Merge branch 'main' into fix_gcc7_arm

contrib/clustering.py

@@ -151,14 +151,12 @@ def assign_to(self, centroids, weights=None):
 
         I = I.ravel()
         D = D.ravel()
-        n = len(self.x)
+        nc, d = centroids.shape
+        sum_per_centroid = np.zeros((nc, d), dtype='float32')
         if weights is None:
-            weights = np.ones(n, dtype='float32')
-        nc = len(centroids)
-        m = scipy.sparse.csc_matrix(
-            (weights, I, np.arange(n + 1)),
-            shape=(nc, n))
-        sum_per_centroid = m * self.x
+            np.add.at(sum_per_centroid, I, self.x)
+        else:
+            np.add.at(sum_per_centroid, I, weights[:, np.newaxis] * self.x)
 
         return I, D, sum_per_centroid
 
@@ -185,7 +183,8 @@ def perform_search(self, centroids):
 
 def sparse_assign_to_dense(xq, xb, xq_norms=None, xb_norms=None):
     """ assignment function for xq is sparse, xb is dense
-    uses a matrix multiplication. The squared norms can be provided if available.
+    uses a matrix multiplication. The squared norms can be provided if
+    available.
     """
     nq = xq.shape[0]
     nb = xb.shape[0]
@@ -272,6 +271,7 @@ def assign_to(self, centroids, weights=None):
         if weights is None:
             weights = np.ones(n, dtype='float32')
         nc = len(centroids)
+
         m = scipy.sparse.csc_matrix(
             (weights, I, np.arange(n + 1)),
             shape=(nc, n))
@@ -285,25 +285,40 @@ def imbalance_factor(k, assign):
     return faiss.imbalance_factor(len(assign), k, faiss.swig_ptr(assign))
 
 
+def check_if_torch(x):
+    if x.__class__ == np.ndarray:
+        return False
+    import torch
+    if isinstance(x, torch.Tensor):
+        return True
+    raise NotImplementedError(f"Unknown tensor type {type(x)}")
+
+
 def reassign_centroids(hassign, centroids, rs=None):
     """ reassign centroids when some of them collapse """
     if rs is None:
         rs = np.random
     k, d = centroids.shape
     nsplit = 0
+    is_torch = check_if_torch(centroids)
+
     empty_cents = np.where(hassign == 0)[0]
 
-    if empty_cents.size == 0:
+    if len(empty_cents) == 0:
         return 0
 
-    fac = np.ones(d)
+    if is_torch:
+        import torch
+        fac = torch.ones_like(centroids[0])
+    else:
+        fac = np.ones_like(centroids[0])
     fac[::2] += 1 / 1024.
     fac[1::2] -= 1 / 1024.
 
     # this is a single pass unless there are more than k/2
     # empty centroids
-    while empty_cents.size > 0:
-        # choose which centroids to split
+    while len(empty_cents) > 0:
+        # choose which centroids to split (numpy)
         probas = hassign.astype('float') - 1
         probas[probas < 0] = 0
         probas /= probas.sum()
@@ -327,13 +342,17 @@ def reassign_centroids(hassign, centroids, rs=None):
     return nsplit
 
 
+
 def kmeans(k, data, niter=25, seed=1234, checkpoint=None, verbose=True,
            return_stats=False):
     """Pure python kmeans implementation. Follows the Faiss C++ version
     quite closely, but takes a DatasetAssign instead of a training data
-    matrix. Also redo is not implemented. """
-    n, d = data.count(), data.dim()
+    matrix. Also redo is not implemented.
 
+    For the torch implementation, the centroids are tensors (possibly on GPU),
+    but the indices remain numpy on CPU.
+    """
+    n, d = data.count(), data.dim()
     log = print if verbose else print_nop
 
     log(("Clustering %d points in %dD to %d clusters, " +
@@ -345,6 +364,7 @@ def kmeans(k, data, niter=25, seed=1234, checkpoint=None, verbose=True,
     # initialization
     perm = rs.choice(n, size=k, replace=False)
     centroids = data.get_subset(perm)
+    is_torch = check_if_torch(centroids)
 
     iteration_stats = []
 
