Alex Black 1170827c18 Merge master to upstream (#7945)
* Shugeo strided slice zeros (#14)

* Modified strided_slice op to properly work with empty-like shapes.

* Fixed test for reduce_mean with empty-like input.

* [WIP] Last merge (#15)

* correct logsoftmax looss (#2)

* Small SameDiff listener fix (#4)

* Various fixes (#6)

* #7839 Fix for asXMatrix and tests

* #7866 EmbeddingSequenceLayer dtype fix + test

* #7856 SameDiff save/load stream methods

* #7859 RegressionEvaluation rank 4 fix + tests + axis configuration

* EvaluationBinary 3d/4d

* More evaluation 3d/4d tests

* #7847 Evaluation empty checks

* Small test ifx

* #7848 Fix median edge case

* Improve DL4J samediff layer tests

* [WIP] FastText wrapper implemented (#8)

* FastText implemented

* Some fixes

* Fix shapes for wordsNearest

* Validation of input vectors

* Fixes

* Fixed test

* Thread tagged

* Some tweaks

* setContextClassLoader for DeallocatorServiceThread

* Numpy format tests (#1)

* Various fixes (#11)

* #7852 SameDiff gather fix

* #7892 SameDiff placeholder to constant conversion

* #7890 validate input rank for MLN/CG init methods

* Fix broken permute shape calculation

* Permute and gather fixes

* Tests

* #7850 LogSumExp fix + test

* Handful of test fixes

* Empty arrays with non-scalar shapes (#10)

* minor rearrangements for lambdas

* empty tensors with non-scalar shapes

* numpy empty tensors with non-scalar shapes

* few more empty tweaks

* Small fixes

* conv3d signature update

* micro fix in batchnorm mkldnn

* Import fixes

* Fix

* MKL-DNN update

* Small fill fix

* fill with empty input + test

* Fixes

* Small error improvement

* Fix

* one special test

* couple of fixes for lstm

* Rewrite TFGraphMapper.getNDArrayFromTensor to be maintainable and less error prone

* Fixes

* FP16

* Unsigned

* BFloat16

* Fill op - empty tweaks

* - couple of fixes for empty arrays construction
- stack updated

* strided slice fix

* one transform test

* provide method for reducing shapeInfo in case of input array is empty

* Fixed reduceAlongDimensions to use empty input properly.

* couple of broadcast tests

* couple of tests broadcast tests + tweak to make them pass

* add check of non-empty to methods producing sub-arrays

* Fixed reshapeC with zeros in shape.

* complete empty check in reduce_... legacy ops

* Concat and cumsum/prod

* Tweak to empty shape inference on import

* add empty check to the rest of reduce legacy ops

* one more test

* correct typo in evalReduceShapeInfoEmpty

* Added tests for reduce_* ops to tests with zero shapes.

* few more tests for empty reductions

* Fixed strided_slice op with empty case and tests.

* one more empty reduction test

* Fixed strided_slice test.

* add empty check to NDArray::reshapei

* infOrMax

* empty min/max with infinity tests

* made unstack working correctly with empty arrays

* few IndexReduce tests + tweaks for empty shapes

* add test for empty concat

* few tests fixed

* Validation fix for reductions on empty shapes

* Reverse fix

* Reduction shape calc fixes

* SameDiff.generateOutputVariable: don't use shape function to determine number of outputs

* Range fix

* - NDArray constructor updated for scalars/empty arrays
- few tests fixed

* More fixes

* Empty creator fixes

* concat fix

* concat fix

* TF import tests: allow 'both all NaN' and 'both all inf' to pass

* Slice, zero fraction, and reshape fixes

* transpose, gather

* Zero fraction

* scalar cast fix

* Empty reduction axis support

* few more tests fixed

* Fixed input checks conforming with TF for concat op and tests.

* few tests fixed

* matmul scalar shape fix

* Fixed checkout for data type and scalarity with concat to allow non-empty scalars with vector concats.

