Merge branch 'release-v0.99'

============================== Release Notes: v0.99 ==============================
Support for new training algorithms:
 - Improvements to LTFB infrastructure (including transfer of SGD and Adam hyperparameters)

Support for new network structures:
 - Support for Wide ResNets

Support for new layers:

Python front-end:
 - Python front-end for generating neural network architectures (lbann namespace):
   including layers, objective functions, callbacks, metrics, and optimizers.
 - Python interface for launching (SLURM or LSF) jobs on HPC systems
 - Support for running LBANN experiments and capturing experimental output
 - Network templates for AlexNet, LeNet, arbitrary ResNet models, and Wide ResNet models
 - Python scripts for LeNet, AlexNet, and (Wide) ResNets in model zoo.

Performance optimizations:
 - GPU implementation of RMSprop optimizer.
 - cuDNN convolution algorithms are determined by empirically measuring
   performance rather than using heuristics.
 - Avoid setting up unused bias weights.
 - Perform gradient accumulations in-place when possible.

Model portability & usability:

Internal features:
 - Weight gradient allreduces are in-place rather than on a staging buffer.
 - Fully connected and convolution layers only create bias weights when
   needed.
 - Optimizer exposes gradient buffers so they can be updated in-place.
 - Added callback support to explicitly save model
 - Min-max metric for reporting on multiple LTFB trainers
 - Cleanup of Hydrogen interface to match Hydrogen v1.2.0
 - Added type-erased matrix class for internal refactoring
 - Make CUB always log performance critical events

I/O & data readers:
 - Python data reader that interacts with an embedded Python session.
 - Optimized data store to provide preload option
 - Extended data store to operate with Cosmoflow-numpy data reader

Build system:
 - Added documentation for how users can use Spack to install LBANN
   either directly or via environments.
 - Conduit is a required dependency.
 - Provided Spack environment for installing LBANN as a user
 - Improved documentation on lbann.readthedocs.io
 - CMake installs a module file in the installation directory that
   sets up PATH and PYTHONPATH variables appropriately

Bug fixes:
 - Models can now be copied or setup multiple times.
 - Fixed incorrect weight initialization with multiple trainers.
 - Updated I/O random number generators to be C++ thread safe (rather than OpenMP)
 - Added an I/O random number generator for preprocessing that is independent
   of the data sequence RNG.
 - Fixed initialization order of RNGs and multiple models / trainers.
 - General fixes for I/O and LTFB interaction.

Retired features:
 - "Zero" layer (hack for early GAN implementation).
 - Removed data reader specific implementations of data store (in favor of Conduit-based
   data store)

Author: bvanessen

.readthedocs.yml

@@ -0,0 +1,7 @@
+# .readthedocs.yml
+
+build:
+  image: latest
+
+python:
+  version: 3.7

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.8)
+cmake_minimum_required(VERSION 3.12)
 
 project(LBANN CXX)
 
@@ -48,8 +48,8 @@ endif ()
 #
 
 set(LBANN_VERSION_MAJOR 0)
-set(LBANN_VERSION_MINOR 98)
-set(LBANN_VERSION_PATCH 1)
+set(LBANN_VERSION_MINOR 99)
+set(LBANN_VERSION_PATCH 0)
 
 set(LBANN_VERSION "${LBANN_VERSION_MAJOR}.${LBANN_VERSION_MINOR}.${LBANN_VERSION_PATCH}")
 
@@ -100,7 +100,7 @@ option(LBANN_WITH_ALUMINUM "Enable Aluminum all-reduce library" OFF)
 
 option(LBANN_WITH_CNPY "Include cnpy" ON)
 
-option(LBANN_WITH_CONDUIT "Enable Conduit library" OFF)
+option(LBANN_WITH_CONDUIT "Enable Conduit library" ON)
 
 option(LBANN_WITH_CUDNN "Include Nvidia cuDNN" ON)
 
@@ -110,12 +110,17 @@ option(LBANN_WITH_HWLOC
 option(LBANN_WITH_NVPROF
   "Enable NVTX-based instrumentation for nvprof" OFF)
 
