Merge branch 'release/1.0.0-rc.1'

cp2k · Nov 14, 2018 · 3b5a263 · 3b5a263
2 parents fbfce30 + ab16dd0
commit 3b5a263
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diff --git a/.flake8 b/.flake8
@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 120
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,4 @@
+.gitattributes export-ignore
+.gitignore export-ignore
+.gitmodules export-ignore
+.travis.yml export-ignore
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is, including the stacktrace (if there was one).
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Built with the command: '...'
+2. Run like this: '....'
+3. On the architecture/host/platform: '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment:**
+ - Operating system & version
+ - Compiler vendor & version
+ - Build environment (make or cmake)
+ - Configuration of DBCSR (either the cmake flags or the `Makefile.inc`)
+ - MPI implementation and version
+ - If CUDA is being used: CUDA version and GPU architecture
+ - BLAS/LAPACK implementation and version
+ - If applicable: Runtime information (how many nodes, type of nodes, ...)
diff --git a/.gitignore b/.gitignore
@@ -1,17 +1,16 @@
 # ignore project specific locations & files
-lib/
-obj/
-bin/
-doc/
-src/acc/libsmm_acc/libcusmm/parameters.h
-src/acc/libsmm_acc/libcusmm/cusmm_kernels.h
-src/acc/libsmm_acc/libcusmm/libcusmm_parameters_utils.so
-install/
-examples/*.x
+/lib/
+/obj/
+/bin/
+/doc/
+/src/acc/libsmm_acc/libcusmm/parameters.h
+/src/acc/libsmm_acc/libcusmm/cusmm_kernels.h
+/src/acc/libsmm_acc/libcusmm/libcusmm_parameters_utils.so
+/install/
 *.callgraph
 
 # exclude personal makefile
-Makefile.inc.*
+/Makefile.inc.*
 
 # The following covers some more,
 # Created by https://www.gitignore.io/api/vim,emacs,python,fortran

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,11 @@
+exclude: '^tools/(prettify/fprettify|build_utils/fypp)'
+fail_fast: false
+repos:
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.24.0
+  hooks:
+  - id: yapf
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+  - id: flake8
diff --git a/.style.yapf b/.style.yapf
@@ -0,0 +1,3 @@
+[style]
+based_on_style = pep8
+column_limit = 120
diff --git a/.travis.yml b/.travis.yml
@@ -3,65 +3,126 @@ language: c
 addons:
   apt:
     sources:
-      - ubuntu-toolchain-r-test
+    - ubuntu-toolchain-r-test
     packages:
-      - gfortran
-      - libblas-dev
-      - liblapack-dev
-      - libopenmpi-dev
-      - openmpi-bin
+    - gfortran
+    - libblas-dev
+    - liblapack-dev
+    - libopenmpi-dev
+    - openmpi-bin
+  homebrew:
+    packages:
+    - cmake
+
+cache:
+  pip: true
+  directories:
+    - $HOME/deps
+
+env:
+  global:
+  - LIBXSMM_VERSION=1.10
+  - CMAKE_VERSION=3.10.3
 
 install:
   # Update cmake to the minimal required version (shamelessly copied from the boost travis config):
   - DEPS_DIR="${HOME}/deps"
   - mkdir -p ${DEPS_DIR} && cd ${DEPS_DIR}
   - |
-    if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
-      CMAKE_URL="https://cmake.org/files/v3.10/cmake-3.10.0-Linux-x86_64.tar.gz"
-      mkdir cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C cmake
-      export PATH=${DEPS_DIR}/cmake/bin:${PATH}
-    else
-      brew install cmake || brew upgrade cmake
+    if [[ "${TRAVIS_OS_NAME}" == "linux" ]] ; then
+      CMAKE_URL="https://cmake.org/files/v${CMAKE_VERSION%.*}/cmake-${CMAKE_VERSION}-Linux-x86_64.tar.gz"
+      CMAKE_DIR="cmake-${CMAKE_VERSION}"
+      if [[ ! -e "${CMAKE_DIR}" ]] ; then
+        rm -rf cmake-*
+        mkdir "${CMAKE_DIR}"
+        travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C "${CMAKE_DIR}"
+      fi
+      export PATH=${DEPS_DIR}/${CMAKE_DIR}/bin:${PATH}
     fi
   - cmake --version
+  - |
+    LIBXSMM_URL="https://github.com/hfp/libxsmm/archive/${LIBXSMM_VERSION}.tar.gz"
+    LIBXSMM_DIR="libxsmm-${LIBXSMM_VERSION}"
+    if [[ ! -e "${LIBXSMM_DIR}" ]] ; then
+      rm -rf libxsmm-*
+      mkdir "${LIBXSMM_DIR}"
+      travis_retry wget --no-check-certificate --quiet -O - ${LIBXSMM_URL} | tar --strip-components=1 -xz -C "${LIBXSMM_DIR}"
+      make -C "${LIBXSMM_DIR}" -j
+    fi
+    export PKG_CONFIG_PATH=${DEPS_DIR}/${LIBXSMM_DIR}/lib
+  - pkg-config libxsmm --exists
 
