Add TileDB support as external storage

.travis.yml

@@ -55,7 +55,7 @@ install:
     fi
   - pip install -r requirements-dev.txt &&
     pip install -r requirements-extra.txt &&
-    pip install virtualenv coveralls flake8 etcd-gevent
+    pip install virtualenv coveralls flake8 etcd-gevent tiledb
   - virtualenv testenv && source testenv/bin/activate
   - pip install -r requirements.txt && pip install pytest pytest-timeout
   - if [ -z "$DEFAULT_VENV" ]; then deactivate; else source $DEFAULT_VENV/bin/activate; fi

mars/lib/sparse/__init__.py

@@ -26,11 +26,11 @@
 from .coo import COONDArray
 
 
-def asarray(x):
+def asarray(x, shape=None):
     from .core import issparse
 
     if issparse(x):
-        return SparseNDArray(x)
+        return SparseNDArray(x, shape=shape)
 
     return x
 
@@ -460,7 +460,7 @@ def matmul(a, b, sparse=True, **_):
 def concatenate(tensors, axis=0):
     has_sparse = any(issparse(t) for t in tensors)
     if has_sparse:
-        tensors = [asarray(get_sparse_module(t).csr_matrix(t)) for t in tensors]
+        tensors = [asarray(get_sparse_module(t).csr_matrix(t), t.shape) for t in tensors]
 
     return reduce(lambda a, b: _call_bin('concatenate', a, b, axis=axis), tensors)
 

mars/lib/sparse/matrix.py

@@ -106,6 +106,9 @@ def __init__(self, spmatrix, shape=()):
     def ndim(self):
         return self.spmatrix.ndim
 
+    def tocsr(self):
+        return self
+
     def toarray(self):
         return self.spmatrix.toarray()
 

mars/lib/sparse/vector.py

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 from .array import SparseNDArray
-from .core import get_array_module, cp, cps, naked, issparse
+from .core import get_array_module, get_sparse_module, cp, cps, naked, issparse
 
 
 class SparseVector(SparseNDArray):
@@ -39,6 +39,9 @@ def toarray(self):
     def todense(self):
         return self.spmatrix.toarray().reshape(self.shape)
 
+    def tocsr(self):
+        return self
+
     def ascupy(self):
         is_cp = get_array_module(self.spmatrix) is cp
         if is_cp:
@@ -118,3 +121,22 @@ def dot(self, other, sparse=True):
             shape = (other.shape[1],)
             return SparseNDArray(x, shape=shape)
         return get_array_module(x).asarray(x)
+
+    def concatenate(self, other, axis=0):
+        try:
+            other = naked(other)
+        except TypeError:
+            return NotImplemented
+
+        if issparse(other):
+            xps = get_sparse_module(self.spmatrix)
+            if axis != 0:
+                raise ValueError('axis can only be 0')
+            x = xps.hstack((self.spmatrix, other))
+        else:
+            xp = get_array_module(self.spmatrix)
+            x = xp.concatenate((self.spmatrix.toarray().reshape(self.shape), other), axis=axis)
+
+        if issparse(x):
+            return SparseNDArray(x, shape=(x.shape[1],))
+        return get_array_module(x).asarray(x)

mars/opcodes.py

@@ -16,6 +16,8 @@
 TENSOR_LINSPACE = 14
 TENSOR_TRIU = 15
 TENSOR_TRIL = 16
+TENSOR_FROM_TILEDB = 18
+TENSOR_STORE_TILEDB = 19
 DATAFRAME_DATA_SOURCE = 17
 RAND_RAND = 41
 RAND_RANDN = 42

mars/operands/datastore.py

@@ -14,8 +14,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .core import Operand
+from .base import HasInput
 