-option(LBANN_WITH_TBINF "Include Tensorboard interface" ON)
+option(LBANN_WITH_PYTHON
+  "Install Python frontend and enable embedded Python" ON)
 
+option(LBANN_WITH_TBINF "Include Tensorboard interface" ON)
 
 option(LBANN_WITH_VTUNE
   "Link the Intel VTune profiling library" OFF)
 
+option(LBANN_WITH_UNIT_TESTING
+  "Enable the unit testing framework (requires Catch2)" OFF)
+
 # Enable parallel random matrix generation, if possible
 option(LBANN_DETERMINISTIC
   "Use deterministic algorithms as much as possible." OFF)
@@ -167,12 +172,12 @@ set(LBANN_HAS_CEREAL ${CEREAL_FOUND})
 # The imported target is just called "cereal". Super.
 
 # Setup the linear algebra library
-find_package(Hydrogen 1.1.0 NO_MODULE QUIET
+find_package(Hydrogen 1.2.0 NO_MODULE QUIET
   HINTS ${Hydrogen_DIR} ${HYDROGEN_DIR} $ENV{Hydrogen_DIR} $ENV{HYDROGEN_DIR}
   PATH_SUFFIXES lib/cmake/hydrogen
   NO_DEFAULT_PATH)
 if (NOT Hydrogen_FOUND)
-  find_package(Hydrogen 1.1.0 NO_MODULE QUIET REQUIRED)
+  find_package(Hydrogen 1.2.0 NO_MODULE QUIET REQUIRED)
 endif ()
 message(STATUS "Found Hydrogen: ${Hydrogen_DIR}")
 set(LBANN_HAS_HYDROGEN ${Hydrogen_FOUND})
@@ -209,13 +214,13 @@ endif ()
 if (LBANN_WITH_ALUMINUM)
   # Aluminum may have already been found by Hydrogen
   if (NOT Aluminum_FOUND)
-    find_package(Aluminum NO_MODULE QUIET
+    find_package(Aluminum 0.2.0 NO_MODULE QUIET
       HINTS ${Aluminum_DIR} ${ALUMINUM_DIR} ${AL_DIR}
       $ENV{Aluminum_DIR} $ENV{ALUMINUM_DIR} $ENV{AL_DIR}
       PATH_SUFFIXES lib64/cmake/aluminum lib/cmake/aluminum
       NO_DEFAULT_PATH)
     if (NOT Aluminum_FOUND)
-      find_package(Aluminum NO_MODULE QUIET)
+      find_package(Aluminum 0.2.0 NO_MODULE QUIET)
     endif ()
   endif ()
   set(LBANN_HAS_ALUMINUM ${Aluminum_FOUND})
@@ -287,6 +292,29 @@ if (LBANN_WITH_TBINF)
   add_subdirectory(external/TBinf)
 endif ()
 
+# Find Python
+# Note: This uses the Python module in cmake/modules, not the module
+# that comes included with CMake. See the file for a discussion of the
+# differences.
+if (LBANN_WITH_PYTHON)
+  find_package(Python REQUIRED)
+  set(LBANN_HAS_PYTHON "${Python_FOUND}")
+  if (NOT Python_VERSION_MAJOR EQUAL 3)
+    set(LBANN_HAS_PYTHON FALSE)
+    message(FATAL_ERROR "Python 2 is not supported.")
+  endif ()
+
+  # Setup the installation stuff
+  set(PYTHON_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}"
+    CACHE PATH "The prefix for the python installation")
+
+  set(CMAKE_INSTALL_PYTHONDIR
+    "lib/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages"
+    CACHE PATH
+    "Relative path from PYTHON_INSTALL_PREFIX to the python package install")
+
+endif (LBANN_WITH_PYTHON)
+
 if (LBANN_WITH_VTUNE)
   find_package(VTune MODULE)
 
@@ -305,7 +333,7 @@ if (LBANN_WITH_VTUNE)
   endif (VTune_FOUND)
 endif (LBANN_WITH_VTUNE)
 
