Merge remote-tracking branch 'dmlc/master'

.gitignore

@@ -129,3 +129,19 @@ lib
 
 # Mac OS X
 .DS_Store
+
+#Notebook Automated Test
+!tests/nightly/test_config.txt
+!tests/nightly/TestNotebook
+
+# pip building tools
+tools/pip_package/build
+tools/pip_package/dist
+tools/pip_package/mxnet.egg-info
+tools/pip_package/mxnet
+
+# temporary path for building dependencies when building wheel
+deps/
+
+*.jar
+target

.gitmodules

@@ -10,3 +10,7 @@
 [submodule "nnvm"]
 	path = nnvm
 	url = https://github.com/dmlc/nnvm
+[submodule "cub"]
+	path = cub
+	url = https://github.com/NVlabs/cub
+	shallow = true

CMakeLists.txt

@@ -72,6 +72,7 @@ list(APPEND mxnet_LINKER_LIBS ${mshadow_LINKER_LIBS})
 
 include_directories("include")
 include_directories("mshadow")
+include_directories("cub")
 include_directories("nnvm/include")
 include_directories("dmlc-core/include")
 
@@ -127,6 +128,7 @@ mxnet_source_group("Include\\io"   GLOB "src/io/*.h")
 mxnet_source_group("Include\\kvstore"   GLOB "src/kvstore/*.h")
 mxnet_source_group("Include\\ndarray"   GLOB "src/ndarray/*.h")
 mxnet_source_group("Include\\operator"   GLOB "src/operator/*.h")
+mxnet_source_group("Include\\operator\\tensor"   GLOB "src/operator/tensor/*.h")
 mxnet_source_group("Include\\optimizer"   GLOB "src/optimizer/*.h")
 mxnet_source_group("Include\\resource.cc"   GLOB "src/resource.cc/*.h")
 mxnet_source_group("Include\\storage"   GLOB "src/storage/*.h")
@@ -140,7 +142,7 @@ mxnet_source_group("Cuda\\io"   GLOB "src/io/*.cu")
 mxnet_source_group("Cuda\\kvstore"   GLOB "src/kvstore/*.cu")
 mxnet_source_group("Cuda\\ndarray"   GLOB "src/ndarray/*.cu")
 mxnet_source_group("Cuda\\operator"   GLOB "src/operator/*.cu")
-mxnet_source_group("Cuda\\operator\\tensor"   GLOB "src/operator/tensor/*.cu")
+mxnet_source_group("Cuda\\operator\\tensor"   GLOB "src/operator/tensor/*.cu"  "src/operator/tensor/*.cuh")
 mxnet_source_group("Cuda\\optimizer"   GLOB "src/optimizer/*.cu")
 mxnet_source_group("Cuda\\resource.cc"   GLOB "src/resource.cc/*.cu")
 mxnet_source_group("Cuda\\storage"   GLOB "src/storage/*.cu")
@@ -164,7 +166,7 @@ mxnet_source_group("Source\\nnvm"   GLOB "src/nnvm/*.cc")
 
 
 FILE(GLOB_RECURSE SOURCE "src/*.cc" "src/*.h")
-FILE(GLOB_RECURSE CUDA "src/*.cu")
+FILE(GLOB_RECURSE CUDA "src/*.cu" "src/*.cuh")
 
 # add nnvm to source
 
@@ -184,12 +186,14 @@ list(APPEND SOURCE ${NNVMSOURCE})
 
 # add mshadow file
 mxnet_source_group("mshadow\\Include"   GLOB "mshadow/mshadow/*.h")
-mxnet_source_group("mshadow\\Include\\cuda"   GLOB "mshadow/mshadow/cuda/*.h")
+mxnet_source_group("mshadow\\Include\\cuda"   GLOB "mshadow/mshadow/cuda/*.h" "mshadow/mshadow/cuda/*.cuh")
 mxnet_source_group("mshadow\\Include\\extension"   GLOB "mshadow/mshadow/extension/*.h")
 mxnet_source_group("mshadow\\Include\\packet"   GLOB "mshadow/mshadow/packet/*.h")
 
 FILE(GLOB_RECURSE MSHADOWSOURCE "mshadow/mshadow/*.h")
+FILE(GLOB_RECURSE MSHADOW_CUDASOURCE "mshadow/mshadow/*.cuh")
 list(APPEND SOURCE ${MSHADOWSOURCE})
+list(APPEND CUDA ${MSHADOW_CUDASOURCE})
 
 if(USE_PLUGINS_WARPCTC)
 	set(WARPCTC_INCLUDE  "" CACHE PATH "WARPCTC include")

CONTRIBUTORS.md

@@ -120,3 +120,5 @@ List of Contributors
 * [Wei Wu](https://github.com/lazyparser)
 * [Shishi Duan](https://github.com/burness)
 * [Yu Du](https://github.com/Answeror)
+* [Xu Dong](https://github.com/dsqx71)
+* [Chihiro Komaki](https://github.com/ckomaki)

MKL_README.md

@@ -12,7 +12,7 @@ This README shows the user how to setup and install MKL2017 library with mxnet.
 
