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Posted to commits@mxnet.apache.org by GitBox <gi...@apache.org> on 2020/08/26 01:29:22 UTC
[GitHub] [incubator-mxnet] Zha0q1 opened a new pull request #19015: Numpy nonzero large tensor fix
Zha0q1 opened a new pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015
This fixes nonzero against large tensors.
Also cleaned up the loop a little bit.
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[GitHub] [incubator-mxnet] mxnet-bot commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
mxnet-bot commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-683186130
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478563458
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
This int64_t is actually the output data type. According to the original author this "must be int 64" https://github.com/apache/incubator-mxnet/blob/a2b77fb311204488bd72f99b681fc0ff334bca8d/src/operator/numpy/np_nonzero_op.cc#L33.
I think the reasoning is because the tensor is flattened, even with int64tensorsize=off we can have > int32_max many elements e.g.(2**20, 2**20)
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[GitHub] [incubator-mxnet] mxnet-bot commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
mxnet-bot commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-683186026
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[GitHub] [incubator-mxnet] access2rohit commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478477723
##########
File path: src/operator/numpy/np_nonzero_op.cc
##########
@@ -88,17 +88,16 @@ void NonzeroForwardCPU(const nnvm::NodeAttrs& attrs,
const_cast<NDArray &>(out).Init(s);
return;
}
- std::vector<int32_t> prefix_sum(in_size, 0);
+ std::vector<index_t> prefix_sum(in_size, 0);
size_t valid_num = 0;
// Calculate prefix sum
MSHADOW_TYPE_SWITCH_WITH_BOOL(in.dtype(), DType, {
DType* in_dptr = in.data().dptr<DType>();
for (size_t i = 0; i < in_size; i++) {
- prefix_sum[i] = (i == 0) ? 0 : prefix_sum[i - 1];
- prefix_sum[i] += (in_dptr[i]) ? 1 : 0;
+ valid_num += (in_dptr[i] != 0);
Review comment:
Nice work ! its actually correct : https://stackoverflow.com/questions/2725044/can-i-assume-booltrue-int1-for-any-c-compiler
But for the sake of readability can you still keep it
```
(in_dptr[i]) ? 1 : 0;
```
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[GitHub] [incubator-mxnet] access2rohit commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-682205111
> Again pytest run results ?
?? rest LGTM!
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[GitHub] [incubator-mxnet] Zha0q1 commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-683186017
@mxnet-bot add [pr-awaiting-merge]
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478563458
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
This int64_t is actually the output data type. According to the original author this "must be int 64" https://github.com/apache/incubator-mxnet/blob/a2b77fb311204488bd72f99b681fc0ff334bca8d/src/operator/numpy/np_nonzero_op.cc#L33.
although I do agree that both these places can be changed to index_t
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[GitHub] [incubator-mxnet] mxnet-bot commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
mxnet-bot commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-680406692
Hey @Zha0q1 , Thanks for submitting the PR
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[GitHub] [incubator-mxnet] access2rohit commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478710967
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
+ const index_t* idx,
+ const mshadow::Shape<ndim> shape) {
+ index_t prev = (i == 0) ? 0 : idx[i - 1];
+ index_t curr = idx[i];
+ if (prev != curr) {
+ mshadow::Shape<ndim> coord = mxnet_op::unravel<ndim>(i, shape);
+ for (int j = 0; j < ndim; j++) {
+ out[prev * ndim + j] = coord[j];
+ }
+ }
+ }
+};
+
+struct NonzeroForwardKernelGPU {
+ // for gpu implementation because it does not support int 64 indexing
Review comment:
aah ... makes sense two Fcompute each for CPU and GPU comes to same kernel eventually but for GPU's FCompute there is a prior call to cub that expects an int32_t pointer that it populates and returns.