-if (LBANN_WITH_NVPROF)
+if (LBANN_WITH_CUDA AND LBANN_WITH_NVPROF)
   set(LBANN_NVPROF TRUE)
 endif ()
 
@@ -336,15 +364,15 @@ if (LBANN_WITH_CONDUIT)
     message(STATUS "Found HDF5: ${HDF5_DIR}")
   endif ()
 
-  find_package(CONDUIT CONFIG QUIET
-    HINTS ${CONDUIT_DIR} $ENV{CONDUIT_DIR}
+  find_package(Conduit CONFIG QUIET
+    HINTS ${Conduit_DIR} $ENV{Conduit_DIR} ${CONDUIT_DIR} $ENV{CONDUIT_DIR}
     PATH_SUFFIXES lib64/cmake lib/cmake
     NO_DEFAULT_PATH)
-  if (NOT CONDUIT_FOUND)
-    find_package(CONDUIT CONFIG QUIET REQUIRED
+  if (NOT Conduit_FOUND)
+    find_package(Conduit CONFIG QUIET REQUIRED
       PATH_SUFFIXES lib64/cmake lib/cmake)
   endif ()
-  message(STATUS "Found CONDUIT: ${CONDUIT_DIR}")
+  message(STATUS "Found CONDUIT: ${Conduit_DIR}")
 
   # Ugh. I don't like that this requires intimate knowledge of
   # specific targets that CONDUIT exports. It should support
@@ -402,9 +430,28 @@ if (LBANN_WITH_CONDUIT)
     "${_conduit_interface_link_libs}")
 
   set(CONDUIT_LIBRARIES conduit::conduit)
-  set(LBANN_HAS_CONDUIT ${CONDUIT_FOUND})
+  set(LBANN_HAS_CONDUIT ${Conduit_FOUND})
 endif (LBANN_WITH_CONDUIT)
 
+if (LBANN_WITH_UNIT_TESTING)
+  find_package(Catch2 2.0.0 CONFIG QUIET
+    HINTS ${CATCH2_DIR} $ENV{CATCH2_DIR} ${CATCH_DIR} $ENV{CATCH_DIR}
+    PATH_SUFFIXES lib64/cmake/Catch2 lib/cmake/Catch2
+    NO_DEFAULT_PATH)
+  if (NOT Catch2_FOUND)
+    find_package(Catch2 2.0.0 CONFIG QUIET REQUIRED)
+  endif ()
+  message(STATUS "Found Catch2: ${Catch2_DIR}")
+
+  # Now that Catch2 has been found, start adding the unit tests
+  include(CTest)
+  include(Catch)
+  add_subdirectory(src/utils/unit_test)
+
+  # Add this one last
+  add_subdirectory(unit_test)
+endif (LBANN_WITH_UNIT_TESTING)
+
 # Handle the documentation
 add_subdirectory(docs)
 
@@ -430,6 +477,10 @@ target_include_directories(lbann PUBLIC
   $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/include>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}>)
 
+if (LBANN_HAS_PYTHON)
+  target_include_directories(lbann PUBLIC ${Python_INCLUDE_DIRS})
+endif ()
+
 # Use the IMPORTED targets when possible.
 target_link_libraries(lbann PUBLIC LbannProto)
 target_link_libraries(lbann PUBLIC cereal)
@@ -460,6 +511,10 @@ if (LBANN_HAS_VTUNE)
   target_link_libraries(lbann PUBLIC ${VTUNE_STATIC_LIB})
 endif ()
 
+if (LBANN_HAS_PYTHON)
+  target_link_libraries(lbann PUBLIC ${Python_LIBRARIES})
+endif ()
+
 if (TARGET LBANN_CXX_FLAGS_werror)
   target_link_libraries(lbann PUBLIC LBANN_CXX_FLAGS_werror)
 endif ()
@@ -516,8 +571,8 @@ export(EXPORT LBANNTargets NAMESPACE LBANN:: FILE LBANNTargets.cmake)
 