 before_script:
   # make sure we are back into the top directory again
   - cd "${TRAVIS_BUILD_DIR}"
+  - export PATH=$HOME/.local/bin:$PATH
+  - pip install --user git-archive-all pre-commit
 
 jobs:
   include:
-    - stage: build
-      name: "Build and test MPI+OpenMP version with make"
-      script:
-        - make -j FC="mpif90" LD="mpif90" OPTFLAGS="-fprofile-arcs -ftest-coverage -O0 -D__MPI_VERSION=2" all
-        - make test
-        - bash <(curl -s https://codecov.io/bash)
-    - # run this in parallel with the other builds
-      name: "Build and test MPI+OpenMP version with cmake"
-      script:
-        - mkdir -p build
-        - cd build
-        # C++ example fails with this ancient version of MPI,
-        # we see all system CPUs, but can use only 1, causing nproc auto-detection to fail
-        - cmake -DCMAKE_BUILD_TYPE=Coverage -DWITH_EXAMPLES=OFF -DTEST_MPI_RANKS=1 ..
-        - make -j
-        - make CTEST_OUTPUT_ON_FAILURE=1 test
-    - # run this in parallel with the other builds
-      name: "Build and test OpenMP version with cmake"
-      script:
-        - mkdir -p build
-        - cd build
-        # all examples need MPI atm
-        - cmake -DCMAKE_BUILD_TYPE=Coverage -DUSE_MPI=OFF -DWITH_EXAMPLES=OFF ..
-        - make -j
-        - make CTEST_OUTPUT_ON_FAILURE=1 test
-    - # run this in parallel with the other builds
-      name: "Build and test MPI version with cmake"
-      script:
-        - mkdir -p build
-        - cd build
-        # all examples need MPI atm
-        - cmake -DCMAKE_BUILD_TYPE=Coverage -DUSE_OPENMP=OFF -DWITH_EXAMPLES=OFF -DTEST_MPI_RANKS=1 ..
-        - make -j
-        - make CTEST_OUTPUT_ON_FAILURE=1 test
+  - stage: build
+    name: "Build and test MPI+OpenMP version with make"
+    script:
+    - make -j FC="mpif90" LD="mpif90" OPTFLAGS="-fprofile-arcs -ftest-coverage -O0 -D__MPI_VERSION=2" all
+    - make test
+    - bash <(curl -s https://codecov.io/bash)
+  - # run this in parallel with the other builds
+    name: "Build and test MPI+OpenMP version with cmake"
+    script:
+    - mkdir -p build
+    - cd build
+    # C++ example fails with this ancient version of MPI,
+    # we see all system CPUs, but can use only 1, causing nproc auto-detection to fail
+    - cmake -DCMAKE_BUILD_TYPE=Coverage -DTEST_MPI_RANKS=1 ..
+    - make -j
+    - make CTEST_OUTPUT_ON_FAILURE=1 test
+  - # run this in parallel with the other builds
+    name: "Build and test OpenMP version with cmake"
+    script:
+    - mkdir -p build
+    - cd build
+    # all examples need MPI atm
+    - cmake -DCMAKE_BUILD_TYPE=Coverage -DUSE_MPI=OFF ..
+    - make -j
+    - make CTEST_OUTPUT_ON_FAILURE=1 test
+  - # run this in parallel with the other builds
+    name: "Build and test OpenMP version with cmake and libxsmm"
+    script:
+    - mkdir -p build
+    - cd build
+    # all examples need MPI atm
+    - cmake -DCMAKE_BUILD_TYPE=Coverage -DUSE_MPI=OFF -DUSE_SMM=libxsmm ..
+    - make -j
+    - make CTEST_OUTPUT_ON_FAILURE=1 test
+  - # run this in parallel with the other builds
+    name: "Build and test MPI version with cmake"
+    script:
+    - mkdir -p build
+    - cd build
+    # all examples need MPI atm
+    - cmake -DCMAKE_BUILD_TYPE=Coverage -DUSE_OPENMP=OFF -DTEST_MPI_RANKS=1 ..
+    - make -j
+    - make CTEST_OUTPUT_ON_FAILURE=1 test
+  - # run this in parallel with the other builds
+    name: "Run pre-commit hook on changed files"
+    script:
+    - set -o pipefail
+    - git diff --name-only --diff-filter=AM HEAD...$TRAVIS_BRANCH | xargs pre-commit run --files
+  - stage: release
+    name: "Build release tarball and deploy to GitHub"
+    if: tag IS present
+    script:
+      # do an in-source config for simplicity since we are not building anything here
+      - cmake .
+      - make dist
+    deploy:
+      provider: releases
+      api_key:  # encrypted token of the `dbcsr` GitHub service user
+        secure: 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
+      skip_cleanup: true
+      file_glob: true
+      file: dist/*
+      draft: true
+      # the following 2 lines work around an issue in TravisCI with draft=true:
+      tag_name: $TRAVIS_TAG
+      target_commitish: $TRAVIS_COMMIT
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -9,26 +9,68 @@ include(CMakeDependentOption)
 
