From e345f6eebc0e375433bd891b36e488243bcbb9cf Mon Sep 17 00:00:00 2001 From: Marcel Stimberg Date: Fri, 15 Dec 2023 15:48:33 +0100 Subject: [PATCH 1/5] Fix C++ implementation of floor division for integers Fixes #1495 --- LICENSE | 182 +++++++++++++++++++++ brian2/codegen/generators/cpp_generator.py | 32 +++- brian2/tests/test_neurongroup.py | 24 +-- 3 files changed, 225 insertions(+), 13 deletions(-) diff --git a/LICENSE b/LICENSE index 57bfc03fb..91098d6bf 100644 --- a/LICENSE +++ b/LICENSE @@ -729,3 +729,185 @@ Magnus Jonsson. -- Constants used in the rk_double implementation by Isaku Wada. + +-- + +The floor division implementation for integer numbers in C++ standalone is based +on the implementation in Cython (https://github.com/cython/cython), published under +the Apache License 2.0: + Apache License + Version 2.0, January 2004 + https://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS \ No newline at end of file diff --git a/brian2/codegen/generators/cpp_generator.py b/brian2/codegen/generators/cpp_generator.py index 203902cd8..b2be9eb8e 100644 --- a/brian2/codegen/generators/cpp_generator.py +++ b/brian2/codegen/generators/cpp_generator.py @@ -111,13 +111,43 @@ def c_data_type(dtype): """ floordiv_support_code = """ - +// General template for floating point types template < typename T1, typename T2 > static inline typename _higher_type::type _brian_floordiv(T1 x, T2 y) {{ return floor(1.0*x/y); }} + +// Specific templates for integer types +template <> +inline int _brian_floordiv(int a, int b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} +template <> +inline long _brian_floordiv(int a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} +template <> +inline long _brian_floordiv(long a, int b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} +template <> +inline long _brian_floordiv(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} """ pow_support_code = """ diff --git a/brian2/tests/test_neurongroup.py b/brian2/tests/test_neurongroup.py index ff8fb7aa5..1aa797ff6 100644 --- a/brian2/tests/test_neurongroup.py +++ b/brian2/tests/test_neurongroup.py @@ -2114,9 +2114,9 @@ def test_run_regularly_shared(): @pytest.mark.standalone_compatible def test_semantics_floor_division(): - # See github issues #815 and #661 + # See github issues #815, #661, and #1495 G = NeuronGroup( - 11, + 300, """ a : integer b : integer @@ -2127,25 +2127,25 @@ def test_semantics_floor_division(): """, dtype={"a": np.int32, "b": np.int64, "x": float, "y": float}, ) - int_values = np.arange(-5, 6) - float_values = np.arange(-5.0, 6.0, dtype=np.float64) + int_values = np.arange(-150, 150) + float_values = np.linspace(-100, 100, 300, dtype=np.float64) G.ivalue = int_values G.fvalue = float_values with catch_logs() as l: G.run_regularly( """ - a = ivalue//3 - b = ivalue//3 - x = fvalue//3 - y = fvalue//3 + a = ivalue//98 + b = ivalue//98 + x = fvalue//98 + y = fvalue//98 """ ) run(defaultclock.dt) assert len(l) == 0 - assert_equal(G.a[:], int_values // 3) - assert_equal(G.b[:], int_values // 3) - assert_allclose(G.x[:], float_values // 3) - assert_allclose(G.y[:], float_values // 3) + assert_equal(G.a[:], int_values // 98) + assert_equal(G.b[:], int_values // 98) + assert_allclose(G.x[:], float_values // 98) + assert_allclose(G.y[:], float_values // 98) @pytest.mark.standalone_compatible From 454dc5dff395cdbac298d48a0057652b9d62ed07 Mon Sep 17 00:00:00 2001 From: Marcel Stimberg Date: Fri, 15 Dec 2023 16:04:29 +0100 Subject: [PATCH 2/5] Fix C++ modulo for integers as well Same issue as #1495 --- LICENSE | 6 +-- brian2/codegen/generators/cpp_generator.py | 49 ++++++++++++++++++---- brian2/tests/test_neurongroup.py | 23 +++++----- 3 files changed, 56 insertions(+), 22 deletions(-) diff --git a/LICENSE b/LICENSE index 91098d6bf..c06e706f5 100644 --- a/LICENSE +++ b/LICENSE @@ -732,9 +732,9 @@ Constants used in the rk_double implementation by Isaku Wada. -- -The floor division implementation