clean write version

cbg-ethz · Oct 15, 2024 · d2587fd · d2587fd
1 parent 8e71f09
commit d2587fd
Showing 1 changed file with 15 additions and 17 deletions.
diff --git a/lollipop/cli/deconvolute.py b/lollipop/cli/deconvolute.py
@@ -14,7 +14,7 @@
 import pandas as pd
 import numpy as np
 from tqdm import tqdm, trange
-from threadpoolctl import threadpool_info, ThreadpoolController, threadpool_limits
+from threadpoolctl import ThreadpoolController
 
 import lollipop as ll
 
@@ -147,11 +147,10 @@ def _deconvolute_bootstrap(
     List[pd.DataFrame]
         The deconvolution results for the location and bootstrap iterations.
     """
-    print("Threadpool: ", threadpool_info())
-
-    logging.warning(threadpool_info())
 
+    # monitor the number of threads, to prevent oversubscription on blas / cluster systmes
     controller = ThreadpoolController()
+    logging.info(f"Threading configuration:\n {controller.info()}")
 
     # deconvolution results
     deconv = []
@@ -238,17 +237,19 @@ def _deconvolute_bootstrap(
                 # just run one on everything
                 weights = {}
 
+            # define deconvolution kernel
+            t_kdec = ll.KernelDeconv(
+                temp_df2[var_dates["var_dates"][mindate] + ["undetermined"]],
+                temp_df2["frac"],
+                temp_df2["date"],
+                kernel=kernel(**kernel_params),
+                reg=regressor(**regressor_params),
+                confint=confint(**confint_params),
+                **weights,
+            )
+            # limit the number of threads, to prevent oversubscription on blas / cluster systmes
             with controller.limit(limits=1, user_api='blas'):
-                # deconvolution
-                t_kdec = ll.KernelDeconv(
-                    temp_df2[var_dates["var_dates"][mindate] + ["undetermined"]],
-                    temp_df2["frac"],
-                    temp_df2["date"],
-                    kernel=kernel(**kernel_params),
-                    reg=regressor(**regressor_params),
-                    confint=confint(**confint_params),
-                    **weights,
-                )
+                # do the deconvolution
                 t_kdec = t_kdec.deconv_all(**deconv_params)
 
             if have_confint:
@@ -397,9 +398,6 @@ def deconvolute(
     tally_data,
     namefield,
 ):
-
-    controller = ThreadpoolController()
-    logging.warning(f"Controller {controller.info()}")
 
     # load data
     yaml = ruamel.yaml.YAML(typ="rt")