 option(USE_MPI "Build with MPI support" ON)
 option(USE_OPENMP "Build with OpenMP support" ON)
-option(WITH_C_API "Build the C API library" ON)
+cmake_dependent_option(WITH_C_API "Build the C API (ISO_C_BINDINGS)" ON "USE_MPI" OFF) # the ISO_C_BINDINGS require MPI unconditionally
 cmake_dependent_option(WITH_EXAMPLES "Build the examples" ON "USE_MPI" OFF) # all examples require MPI
+
 set(TEST_MPI_RANKS "auto" CACHE STRING "Number of MPI ranks for testing")
 
+set(USE_SMM "blas" CACHE STRING "Small Matrix Multiplication implementation to use (default: blas)")
+set_property(CACHE USE_SMM PROPERTY STRINGS blas libxsmm)
+
+option(USE_CUDA "Build with CUDA support" OFF)
+cmake_dependent_option(USE_CUBLAS "Build with CUBLAS support" OFF "USE_CUDA" OFF)
+set(WITH_GPU "P100" CACHE STRING "Set the CUDA GPU architecture if CUDA is enabled (default: P100)")
+set_property(CACHE WITH_GPU PROPERTY STRINGS K20X K40 K80 P100)
+
+enable_language(Fortran)
+enable_testing() # enables the `make test` target
+
 if (WITH_C_API AND WITH_EXAMPLES)
-  set(ENABLED_LANGUAGES Fortran CXX)
-else ()
-  set(ENABLED_LANGUAGES Fortran)
+  enable_language(CXX)
+endif ()
+
+if (USE_CUDA)
+  enable_language(CXX CUDA)
+
+  set(CUDA_ARCH_NUMBER_K20X 35)
+  set(CUDA_ARCH_NUMBER_K40  35)
+  set(CUDA_ARCH_NUMBER_K80  37)
+  set(CUDA_ARCH_NUMBER_P100 60)
+  set(CUDA_ARCH_NUMBER ${CUDA_ARCH_NUMBER_${WITH_GPU}})
 endif ()
 
-enable_language(${ENABLED_LANGUAGES})
-enable_testing() # enables the `make test` target
 
 # PACKAGE DISCOVERY:
 
 find_package(BLAS REQUIRED)
 find_package(LAPACK REQUIRED)
+find_package(PkgConfig)
 
 if (USE_MPI)
-  find_package(MPI COMPONENTS ${ENABLED_LANGUAGES} REQUIRED)
+  get_property(REQUIRED_MPI_COMPONENTS GLOBAL PROPERTY ENABLED_LANGUAGES)
+  find_package(MPI COMPONENTS ${REQUIRED_MPI_COMPONENTS} REQUIRED)
+endif ()
+
+if (USE_SMM MATCHES "blas")
+  message("-- Using BLAS for Small Matrix Multiplication")
+elseif (USE_SMM MATCHES "libxsmm")
+  # rely on pkg-config since it's quiet hard to link against libxsmm properly
+  pkg_check_modules(deps REQUIRED IMPORTED_TARGET GLOBAL libxsmmf)
+  message("-- Using libxsmm for Small Matrix Multiplication")
+else()
+  message(FATAL_ERROR "Unknown SMM library specified" )
+endif ()
+
+if (USE_CUBLAS)
+  # the rest of CUDA is detected by enabling the language
+  find_library(CUBLAS cublas HINT ${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES})
+  if (NOT CUBLAS)
+    message(FATAL_ERROR "cuBLAS library not found but support requested")
+  endif ()
+endif ()
+
+if (USE_OPENMP)
+  find_package(OpenMP REQUIRED)
 endif ()
 
