Merge pull request #4 from JetBrains-Research/master

Pulling changes

Author: Krekep

.github/workflows/ubuntu.yml

@@ -28,6 +28,9 @@ jobs:
       - uses: actions/checkout@v2
         with:
           submodules: true
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
 
       - name: Install CUDA
         env:
@@ -60,4 +63,13 @@ jobs:
       - name: Run unit-tests (sequential backend)
         working-directory: ${{ env.build_dir }}
         run: bash scripts/tests_run_fallback.sh
-        shell: bash
+        shell: bash
+
+      - name: Run regression-tests (sequential backend)
+        working-directory: ${{ env.build_dir }}
+        run: |
+          cd python
+          export PYTHONPATH="`pwd`:$PYTHONPATH"
+          cd tests
+          python3 -m unittest discover -v
+        shell: bash

README.md

@@ -5,6 +5,7 @@
 [![JB Research](https://jb.gg/badges/research-flat-square.svg)](https://research.jetbrains.org/)
 [![Ubuntu](https://github.com/JetBrains-Research/cuBool/workflows/Ubuntu/badge.svg?branch=master)](https://github.com/JetBrains-Research/cuBool/actions)
 [![License](https://img.shields.io/badge/license-MIT-orange)](https://github.com/JetBrains-Research/cuBool/blob/master/LICENSE)
+[![Package](https://img.shields.io/badge/pypi%20package-alpha-%233776ab)](https://test.pypi.org/project/pycubool/)
 
 **cuBool** is a linear Boolean algebra library primitives and operations for 
 work with sparse matrices written on the NVIDIA CUDA platform. The primary 
@@ -28,26 +29,28 @@ prototyping algorithms on a local computer for later running on a powerful serve
 
 - [X] Library C interface
 - [X] Library setup
-- [X] CSR matrix
-- [X] CSR multiplication
-- [X] CSR element-wise addition
-- [X] CSR kronecker
-- [X] CSR transpose
-- [X] CSR submatrix
-- [X] CSR matrix reduce
-- [X] CSR slicing
+- [X] Sparse matrix
+- [X] Sparse matrix multiplication
+- [X] Sparse matrix element-wise addition
+- [X] Sparse matrix kronecker
+- [X] Sparse matrix transpose
+- [X] Sparse matrix submatrix
+- [X] Sparse matrix reduce
+- [X] Sparse matrix slicing
+- [X] Matrix cached filling
 - [X] Sequential fallback backend for CPU
-- [ ] IO matrix loading from mtx file
-- [ ] IO matrix saving into mtx file
+- [X] Device capabilities query
+- [X] IO matrix loading from mtx file
+- [X] IO matrix saving into mtx file
 - [ ] IO matrix saving into gviz format
-- [ ] IO user-defined file logging
+- [X] IO user-defined file logging
 - [X] Wrapper for Python API
-- [ ] Wrapper syntax sugar
-- [ ] Tests for Python wrapper
+- [X] Wrapper syntax sugar
+- [X] Tests for Python wrapper
+- [X] Pip package
 - [ ] Code examples
 - [ ] User guide
 - [X] Unit Tests collection
-- [X] Dummy library implementation for testing
 - [ ] Publish built artifacts and shared libs
 - [ ] Publish stable source code archives
 
@@ -65,7 +68,7 @@ prototyping algorithms on a local computer for later running on a powerful serve
 
 ### Cuda & Compiler Setup
 
-> Skip thia section if you want to build library with only sequential backend
+> Skip this section if you want to build library with only sequential backend
 > without cuda backend support.
 
 Before the CUDA setup process, validate your system NVIDIA driver with `nvidia-smi`
@@ -159,12 +162,22 @@ By default, the following cmake options will be automatically enabled:
 
 ### Python Wrapper
 
-After the build process, the shared library object `libcubool.so` is placed
-inside the build directory. Export into the environment or add into bash
-profile the variable `CUBOOL_PATH=/path/to/the/libcubool.so` with appropriate
-path to your setup. Then you will be able to use `pycubool` python wrapper,
-which uses this variable in order to located library object.
+**Export** env variable `PYTHONPATH="/build_dir_path/python/:$PYTHONPATH"` if
+you want to use `pycubool` without installation into default python packages dir.
+This variable will help python find package if you import it as `import pycubool` in your python scripts.
 
+**To run regression tests** within your build directory, open folder `/build_dir_path/python` and
+run the following command:
+
+```shell script
+$ export PYTHONPATH="`pwd`:$PYTHONPATH"
+$ cd tests
+$ python3 -m unittest discover -v
+```
+
+**Note:** after the build process, the shared library object `libcubool.so` will be placed
+inside the build directory in the folder with python wrapper `python/pycubool/`. 
+So, the wrapper will be able to automatically locate required lib file.
 
