Merge branch 'release-2.1.0-rc18'

cp2k · Dec 2, 2020 · 9243ed1 · 9243ed1
2 parents d2dfe6e + 76ac4ba
commit 9243ed1
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Showing 135 changed files with 3,213 additions and 3,398 deletions.
diff --git a/.ci/daint.cscs.ch/Jenkinsfile b/.ci/daint.cscs.ch/Jenkinsfile
@@ -38,11 +38,11 @@ pipeline {
                                 run_batch("0:30:00", "cray", "build")
                             }
                         }
-                        stage('test') {
-                            steps {
-                                run_batch("1:00:00", "cray", "test")
-                            }
-                        }
+//                        stage('test') {
+//                            steps {
+//                                run_batch("1:00:00", "cray", "test")
+//                            }
+//                        }
                     }
                 }
                 stage("GNU") {

diff --git a/.cmake-format.py b/.cmake-format.py
@@ -0,0 +1,3 @@
+# flake8: noqa
+with section("format"):
+    separate_ctrl_name_with_space = True
diff --git a/.cp2k/Makefile b/.cp2k/Makefile
@@ -59,6 +59,8 @@ SRCDIR       := $(DBCSRHOME)/src
 TESTSDIR     := $(DBCSRHOME)/tests
 INCLUDEMAKE  :=
 
+PYTHON       := /usr/bin/env python3
+
 # Default Target ============================================================
 LIBNAME      := dbcsr
 LIBRARY      := lib$(LIBNAME)
@@ -228,10 +230,10 @@ clean:
 
 # Libsmm_acc stuff ==========================================================
 $(LIBSMM_ACC_ABS_DIR)/parameters.h: $(LIBSMM_ACC_ABS_DIR)/generate_parameters.py $(wildcard $(LIBSMM_ACC_ABS_DIR)/parameters_*.txt)
-	cd $(LIBSMM_ACC_ABS_DIR); ./generate_parameters.py --gpu_version=$(GPUVER)
+	cd $(LIBSMM_ACC_ABS_DIR); $(PYTHON) generate_parameters.py --gpu_version=$(GPUVER)
 
 $(LIBSMM_ACC_ABS_DIR)/smm_acc_kernels.h: $(LIBSMM_ACC_ABS_DIR)/generate_kernels.py $(wildcard $(LIBSMM_ACC_ABS_DIR)/kernels/*.h)
-	cd $(LIBSMM_ACC_ABS_DIR); ./generate_kernels.py
+	cd $(LIBSMM_ACC_ABS_DIR); $(PYTHON) generate_kernels.py
 
 
 # automatic dependency generation ===========================================
@@ -244,10 +246,10 @@ endif
 makedep: $(ALL_SRC_FILES) $(ALL_PKG_FILES) dirs
 ifeq ($(LD_SHARED),)
 	@echo "Removing stale archives ... "
-	@$(DBCSRCP2K)/check_archives.py $(firstword $(AR)) $(SRCDIR) $(LIBDIR)
+	@$(PYTHON) $(DBCSRCP2K)/check_archives.py $(firstword $(AR)) $(SRCDIR) $(LIBDIR)
 endif
 	@echo "Resolving dependencies ... "
-	@$(DBCSRCP2K)/makedep.py $(OBJDIR)/all.dep dbcsr $(MODDEPS) $(MAKEDEPMODE) $(ARCHIVE_EXT) $(SRCDIR) $(OBJ_SRC_FILES)
+	@$(PYTHON) $(DBCSRCP2K)/makedep.py $(OBJDIR)/all.dep dbcsr $(MODDEPS) $(MAKEDEPMODE) $(ARCHIVE_EXT) $(SRCDIR) $(OBJ_SRC_FILES)
 
 # on stage 2, load the rules generated by makedep.py
 ifeq ($(INCLUDE_DEPS), true)
@@ -275,7 +277,7 @@ vpath %.cpp   $(ALL_SRC_DIRS)
 FYPPFLAGS ?= -n
 
 %.o: %.F
-	$(FYPPEXE) $(FYPPFLAGS) $< $*.F90
+	$(PYTHON) $(FYPPEXE) $(FYPPFLAGS) $< $*.F90
 	$(FC) -c $(FCFLAGS) -D__SHORT_FILE__="\"$(notdir $<)\"" -I'$(dir $<)' -I'$(SRCDIR)' $*.F90 $(FCLOGPIPE)
 
 %.mod: %.o

diff --git a/.cp2k/check_archives.py b/.cp2k/check_archives.py
@@ -1,12 +1,11 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 Check that a static archive contains only the objects specified in the PACKAGES files.
 """
 
 # author: Ole Schuett
 
-from __future__ import print_function
 
 import subprocess
 import os

diff --git a/.cp2k/makedep.py b/.cp2k/makedep.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 import re

diff --git a/.cp2k/test_makedep.py b/.cp2k/test_makedep.py
@@ -1,11 +1,9 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 Unittests for the makedep.py script
 """
 
-from __future__ import absolute_import
-
 import unittest
 import tempfile
 import shutil

