[MRG] ENH Add BLIS support

.azure_pipeline.yml

@@ -73,6 +73,31 @@ jobs:
         VERSION_PYTHON: '*'
         CC_OUTER_LOOP: 'gcc'
         CC_INNER_LOOP: 'clang-8'
+      # Linux environment with numpy linked to BLIS
+      pylatest_blis_gcc_clang:
+        PACKAGER: 'conda'
+        VERSION_PYTHON: '*'
+        INSTALL_BLIS: 'true'
+        BLIS_NUM_THREADS: '4'
+        CC_OUTER_LOOP: 'gcc'
+        CC_INNER_LOOP: 'gcc'
+        BLIS_CC: 'clang-8'
+      pylatest_blis_clang_gcc:
+        PACKAGER: 'conda'
+        VERSION_PYTHON: '*'
+        INSTALL_BLIS: 'true'
+        BLIS_NUM_THREADS: '4'
+        CC_OUTER_LOOP: 'clang-8'
+        CC_INNER_LOOP: 'clang-8'
+        BLIS_CC: 'gcc'
+      pylatest_blis_sinlge_threaded:
+        PACKAGER: 'conda'
+        VERSION_PYTHON: '*'
+        INSTALL_BLIS: 'true'
+        BLIS_NUM_THREADS: '1'
+        CC_OUTER_LOOP: 'gcc'
+        CC_INNER_LOOP: 'gcc'
+        BLIS_CC: 'gcc'
 
 - template: continuous_integration/posix.yml
   parameters:

continuous_integration/install_with_blis.sh

@@ -0,0 +1,53 @@
+#!/bin/bash
+
+set -e
+
+pushd ..
+ABS_PATH=$(pwd)
+popd
+
+# Assume Ubuntu: install a recent version of clang and libomp
+echo "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" | sudo tee -a /etc/apt/sources.list.d/llvm.list
+echo "deb-src http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main" | sudo tee -a /etc/apt/sources.list.d/llvm.list
+wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+sudo apt update
+sudo apt install clang-8 libomp-8-dev
+
+# create conda env
+conda create -n $VIRTUALENV -q --yes python=$VERSION_PYTHON pip cython
+source activate $VIRTUALENV
+
+pushd ..
+
+# build & install blis
+mkdir BLIS_install
+git clone https://github.com/flame/blis.git
+pushd blis
+./configure --prefix=$ABS_PATH/BLIS_install --enable-cblas --enable-threading=openmp CC=$BLIS_CC auto
+make -j4
+make install
+popd
+
+# build & install numpy
+git clone https://github.com/numpy/numpy.git
+pushd numpy
+echo "[blis]
+libraries = blis
+library_dirs = $ABS_PATH/BLIS_install/lib
+include_dirs = $ABS_PATH/BLIS_install/include/blis
+runtime_library_dirs = $ABS_PATH/BLIS_install/lib" > site.cfg
+python setup.py build_ext -i
+pip install -e .
+popd
+
+popd
+
+python -m pip install -q -r dev-requirements.txt
+CFLAGS=-I$ABS_PATH/BLIS_install/include/blis LDFLAGS=-L$ABS_PATH/BLIS_install/lib \
+    bash ./continuous_integration/build_test_ext.sh
+
+python --version
+python -c "import numpy; print('numpy %s' % numpy.__version__)" || echo "no numpy"
+python -c "import scipy; print('scipy %s' % scipy.__version__)" || echo "no scipy"
+
+python -m flit install --symlink

continuous_integration/posix.yml

@@ -22,7 +22,12 @@ jobs:
       condition: eq('${{ parameters.name }}', 'macOS')
     - script: |
         continuous_integration/install.sh
-      displayName: 'Install'
+      displayName: 'Install without BLIS'
+      condition: ne(variables['INSTALL_BLIS'], 'true')
+    - script: |
+        continuous_integration/install_with_blis.sh
+      displayName: 'Install with BLIS'
+      condition: eq(variables['INSTALL_BLIS'], 'true')
     - script: |
         continuous_integration/test_script.sh
       displayName: 'Test Library'

