Numpy 1.24 and numba 0.57

docs/manual.txt

@@ -262,7 +262,7 @@ to find more details of the MFEM library.
 	  GridFunction(fes, vec.GetData() + sc)
       the same is used for ParGridFunction
 
-      GridFunction::Save(std::ostream &out) is wrapped as Save(filename, precision=8)
+      GridFunction::Save(std::ostream &out) is wrapped as Save(filename, precision)
       QuadratureFunction::Save(std::ostream &out) is wrapped as Save(filename, precision=8)
 
       GridFunction::WriteToStream(IOString) writes data to io.IOString

examples/ex24.py

@@ -90,7 +90,7 @@ def p_coef(x):
 
         @mfem.jit.vector(shape=(sdim,))
         def gradp_coef(x):
-            out = np.zeros(shape, dtype=np.float)
+            out = np.zeros(shape, dtype=np.float64)
             if dim == 3:
                 out[0] = cos(x[0]) * sin(x[1]) * sin(x[2])
                 out[1] = sin(x[0]) * cos(x[1]) * sin(x[2])
@@ -104,7 +104,7 @@ def gradp_coef(x):
 
         @mfem.jit.vector(vdim=sdim, interface="c++")
         def v_coef(x, out):
-            out = np.zeros(shape, dtype=np.float)
+            out = np.zeros(shape, dtype=np.float64)
             if dim == 3:
                 out[0] = sin(kappa * x[1])
                 out[1] = sin(kappa * x[2])

examples/ex25p.py

@@ -670,7 +670,7 @@ def detJ_JT_J_inv_f(x):
 
 def detJ_JT_J_inv_abs_f(x):
     dim = shape[0]
-    D = np.zeros(dim, dtype=np.float)
+    D = np.zeros(dim, dtype=np.float64)
 
     dxs = np.empty(dim, dtype=np.complex128)
     det = complex(1.0)
@@ -702,7 +702,7 @@ def detJ_inv_JT_J_f(x):
 
 def detJ_inv_JT_J_abs_f(x):
     dim = shape[0]
-    D = np.zeros(dim, dtype=np.float)
+    D = np.zeros(dim, dtype=np.float64)
 
     dxs = np.empty(dim, dtype=np.complex128)
     det = 1.0

examples/ex31.py

@@ -281,7 +281,7 @@ def run(order=1,
 
 
 def E_exact(x):
-    E = np.zeros(shape, dtype=np.float)
+    E = np.zeros(shape, dtype=np.float64)
     if dim == 1:
         E[0] = 1.1 * sin(kappa * x[0] + 0.0 * pi)
         E[1] = 1.2 * sin(kappa * x[0] + 0.4 * pi)
@@ -301,7 +301,7 @@ def E_exact(x):
 
 
 def CurlE_exact(x):
-    dE = np.zeros(shape, dtype=np.float)
+    dE = np.zeros(shape, dtype=np.float64)
     if dim == 1:
         c4 = cos(kappa * x[0] + 0.4 * pi)
         c9 = cos(kappa * x[0] + 0.9 * pi)
@@ -341,7 +341,7 @@ def CurlE_exact(x):
 
 
 def f_exact(x):
-    f = np.zeros(shape, dtype=np.float)
+    f = np.zeros(shape, dtype=np.float64)
     if dim == 1:
         s0 = sin(kappa * x[0] + 0.0 * pi)
         s4 = sin(kappa * x[0] + 0.4 * pi)

examples/ex31p.py

@@ -382,7 +382,7 @@ def CurlE_exact(x):
 
 
 def f_exact(x):
-    f = np.zeros(vdim, dtype=np.float)
+    f = np.zeros(vdim, dtype=np.float64)
     if dim == 1:
         s0 = sin(kappa * x[0] + 0.0 * pi)
         s4 = sin(kappa * x[0] + 0.4 * pi)

examples/ex3p.py

@@ -226,7 +226,7 @@ def EvalValue(self, x):
 
     # 16. Save the refined mesh and the solution in parallel. This output can
     #     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-    x.Save('sol.'+smyid)
+    x.Save('sol.'+smyid, 8)
     pmesh.Print('mesh.'+smyid)
 