 # Write the configure file for the install tree
 set(INCLUDE_INSTALL_DIRS include)
-set(LIB_INSTALL_DIR lib)
-set(CMAKE_INSTALL_DIR lib/cmake/lbann)
+set(LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR})
+set(CMAKE_INSTALL_DIR ${LIB_INSTALL_DIR}/cmake/lbann)
 set(EXTRA_CMAKE_MODULE_DIR)
 configure_package_config_file(cmake/configure_files/LBANNConfig.cmake.in
   "${CMAKE_BINARY_DIR}/LBANNConfig.cmake.install"
@@ -559,6 +614,64 @@ install(
   FILES "${PROJECT_BINARY_DIR}/lbann_config.hpp"
   DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
 
+# Install Python frontend
+# Note (tym): Python best practices are to put setup.py at the package
+# root and setuptools only accepts relative paths. However, we need to
+# insert a config file containing install-specific file paths and make
+# sure setup.py can pick it up. I see three approaches for the build
+# process:
+#   1) Inject the config file into a known location in the source
+#      directory so that setup.py can pick it up.
+#   2) Copy the Python source tree into the build directory and insert
+#      setup.py and the config file.
+#   3) Create setup.py and the config file in the build directory and
+#      pass the source directory as a relative path.
+# We go for option 3 since it's simple and lightweight, but it runs
+# counter to the intent of setuptools. If we learn about any nicer
+# approaches, we should use them.
+if (LBANN_HAS_PYTHON)
+
+  # Construct config file
+  # NOTE (trb): python_config.ini is installed by setup.py
+  set(_PYTHON_CONFIG_INI ${CMAKE_BINARY_DIR}/python_config.ini)
+  set(_LBANN_PB2_PY ${PYTHON_INSTALL_PREFIX}/${CMAKE_INSTALL_PYTHONDIR}/lbann_pb2.py)
+  set(_LBANN_EXE ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}/lbann)
+  configure_file(
+    "${CMAKE_SOURCE_DIR}/cmake/configure_files/python_config.ini.in"
+    "${_PYTHON_CONFIG_INI}"
+    @ONLY)
+
+  # Construct setup.py
+  set(_SETUP_PY ${CMAKE_BINARY_DIR}/setup.py)
+  set(_LBANN_PYTHON_DIR "${CMAKE_SOURCE_DIR}/python")
+  configure_file(
+    "${CMAKE_SOURCE_DIR}/cmake/configure_files/setup.py.in"
+    "${_SETUP_PY}"
+    @ONLY)
+
+  # Install Python package with setuptools
+  set(_PY_INSTALL_DIR "${PYTHON_INSTALL_PREFIX}/${CMAKE_INSTALL_PYTHONDIR}")
+  set(_SETUP_PY_ARGS
+    "${_SETUP_PY_ARGS} --root ${_PY_INSTALL_DIR} --install-lib . --install-data .")
+  install(CODE
+    "execute_process(COMMAND ${Python_EXECUTABLE} ${_SETUP_PY} install ${_SETUP_PY_ARGS})")
+
+  set(_PY_INSTALL_MSG
+    "
+\n**********************************************************************
+
+A Python package has been installed to ${_PY_INSTALL_DIR}. To use
+this package, be sure to add this directory to your PYTHONPATH, e.g.:
+
+  export PYTHONPATH=${_PY_INSTALL_DIR}:\\$\{PYTHONPATH\}
+
+**********************************************************************\n
+")
+  install(CODE
+    "execute_process(COMMAND ${CMAKE_COMMAND} -E echo \"${_PY_INSTALL_MSG}\")")
+
+endif (LBANN_HAS_PYTHON)
+
 # Install contributor list, license, readme
 install(
   FILES "${PROJECT_SOURCE_DIR}/CONTRIBUTORS"
@@ -583,8 +696,10 @@ macro(append_str_tf STRING_VAR)
     math(EXPR _num_spaces "${_max_length} - ${_var_length}")
     lbann_get_space_string(_spaces ${_num_spaces})
     if (${var})
+      set(${var} "TRUE")
       string(APPEND ${STRING_VAR} "  ${var}:" "${_spaces}" "TRUE\n")
     else ()
+      set(${var} "FALSE")
       string(APPEND ${STRING_VAR} "  ${var}:" "${_spaces}" "FALSE\n")
     endif ()
   endforeach()
@@ -632,10 +747,33 @@ append_str_tf(_str
   LBANN_HAS_DOXYGEN
   LBANN_HAS_LBANN_PROTO
   LBANN_HAS_ALUMINUM
-  LBANN_HAS_CONDUIT)
+  LBANN_HAS_CONDUIT
+  LBANN_HAS_PYTHON)
 string(APPEND _str
   "\n== End LBANN Configuration Summary ==\n")
 