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[GitHub] [incubator-mxnet] Zha0q1 edited a comment on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 edited a comment on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-683186017
@mxnet-bot add [awaiting-merge]
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478563458
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
This int64_t is actually the output data type. According to the original author this "must be int 64" https://github.com/apache/incubator-mxnet/blob/a2b77fb311204488bd72f99b681fc0ff334bca8d/src/operator/numpy/np_nonzero_op.cc#L33.
I do also agree that both these places can be changed to index_t
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[GitHub] [incubator-mxnet] access2rohit commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478467906
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
int64_t -> index_t
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[GitHub] [incubator-mxnet] access2rohit commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-681998737
Again pytest run results ?
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478598552
##########
File path: src/operator/numpy/np_nonzero_op.cc
##########
@@ -88,17 +88,16 @@ void NonzeroForwardCPU(const nnvm::NodeAttrs& attrs,
const_cast<NDArray &>(out).Init(s);
return;
}
- std::vector<int32_t> prefix_sum(in_size, 0);
+ std::vector<index_t> prefix_sum(in_size, 0);
size_t valid_num = 0;
// Calculate prefix sum
MSHADOW_TYPE_SWITCH_WITH_BOOL(in.dtype(), DType, {
DType* in_dptr = in.data().dptr<DType>();
for (size_t i = 0; i < in_size; i++) {
- prefix_sum[i] = (i == 0) ? 0 : prefix_sum[i - 1];
- prefix_sum[i] += (in_dptr[i]) ? 1 : 0;
+ valid_num += (in_dptr[i] != 0);
Review comment:
I will add a comment there explaining the logic. This way of writing it is faster than branching
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[GitHub] [incubator-mxnet] Zha0q1 commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-680680675
@mxnet-bot run ci [unix-gpu ]
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[GitHub] [incubator-mxnet] Zha0q1 commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-682206330
> > Again pytest run results ?
>
> ?? rest LGTM!
Sorry I was working on another task. Will make the changes and paste run results here before requesting for merge.
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[GitHub] [incubator-mxnet] access2rohit commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
access2rohit commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478478710
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
+ const index_t* idx,
+ const mshadow::Shape<ndim> shape) {
+ index_t prev = (i == 0) ? 0 : idx[i - 1];
+ index_t curr = idx[i];
+ if (prev != curr) {
+ mshadow::Shape<ndim> coord = mxnet_op::unravel<ndim>(i, shape);
+ for (int j = 0; j < ndim; j++) {
+ out[prev * ndim + j] = coord[j];
+ }
+ }
+ }
+};
+
+struct NonzeroForwardKernelGPU {
+ // for gpu implementation because it does not support int 64 indexing
Review comment:
Can you point me to where the cub library is getting called ?
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[GitHub] [incubator-mxnet] mxnet-bot commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
mxnet-bot commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-680680726
Jenkins CI successfully triggered : [unix-gpu]
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[GitHub] [incubator-mxnet] Zha0q1 commented on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-682268611
test result:
```
ubuntu@ip-172-31-38-169:~/incubator-mxnet$ pytest tests/nightly/test_np_large_array.py::test_nonzero
/home/ubuntu/anaconda3/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
return f(*args, **kwds)
/home/ubuntu/anaconda3/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
return f(*args, **kwds)
/home/ubuntu/anaconda3/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
return f(*args, **kwds)
============================================ test session starts =============================================
platform linux -- Python 3.7.7, pytest-5.4.1, py-1.8.1, pluggy-0.13.1
rootdir: /home/ubuntu/incubator-mxnet, inifile: pytest.ini
plugins: remotedata-0.3.2, openfiles-0.4.0, astropy-header-0.1.2, hypothesis-5.8.3, arraydiff-0.3, doctestplus-0.5.0
collected 1 item