* broadcast bool fix

* few more tests

* few more tests

* correct evalReduceShapeInfoEmpty

* argmax/argmin + tests

* one more empty edge case + one more test

* argmax/argmin/realdiv_bp tweaks

* empty reshape test + fix

* Helper fixes

* Small fixes

* Gather test fix

* Gather test fix

* Small fixes

* reduce scalar zero values

* scalar mean workaround

* Remove debug code

* along dim mean workaround

* one more test

* - equalsTo() tweak for empty arrays
- one more test

* broadcast tweaks

* [WIP] Fixing outstanding issues for NLP (#9)

* Avoid using not-inited objects

* Test fixed.

* Redundant method avoided for models like FastText

* KMeans++ implementation

* KMeans++ implementation

* Disable parallel execution

* KMeans++

* Tests

* Dev branch merge (#16)

* SameDiff: convertDataType and gradient check util improvements (#12)

* GradCheck util improvements

* StopGradient constructor + test

* SameDiff: Add datatype conversion

* Javadoc and add DataType.isNumerical()

* Small fix

* Fix SameDiff TF import test cases intermediate naming (workaround for bad default)

* TFGraphTestAllHelper: check intermediates in execution order

* Add missing debug listener

* [WIP] lstmBlock fix + other changes (#13)

- fixes lstmBlock issue
- changes NDArray method reshape(), permute(), transpose() by making them return instance instead of pointer
- CheckNumerics op
- fixes for ReduceBool IsInfOrNan & IsFinite

* Small test fix

* CheckNumerics op wrapper

* Fix some issues on master (#17)

* Fix DataVec test issue

* Fix issue with dl4j SameDiff output layer

* Dtype fix for lambda layers

* #7912 BertIterator dtype fix (use float32 not global default)

* [WIP] Next set of CUDA stuff (#7)

New CUDA implementations and improvements

* bad file

* Dev branch master merge (#23)

* SameDiff: convertDataType and gradient check util improvements (#12)

* GradCheck util improvements

* StopGradient constructor + test

* SameDiff: Add datatype conversion

* Javadoc and add DataType.isNumerical()

* Small fix

* Fix SameDiff TF import test cases intermediate naming (workaround for bad default)

* TFGraphTestAllHelper: check intermediates in execution order

* Add missing debug listener

* [WIP] lstmBlock fix + other changes (#13)

- fixes lstmBlock issue
- changes NDArray method reshape(), permute(), transpose() by making them return instance instead of pointer
- CheckNumerics op
- fixes for ReduceBool IsInfOrNan & IsFinite

* Small test fix

* CheckNumerics op wrapper

* Compatibility of deserialization (#18)

Signed-off-by: Alexander Stoyakin <alexander.stoyakin@gmail.com>

* SameDiff: add activation gradient checking support for debugging (#19)

* SameDiff gradient checker: first pass on activation gradient checks

* Fixes + tests for activation gradient checking

* Javadoc

* [WIP] Some nd4j data type corrections (#20)

* Adjust data type

* Set correct Data type.

* Size of proper data type.

* fix averaged cpu load (#22)

* SameDiff ops, TF import and fixes (#24)

* CheckNumerics tests + fixes + misc fixes

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Fake quant

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Fixes

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* FakeQuantWithMinMaxArgs

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* CheckNumerics fix

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* Fix libnd4j ALL_INTS and ALL_FLOATS declaration (uint and bfloat types)

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Small fix

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* Javadoc

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* Exception tweak

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* fix

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* Fix for out of scope stack allocated var use

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* Ignores

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* Ignore for known failing test (already logged issue)

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* Merge upstream to fork (#25)

* Add thousand-separator commas to TotalParams (#7915)

* Add thousand-separator commas to TotalParams

The number of parameters can be quite large, and it would help the reading of the summary printout to have the TotalParams column & values at the bottom have thousand-separator-commas in them.