for integer numbers in C++ standalone is based -on the implementation in Cython (https://github.com/cython/cython), published under -the Apache License 2.0: +The floor division and modulo implementations for integer numbers in C++ standalone +are based on the implementation in Cython (https://github.com/cython/cython), published +under the Apache License 2.0: Apache License Version 2.0, January 2004 https://www.apache.org/licenses/ diff --git a/brian2/codegen/generators/cpp_generator.py b/brian2/codegen/generators/cpp_generator.py index b2be9eb8e..c4c4c6a9f 100644 --- a/brian2/codegen/generators/cpp_generator.py +++ b/brian2/codegen/generators/cpp_generator.py @@ -101,17 +101,51 @@ def c_data_type(dtype): """ mod_support_code = """ - +// General template, used for floating point types template < typename T1, typename T2 > static inline typename _higher_type::type _brian_mod(T1 x, T2 y) -{{ +{ return x-y*floor(1.0*x/y); -}} +} + +// Specific implementations for integer types +// (from Cython, see LICENSE file) +template <> +inline int _brian_mod(int x, int y) +{ + int r = x % y; + r += ((r != 0) & ((r ^ y) < 0)) * y; + return r; +} + +template <> +inline long _brian_mod(int x, long y) +{ + long r = x % y; + r += ((r != 0) & ((r ^ y) < 0)) * y; + return r; +} + +template <> +inline long _brian_mod(long x, int y) +{ + long r = x % y; + r += ((r != 0) & ((r ^ y) < 0)) * y; + return r; +} + +template <> +inline long _brian_mod(long x, long y) +{ + long r = x % y; + r += ((r != 0) & ((r ^ y) < 0)) * y; + return r; +} """ floordiv_support_code = """ -// General template for floating point types +// General implementation, used for floating point types template < typename T1, typename T2 > static inline typename _higher_type::type _brian_floordiv(T1 x, T2 y) @@ -119,11 +153,12 @@ def c_data_type(dtype): return floor(1.0*x/y); }} -// Specific templates for integer types +// Specific implementations for integer types +// (from Cython, see LICENSE file) template <> inline int _brian_floordiv(int a, int b) { - long q = a / b; - long r = a - q*b; + int q = a / b; + int r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } diff --git a/brian2/tests/test_neurongroup.py b/brian2/tests/test_neurongroup.py index 1aa797ff6..8c8a240b9 100644 --- a/brian2/tests/test_neurongroup.py +++ b/brian2/tests/test_neurongroup.py @@ -2188,7 +2188,7 @@ def test_semantics_floating_point_division(): def test_semantics_mod(): # See github issues #815 and #661 G = NeuronGroup( - 11, + 300, """ a : integer b : integer @@ -2199,26 +2199,25 @@ def test_semantics_mod(): """, dtype={"a": np.int32, "b": np.int64, "x": float, "y": float}, ) - int_values = np.arange(-5, 6) - float_values = np.arange(-5.0, 6.0, dtype=np.float64) + int_values = np.arange(-150, 150) + float_values = np.linspace(-100, 100, 300, dtype=np.float64) G.ivalue = int_values G.fvalue = float_values with catch_logs() as l: G.run_regularly( """ - a = ivalue % 3 - b = ivalue % 3 - x = fvalue % 3 - y = fvalue % 3 + a = ivalue % 98 + b = ivalue % 98 + x = fvalue % 98 + y = fvalue % 98 """ ) run(defaultclock.dt) assert len(l) == 0 - assert_equal(G.a[:], int_values % 3) - assert_equal(G.b[:], int_values % 3) - assert_allclose(G.x[:], float_values % 3) - assert_allclose(G.y[:], float_values % 3) - + assert_equal(G.a[:], int_values % 98) + assert_equal(G.b[:], int_values % 98) + assert_allclose(G.x[:], float_values % 98) + assert_allclose(G.y[:], float_values % 98) if __name__ == "__main__": test_set_states() From 92a7c39f36eacaf1cae73820e8ce772c0a4d716a Mon Sep 17 00:00:00 2001 From: Marcel Stimberg Date: Fri, 15 Dec 2023 16:07:28 +0100 Subject: [PATCH 3/5] C++: Use int32_t and int64_t instead of int/long/long long Either long or long long is redundant, depending on whether we are on Unix or Windows --- brian2/codegen/generators/cpp_generator.py | 42 +++++++++++----------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/brian2/codegen/generators/cpp_generator.py