@@ -362,12 +382,17 @@ def kmeans(k, data, niter=25, seed=1234, checkpoint=None, verbose=True,
         t_search_tot += time.time() - t0s;
 
         err = D.sum()
+        if is_torch:
+            err = err.item()
         obj.append(err)
 
         hassign = np.bincount(assign, minlength=k)
 
         fac = hassign.reshape(-1, 1).astype('float32')
-        fac[fac == 0] = 1 # quiet warning
+        fac[fac == 0] = 1  # quiet warning
+        if is_torch:
+            import torch
+            fac = torch.from_numpy(fac).to(sums.device)
 
         centroids = sums / fac
 
@@ -377,7 +402,7 @@ def kmeans(k, data, niter=25, seed=1234, checkpoint=None, verbose=True,
             "obj": err,
             "time": (time.time() - t0),
             "time_search": t_search_tot,
-            "imbalance_factor": imbalance_factor (k, assign),
+            "imbalance_factor": imbalance_factor(k, assign),
             "nsplit": nsplit
         }
 
@@ -391,7 +416,11 @@ def kmeans(k, data, niter=25, seed=1234, checkpoint=None, verbose=True,
 
         if checkpoint is not None:
             log('storing centroids in', checkpoint)
-            np.save(checkpoint, centroids)
+            if is_torch:
+                import torch
+                torch.save(centroids, checkpoint)
+            else:
+                np.save(checkpoint, centroids)
 
     if return_stats:
         return centroids, iteration_stats

contrib/torch/README.md

@@ -0,0 +1,6 @@
+# The Torch contrib
+
+This contrib directory contains a few Pytorch routines that
+are useful for similarity search. They do not necessarily depend on Faiss.
+
+The code is designed to work with CPU and GPU tensors.

contrib/torch/clustering.py

@@ -0,0 +1,59 @@
+# Copyright (c) Facebook, Inc. and its affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+"""
+This contrib module contains Pytorch code for k-means clustering
+"""
+import faiss
+import faiss.contrib.torch_utils
+import torch
+
+# the kmeans can produce both torch and numpy centroids
+from faiss.contrib.clustering import kmeans
+
+class DatasetAssign:
+    """Wrapper for a tensor that offers a function to assign the vectors
+    to centroids. All other implementations offer the same interface"""
+
+    def __init__(self, x):
+        self.x = x
+
+    def count(self):
+        return self.x.shape[0]
+
+    def dim(self):
+        return self.x.shape[1]
+
+    def get_subset(self, indices):
+        return self.x[indices]
+
+    def perform_search(self, centroids):
+        return faiss.knn(self.x, centroids, 1)
+
+    def assign_to(self, centroids, weights=None):
+        D, I = self.perform_search(centroids)
+
+        I = I.ravel()
+        D = D.ravel()
+        nc, d = centroids.shape
+
+        sum_per_centroid = torch.zeros_like(centroids)
+        if weights is None:
+            sum_per_centroid.index_add_(0, I, self.x)
+        else:
+            sum_per_centroid.index_add_(0, I, self.x * weights[:, None])
+
+        # the indices are still in numpy.
+        return I.cpu().numpy(), D, sum_per_centroid
+
+
+class DatasetAssignGPU(DatasetAssign):
+
+    def __init__(self, res, x):
+        DatasetAssign.__init__(self, x)
+        self.res = res
+
+    def perform_search(self, centroids):
+        return faiss.knn_gpu(self.res, self.x, centroids, 1)

contrib/torch/quantization.py

@@ -0,0 +1,53 @@
+# Copyright (c) Facebook, Inc. and its affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+"""
+This contrib module contains Pytorch code for quantization.
+"""
+
+import numpy as np
+import torch
+import faiss
+
+from faiss.contrib import torch_utils
+
+
+class Quantizer:
+
+    def __init__(self, d, code_size):
+        self.d = d
+        self.code_size = code_size
+
+    def train(self, x):
+        pass
+
+    def encode(self, x):
+        pass
+
+    def decode(self, x):
+        pass
+
+
+class VectorQuantizer(Quantizer):
+
+    def __init__(self, d, k):
+        code_size = int(torch.ceil(torch.log2(k) / 8))
+        Quantizer.__init__(d, code_size)
+        self.k = k
+
+    def train(self, x):
+        pass
+
+
+class ProductQuantizer(Quantizer):
+
+    def __init__(self, d, M, nbits):
+        code_size = int(torch.ceil(M * nbits / 8))
+        Quantizer.__init__(d, code_size)
+        self.M = M
+        self.nbits = nbits
+
+    def train(self, x):
+        pass

contrib/torch_utils.py

@@ -28,13 +28,18 @@
 import sys
 import numpy as np
 
+##################################################################
+# Equivalent of swig_ptr for Torch tensors
+##################################################################
+
 def swig_ptr_from_UInt8Tensor(x):
     """ gets a Faiss SWIG pointer from a pytorch tensor (on CPU or GPU) """
     assert x.is_contiguous()
     assert x.dtype == torch.uint8
     return faiss.cast_integer_to_uint8_ptr(
         x.untyped_storage().data_ptr() + x.storage_offset())
 
