Update licensing information

Author: jussienko

COPYING

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+All material Copyright (c) CSC - IT Center for Science Ltd. <www.csc.fi> unless otherwise noted.
+
+All text and image material licensed under Creative Commons BY-NC-SA 4.0 unless
+otherwise noted. 
+
+All code samples licensed under MIT license unless otherwise noted.
+
+See LICENSES/ and individual file headers for more details.

LICENSE

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+MIT License
+
+Copyright (c) <year> <copyright holders>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
+associated documentation files (the "Software"), to deal in the Software without restriction, including 
+without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 
+copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the 
+following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial 
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT 
+LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO 
+EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE 
+USE OR OTHER DEALINGS IN THE SOFTWARE.

LICENSES/CC-BY-NC-SA-4.0.txt

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 # Python in High Performance Computing
 
 Exercise material and model answers for the CSC course "Python in High Performance Computing". The course is part of PRACE Training activity at CSC.

LICENSES/MIT.txt

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 ## Using C-functions
 
 Fibonacci numbers are a sequence of integers defined by the recurrence 

README.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 def fibonacci(n):
     if n < 2:
         return n

cython/c-functions/README.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 cpdef int fibonacci(int n):
     if n < 2:
         return n

cython/c-functions/fib.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from functools import lru_cache
 
 def fibonacci(n):

cython/c-functions/solution/fib.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 

cython/c-functions/solution/fib_py.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from fib import fibonacci
 from fib_py import fibonacci as fibonacci_py, fibonacci_cached
 from timeit import repeat

cython/c-functions/solution/setup.py

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 ## Optimising heat equation with Cython
 
 ### Creating a Cython extension

cython/c-functions/solution/test_fib.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 import numpy as np
 import matplotlib
 matplotlib.use('Agg')

cython/heat-equation/README.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from __future__ import print_function
 import time
 import argparse

cython/heat-equation/heat.py

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 ## Example profile for heat equation solver
 
 ```

cython/heat-equation/heat_main.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
+# cython: profile=True
+
+import numpy as np
+cimport numpy as cnp
+
+import cython
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+@cython.cdivision(True)
+cdef laplacian(cnp.ndarray[cnp.double_t, ndim=2]u, cnp.ndarray[cnp.double_t, ndim=2]du, double dx2, double dy2):
+
+    cdef int n = u.shape[0]
+    cdef int m = u.shape[1]
+
+    cdef int i,j
+
+    # Multiplication is more efficient than division
+    cdef double dx2inv = 1. / dx2
+    cdef double dy2inv = 1. / dy2
+
+    for i in range(1, n-1):
+        for j in range(1, m-1):
+            du[i, j] = (u[i+1, j] - 2*u[i, j] + u[i-1, j]) * dx2inv + \
+                       (u[i, j+1] - 2*u[i, j] + u[i, j-1]) * dy2inv
+
+    
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+@cython.cdivision(True)
+def evolve(cnp.ndarray[cnp.double_t, ndim=2]u, 
+           cnp.ndarray[cnp.double_t, ndim=2]u_previous, 
+           double a, double dt, double dx2, double dy2):
+    """Explicit time evolution.
+       u:            new temperature field
+       u_previous:   previous field
+       a:            diffusion constant
+       dt:           time step. """
+
+    laplacian(u_previous, u, dx2, dy2)
+    # u *= a * dt
+    u = u_previous + a*dt * u
+
+    u_previous[:] = u[:]
+

cython/heat-equation/profile.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
+import numpy as np
+from numba import jit, void, double
+
+# @jit(void(double[:,:], double[:,:], double, double, double, double), nopython=True, cache=True, fastmath=True, error_model='numpy')
+# @jit(nopython=True, cache=True, fastmath=True)
+@jit(nopython=True)
+def evolve(u, u_previous, a, dt, dx2, dy2):
+    """Explicit time evolution.
+       u:            new temperature field
+       u_previous:   previous field
+       a:            diffusion constant
+       dt:           time step. """
+
+    n, m = u.shape
+
+    # dx2inv = 1.0 / dx2
+    # dy2inv = 1.0 / dy2
+    for i in range(1, n-1):
+        for j in range(1, m-1):
+            u[i, j] = u_previous[i, j] + a * dt * ( \
+             (u_previous[i+1, j] - 2*u_previous[i, j] + \
+              u_previous[i-1, j]) / dx2 + \
+              # u_previous[i-1, j]) * dx2inv + \
+             (u_previous[i, j+1] - 2*u_previous[i, j] + \
+              u_previous[i, j-1]) / dy2 )
+              # u_previous[i, j-1]) * dy2inv )
+    u_previous[:] = u[:]
+

cython/heat-equation/solution/evolve_new.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 import numpy as np
 cimport numpy as cnp
 import cython

cython/heat-equation/solution/evolve_py.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from __future__ import print_function
 import time
 import argparse

cython/heat-equation/solution/heat.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 

cython/heat-equation/solution/heat_main.py

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 ## Simple Cython extension
 
 ### Creating a Cython extension

cython/heat-equation/solution/setup.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 def subtract(x, y):
     result = x - y
     return result

cython/simple-extension/README.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 

cython/simple-extension/solution/cyt_module.pyx

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+<!--
+SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+
+SPDX-License-Identifier: CC-BY-NC-SA-4.0
+-->
+
 ## Using static typing 
 
 Continue with the simple Cython module for subtracting two numbers:

cython/simple-extension/solution/setup.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 def subtract(x, y):
     result = x - y
     return result

cython/static-typing/README.md

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 

cython/static-typing/cyt_module.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 def subtract(int x, int y):
     cdef int result
     result = x - y

cython/static-typing/setup.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 

cython/static-typing/solution/cyt_module.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 import numpy as np
 
 a1 = np.random.random((10,3))

cython/static-typing/solution/setup.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 

demos/broadcasting.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 cimport numpy as cnp

demos/cython/mandel.py

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 

demos/cython/mandel_cyt.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 

demos/cython/mandel_cyt_1.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 cimport numpy as cnp

demos/cython/mandel_cyt_2.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 cimport numpy as cnp

demos/cython/mandel_cyt_3.pyx

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+# SPDX-FileCopyrightText: 2019 CSC - IT Center for Science Ltd. <www.csc.fi>
+#
+# SPDX-License-Identifier: MIT
+
 from time import time
 import numpy as np
 cimport numpy as cnp