* Add thousand-separator commas to MultiLayerNetwork

Corresponding change to MultiLayerNetwork

Signed-off-by: Jxtps Jxtps <jxtps435@gmail.com>

* Update contributing and issue/PR templates (#7934)

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Fix link to AdaDelta paper (#7942)

Fix link to AdaDelta paper hosted on matthewzeiler.com

Signed-off-by: Jxtps

* Fixes, and ignores for known/logged failing issues (#7943)

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* SameDiff + DL4J/SameDiff: Multiple fixes (#28)

* #7919 HDF5 attribute buffer length fix

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* #7909 Arbiter constructor exception ux improvements

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* #7925 RNN output layer length checks

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* #7939 Add listener for validating inputs are not incorrectly modified

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* #7939 Integrate NonInplaceValidationListener into tests

* #7844 DL4J SameDiff fixes for variable minibatch size

* DL4J SameDiff fixes - ensure gradient for input placeholder is available

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Tweaks to ExternalErrorsFunction - use placeholders, make more robust

* Another fix

* More fixes

* More SameDiff/DL4J fixes

* Scope out scalar array creation in BaseScalarOp

* Remove debug code

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* [WIP] Final dev branch merge (#29)

* SameDiff: convertDataType and gradient check util improvements (#12)

* GradCheck util improvements

* StopGradient constructor + test

* SameDiff: Add datatype conversion

* Javadoc and add DataType.isNumerical()

* Small fix

* Fix SameDiff TF import test cases intermediate naming (workaround for bad default)

* TFGraphTestAllHelper: check intermediates in execution order

* Add missing debug listener

* [WIP] lstmBlock fix + other changes (#13)

- fixes lstmBlock issue
- changes NDArray method reshape(), permute(), transpose() by making them return instance instead of pointer
- CheckNumerics op
- fixes for ReduceBool IsInfOrNan & IsFinite

* Small test fix

* CheckNumerics op wrapper

* Compatibility of deserialization (#18)

Signed-off-by: Alexander Stoyakin <alexander.stoyakin@gmail.com>

* SameDiff: add activation gradient checking support for debugging (#19)

* SameDiff gradient checker: first pass on activation gradient checks

* Fixes + tests for activation gradient checking

* Javadoc

* [WIP] Some nd4j data type corrections (#20)

* Adjust data type

* Set correct Data type.

* Size of proper data type.

* fix averaged cpu load (#22)

* [WIP] Multiple dataset iterators (#27)

* Splitting dataset into arbitrary number

* Fixes

* Multiple split of iterator

* Test

* Test

* Some fixes

* signature change

* one more tweak

Signed-off-by: raver119 <raver119@gmail.com>

* one more test for sequential use of DataSetIteratorSplitter

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* Fixes

* Fixes

* one more test for Alexander

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* Some fixes

* Some fixes

* one more test for Alexander

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* minor test fix

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* Some fixes

* Some fixes

* couple of assertions tweaked

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* MDS splitter test :/

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* Minor refactoring

* Multi dataset

* Some fixes

* More tests

* Small number of test fixes/improvements (failures on CI) (#31)

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* [WIP] More CUDA stuff (#26)

* initial commit

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* LRN BP CUDA

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* less memory

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* Fixed bug with crop_and_resize op helper.

* get rid of unnecessary index-calculation dunction

Signed-off-by: Yurii <yurii@skymind.io>

* Fixed sort with nth_element cuda-based helper.

* Refactored nth_element.

* Refactored nth_element op and tests.

* Modified usage of dim array with sortTad routine.

* Refactored main routine of helper for non_max_image_suppression op.

* non_max_image_suppression op helper with cuda kernel implementation. Initial revision.

* fix vol2col cuda kernel

* meh

Signed-off-by: raver119 <raver119@gmail.com>

* topK concept

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* unsorted topK with scanWitdh of 1

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* correct vol2col tests

* sorted/unsorted topK

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* implementation and fixing col2im/col2vol

* Corrected usage flags with input/output with reverse op.

* dup is const now

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* percentile op

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* group tests for mapool2d

Signed-off-by: Yurii <yurii@skymind.io>

* special test for george

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* less threads for sortTad

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* provide conv2d for cuda

Signed-off-by: Yurii <yurii@skymind.io>

* remove auther in sort tad kernel code

Signed-off-by: Yurii <yurii@skymind.io>

* provide depthwise_conv2d for cuda

Signed-off-by: Yurii <yurii@skymind.io>

* - max_pooling_with_argmax
- null check for special use

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* dts cuda

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* provide sconv2d for cuda

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* std cuda

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* Refactored non_max_suppression op to conform TF implementation.