+
 def swig_ptr_from_HalfTensor(x):
     """ gets a Faiss SWIG pointer from a pytorch tensor (on CPU or GPU) """
     assert x.is_contiguous()
@@ -43,27 +48,34 @@ def swig_ptr_from_HalfTensor(x):
     return faiss.cast_integer_to_void_ptr(
         x.untyped_storage().data_ptr() + x.storage_offset() * 2)
 
+
 def swig_ptr_from_FloatTensor(x):
     """ gets a Faiss SWIG pointer from a pytorch tensor (on CPU or GPU) """
     assert x.is_contiguous()
     assert x.dtype == torch.float32
     return faiss.cast_integer_to_float_ptr(
         x.untyped_storage().data_ptr() + x.storage_offset() * 4)
 
+
 def swig_ptr_from_IntTensor(x):
     """ gets a Faiss SWIG pointer from a pytorch tensor (on CPU or GPU) """
     assert x.is_contiguous()
     assert x.dtype == torch.int32, 'dtype=%s' % x.dtype
     return faiss.cast_integer_to_int_ptr(
         x.untyped_storage().data_ptr() + x.storage_offset() * 4)
 
+
 def swig_ptr_from_IndicesTensor(x):
     """ gets a Faiss SWIG pointer from a pytorch tensor (on CPU or GPU) """
     assert x.is_contiguous()
     assert x.dtype == torch.int64, 'dtype=%s' % x.dtype
     return faiss.cast_integer_to_idx_t_ptr(
         x.untyped_storage().data_ptr() + x.storage_offset() * 8)
 
+##################################################################
+# utilities
+##################################################################
+
 @contextlib.contextmanager
 def using_stream(res, pytorch_stream=None):
     """ Creates a scoping object to make Faiss GPU use the same stream
@@ -107,6 +119,10 @@ def torch_replace_method(the_class, name, replacement,
     setattr(the_class, name + '_numpy', orig_method)
     setattr(the_class, name, replacement)
 
+##################################################################
+# Setup wrappers
+##################################################################
+
 def handle_torch_Index(the_class):
     def torch_replacement_add(self, x):
         if type(x) is np.ndarray:
@@ -493,6 +509,52 @@ def torch_replacement_sa_decode(self, codes, x=None):
             handle_torch_Index(the_class)
 
 
+# allows torch tensor usage with knn
+def torch_replacement_knn(xq, xb, k, metric=faiss.METRIC_L2, metric_arg=0):
+    if type(xb) is np.ndarray:
+        # Forward to faiss __init__.py base method
+        return faiss.knn_numpy(xq, xb, k, metric=metric, metric_arg=metric_arg)
+
+    nb, d = xb.size()
+    assert xb.is_contiguous()
+    assert xb.dtype == torch.float32
+    assert not xb.is_cuda, "use knn_gpu for GPU tensors"
+
+    nq, d2 = xq.size()
+    assert d2 == d
+    assert xq.is_contiguous()
+    assert xq.dtype == torch.float32
+    assert not xq.is_cuda, "use knn_gpu for GPU tensors"
+
+    D = torch.empty(nq, k, device=xb.device, dtype=torch.float32)
+    I = torch.empty(nq, k, device=xb.device, dtype=torch.int64)
+    I_ptr = swig_ptr_from_IndicesTensor(I)
+    D_ptr = swig_ptr_from_FloatTensor(D)
+    xb_ptr = swig_ptr_from_FloatTensor(xb)
+    xq_ptr = swig_ptr_from_FloatTensor(xq)
+
+    if metric == faiss.METRIC_L2:
+        faiss.knn_L2sqr(
+            xq_ptr, xb_ptr,
+            d, nq, nb, k, D_ptr, I_ptr
+        )
+    elif metric == faiss.METRIC_INNER_PRODUCT:
+        faiss.knn_inner_product(
+            xq_ptr, xb_ptr,
+            d, nq, nb, k, D_ptr, I_ptr
+        )
+    else:
+        faiss.knn_extra_metrics(
+            xq_ptr, xb_ptr,
+            d, nq, nb, metric, metric_arg, k, D_ptr, I_ptr
+        )
+
+    return D, I
+
+
+torch_replace_method(faiss_module, 'knn', torch_replacement_knn, True, True)
+
+
 # allows torch tensor usage with bfKnn
 def torch_replacement_knn_gpu(res, xq, xb, k, D=None, I=None, metric=faiss.METRIC_L2, device=-1, use_raft=False):
     if type(xb) is np.ndarray: