Remove nothreading() as it is redundant with using environment variables.

CHANGELOG.md

@@ -26,7 +26,7 @@
 - Some labels and the title for the SED plots has been improved to avoid overlaps and overflows. (Médéric Boquien)
 - Ensure that best models are properly computed when models are computed by blocks and that no fit could be made in one or more blocks. This can be case if all the models in the block are older than the age of the universe. (Médéric)
 - Make sure that the parameters are saved with the proper scale (linear or logarithmic) in the χ² files. (Médéric Boquien)
-- Some math libraries such as MKL or OpenBLAS sometime try to be (too) smart, starting computation threads on their own. As cigale is already parallel, this just oversubscribes the CPU and can lead to important slowdowns. An environment variable could be set to disable this, but this is cumbersome. Disabling within the code did not seem to work. A different method has been implement, which should address the issue to forcefully disable threading in these libraries. (Médéric Boquien)
+- Some math libraries such as MKL or OpenBLAS sometime try to be (too) smart, starting computation threads on their own. As cigale is already parallel, this just oversubscribes the CPU and can lead to important slowdowns. An environment variable could be set by the user to disable this, but this is cumbersome. Rather, we set these variables directly in the code at the startup of cigale. (Yannick Roehlly & Médéric Boquien)
 ### Optimised
 - Slight speedup of the computation of the likelihood from the χ² using a multiplication rather than a division. (Médéric Boquien)
 - Speedup of the computation of the χ² by ~10% taking the opposite of a scalar rather than of an array. (Médéric Boquien)

pcigale/analysis_modules/pdf_analysis/workers.py

@@ -11,7 +11,6 @@ from copy import deepcopy
 import numpy as np
 
 from .utils import save_chi2, compute_corr_dz, compute_chi2, weighted_param
-from ..utils import nothreading
 from ...warehouse import SedWarehouse
 
 
@@ -28,10 +27,6 @@ def init_sed(models, counter):
     """
     global gbl_warehouse, gbl_models, gbl_counter
 
-    # Limit the number of threads to 1 if we use MKL in order to limit the
-    # oversubscription of the CPU/RAM.
-    nothreading()
-
     gbl_warehouse = SedWarehouse()
 
     gbl_models = models
@@ -53,9 +48,6 @@ def init_analysis(models, results, counter):
     """
     global gbl_models, gbl_obs, gbl_results, gbl_counter
 
-    # Limit the number of threads to 1 to limit the oversubscription of the CPU
-    nothreading()
-
     gbl_models = models
     gbl_obs = models.obs
     gbl_results = results
@@ -82,9 +74,6 @@ def init_bestfit(conf, params, observations, results, counter):
     global gbl_warehouse, gbl_conf, gbl_params, gbl_obs
     global gbl_results, gbl_counter
 
-    # Limit the number of threads to 1 to limit the oversubscription of the CPU
-    nothreading()
-
     gbl_warehouse = SedWarehouse()
 
     gbl_conf = conf

pcigale/analysis_modules/savefluxes/workers.py

@@ -7,7 +7,6 @@
 
 import numpy as np
 
-from ..utils import nothreading
 from ...warehouse import SedWarehouse
 
 
@@ -26,9 +25,6 @@ def init_fluxes(models, counter):
     """
     global gbl_warehouse, gbl_models, gbl_obs, gbl_save, gbl_counter
 
-    # Limit the number of threads to 1 to limit the oversubscription of the CPU
-    nothreading()
-
     gbl_warehouse = SedWarehouse()
 
     gbl_models = models

pcigale/analysis_modules/utils.py

@@ -6,52 +6,11 @@
 """
 Various utility functions for pcigale analysis modules
 """
-import ctypes
-from ctypes.util import find_library
+
 import multiprocessing as mp
 import time
 