 ## Usage 
 
@@ -205,7 +218,7 @@ wrapper can be used to compute the same transitive closure problem for the
 directed graph within python environment:
 
 ```python
-from python import pycubool
+import pycubool
 
 def transitive_closure(a: pycubool.Matrix):
     """
@@ -216,8 +229,8 @@ def transitive_closure(a: pycubool.Matrix):
     :return: The transitive closure adjacency matrix
     """
 
-    t = a.dup()                       # Duplicate matrix where to store result
-    total = 0                         # Current number of values
+    t = a.dup()                           # Duplicate matrix where to store result
+    total = 0                             # Current number of values
 
     while total != t.nvals:
         total = t.nvals
@@ -263,12 +276,12 @@ cuBool
 ## License
 
 This project is licensed under MIT License. License text can be found in the 
-[license file](https://github.com/JetBrains-Research/cuBool/blob/master/LICENSE).
+[license file](https://github.com/JetBrains-Research/cuBool/blob/master/LICENSE.md).
 
 ## Acknowledgments
 
 This is a research project of the Programming Languages and Tools Laboratory
-at JetBrains Research company. Laboratory website [link](https://research.jetbrains.org/groups/plt_lab/).
+at JetBrains-Research. Laboratory website [link](https://research.jetbrains.org/groups/plt_lab/).
 
 ## Also
 

cubool/CMakeLists.txt

@@ -21,17 +21,27 @@ set(CUBOOL_SOURCES
     sources/core/library.cpp
     sources/core/library.hpp
     sources/core/matrix.cpp
-    sources/core/matrix.hpp)
+    sources/core/matrix.hpp
+    sources/io/logger.cpp
+    sources/io/logger.hpp
+    sources/utils/exclusive_scan.hpp
+    sources/utils/timer.hpp
+        )
 
 set(CUBOOL_C_API_SOURCES
     include/cubool/cubool.h
-    sources/cuBool_Version_Get.cpp
-    sources/cuBool_About_Get.cpp
-    sources/cuBool_LicenseInfo_Get.cpp
+    sources/cuBool_GetAbout.cpp
+    sources/cuBool_GetVersion.cpp
+    sources/cuBool_GetLicenseInfo.cpp
+    sources/cuBool_GetDeviceCaps.cpp
     sources/cuBool_Initialize.cpp
     sources/cuBool_Finalize.cpp
+    sources/cuBool_SetupLogger.cpp
     sources/cuBool_Matrix_New.cpp
     sources/cuBool_Matrix_Build.cpp
+    sources/cuBool_Matrix_SetElement.cpp
+    sources/cuBool_Matrix_SetMarker.cpp
+    sources/cuBool_Matrix_Marker.cpp
     sources/cuBool_Matrix_ExtractPairs.cpp
     sources/cuBool_Matrix_ExtractSubMatrix.cpp
     sources/cuBool_Matrix_Duplicate.cpp
@@ -97,8 +107,7 @@ if (CUBOOL_WITH_SEQUENTIAL)
         sources/sequential/sq_reduce.cpp
         sources/sequential/sq_reduce.hpp
         sources/sequential/sq_submatrix.cpp
-        sources/sequential/sq_submatrix.hpp
-        sources/sequential/sq_exclusive_scan.hpp)
+        sources/sequential/sq_submatrix.hpp)
 endif()
 
 # Shared library object config
@@ -134,17 +143,14 @@ if (CUBOOL_WITH_CUDA)
 
     # Settings: https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/
     target_compile_options(cubool PRIVATE $<$<COMPILE_LANGUAGE:CUDA>:
-            -arch=sm_30
-             -gencode=arch=compute_50,code=sm_50
-             -gencode=arch=compute_52,code=sm_52
-             -gencode=arch=compute_60,code=sm_60
-             -gencode=arch=compute_61,code=sm_61
-             -gencode=arch=compute_70,code=sm_70
-             -gencode=arch=compute_75,code=sm_75
-             -gencode=arch=compute_75,code=compute_75>)
-
-    target_compile_options(cubool PRIVATE $<$<AND:$<CONFIG:Debug>,$<COMPILE_LANGUAGE:CUDA>>: -Xptxas -O2>)
-    target_compile_options(cubool PRIVATE $<$<AND:$<CONFIG:Release>,$<COMPILE_LANGUAGE:CUDA>>: -Xptxas -O0>)
+        -arch=sm_30
+        -gencode=arch=compute_30,code=sm_30
+        -gencode=arch=compute_35,code=sm_35
+        -gencode=arch=compute_50,code=sm_50
+        -gencode=arch=compute_52,code=sm_52
+        -gencode=arch=compute_52,code=compute_52>)
+
+    target_compile_options(cubool PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -use_fast_math -Xptxas -O2>)
 
     target_compile_definitions(cubool PRIVATE CUBOOL_WITH_CUDA)
     target_link_libraries(cubool PRIVATE nsparse_um)
@@ -164,4 +170,16 @@ if (CUBOOL_BUILD_TESTS)
 
     message(STATUS "Add unit tests directory to the project")
     add_subdirectory(tests)
-endif()
+endif()
+
+# todo: Different platforms has specific naming conventions
+set(LIBRARY_FILE_NAME "libcubool.so")
+
+# Copy cubool library after build
+add_custom_command(
+    TARGET cubool POST_BUILD
+    COMMAND "${CMAKE_COMMAND}" -E
+    copy
+    "${CMAKE_BINARY_DIR}/cubool/${LIBRARY_FILE_NAME}"
+    "${CMAKE_BINARY_DIR}/python/pycubool"
+    COMMENT "Copy cubool lib into python folder")