Merge pull request #71 from Tieqiong/examples

correct parrallel example for all platforms

Author: sbillinge

docs/examples/parallelPDF.py

@@ -20,68 +20,85 @@
 from diffpy.srreal.pdfcalculator import PDFCalculator
 from diffpy.structure import Structure
 
-mydir = os.path.dirname(os.path.abspath(__file__))
-mentholcif = os.path.join(mydir, "datafiles", "menthol.cif")
-Uisodefault = 0.005
-
-# configure options parsing
-parser = optparse.OptionParser("%prog [options]\n" + __doc__)
-parser.add_option(
-    "--pyobjcryst",
-    action="store_true",
-    help="Use pyobjcryst to load the CIF file.",
-)
-parser.allow_interspersed_args = True
-opts, args = parser.parse_args(sys.argv[1:])
 
 # load menthol structure and make sure Uiso values are non-zero
-if opts.pyobjcryst:
-    # use pyobjcryst if requested by the user
-    from numpy import pi
-    from pyobjcryst.crystal import create_crystal_from_cif
-
-    menthol = create_crystal_from_cif(mentholcif)
-    for sc in menthol.GetScatteringComponentList():
-        sp = sc.mpScattPow
-        sp.Biso = sp.Biso or 8 * pi**2 * Uisodefault
-else:
-    # or use diffpy.structure by default
-    menthol = Structure(filename=mentholcif)
-    for a in menthol:
-        a.Uisoequiv = a.Uisoequiv or Uisodefault
-
-# configuration of a PDF calculator
-cfg = {
-    "qmax": 25,
-    "rmin": 0,
-    "rmax": 30,
-}
-
-# number of CPUs for parallel calculation
-ncpu = multiprocessing.cpu_count()
-
-# calculate PDF on a single core
-t0 = time.time()
-pc0 = PDFCalculator(**cfg)
-r0, g0 = pc0(menthol)
-t0 = time.time() - t0
-print("Calculation time on 1 CPU: %g" % t0)
-
-# create a pool of workers
-pool = multiprocessing.Pool(processes=ncpu)
-
-t1 = time.time()
-# create a proxy parallel calculator to PDFCalculator pc0,
-# that uses ncpu parallel jobs submitted via pool.imap_unordered
-pc1 = createParallelCalculator(pc0, ncpu, pool.imap_unordered)
-r1, g1 = pc1(menthol)
-t1 = time.time() - t1
-print("Calculation time on %i CPUs: %g" % (ncpu, t1))
-print("Time ratio: %g" % (t0 / t1))
-
-# plot both results and the difference curve
-
-clf()
-gd = g0 - g1
-plot(r0, g0, r1, g1, r0, gd - 3)
-show()
+def load_structure(opts, mentholcif, Uisodefault):
+    if opts.pyobjcryst:
+        # use pyobjcryst if requested by the user
+        from numpy import pi
+        from pyobjcryst.crystal import create_crystal_from_cif
+
+        menthol = create_crystal_from_cif(mentholcif)
+        for sc in menthol.GetScatteringComponentList():
+            sp = sc.mpScattPow
+            sp.Biso = sp.Biso or 8 * pi**2 * Uisodefault
+    else:
+        # or use diffpy.structure by default
+        menthol = Structure(filename=mentholcif)
+        for a in menthol:
+            a.Uisoequiv = a.Uisoequiv or Uisodefault
+    return menthol
+
+
+def calculate_pdf(menthol, cfg, ncpu):
+    # calculate PDF on a single core
+    t0 = time.time()
+    pc0 = PDFCalculator(**cfg)
+    r0, g0 = pc0(menthol)
+    t0 = time.time() - t0
+    print(f"Calculation time on 1 CPU: {t0:g}")
+
+    # create a pool of workers
+    pool = multiprocessing.Pool(processes=ncpu)
+
+    t1 = time.time()
+    # create a proxy parallel calculator to PDFCalculator pc0,
+    # that uses ncpu parallel jobs submitted via pool.imap_unordered
+    pc1 = createParallelCalculator(pc0, ncpu, pool.imap_unordered)
+    r1, g1 = pc1(menthol)
+    t1 = time.time() - t1
+    pool.close()
+    pool.join()
+
+    print(f"Calculation time on {ncpu} CPUs: {t1:g}")
+    print(f"Time ratio: {t0 / t1:g}")
+
+    # plot both results and the difference curve
+
+    clf()
+    gd = g0 - g1
+    plot(r0, g0, label="1 CPU")
+    plot(r1, g1, label=f"{ncpu} CPUs")
+    plot(r0, gd - 3, label="Difference − 3")
+    show()
+
+
+def main():
+    mydir = os.path.dirname(os.path.abspath(__file__))
+    mentholcif = os.path.join(mydir, "datafiles", "menthol.cif")
+    Uisodefault = 0.005
+
+    # configure options parsing
+    parser = optparse.OptionParser("%prog [options]\n" + __doc__)
+    parser.add_option(
+        "--pyobjcryst",
+        action="store_true",
+        help="Use pyobjcryst to load the CIF file.",
+    )
+    parser.allow_interspersed_args = True
+    opts, args = parser.parse_args(sys.argv[1:])
+
+    # load the structure
+    menthol = load_structure(opts, mentholcif, Uisodefault)
+
+    # configuration of a PDF calculator
+    cfg = {"qmax": 25, "rmin": 0, "rmax": 30}
+
+    # number of CPUs for parallel calculation
+    ncpu = multiprocessing.cpu_count()
+    calculate_pdf(menthol, cfg, ncpu)
+
+
+if __name__ == "__main__":
+    multiprocessing.freeze_support()
+    main()

news/examples.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed `parallelPDF.py` example multiprocessing safe importing of main module issue.
+
+**Security:**
+
+* <news item>