 
-class DataStore(Operand):
+class DataStore(HasInput):
     __slots__ = ()

mars/serialize/protos/operand.proto

@@ -26,6 +26,9 @@ message OperandDef {
         TENSOR_LINSPACE = 14;
         TENSOR_TRIU = 15;
         TENSOR_TRIL = 16;
+        // external storage
+        TENSOR_FROM_TILEDB = 18;
+        TENSOR_STORE_TILEDB = 19;
         // dataframe
         DATAFRAME_DATA_SOURCE = 17;
 

mars/tensor/__init__.py

@@ -18,7 +18,8 @@
 from .expressions.datasource import tensor, array, asarray, scalar, \
     empty, empty_like, ones, ones_like, zeros, zeros_like, \
     full, arange, diag, diagflat, eye, identity, linspace, \
-    meshgrid, indices, tril, triu
+    meshgrid, indices, tril, triu, fromtiledb
+from .expressions.datastore import totiledb
 from .expressions.base import result_type, copyto, transpose, where, broadcast_to, broadcast_arrays, \
     expand_dims, rollaxis, swapaxes, moveaxis, ravel, atleast_1d, atleast_2d, atleast_3d, argwhere, \
     array_split, split, hsplit, vsplit, dsplit, roll, squeeze, ptp, diff, ediff1d, digitize, \

mars/tensor/core.py

@@ -173,6 +173,11 @@ def ravel(self):
     def _equals(self, o):
         return self is o
 
+    def totiledb(self, uri, ctx=None, key=None, timestamp=None):
+        from .expressions.datastore import totiledb
+
+        return totiledb(uri, self, ctx=ctx, key=key, timestamp=timestamp)
+
     def execute(self, session=None, **kw):
         from ..session import Session
 
@@ -361,6 +366,11 @@ def reshape(self, shape, *shapes):
         """
         return self._data.reshape(shape, *shapes)
 
+    def totiledb(self, uri, ctx=None, key=None, timestamp=None):
+        from .expressions.datastore import totiledb
+
+        return totiledb(uri, self, ctx=ctx, key=key, timestamp=timestamp)
+
 
 class SparseTensor(Tensor):
     __slots__ = ()

mars/tensor/execution/core.py

@@ -15,6 +15,7 @@
 # limitations under the License.
 
 from .datasource import register_data_source_handler
+from .datastore import register_data_store_handler
 from .random import register_random_handler
 from .base import register_basic_handler
 from .arithmetic import register_arithmetic_handler
@@ -48,6 +49,7 @@ def register_tensor_execution_handler():
         from .cp import register_cp_handler
         register_cp_handler()
     register_data_source_handler()
+    register_data_store_handler()
     register_random_handler()
     register_basic_handler()
     register_arithmetic_handler()

mars/tensor/execution/datasource.py

@@ -21,6 +21,7 @@
 from ...lib.sparse.core import get_sparse_module, get_array_module, cps, sps, naked
 from ...lib.sparse import SparseNDArray
 from ..expressions import datasource
+from .utils import get_tiledb_ctx
 
 logger = logging.getLogger(__name__)
 
@@ -155,6 +156,52 @@ def _tensor_dense_to_sparse(ctx, chunk):
     ctx[chunk.key] = SparseNDArray(xps.csr_matrix(in_data))
 