* Improved suppression helper.

* provide pooling3d for cuda

Signed-off-by: Yurii <yurii@skymind.io>

* minor lstm rearrangements

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* more of minor lstm rearrangements

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* (bi)dynamic_rnn

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* templates init order

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* Refactored non_max_suppression op.

* Added cuda kernel for non_max_suppression.

* CPU sort by key/value

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* CPU sort TAD by key/value

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* CPU sort TAD by key/value tests

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* Eliminate compiler error with cuda implementation.

* - repaired gradCheck in cuda
- provide conv2d_bp for cuda

Signed-off-by: Yurii <yurii@skymind.io>

* missed signature

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* provide depthwise_conv2d_bp for cuda

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* Implementation of lup helper with cuda kernel. Initial commit.

* further work on backprops for convolutions

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* CUDA linear sort by key/val

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* CUDA tad sort by key/val

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* start providing of backprop for pooling2d/3d

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* Added atomicAdd for bool datatype.

* dynamic partition concept

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* dynamic partition concept

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* dynamic partition scalar CUDA

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* important comment

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* fix pooling2d/3d backprop helpers

Signed-off-by: Yurii <yurii@skymind.io>

* Added non-linear test with dynamic_partition.

* Improved test for dynamic_partition.

* dynamic_partition TAD concept

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* - dynamic_partition TAD CUDA impl
- dynamic_partition TAD CPU fix

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* - rewrite cpu code for usampling2d/3d
- write cuda code for usampling2d/3d

Signed-off-by: Yurii <yurii@skymind.io>

* dynamic_stitch CUDA vector case

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* dynamic_stitch CUDA TAD case concept

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* dynamic_stitch CUDA TAD case impl

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* Added tests for dynamic_stitch 3D-4D cases.

* minor tests tweaks

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* Fixed type check for dynamic stitch.

* min/max bp

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* rewrite code for upsampling2d/3d cpu

Signed-off-by: Yurii <yurii@skymind.io>

* reduce min/max/norm_max bp

Signed-off-by: raver119 <raver119@gmail.com>

* lup implementation. Additional enhancements.

* provide code for upsamling2d/3d backprop

Signed-off-by: Yurii <yurii@skymind.io>

* weightedCrossEntropyWithLogits

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* Fixed template math atomicMul for 64bit ints.

* Refactored dynamic_partition_bp op.

* inverseBroadcast fix

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* DynamicPartitionBP test datatype fixed.