     1.1 By default, MKL_2017_EXPRIEMENTAL=0. If setting MKL_2017_EXPRIEMENTAL=1, MKL buffer will be created and transferred between layers to achiever much higher performance.
 
-    1.2 By default, USE_BLAS=atlas, MKLML_ROOT=/usr/local, MKL2017_ML will be used
+    1.2 By default, MKLML_ROOT=/usr/local, MKL2017_ML will be used
 
       1.2.1 when excute make, Makefile will execute "prepare_mkl.sh" to download the MKL2017_ML library under <MKLML_ROOT>
 
@@ -28,11 +28,11 @@ This README shows the user how to setup and install MKL2017 library with mxnet.
 
     1.3 If setting USE_BLAS=mkl
 
-      1.3.1 please navigate here to do a full MKL installation: https://registrationcenter.intel.com/en/forms/?productid=2558&licensetype=2  
+      1.3.1 mshadow can also utilize mkl blas function in mklml package  
 
-      1.3.2 do not use MKL2017 and MKL2017_ML at the same time
+    1.4 MKL version compatibility
 
-        1.3.2.1 Do not execute MKL2017 compilervars.sh or mklvars.sh script before MxNet compilation. Otherwise, MKL2017 may conflict with MKL2017_ML and MxNet may not be compiled.   
+        1.3.2.1 If you already have MKL installed and MKLROOT being set in your system, by default, it will not attempt to download the latest mklml package unless you unset MKLROOT. 
 
   2. Run 'make -jX'
 

Makefile

@@ -22,8 +22,16 @@ ifneq ($(USE_OPENMP), 1)
 	export NO_OPENMP = 1
 endif
 
+
 # use customized config file
 include $(config)
+
+ifeq ($(USE_MKL2017), 1)
+	RETURN_STRING=$(shell ./prepare_mkl.sh $(MKLML_ROOT))
+	MKLROOT=$(firstword $(RETURN_STRING))
+	export USE_MKLML=$(lastword $(RETURN_STRING))
+endif
+
 include mshadow/make/mshadow.mk
 include $(DMLC_CORE)/make/dmlc.mk
 
@@ -85,18 +93,6 @@ ifeq ($(USE_MKL2017_EXPERIMENTAL), 1)
 else
 	CFLAGS += -DMKL_EXPERIMENTAL=0
 endif
-ifneq ($(USE_BLAS), mkl)
-	ICC_ON=0
-	RETURN_STRING=$(shell ./prepare_mkl.sh $(ICC_ON) $(MKLML_ROOT))
-	MKLROOT=$(firstword $(RETURN_STRING))
-	MKL_LDFLAGS=-l$(word 2, $(RETURN_STRING))
-	MKL_EXTERNAL=$(lastword $(RETURN_STRING))
-ifeq ($(MKL_EXTERNAL), 1)
-	MKL_LDFLAGS+=-Wl,-rpath,$(MKLROOT)/lib
-	CFLAGS += -I$(MKLROOT)/include
-	LDFLAGS += -Wl,--as-needed -L$(MKLROOT)/lib/ -liomp5 -lmklml_intel
-endif
-endif
 endif
 
 ifeq ($(USE_CUDNN), 1)
@@ -180,6 +176,7 @@ LIB_DEP += $(DMLC_CORE)/libdmlc.a $(NNVM_PATH)/lib/libnnvm.a
 ALL_DEP = $(OBJ) $(EXTRA_OBJ) $(PLUGIN_OBJ) $(LIB_DEP)
 
 ifeq ($(USE_CUDA), 1)
+	CFLAGS += -I$(ROOTDIR)/cub
 	ALL_DEP += $(CUOBJ) $(EXTRA_CUOBJ) $(PLUGIN_CUOBJ)
 	LDFLAGS += -lcuda
 	SCALA_PKG_PROFILE := $(SCALA_PKG_PROFILE)-gpu
@@ -245,12 +242,12 @@ PSLITE:
 $(DMLC_CORE)/libdmlc.a: DMLCCORE
 