 
+def _tensor_tiledb(ctx, chunk):
+    import tiledb
+
+    xp = array_module(chunk.op.gpu)
+
+    axis_offsets = [offset + dim_start for offset, dim_start
+                    in zip(chunk.op.axis_offsets, chunk.op.tiledb_dim_starts)]
+    tiledb_ctx = get_tiledb_ctx(chunk.op.tiledb_config)
+    uri = chunk.op.tiledb_uri
+    key = chunk.op.tiledb_key
+    timestamp = chunk.op.tiledb_timestamp
+
+    slcs = []
+    for axis in range(chunk.ndim):
+        axis_offset = axis_offsets[axis]
+        axis_length = chunk.shape[axis]
+        slcs.append(slice(axis_offset, axis_offset + axis_length))
+
+    if not chunk.issparse():
+        # read dense array from tiledb
+        with tiledb.DenseArray(tiledb_ctx, uri, key=key, timestamp=timestamp) as tiledb_arr:
+            ctx[chunk.key] = tiledb_arr[tuple(slcs)]
+    else:
+        # read sparse array from tiledb
+        with tiledb.SparseArray(tiledb_ctx, uri, key=key, timestamp=timestamp) as tiledb_arr:
+            if tiledb_arr.ndim > 2:
+                raise NotImplementedError(
+                    'Does not support to read array with more than 2 dimensions')
+
+            data = tiledb_arr[tuple(slcs)]
+            coords = data['coords']
+            value = data[tiledb_arr.attr(0).name]
+            if tiledb_arr.ndim == 2:
+                # 2-d
+                ij = tuple(coords[tiledb_arr.domain.dim(k).name] - axis_offsets[k]
+                           for k in range(tiledb_arr.ndim))
+                spmatrix = sps.coo_matrix((value, ij), shape=chunk.shape)
+                ctx[chunk.key] = SparseNDArray(spmatrix)
+            else:
+                # 1-d
+                ij = xp.zeros(coords.shape), \
+                     coords[tiledb_arr.domain.dim(0).name] - axis_offsets[0]
+                spmatrix = sps.coo_matrix((value, ij), shape=(1,) + chunk.shape)
+                ctx[chunk.key] = SparseNDArray(spmatrix, shape=chunk.shape)
+
+
 def _tensor_fetch_chunk(ctx, chunk):
     # nothing need to do
     return
@@ -187,5 +234,7 @@ def register_data_source_handler():
     register(datasource.CSRMatrixDataSource, _tensor_csr_matrix_data_source)
     register(datasource.SparseToDense, _tensor_sparse_to_dense)
     register(datasource.DenseToSparse, _tensor_dense_to_sparse)
+    register(datasource.TensorTileDBDataSource, _tensor_tiledb)
     register(datasource.TensorFetch, _tensor_fetch_chunk)
     register(datasource.Scalar, _scalar)
+

mars/tensor/execution/datastore.py

@@ -14,10 +14,55 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import numpy as np
+try:
+    import tiledb
+except ImportError:  # pragma: no cover
+    tiledb = None
 
-def _data_store(ctx, chunk):
-    raise NotImplementedError
+from ...lib.sparse import SparseNDArray
+from ...lib.sparse.core import sps
+from ..expressions import datastore
+from .utils import get_tiledb_ctx
+
+
+def _store_tiledb(ctx, chunk):
+    tiledb_ctx = get_tiledb_ctx(chunk.op.tiledb_config)
+    uri = chunk.op.tiledb_uri
+    key = chunk.op.tiledb_key
+    timestamp = chunk.op.tiledb_timestamp
+    axis_offsets = chunk.op.axis_offsets
+
+    if not chunk.issparse():
+        # dense
+        to_store = np.ascontiguousarray(ctx[chunk.op.input.key])
+        slcs = []
+        for axis in range(chunk.ndim):
+            axis_offset = axis_offsets[axis]
+            axis_length = chunk.op.input.shape[axis]
+            slcs.append(slice(axis_offset, axis_offset + axis_length))
+        with tiledb.DenseArray(tiledb_ctx, uri, mode='w',
+                               key=key, timestamp=timestamp) as arr:
+            arr[tuple(slcs)] = to_store
+        ctx[chunk.key] = np.empty((0,) * chunk.ndim, dtype=chunk.dtype)
+    else:
+        # sparse
+        to_store = ctx[chunk.op.input.key].spmatrix.tocoo()
+        if to_store.nnz > 0:
+            with tiledb.SparseArray(tiledb_ctx, uri, mode='w',
+                                    key=key, timestamp=timestamp) as arr:
+                if chunk.ndim == 1:
+                    vec = to_store.col if to_store.shape[0] == 1 else to_store.row
+                    vec += axis_offsets[0]
+                    arr[vec] = to_store.data
+                else:
+                    i, j = to_store.row + axis_offsets[0], to_store.col + axis_offsets[1]
+                    arr[i, j] = to_store.data
+        ctx[chunk.key] = SparseNDArray(sps.csr_matrix((0, 0), dtype=chunk.dtype),
+                                       shape=chunk.shape)
 
 
 def register_data_store_handler():
-    pass
+    from ...executor import register
+
+    register(datastore.TensorTileDBDataStore, _store_tiledb)

mars/tensor/execution/tests/test_datasource_execute.py

@@ -14,14 +14,22 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import tempfile
+import shutil
+import unittest
+
 import numpy as np
 import scipy.sparse as sps
+try:
+    import tiledb
+except ImportError:  # pragma: no cover
+    tiledb = None
 
 from mars.executor import Executor
 from mars.tests.core import TestBase
 from mars.tensor.expressions.datasource import tensor, ones_like, zeros, zeros_like, full, \
     arange, empty, empty_like, diag, diagflat, eye, linspace, meshgrid, indices, \
-    triu, tril
+    triu, tril, fromtiledb
 from mars.lib.sparse import SparseNDArray
 from mars.tensor.expressions.lib import nd_grid
 