 
-def nothreading():
-    """Some libraries such as Intel's MKL have automatic threading. This is
-    good when having only one process. However we already do our own
-    parallelisation. The additional threads created by the MKL increase in
-    excess the pressure on the CPU and on the RAM slowing everything down.
-
-    Parameters
-    ----------
-    None
-
-    Returns
-    -------
-    None
-
-    """
-    for basename in ['iomp', 'gomp', 'omp', 'vcomp']:
-        try:  # Disable threading for OpenMP
-            name = find_library(basename)
-            if name:
-                lib = ctypes.cdll.LoadLibrary(name)
-                lib.omp_set_num_threads(ctypes.c_int(1))
-        except:
-            continue
-
-    try:  # Disable threading for MKL
-        name = find_library('mkl_rt')
-        if name:
-            lib = ctypes.cdll.LoadLibrary(name)
-            lib.mkl_set_num_threads(ctypes.byref(ctypes.c_int(1)))
-    except:
-        pass
-
-    try:  # Disable threading for OpenBLAS
-        name = find_library('openblas')
-        if name:
-            lib = ctypes.cdll.LoadLibrary(name)
-            lib.openblas_set_num_threads(ctypes.c_int(1))
-    except:
-        pass
-
 class Counter:
     """Class to count the number of models computers/objects analysed. It has
     two internal counters. One is internal to the process and is incremented at

pcigale_plots/plot_types/chi2.py

@@ -17,7 +17,7 @@ import matplotlib.pyplot as plt
 import multiprocessing as mp
 import numpy as np
 from pcigale.utils import read_table
-from pcigale.analysis_modules.utils import Counter, nothreading
+from pcigale.analysis_modules.utils import Counter
 
 
 def pool_initializer(counter):
@@ -27,9 +27,7 @@ def pool_initializer(counter):
     :param counter: Counter class object for the number of models plotted
     """
     global gbl_counter
-    # Limit the number of threads to 1 if we use MKL in order to limit the
-    # oversubscription of the CPU/RAM.
-    nothreading()
+
     gbl_counter = counter
 
 

pcigale_plots/plot_types/mock.py

@@ -17,7 +17,7 @@ import multiprocessing as mp
 import numpy as np
 import pkg_resources
 from scipy import stats
-from pcigale.analysis_modules.utils import Counter, nothreading
+from pcigale.analysis_modules.utils import Counter
 
 # Name of the file containing the best models information
 BEST_RESULTS = "results.fits"
@@ -31,9 +31,7 @@ def pool_initializer(counter):
     :param counter: Counter class object for the number of models plotted
     """
     global gbl_counter
-    # Limit the number of threads to 1 if we use MKL in order to limit the
-    # oversubscription of the CPU/RAM.
-    nothreading()
+
     gbl_counter = counter
 
 

pcigale_plots/plot_types/pdf.py

@@ -16,7 +16,7 @@ import matplotlib.pyplot as plt
 import multiprocessing as mp
 import numpy as np
 from pcigale.utils import read_table
-from pcigale.analysis_modules.utils import Counter, nothreading
+from pcigale.analysis_modules.utils import Counter
 
 
 def pool_initializer(counter):
@@ -26,9 +26,7 @@ def pool_initializer(counter):
     :param counter: Counter class object for the number of models plotted
     """
     global gbl_counter
-    # Limit the number of threads to 1 if we use MKL in order to limit the
-    # oversubscription of the CPU/RAM.
-    nothreading()
+
     gbl_counter = counter
 
 

pcigale_plots/plot_types/sed.py

@@ -22,7 +22,7 @@ from scipy.constants import c
 from pcigale.data import Database
 from pcigale.utils import read_table
 import matplotlib.gridspec as gridspec
-from pcigale.analysis_modules.utils import Counter, nothreading
+from pcigale.analysis_modules.utils import Counter
 
 # Name of the file containing the best models information
 BEST_RESULTS = "results.fits"
@@ -46,9 +46,7 @@ def pool_initializer(counter):
     :param counter: Counter class object for the number of models plotted
     """
     global gbl_counter
-    # Limit the number of threads to 1 if we use MKL in order to limit the
-    # oversubscription of the CPU/RAM.
-    nothreading()
+
     gbl_counter = counter