     # 17. Send the solution by socket to a GLVis server

mfem/_par/dist_solver.i

@@ -1,7 +1,7 @@
 %module(package="mfem._par") dist_solver
 %{
 #include "mfem.hpp"      
-#include "miniapps/shifted/dist_solver.hpp"
+#include "miniapps/common/dist_solver.hpp"
 #include "pyoperator.hpp"
 #include "../common/pysolvers.hpp"
 #include "../common/pycoefficient.hpp"  
@@ -13,7 +13,7 @@ import_array();
 %}
 
 %inline %{
-#include "miniapps/shifted/dist_solver.cpp"
+#include "miniapps/common/dist_solver.cpp"
 %}
 
 
@@ -26,5 +26,5 @@ import_array();
 %import "pmesh.i"
 %import "solvers.i"
 
-%include "miniapps/shifted/dist_solver.hpp"
+%include "miniapps/common/dist_solver.hpp"
 

test/run_examples.py

@@ -66,8 +66,8 @@ class bcolors:
 # special handling of text (needs to be set manually)
 ignore_txt_def = ['seconds', 'residual']
 ignore_txt_dict = {'ex15p': ['seconds', 'residual', ],
-                   'ex12p' : ['seconds'],
-                   'ex18p': ['time step' ],
+                   'ex12p': ['seconds'],
+                   'ex18p': ['time step'],
                    'ex10': ['iteration', 'seconds', 'residual', ],
                    'ex10p': ['iteration', 'seconds', 'residual', 'rtol'],
                    'ex13p': ['iteration', 'seconds', 'residual', ]}
@@ -84,7 +84,8 @@ def run_file(command, num=5):
     lines, errs = p.communicate()
 
     lines = lines.decode('utf-8').split('\n')
-    lines = [x for x in lines if not x.startswith('\x1b')] # remove line with ESC
+    lines = [x for x in lines if not x.startswith(
+        '\x1b')]  # remove line with ESC
 
     # debug print all output....
     # print("\n".join(lines))
@@ -93,6 +94,7 @@ def run_file(command, num=5):
     lines = [l for l in lines if len(l.strip()) != 0]
     return t2-t1, lines[-num:]
 
+
 def pad_lines(lines):
     length = max([len(l.strip()) for l in lines])
     return [l.strip() + " "*(length-len(l.strip())) for l in lines]
@@ -137,10 +139,11 @@ def compare_results(lines1, lines2, case, verbose=True):
         compare.append(flag)
     return all(compare)
 
+
 def do_compare_outputs(dir1, dir2):
     files1 = os.listdir(dir1)
     files2 = os.listdir(dir2)
-    
+
     unique_file = list(set(files1+files2))
     if (len(unique_file) != len(files1) or
             len(unique_file) != len(files2)):
@@ -158,50 +161,77 @@ def do_compare_outputs(dir1, dir2):
             if not flag:
                 return False
             continue
-        
+
         if not f in files2:
             print("File not found in python outputs", f)
             return False
         l1 = open(os.path.join(dir1, f), 'r').readlines()
         l2 = open(os.path.join(dir2, f), 'r').readlines()
 
         mismatch = 0
+
+        # compute average of all the values in file
+        total = 0
+        for ll1 in l1:
+            try:
+                total = total + sum([abs(float(x)) for x in ll1.split(' ')])
+            except:
+                pass
+
+        www = total/len(l1)
+
         for ll1, ll2 in zip(l1, l2):
             if ll1 != ll2:
                 try:
-                    # compare 3 digits
-                    d1 = ['%s' % float('%.3g' % float(x)) for x in ll1.split(' ')]
-                    d2 = ['%s' % float('%.3g' % float(x)) for x in ll2.split(' ')]
-                    if d1 == d2:
-                        continue
+                    check = [abs(float(x))/www for x in ll1.split(' ')]
+                    flag = sum([x < 1e-7 for x in check])
+
+                    # find ratio as number
+                    dd1 = [float(x) for x in ll1.split(' ')]
+                    dd2 = [float(x) for x in ll2.split(' ')]
+                    mratio = max([abs(v1-v2)/abs(v1+v2)
+                                 for v1, v2 in zip(dd1, dd2)])
+
+                    # compare 5 digits in text
+                    d1 = ['%s' % float('%.5g' % float(x))
+                          for x in ll1.split(' ')]
+                    d2 = ['%s' % float('%.5g' % float(x))
+                          for x in ll2.split(' ')]
+                    if d1 != d2 and flag == 0:  # and mratio > 1e-7:
+                        print("line with difference", d1, d2, check, maratio)
+                        mismatch += 1
                     else:
-                        #print("line with difference", d1, d2)
-                        mismatch += 1                        
+                        #print("line with the same", d1, d2, check)
+                        continue
+
                 except:
                     #print("found a line mismatch :", ll1, ll2)
                     mismatch += 1
         if mismatch > 3:
-           print("Contents does not agree: ", f)
-           print("# "+str(mismatch) + " lines do not agree out of "+str(len(l1)))
-           fail = True
-           
+            print("Contents does not agree: ", f)
+            print("# "+str(mismatch) + " lines do not agree out of "+str(len(l1)))
+            fail = True
+
     if not fail:
-        print("No difference in generate files (Passed output file check) in " + os.path.basename(dir1))
-
+        print("No difference in generate files (Passed output file check) in " +
+              os.path.basename(dir1))
+
     return not fail
 