* - nd4j_atomicMul Windows fix
- cpu/NDArrayLambda.hpp excluded from CUDA

Signed-off-by: raver119 <raver119@gmail.com>
2019-06-27 18:37:04 +03:00

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/*******************************************************************************
* Copyright (c) 2015-2018 Skymind, Inc.
*
* This program and the accompanying materials are made available under the
* terms of the Apache License, Version 2.0 which is available at
* https://www.apache.org/licenses/LICENSE-2.0.
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations
* under the License.
*
* SPDX-License-Identifier: Apache-2.0
******************************************************************************/
//
// @author Yurii Shyrma (iuriish@yahoo.com), created on 07.03.2019
//
#include <ops/declarable/helpers/gather.h>
#include <numeric>
#include <PointersManager.h>
#include <ShapeUtils.h>
namespace nd4j {
namespace ops {
namespace helpers {
template<typename X, typename Y>
__global__ static void gatherCudaLinearKernel(const void* vx, const Nd4jLong* xShapeInfo, const void* vy, const Nd4jLong* yShapeInfo,
void* vz, const Nd4jLong* zShapeInfo) {
__shared__ const X* x;
__shared__ const Y* y;
__shared__ X* z;
__shared__ Nd4jLong xLen, yLen, zLen;
if (threadIdx.x == 0) {
x = reinterpret_cast<const X*>(vx);
z = reinterpret_cast<X*>(vz);
y = reinterpret_cast<const Y *>(vy);
xLen = shape::length(xShapeInfo);
yLen = shape::length(yShapeInfo);
zLen = shape::length(zShapeInfo);
}
__syncthreads();
//const Nd4jLong zLen = shape::length(zShapeInfo);
auto start = blockIdx.x * blockDim.x + threadIdx.x;
auto step = blockDim.x * gridDim.x;
for (int j = start; j < zLen; j += step) {
auto zIndex = shape::getIndexOffset(j, zShapeInfo, zLen);
auto yIndex = shape::getIndexOffset(j, yShapeInfo, yLen);
auto xIndex = shape::getIndexOffset(y[yIndex], xShapeInfo, xLen);
//printf("%lld , %lld\n", zIndex, xIndex);
z[zIndex] = x[xIndex];
}
}
//////////////////////////////////////////////////////////////////////
template<typename X, typename Y>
__global__ static void gatherCuda(const int numOfSubArrs,
const void* vx, const Nd4jLong* xShapeInfo, const Nd4jLong* xOffsets,
const void* vy, const Nd4jLong* yShapeInfo,
void* vz, const Nd4jLong* zShapeInfo, const Nd4jLong* zOffsets) {
const Y* y = reinterpret_cast<const Y*>(vy);
__shared__ const X* x;
__shared__ X* z;
const Nd4jLong len = shape::length(xShapeInfo);
//const Nd4jLong zLen = shape::length(zShapeInfo);
for (int i = blockIdx.x; i < numOfSubArrs; i += gridDim.x) {
if (threadIdx.x == 0) {
x = reinterpret_cast<const X*>(vx) + xOffsets[y[shape::getIndexOffset(i, yShapeInfo, numOfSubArrs)]];
z = reinterpret_cast<X*>(vz) + zOffsets[i];
}
__syncthreads();
for (int j = threadIdx.x; j < len; j += blockDim.x) {
auto zIndex = shape::getIndexOffset(j, zShapeInfo, len);
auto xIndex = shape::getIndexOffset(j, xShapeInfo, len);
//printf("%lld , %lld\n", zIndex, xIndex);
z[zIndex] = x[xIndex];
}
__syncthreads();
}
}
template<typename X, typename Y>
__host__ static void gatherCudaLinear(const cudaStream_t *stream, const void* vx, const Nd4jLong* xShapeInfo, const void* vy, const Nd4jLong* yShapeInfo,
void* vz, const Nd4jLong* zShapeInfo) {
gatherCudaLinearKernel<X,Y><<<128, 256, 1024, *stream>>>(vx, xShapeInfo, vy, yShapeInfo, vz, zShapeInfo);
}
//////////////////////////////////////////////////////////////////////
template<typename X, typename Y>
__host__ static void gatherCudaLauncher(const cudaStream_t *stream, const int numOfSubArrs,
const void* vx, const Nd4jLong* xShapeInfo, const Nd4jLong* xOffsets,
const void* vy, const Nd4jLong* yShapeInfo,
void* vz, const Nd4jLong* zShapeInfo, const Nd4jLong* zOffsets) {
gatherCuda<X,Y><<<numOfSubArrs, MAX_NUM_THREADS, 1024, *stream>>>(numOfSubArrs, vx, xShapeInfo, xOffsets, vy, yShapeInfo, vz, zShapeInfo, zOffsets);