b/brian2/codegen/generators/cpp_generator.py index c4c4c6a9f..269dde25b 100644 --- a/brian2/codegen/generators/cpp_generator.py +++ b/brian2/codegen/generators/cpp_generator.py @@ -90,7 +90,7 @@ def c_data_type(dtype): ) -typestrs = ["int", "long", "long long", "float", "double", "long double"] +typestrs = ["int32_t", "int64_t", "float", "double", "long double"] floattypestrs = ["float", "double", "long double"] hightype_support_code = "template < typename T1, typename T2 > struct _higher_type;\n" for ix, xtype in enumerate(typestrs): @@ -112,33 +112,33 @@ def c_data_type(dtype): // Specific implementations for integer types // (from Cython, see LICENSE file) template <> -inline int _brian_mod(int x, int y) +inline int32_t _brian_mod(int32_t x, int32_t y) { - int r = x % y; + int32_t r = x % y; r += ((r != 0) & ((r ^ y) < 0)) * y; return r; } template <> -inline long _brian_mod(int x, long y) +inline int64_t _brian_mod(int32_t x, int64_t y) { - long r = x % y; + int64_t r = x % y; r += ((r != 0) & ((r ^ y) < 0)) * y; return r; } template <> -inline long _brian_mod(long x, int y) +inline int64_t _brian_mod(int64_t x, int32_t y) { - long r = x % y; + int64_t r = x % y; r += ((r != 0) & ((r ^ y) < 0)) * y; return r; } template <> -inline long _brian_mod(long x, long y) +inline int64_t _brian_mod(int64_t x, int64_t y) { - long r = x % y; + int64_t r = x % y; r += ((r != 0) & ((r ^ y) < 0)) * y; return r; } @@ -156,30 +156,30 @@ def c_data_type(dtype): // Specific implementations for integer types // (from Cython, see LICENSE file) template <> -inline int _brian_floordiv(int a, int b) { - int q = a / b; - int r = a - q*b; +inline int32_t _brian_floordiv(int32_t a, int32_t b) { + int32_t q = a / b; + int32_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } template <> -inline long _brian_floordiv(int a, long b) { - long q = a / b; - long r = a - q*b; +inline int64_t _brian_floordiv(int32_t a, int64_t b) { + int64_t q = a / b; + int64_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } template <> -inline long _brian_floordiv(long a, int b) { - long q = a / b; - long r = a - q*b; +inline int64_t _brian_floordiv(int64_t a, int32_t b) { + int64_t q = a / b; + int64_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } template <> -inline long _brian_floordiv(long a, long b) { - long q = a / b; - long r = a - q*b; +inline int64_t _brian_floordiv(int64_t a, int64_t b) { + int64_t q = a / b; + int64_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } From f248d53a38f8bc2bca85c4677f670d659460175d Mon Sep 17 00:00:00 2001 From: Marcel Stimberg Date: Fri, 15 Dec 2023 16:15:41 +0100 Subject: [PATCH 4/5] Remove unused variable --- brian2/codegen/generators/cpp_generator.py | 1 - 1 file changed, 1 deletion(-) diff --git a/brian2/codegen/generators/cpp_generator.py b/brian2/codegen/generators/cpp_generator.py index 269dde25b..1868ba56f 100644 --- a/brian2/codegen/generators/cpp_generator.py +++ b/brian2/codegen/generators/cpp_generator.py @@ -91,7 +91,6 @@ def c_data_type(dtype): typestrs = ["int32_t", "int64_t", "float", "double", "long double"] -floattypestrs = ["float", "double", "long double"] hightype_support_code = "template < typename T1, typename T2 > struct _higher_type;\n" for ix, xtype in enumerate(typestrs): for iy, ytype in enumerate(typestrs): From 0dfd2a7509ea1fd146886dcfeab7137af799cf0c Mon Sep 17 00:00:00 2001 From: Marcel Stimberg Date: Fri, 15 Dec 2023 16:39:58 +0100 Subject: [PATCH 5/5] Minor formatting fix --- brian2/tests/test_neurongroup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/brian2/tests/test_neurongroup.py b/brian2/tests/test_neurongroup.py index 8c8a240b9..8b22a3240 100644 --- a/brian2/tests/test_neurongroup.py +++ b/brian2/tests/test_neurongroup.py @@ -2219,6 +2219,7 @@ def test_semantics_mod(): assert_allclose(G.x[:], float_values % 98) assert_allclose(G.y[:], float_values % 98) + if __name__ == "__main__": test_set_states() test_creation()