tests/nightly/test_np_large_array.py . [100%]
============================================== warnings summary ==============================================
tests/nightly/test_np_large_array.py:88
/home/ubuntu/incubator-mxnet/tests/nightly/test_np_large_array.py:88: DeprecationWarning: invalid escape sequence \
'''
tests/nightly/test_np_large_array.py:568
/home/ubuntu/incubator-mxnet/tests/nightly/test_np_large_array.py:568: DeprecationWarning: invalid escape sequence \
'''
-- Docs: https://docs.pytest.org/en/latest/warnings.html
================================= 1 passed, 2 warnings in 166.16s (0:02:46) ==================================
```
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478556931
##########
File path: src/operator/numpy/np_nonzero_op.cc
##########
@@ -88,17 +88,16 @@ void NonzeroForwardCPU(const nnvm::NodeAttrs& attrs,
const_cast<NDArray &>(out).Init(s);
return;
}
- std::vector<int32_t> prefix_sum(in_size, 0);
+ std::vector<index_t> prefix_sum(in_size, 0);
size_t valid_num = 0;
// Calculate prefix sum
MSHADOW_TYPE_SWITCH_WITH_BOOL(in.dtype(), DType, {
DType* in_dptr = in.data().dptr<DType>();
for (size_t i = 0; i < in_size; i++) {
- prefix_sum[i] = (i == 0) ? 0 : prefix_sum[i - 1];
- prefix_sum[i] += (in_dptr[i]) ? 1 : 0;
+ valid_num += (in_dptr[i] != 0);
Review comment:
yes sir
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478563458
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
This int64_t is actually the output data type. According to the original author this "must be int 64" https://github.com/apache/incubator-mxnet/blob/a2b77fb311204488bd72f99b681fc0ff334bca8d/src/operator/numpy/np_nonzero_op.cc#L33.
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478563458
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
This int64_t is actually the output data type. According to the original author this "must be int 64" https://github.com/apache/incubator-mxnet/blob/a2b77fb311204488bd72f99b681fc0ff334bca8d/src/operator/numpy/np_nonzero_op.cc#L33.
I do also think this both these places can be changed to index_t
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[GitHub] [incubator-mxnet] sxjscience merged pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
sxjscience merged pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015
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[GitHub] [incubator-mxnet] Zha0q1 commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r478557832
##########
File path: src/operator/numpy/np_nonzero_op-inl.h
##########
@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
+ const index_t* idx,
+ const mshadow::Shape<ndim> shape) {
+ index_t prev = (i == 0) ? 0 : idx[i - 1];
+ index_t curr = idx[i];
+ if (prev != curr) {
+ mshadow::Shape<ndim> coord = mxnet_op::unravel<ndim>(i, shape);
+ for (int j = 0; j < ndim; j++) {
+ out[prev * ndim + j] = coord[j];
+ }
+ }
+ }
+};
+
+struct NonzeroForwardKernelGPU {
+ // for gpu implementation because it does not support int 64 indexing
Review comment:
In our code the cub function is called here: https://github.com/apache/incubator-mxnet/blob/master/src/operator/numpy/np_nonzero_op.cu#L71
You can also refer to https://github.com/apache/incubator-mxnet/issues/19020
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[GitHub] [incubator-mxnet] Zha0q1 removed a comment on pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
Zha0q1 removed a comment on pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#issuecomment-683186017
@mxnet-bot add [awaiting-merge]
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[GitHub] [incubator-mxnet] sxjscience commented on a change in pull request #19015: Numpy nonzero large tensor fix
Posted by GitBox <gi...@apache.org>.
sxjscience commented on a change in pull request #19015:
URL: https://github.com/apache/incubator-mxnet/pull/19015#discussion_r480277134
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File path: src/operator/numpy/np_nonzero_op-inl.h
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@@ -43,6 +43,25 @@ namespace mxnet {
namespace op {
struct NonzeroForwardKernel {
+ // this is for cpu
+ template<int ndim>
+ MSHADOW_XINLINE static void Map(index_t i,
+ int64_t* out,
Review comment:
For me, I feel that it's better to use template because most of the codes are duplicated.
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