 DMLCCORE:
-	+ cd $(DMLC_CORE); make libdmlc.a USE_SSE=$(USE_SSE) config=$(ROOTDIR)/$(config); cd $(ROOTDIR)
+	+ cd $(DMLC_CORE); $(MAKE) libdmlc.a USE_SSE=$(USE_SSE) config=$(ROOTDIR)/$(config); cd $(ROOTDIR)
 
 $(NNVM_PATH)/lib/libnnvm.a: LIBNNVM
 
 LIBNNVM:
-	+ cd $(NNVM_PATH); make lib/libnnvm.a; cd $(ROOTDIR)
+	+ cd $(NNVM_PATH); $(MAKE) lib/libnnvm.a DMLC_CORE_PATH=$(DMLC_CORE); cd $(ROOTDIR)
 
 bin/im2rec: tools/im2rec.cc $(ALLX_DEP)
 
@@ -300,6 +297,7 @@ rpkg:
 	R CMD INSTALL R-package
 	Rscript -e "require(mxnet); mxnet:::mxnet.export(\"R-package\")"
 	rm -rf R-package/NAMESPACE
+	Rscript -e "require(devtools); install_version(\"roxygen2\", version = \"5.0.1\", repos = \"https://cloud.r-project.org/\")"
 	Rscript -e "require(roxygen2); roxygen2::roxygenise(\"R-package\")"
 	R CMD build --no-build-vignettes R-package
 	rm -rf mxnet_current_r.tar.gz
@@ -336,18 +334,18 @@ ifneq ($(EXTRA_OPERATORS),)
 clean: cyclean
 	$(RM) -r build lib bin *~ */*~ */*/*~ */*/*/*~ R-package/NAMESPACE R-package/man R-package/R/mxnet_generated.R \
 		R-package/inst R-package/src/*.o R-package/src/*.so mxnet_*.tar.gz
-	cd $(DMLC_CORE); make clean; cd -
-	cd $(PS_PATH); make clean; cd -
-	cd $(NNVM_PATH); make clean; cd -
+	cd $(DMLC_CORE); $(MAKE) clean; cd -
+	cd $(PS_PATH); $(MAKE) clean; cd -
+	cd $(NNVM_PATH); $(MAKE) clean; cd -
 	$(RM) -r  $(patsubst %, %/*.d, $(EXTRA_OPERATORS)) $(patsubst %, %/*/*.d, $(EXTRA_OPERATORS))
 	$(RM) -r  $(patsubst %, %/*.o, $(EXTRA_OPERATORS)) $(patsubst %, %/*/*.o, $(EXTRA_OPERATORS))
 else
 clean: cyclean
 	$(RM) -r build lib bin *~ */*~ */*/*~ */*/*/*~ R-package/NAMESPACE R-package/man R-package/R/mxnet_generated.R \
 		R-package/inst R-package/src/*.o R-package/src/*.so mxnet_*.tar.gz
-	cd $(DMLC_CORE); make clean; cd -
-	cd $(PS_PATH); make clean; cd -
-	cd $(NNVM_PATH); make clean; cd -
+	cd $(DMLC_CORE); $(MAKE) clean; cd -
+	cd $(PS_PATH); $(MAKE) clean; cd -
+	cd $(NNVM_PATH); $(MAKE) clean; cd -
 endif
 
 clean_all: clean

R-package/DESCRIPTION

@@ -1,21 +1,22 @@
 Package: mxnet
 Type: Package
 Title: MXNet
-Version: 0.9.3
+Version: 0.9.4
 Date: 2015-12-23
 Author: Tianqi Chen, Qiang Kou, Tong He
 Maintainer: Qiang Kou <[email protected]>
 Repository: DMLC
 Description: MXNet is a deep learning framework designed for both efficiency
     and flexibility. It allows you to mix the flavours of deep learning programs
     together to maximize the efficiency and your productivity.
-License: BSD
+License: Apache License (== 2.0)
 URL: https://github.com/dmlc/mxnet/tree/master/R-package
 BugReports: https://github.com/dmlc/mxnet/issues
 Imports:
     methods,
     Rcpp (>= 0.12.1),
     DiagrammeR (>= 0.9.0),
+    visNetwork (>= 1.0.3),
     data.table,
     jsonlite,
     magrittr,
@@ -25,8 +26,7 @@ Suggests:
     mlbench,
     knitr,
     rmarkdown,
-    imager,
-    roxygen2
+    imager
 LinkingTo: Rcpp
-RoxygenNote: 5.0.1
 VignetteBuilder: knitr
+RoxygenNote: 5.0.1