}
//////////////////////////////////////////////////////////////////////
void gather(nd4j::LaunchContext * context, const NDArray* input, const NDArray* indices, NDArray* output, const std::vector<int>& intArgs) {
const int inputRank = input->rankOf();
int axis = intArgs.size() > 0 ? intArgs[0] : 0;
if(axis < 0)
axis += inputRank;
const int numOfIntArgs = intArgs.size();
if (indices == nullptr && numOfIntArgs == 2) { // scalar case
output->assign((*input)(intArgs[1], {axis}));
}
else if (indices != nullptr && indices->isScalar()) {
if(input->rankOf() <= 1) { //For scalar indices, rank 0 or 1 input: can't do tensor along dimension 0 as this is whole array... instead, we want to get a scalar
auto idx = indices->e<Nd4jLong>(0);
auto scalarNDArray = input->e(idx);
output->assign(scalarNDArray);
}
else {
NDArray inSubArr = (*input)(indices->e<Nd4jLong>(0), {axis});
output->assign(inSubArr);
}
}
else {
NDArray* pIndices = const_cast<NDArray*>(indices);
if(indices == nullptr)
pIndices = new NDArray(input->ordering(), {numOfIntArgs-1}, std::vector<double>(intArgs.begin() + 1, intArgs.end()), DataType::INT64, input->getContext());
std::vector<int> dimsOut(pIndices->rankOf());
std::iota(dimsOut.begin(), dimsOut.end(), axis); // fill with axis, axis+1, ... axis+pIndices->rankOf()-1
const Nd4jLong numOfSubArrs = pIndices->lengthOf();
Nd4jLong *outSubArrShapeInfo(nullptr), *inSubArrShapeInfo(nullptr), *outSubArrOffsets(nullptr), *inSubArrOffsets(nullptr);
input-> getSubArrShapeAndOffsets({axis}, inSubArrShapeInfo, inSubArrOffsets);
output->getSubArrShapeAndOffsets(dimsOut, outSubArrShapeInfo, outSubArrOffsets);
if (output->rankOf() > 1) {
PointersManager manager(context, "gather");
auto xShapeInfo = reinterpret_cast<Nd4jLong *>(manager.replicatePointer(inSubArrShapeInfo,
shape::shapeInfoByteLength(
inSubArrShapeInfo)));
auto zShapeInfo = reinterpret_cast<Nd4jLong *>(manager.replicatePointer(outSubArrShapeInfo,
shape::shapeInfoByteLength(
outSubArrShapeInfo)));
auto xOffsets = reinterpret_cast<Nd4jLong *>(manager.replicatePointer(inSubArrOffsets, (input->lengthOf() /
shape::length(
inSubArrShapeInfo)) *
sizeof(Nd4jLong)));
auto zOffsets = reinterpret_cast<Nd4jLong *>(manager.replicatePointer(outSubArrOffsets,
(output->lengthOf() /
shape::length(outSubArrShapeInfo)) *
sizeof(Nd4jLong)));
NDArray::prepareSpecialUse({output}, {input, pIndices});
BUILD_DOUBLE_SELECTOR(input->dataType(), pIndices->dataType(), gatherCudaLauncher, (context->getCudaStream(), numOfSubArrs, input->getSpecialBuffer(), xShapeInfo, xOffsets, pIndices->getSpecialBuffer(), pIndices->getSpecialShapeInfo(), output->getSpecialBuffer(), zShapeInfo, zOffsets), NUMERIC_TYPES, INTEGER_TYPES);
NDArray::registerSpecialUse({output}, {input, pIndices});
manager.synchronize();
}
else {
NDArray::prepareSpecialUse({output}, {input, pIndices});
BUILD_DOUBLE_SELECTOR(input->dataType(), pIndices->dataType(), gatherCudaLinear, (context->getCudaStream(), input->getSpecialBuffer(), input->getSpecialShapeInfo(), pIndices->getSpecialBuffer(), pIndices->getSpecialShapeInfo(), output->specialBuffer(), output->specialShapeInfo()), NUMERIC_TYPES, INTEGER_TYPES);
NDArray::registerSpecialUse({output}, {input, pIndices});
}
if(indices == nullptr)
delete pIndices;
}
}
BUILD_DOUBLE_TEMPLATE(template void gatherCudaLauncher, (const cudaStream_t *stream, const int numOfSubArrs, const void* vx, const Nd4jLong* xShapeInfo, const Nd4jLong* xOffsets, const void* vy, const Nd4jLong* yShapeInfo, void* vz, const Nd4jLong* zShapeInfo, const Nd4jLong* zOffsets), NUMERIC_TYPES, INTEGER_TYPES);
BUILD_DOUBLE_TEMPLATE(template void gatherCudaLinear, (const cudaStream_t *stream, const void* vx, const Nd4jLong* xShapeInfo, const void* vy, const Nd4jLong* yShapeInfo, void* vz, const Nd4jLong* zShapeInfo), NUMERIC_TYPES, INTEGER_TYPES);
}
}
}