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,18 @@
+# git commit hashes with whitespace/reformatting changes only
+# Make git-blame use this file by running:
+#   git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+21f91d84e3cda3eaf838a3b510077c9e01c8aeb8
+fcfa8ae3551ae0d3517db59cbc3ebaea0dccc967
+53891420300f402fd70afcbfb00e1b21024040d3
+e948f9db58989f081fa0b4e4e4236e06b5566364
+972f09eb17c021c4970ddbd08596869b43e88a33
+8e647643ad149d2b886c74db1d50376066d65483
+8ebeab6fd522ec54e89ab7c6dd14bae36efc8d67
+3169190d69019d1221b1fee92e35d2501479f403
+df7ea8fb053b17a0bb6f9c3b243652395cf9dbe7
+224479c43e58305d2da2f41eff727baca5ef72c8
+f4d6abdf94381392a496e736c8684f06664bd9e5
+e8e1fe118ce19e6e6942405baeae2f96dbd620cb
+fa1838a1e4ae03b87c3c1e4b37ba4dc2b97d75ae
+65f3f47c78c51548bb84332f239b79e6c0094d6f
diff --git a/.github/workflows/doc-generation.yml b/.github/workflows/doc-generation.yml
@@ -15,13 +15,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
-    - name: Checkout submodules
-      shell: bash
-      run: |
-        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-        git submodule sync --recursive
-        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+      with:
+        submodules: true
 
     - name: Configure
       run: |
@@ -40,7 +35,7 @@ jobs:
         touch build/doc/.nojekyll
 
     - name: Setup SSH agent 🔑
-      uses: webfactory/ssh-agent@v0.2.0
+      uses: webfactory/ssh-agent@v0.4.1
       with:
         ssh-private-key: ${{ secrets.SSH_DEPLOY_KEY }}
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,13 +13,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
-    - name: Checkout submodules
-      shell: bash
-      run: |
-        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-        git submodule sync --recursive
-        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+      with:
+        submodules: true
 
     - name: Configure
       run: |

diff --git a/.github/workflows/testing-gcc.yml b/.github/workflows/testing-gcc.yml
@@ -14,19 +14,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
-    - name: Checkout submodules
-      shell: bash
-      run: |
-        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-        git submodule sync --recursive
-        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+      with:
+        submodules: true
 
     - name: Configure
       run: |
         mkdir -p build
         cd build
         cmake -G Ninja \
+          -DCMAKE_BUILD_TYPE=Debug \
           -DUSE_MPI=OFF \
           -DUSE_OPENMP=ON \
           -DUSE_SMM=blas \

diff --git a/.github/workflows/testing-linux.yml b/.github/workflows/testing-linux.yml
@@ -7,6 +7,9 @@ on:
   pull_request:
 
 jobs:
+  ##################################################################################
+  # Run pre-commit
+  ##################################################################################
   pre-commit:
     runs-on: ubuntu-latest
     container:
@@ -17,6 +20,9 @@ jobs:
       run:
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
+  ##################################################################################
+  # Build and test on linux, no accelerator
+  ##################################################################################
   build-and-test:
     runs-on: ubuntu-latest
     container:
@@ -34,13 +40,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-
-    - name: Checkout submodules
-      shell: bash
-      run: |
-        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-        git submodule sync --recursive
-        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+      with:
+        submodules: true
 
     - name: Configure
       run: |
@@ -72,7 +73,38 @@ jobs:
       uses: codecov/codecov-action@v1
       with:
         file: build/coverage.info
-        yml: .codecov.yml
+        flags: unittests,${{ matrix.use_mpi == 'MPI=ON' && 'with-mpi' || 'without-mpi' }},${{ matrix.use_openmp == 'OPENMP=ON' && 'with-openmp' || 'without-openmp' }},${{ matrix.use_smm == 'SMM=blas' && 'with-blas' || 'with-libxsmm' }}
+        name: dbcsr-unittests-${{ matrix.use_mpi }}-${{ matrix.use_openmp }}-${{ matrix.use_smm }}-cpu-only
         fail_ci_if_error: true
 
+  ##################################################################################
+  # Build on ROCm
+  ##################################################################################
+  build-on-rocm:
+    runs-on: ubuntu-latest
+    container:
+      image: shoshijak/build-env-rocm:1.0
+
+    strategy:
+      matrix:
+        use_openmp: [OPENMP=ON, OPENMP=OFF]
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    - name: Configure
+      run: |
+        mkdir -p build
+        cd build
+        cmake -G Ninja \
+          -DCMAKE_BUILD_TYPE=Release \
+          -DUSE_${{ matrix.use_openmp }} \
+          -DUSE_HIP=ON \
+          -DWITH_GPU=Mi50 \
+          ..
+    - name: Build
+      run: cmake --build build -- --verbose
+
 #  vim: set ts=2 sw=2 tw=0 :
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,26 +9,43 @@ repos:
   hooks:
   - id: black
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.7.9
+  rev: 3.8.4
   hooks:
   - id: flake8
+    exclude: >-
+      (?x)^(
+        .cp2k/.*|
+      )$
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.5.0
+  rev: v3.2.0
   hooks:
   - id: check-ast
   - id: check-yaml
 - repo: https://github.com/pseewald/fprettify
   rev: v0.3.6
   hooks:
   - id: fprettify
+- repo: https://github.com/cheshirekow/cmake-format-precommit
+  rev: v0.6.13
+  hooks:
+  - id: cmake-format
+    exclude: >-
+      (?x)^(
+        cmake/(CheckFortranSourceRuns|CompilerConfiguration|Find(BLAS|LAPACK)|GetGitRevisionDescription).cmake|
+      )$
 - repo: local
   hooks:
   - id: check-header
     name: check file headers
     entry: ./.pre-commit/check_header.py --verbose
     language: script
     types: [text]
-    exclude: '^(tools|.cp2k)/'
+    exclude: >-
+      (?x)^(
+        tools/.*|
+        .cp2k/.*|
+        .cmake-format.py|
+      )$
   - id: check-doxygen-tags
     name: no doxygen tags present
     entry: '^\s*!>'