 # make sure that the default is a RELEASE
@@ -43,15 +85,10 @@ endif ()
 get_filename_component(Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
 
 if (Fortran_COMPILER_NAME MATCHES "gfortran.*")
-  set(CMAKE_CXX_FLAGS              "")
   set(CMAKE_CXX_FLAGS_RELEASE      "-O3 -funroll-loops")
   set(CMAKE_CXX_FLAGS_COVERAGE     "-O0 -fprofile-arcs -ftest-coverage")
   set(CMAKE_CXX_FLAGS_DEBUG        "-O0 -ggdb")
   set(CMAKE_Fortran_FLAGS          "-ffree-form -ffree-line-length-none -std=f2003")
-  if (USE_OPENMP)
-    set(CMAKE_CXX_FLAGS              "${CMAKE_CXX_FLAGS} -fopenmp")
-    set(CMAKE_Fortran_FLAGS          "${CMAKE_Fortran_FLAGS} -fopenmp")
-  endif ()
   set(CMAKE_Fortran_FLAGS_RELEASE  "-O3 -funroll-loops")
   set(CMAKE_Fortran_FLAGS_DEBUG    "-O0 -ggdb")
   set(CMAKE_Fortran_FLAGS_COVERAGE "-O0 -fprofile-arcs -ftest-coverage")
@@ -60,10 +97,6 @@ elseif (Fortran_COMPILER_NAME MATCHES "ifort.*")
   set(CMAKE_CXX_FLAGS_RELEASE      "-O3")
   set(CMAKE_CXX_FLAGS_DEBUG        "-O0 -debug")
   set(CMAKE_Fortran_FLAGS          "-free -stand f03 -fpp")
-  if (USE_OPENMP)
-    set(CMAKE_CXX_FLAGS              "${CMAKE_CXX_FLAGS} -openmp")
-    set(CMAKE_Fortran_FLAGS          "${CMAKE_Fortran_FLAGS} -openmp")
-  endif ()
   # Disable the line-length-extension warning #5268
   set(CMAKE_Fortran_FLAGS_RELEASE  "-O3 -diag-disable=5268")
   set(CMAKE_Fortran_FLAGS_DEBUG    "-O0 -debug")
@@ -76,10 +109,30 @@ else ()
   set(CMAKE_Fortran_FLAGS_DEBUG    "-O0 -g")
 endif ()
 
+file(STRINGS VERSION VERSION_INFO)
+foreach(line ${VERSION_INFO})
+  if (${line} MATCHES "^([^#].*)=[ \t]*(.*)$")
+    set(key ${CMAKE_MATCH_1})
+    set(value ${CMAKE_MATCH_2})
+    string(REGEX REPLACE "[ \t\n]+$" "" key "${key}")
+    string(REGEX REPLACE "[ \t\n]+$" "" value "${value}")
+    set(VERSION_${key} "${value}")
+    continue ()
+  endif ()
+endforeach()
 
 add_subdirectory(src)
 add_subdirectory(tests)
 
 if (WITH_EXAMPLES)
   add_subdirectory(examples)
 endif ()
+
+set(ARCHIVE_NAME "${CMAKE_PROJECT_NAME}-${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
+add_custom_target(dist
+  COMMAND ${CMAKE_COMMAND} -E echo "Building distribution: ${ARCHIVE_NAME}"
+  COMMAND ${CMAKE_COMMAND} -E make_directory "${CMAKE_BINARY_DIR}/dist"
+  COMMAND git archive-all "${CMAKE_BINARY_DIR}/dist/${ARCHIVE_NAME}.tar.gz"
+  COMMAND ${CMAKE_COMMAND} -E echo "SHA512 Digests:"
+  COMMAND ${CMAKE_COMMAND} -E sha512sum "${CMAKE_BINARY_DIR}/dist/${ARCHIVE_NAME}.tar.gz"
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})