tests/_openmp_test_helper/nested_prange_blas.pyx

@@ -1,8 +1,24 @@
 cimport openmp
-from cython.parallel import prange
+from cython.parallel import parallel, prange
 
 import numpy as np
-from scipy.linalg.cython_blas cimport dgemm
+
+IF USE_BLIS:
+    cdef extern from 'cblas.h' nogil:
+        ctypedef enum CBLAS_ORDER:
+            CblasRowMajor=101
+            CblasColMajor=102
+        ctypedef enum CBLAS_TRANSPOSE:
+            CblasNoTrans=111
+            CblasTrans=112
+            CblasConjTrans=113
+        void dgemm 'cblas_dgemm' (
+            CBLAS_ORDER Order, CBLAS_TRANSPOSE TransA,
+            CBLAS_TRANSPOSE TransB, int M, int N,
+            int K, double alpha, double *A, int lda,
+            double *B, int ldb, double beta, double *C, int ldc)
+ELSE:
+    from scipy.linalg.cython_blas cimport dgemm
 
 from threadpoolctl import threadpool_info
 
@@ -25,18 +41,25 @@ def check_nested_prange_blas(double[:, ::1] A, double[:, ::1] B, int nthreads):
 
         int i
         int prange_num_threads
+        int *prange_num_threads_ptr = &prange_num_threads
 
-    threadpool_infos = None
+    threadpool_infos = [None]
 
-    for i in prange(n_chunks, num_threads=nthreads, nogil=True):
-        dgemm(trans, no_trans, &n, &chunk_size, &k,
-              &alpha, &B[0, 0], &k, &A[i * chunk_size, 0], &k,
-              &beta, &C[i * chunk_size, 0], &n)
+    with nogil, parallel(num_threads=nthreads):
+        if openmp.omp_get_thread_num() == 0:
+            with gil:
+                threadpool_infos[0] = threadpool_info()
 
-        prange_num_threads = openmp.omp_get_num_threads()
+            prange_num_threads_ptr[0] = openmp.omp_get_num_threads()
 
-        if i == 0:
-            with gil:
-                threadpool_infos = threadpool_info()
+        for i in prange(n_chunks):
+            IF USE_BLIS:
+                dgemm(CblasRowMajor, CblasNoTrans, CblasTrans,
+                chunk_size, n, k, alpha, &A[i * chunk_size, 0], k,
+                &B[0, 0], k, beta, &C[i * chunk_size, 0], n)
+            ELSE:
+                dgemm(trans, no_trans, &n, &chunk_size, &k,
+                    &alpha, &B[0, 0], &k, &A[i * chunk_size, 0], &k,
+                    &beta, &C[i * chunk_size, 0], &n)
 
-    return np.asarray(C), prange_num_threads, threadpool_infos
+    return np.asarray(C), prange_num_threads, threadpool_infos[0]

tests/_openmp_test_helper/setup_nested_prange_blas.py

@@ -12,19 +12,24 @@
     set_cc_variables("CC_OUTER_LOOP")
     openmp_flag = get_openmp_flag()
 
+    use_blis = os.getenv('INSTALL_BLIS', False)
+    libraries = ['blis'] if use_blis else []
+
     ext_modules = [
         Extension(
             "nested_prange_blas",
             ["nested_prange_blas.pyx"],
             extra_compile_args=openmp_flag,
-            extra_link_args=openmp_flag
+            extra_link_args=openmp_flag,
+            libraries=libraries
             )
     ]
 
     setup(
         name='_openmp_test_helper_nested_prange_blas',
         ext_modules=cythonize(
             ext_modules,
+            compile_time_env={'USE_BLIS': use_blis},
             compiler_directives={'language_level': 3,
                                  'boundscheck': False,
                                  'wraparound': False})