-def compare_outputs(case):        
+
+def compare_outputs(case):
     dir1 = os.path.join(sandbox, case, 'exe')
     dir2 = os.path.join(sandbox, case, 'py')
     return do_compare_outputs(dir1, dir2)
 
+
 def run_test(mfem_exes, pymfem_exes, sandbox, serial=True, np=2, verbose=False):
     print("mfem examples from : " + os.path.dirname(mfem_exes[0]))
     print("PyMFEM examples from : " + os.path.dirname(pymfem_exes[0]))
     print(',  '.join([os.path.basename(x) for x in mfem_exes]))
 
     cwd = os.getcwd()
-    
+
     if not serial:
         comm_mpi = ["mpirun", "-np", str(np)]
     else:
@@ -219,19 +249,19 @@ def run_test(mfem_exes, pymfem_exes, sandbox, serial=True, np=2, verbose=False):
             continue
         case = os.path.basename(e1)
         opts = options_dict.get(case, options_def)
-        
+
         print("Running : " + case)
-        
+
         path = os.path.join(sandbox, case)
         os.makedirs(path)
         os.chdir(path)
         datadir = os.path.join(os.path.dirname(os.path.dirname(e1)), 'data')
         os.symlink(datadir, 'data')
-        
+
         path = os.path.join(sandbox, case, 'exe')
         os.makedirs(path)
         os.chdir(path)
-        
+
         comm = comm_mpi + [e1] + opts
         t1, l1 = run_file(comm, num=5)
 
@@ -280,7 +310,7 @@ def find_mfem_examples(dir, serial=True, example='all'):
         names = [x for x in names if not x.endswith('p')]
     else:
         names = [x for x in names if x.endswith('p')]
-        
+
     if example != 'all':
         names = [n for n in names if n == example]
     names = [n for n in names if not n in skip_test]
@@ -334,7 +364,7 @@ def print_help(self):
                         help='mfem (parallel) directory')
     parser.add_argument('-mfemsdir',
                         action='store',
-                        default=def_mfemsdir,                        
+                        default=def_mfemsdir,
                         help='mfem (serial) directory')
     parser.add_argument('-sandbox',
                         action='store', default="./sandbox",
@@ -357,9 +387,8 @@ def print_help(self):
     if not os.path.exists(os.path.join(mfempdir, "data")) and testp:
         assert False, "data file (under par dir) does not exist in the package directory"
 
-
     sandbox = os.path.abspath(os.path.expanduser(args.sandbox))
-    
+
     if clean:
         od = os.getcwd()
         files = os.listdir(od)
@@ -374,7 +403,7 @@ def print_help(self):
             shutil.rmtree(sandbox)
         sys.exit()
     import mfem
-    
+
     if os.path.exists(sandbox):
         shutil.rmtree(sandbox)
     os.mkdir(sandbox)
@@ -423,9 +452,9 @@ def print_help(self):
             print("Serial Test \t" + bcolors.FAIL +
                   " ".join(fails) + bcolors.ENDC)
             sys.exit(1)
-        if len(skipped) > 0:            
+        if len(skipped) > 0:
             print("Serial Test Skipped due to the lack of Python vesion \t" + bcolors.FAIL +
-               " ".join(skipped) + bcolors.ENDC)            
+                  " ".join(skipped) + bcolors.ENDC)
 
     if testp and len(resultp) != 0:
         if all(resultp):
@@ -438,4 +467,4 @@ def print_help(self):
 
         if len(skippedp) > 0:
             print("Parallel Test Skipped due to the lack of Python vesion \t" + bcolors.FAIL +
-                 " ".join(skippedp) + bcolors.ENDC)
+                  " ".join(skippedp) + bcolors.ENDC)