@@ -652,3 +660,74 @@ def testIndexTrickExecution(self):
         expected = np.lib.index_tricks.nd_grid(sparse=True)[0:5, 0:5]
         [np.testing.assert_equal(r, e) for r, e in zip(res, expected)]
 
+    @unittest.skipIf(tiledb is None, 'tiledb not installed')
+    def testReadTileDBExecution(self):
+        ctx = tiledb.Ctx()
+
+        tempdir = tempfile.mkdtemp()
+        try:
+            # create TileDB dense array
+            dom = tiledb.Domain(ctx,
+                                tiledb.Dim(ctx, domain=(1, 100), tile=30, dtype=np.int32),
+                                tiledb.Dim(ctx, domain=(0, 90), tile=22, dtype=np.int32),
+                                tiledb.Dim(ctx, domain=(0, 9), tile=8, dtype=np.int32),
+            )
+            schema = tiledb.ArraySchema(ctx, domain=dom, sparse=False,
+                                        attrs=[tiledb.Attr(ctx, dtype=np.float64)])
+            tiledb.DenseArray.create(tempdir, schema)
+
+            expected = np.random.rand(100, 91, 10)
+            with tiledb.DenseArray(ctx, tempdir, mode='w') as arr:
+                arr.write_direct(expected)
+
+            a = fromtiledb(tempdir, ctx=ctx)
+            result = self.executor.execute_tensor(a, concat=True)[0]
+
+            np.testing.assert_allclose(expected, result)
+        finally:
+            shutil.rmtree(tempdir)
+
+        tempdir = tempfile.mkdtemp()
+        try:
+            # create 2-d TileDB sparse array
+            dom = tiledb.Domain(ctx,
+                                tiledb.Dim(ctx, domain=(0, 99), tile=30, dtype=np.int32),
+                                tiledb.Dim(ctx, domain=(2, 11), tile=8, dtype=np.int32),
+            )
+            schema = tiledb.ArraySchema(ctx, domain=dom, sparse=True,
+                                        attrs=[tiledb.Attr(ctx, dtype=np.float64)])
+            tiledb.SparseArray.create(tempdir, schema)
+
+            expected = sps.rand(100, 10, density=0.01)
+            with tiledb.SparseArray(ctx, tempdir, mode='w') as arr:
+                I, J = expected.row, expected.col + 2
+                arr[I, J] = {arr.attr(0).name: expected.data}
+
+            a = fromtiledb(tempdir, ctx=ctx)
+            result = self.executor.execute_tensor(a, concat=True)[0]
+
+            np.testing.assert_allclose(expected.toarray(), result.toarray())
+        finally:
+            shutil.rmtree(tempdir)
+
+        tempdir = tempfile.mkdtemp()
+        try:
+            # create 1-d TileDB sparse array
+            dom = tiledb.Domain(ctx,
+                                tiledb.Dim(ctx, domain=(1, 100), tile=30, dtype=np.int32),
+            )
+            schema = tiledb.ArraySchema(ctx, domain=dom, sparse=True,
+                                        attrs=[tiledb.Attr(ctx, dtype=np.float64)])
+            tiledb.SparseArray.create(tempdir, schema)
+
+            expected = sps.rand(1, 100, density=0.05)
+            with tiledb.SparseArray(ctx, tempdir, mode='w') as arr:
+                I= expected.col + 1
+                arr[I] = expected.data
+
+            a = fromtiledb(tempdir, ctx=ctx)
+            result = self.executor.execute_tensor(a, concat=True)[0]
+
+            np.testing.assert_allclose(expected.toarray()[0], result.toarray())
+        finally:
+            shutil.rmtree(tempdir)