tests/test_threadpoolctl.py

@@ -245,11 +245,17 @@ def test_nested_prange_blas(nthreads_outer):
 
     blas_info = [module for module in threadpool_info()
                  if module["user_api"] == "blas"]
-    for module in threadpool_info():
-        if is_old_openblas(module):
-            # OpenBLAS 0.3.3 and older are known to cause an unrecoverable
-            # deadlock at process shutdown time (after pytest has exited).
-            pytest.skip("Old OpenBLAS: skipping test to avoid deadlock")
+
+    blis_linked = any([module['internal_api'] == 'blis'
+                       for module in threadpool_info()])
+    if not blis_linked:
+        # numpy can be linked to BLIS for CBLAS and OpenBLAS for LAPACK. In that
+        # case this test will run BLIS gemm so no need to skip.
+        for module in threadpool_info():
+            if is_old_openblas(module):
+                # OpenBLAS 0.3.3 and older are known to cause an unrecoverable
+                # deadlock at process shutdown time (after pytest has exited).
+                pytest.skip("Old OpenBLAS: skipping test to avoid deadlock")
 
     from ._openmp_test_helper import check_nested_prange_blas
     A = np.ones((1000, 10))

threadpoolctl.py

@@ -74,6 +74,11 @@ class _dl_phdr_info(ctypes.Structure):
         "internal_api": "mkl",
         "filename_prefixes": ("libmkl_rt", "mkl_rt",),
     },
+    {
+        "user_api": "blas",
+        "internal_api": "blis",
+        "filename_prefixes": ("libblis",),
+    },
 ]
 
 # map a internal_api (openmp, openblas, mkl) to set and get functions
@@ -88,6 +93,9 @@ class _dl_phdr_info(ctypes.Structure):
     "mkl": {
         "set_num_threads": "MKL_Set_Num_Threads",
         "get_num_threads": "MKL_Get_Max_Threads"},
+    "blis": {
+        "set_num_threads": "bli_thread_set_num_threads",
+        "get_num_threads": "bli_thread_get_num_threads"}
 }
 
 # Helpers for the doc and test names
@@ -110,9 +118,8 @@ def decorator(o):
 def _get_limit(prefix, user_api, limits):
     if prefix in limits:
         return limits[prefix]
-    if user_api in limits:
+    else:
         return limits[user_api]
-    return None
 
 
 @_format_docstring(ALL_PREFIXES=_ALL_PREFIXES,
@@ -210,6 +217,10 @@ def threadpool_info():
     modules = _load_modules(user_api=_ALL_USER_APIS)
     for module in modules:
         module['num_threads'] = module['get_num_threads']()
+        # by default BLIS is single-threaded and get_num_threads returns -1.
+        # we map it to 1 for consistency with other libraries.
+        if module['num_threads'] == -1 and module['internal_api'] == 'blis':
+            module['num_threads'] = 1
         # Remove the wrapper for the module and its function
         del module['set_num_threads'], module['get_num_threads']
         del module['dynlib']
@@ -227,6 +238,8 @@ def _get_version(dynlib, internal_api):
         return None
     elif internal_api == "openblas":
         return _get_openblas_version(dynlib)
+    elif internal_api == "blis":
+        return _get_blis_version(dynlib)
     else:
         raise NotImplementedError("Unsupported API {}".format(internal_api))
 
@@ -257,6 +270,13 @@ def _get_openblas_version(openblas_dynlib):
     return None
 
 
+def _get_blis_version(blis_dynlib):
+    """Return the BLIS version"""
+    get_version = getattr(blis_dynlib, "bli_info_get_version_str")
+    get_version.restype = ctypes.c_char_p
+    return get_version().decode('utf-8')
+
+
 # Loading utilities for dynamically linked shared objects
 
 def _load_modules(prefixes=None, user_api=None):