 # Output to stdout
 execute_process(COMMAND ${CMAKE_COMMAND} -E echo "${_str}")
 set(_str)
+
+#
+# Write a basic modulefile
+#
+set(LBANN_MODULEFILE_NAME "lbann-${LBANN_VERSION}.lua"
+  CACHE STRING
+  "The name of the LBANN modulefile to install. Must end in .lua.")
+
+if (NOT (LBANN_MODULEFILE_NAME MATCHES ".+\.lua"))
+  message(WARNING
+    "LBANN_MODULEFILE_NAME must have extension \".lua\". Appending.")
+  set(LBANN_MODULEFILE_NAME "${LBANN_MODULEFILE_NAME}.lua"
+    CACHE STRING "" FORCE)
+endif ()
+
+configure_file(
+  "${CMAKE_SOURCE_DIR}/cmake/configure_files/lbann_module.lua.in"
+  "${CMAKE_BINARY_DIR}/lbann_module.lua.install"
+  @ONLY)
+install(FILES "${CMAKE_BINARY_DIR}/lbann_module.lua.install"
+  RENAME "${LBANN_MODULEFILE_NAME}"
+  DESTINATION "${CMAKE_INSTALL_SYSCONFDIR}/modulefiles")

LICENSE

@@ -1,5 +1,5 @@
-Copyright (c) 2014-2016, Lawrence Livermore National Security, LLC. 
-Produced at the Lawrence Livermore National Laboratory. 
+Copyright (c) 2014-2019, Lawrence Livermore National Security, LLC.
+Produced at the Lawrence Livermore National Laboratory.
 Written by the LBANN Research Team (B. Van Essen, et al.) listed in
 the CONTRIBUTORS file. <lbann-dev@llnl.gov>
 
@@ -8,7 +8,7 @@ All rights reserved.
 
 This file is part of LBANN: Livermore Big Artificial Neural Network
 Toolkit. For details, see http://software.llnl.gov/LBANN or
-https://github.com/LLNL/LBANN. 
+https://github.com/LLNL/LBANN.
 
 Licensed under the Apache License, Version 2.0 (the "Licensee"); you
 may not use this file except in compliance with the License.  You may
@@ -21,4 +21,3 @@ 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.
-

README.md

@@ -21,9 +21,17 @@ methods.
 
 
 ## Building LBANN
-A few options for building LBANN are documented
-[here](docs/BuildingLBANN.md#top).
+The preferred method for LBANN users to install LBANN is to use
+[Spack](https://github.com/llnl/spack). After some system
+configuration, this should be as straightforward as
 
+```bash
+spack install lbann
+```
+
+More detailed instructions for building and installing LBANN are
+available at the [main LBANN
+documentation](https://lbann.readthedocs.io/en/latest/index.html).
 
 ## Running LBANN
 The basic template for running LBANN is
@@ -42,8 +50,12 @@ optimized for the case in which one assigns one GPU per MPI
 the MPI launcher.
 
 More details about running LBANN are documented
-[here](docs/RunningLBANN.md#top).
+[here](https://lbann.readthedocs.io/en/latest/running_lbann.html).
+
+## Publications
 
+A list of publications, presentations and posters are shown
+[here](https://lbann.readthedocs.io/en/latest/publications.html).
 
 ## Reporting issues
 Issues, questions, and bugs can be raised on the [Github issue