 * np.pi) + jnp.log(self.sigma_bulk) + self.bulk_flow ** 2 / 2. / self.sigma_bulk ** 2)
-        # lkl += jnp.sum(0.5 * jnp.log(2 * np.pi) + jnp.log(sigma_bulk) + self.bulk_flow ** 2 / 2. / sigma_bulk ** 2)
             
         # lkl = jnp.clip(lkl, -self.bignum, self.bignum)
         lkl = lax.cond(

borg_velocity/samplers.py

@@ -523,13 +523,19 @@ class TransformedBlackJaxBiasSampler(borg.samplers.PyBaseSampler):
                 adaptation_info_fn=get_info
             )
             rng_key, warmup_key, sample_key = jax.random.split(self.rng_key, 3)
-            (state, self.parameters), info = warmup.run(warmup_key, self.y, num_steps=self.warmup_nsteps)
+            (bj_state, self.parameters), info = warmup.run(warmup_key, self.y, num_steps=self.warmup_nsteps)
             # x = info.state.position
-            self.y[:] = state.position
+            self.y[:] = bj_state.position
             
             # Save results to the borg state object
             state["inverse_mass_matrix"][:] = self.parameters['inverse_mass_matrix']
             state["step_size"] = float(self.parameters['step_size'])
+            
+            # Make and save summary figures
+            dirname = os.getcwd()
+            trace_plot(self.attributes, info.state.position, f'{dirname}/tuning_params.png', ncol=4)
+            trace_plot(self.attributes, info.adaptation_state.inverse_mass_matrix, f'{dirname}/tuning_inverse_mass_matrix.png', ncol=4)
+            trace_plot(['stepsize'], info.adaptation_state.step_size, f'{dirname}/tuning_step_size.png', ncol=4)
 
 
         nuts = blackjax.nuts(logdensity_fn, **self.parameters)

conf/supranta_ini.ini

@@ -29,7 +29,7 @@ ares_heat = 1.0
 
 [mcmc]
 number_to_generate = 15000
-warmup_model = 1000
+warmup_model = 500
 warmup_cosmo = 0
 random_ic = false
 init_random_scaling = 0.1
@@ -42,12 +42,12 @@ max_timesteps = 50
 mixing = 1
 
 [sampling]
-algorithm = BlackJax
+algorithm = TransformedBlackJax
 epsilon = 0.005
 Nsteps = 20
 refresh = 0.1
 rng_seed = 1
-warmup_nsteps = 200
+warmup_nsteps = 400
 warmup_target_acceptance_rate = 0.7
 mvlam_mua = 0.01
 mvlam_alpha = 0.5

scripts/run_borg.sh

@@ -16,7 +16,7 @@ set -e
 
 # Path variables
 BORG=/data101/bartlett/build_borg/tools/hades_python/hades_python
-RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/blackjax_model_ic_v2
+RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/blackjax_model_ic_bf_prior
 
 mkdir -p $RUN_DIR
 cd $RUN_DIR
@@ -30,6 +30,6 @@ set -x
 
 # Just ICs
 INI_FILE=/home/bartlett/fsigma8/borg_velocity/conf/supranta_ini.ini
-cp $INI_FILE ini_file.ini
+# cp $INI_FILE ini_file.ini
-$BORG INIT ini_file.ini
+# $BORG INIT ini_file.ini
-# $BORG RESUME ini_file.ini
+$BORG RESUME ini_file.ini

scripts/submit_borg.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH --job-name=blackjax_model_ic_v2
+#SBATCH --job-name=blackjax_model_ic_bf_prior
 #SBATCH --nodes=1
 #SBATCH --exclusive
 #SBATCH --ntasks=40
@@ -28,7 +28,7 @@ set -e
 
 # Path variables
 BORG=/data101/bartlett/build_borg/tools/hades_python/hades_python
-RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/blackjax_model_ic_v2
+RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/blackjax_model_ic_bf_prior
 
 mkdir -p $RUN_DIR
 cd $RUN_DIR
@@ -42,9 +42,9 @@ set -x
 
 # Run BORG
 INI_FILE=/home/bartlett/fsigma8/borg_velocity/conf/supranta_ini.ini
-cp $INI_FILE ini_file.ini
+# cp $INI_FILE ini_file.ini
-$BORG INIT ini_file.ini
+# $BORG INIT ini_file.ini
-# $BORG RESUME ini_file.ini
+$BORG RESUME ini_file.ini
 
 conda deactivate