Merge branch 'housekeeping_2025-11-14' into 'development'

housekeeping 2025-11-14

Closes #562, #533, #564, #421, #576, and #566

See merge request damask/DAMASK!1154

Author: eisenlohr

.gitlab-ci.yml

@@ -204,14 +204,12 @@ pytest_previous:
 doctest:
   extends: [.processing, .python]
   script:
-    - export DAMASK_ROOT=$(pwd)
-    - PYTHONPATH=${DAMASK_ROOT}/python:${PYTHONPATH}
     - cd python
-    - cp tests/resources/doctest/* .
+    - cp tests/resources/doctest/*.* .
     # pretend neper to be present such that call to /bin/neper does not fail
     - echo '#!/usr/bin/env bash' > /bin/neper
     - chmod +x /bin/neper
-    - python3 -m pytest -v --doctest-modules -k 'not result' damask
+    - PYTHONPATH=${PWD}:${PYTHONPATH} NO_COLOR=1 python3 -m pytest -v --doctest-modules damask
 
 
 ####################################################################################################
@@ -225,7 +223,7 @@ open-source:
     - long_running
   needs: []
   before_script:
-    - cmake -DGRID=ON -DMESH=ON -B build && cmake --build build --parallel 4 --target install
+    - cmake -DGRID=ON -DMESH=ON -B build -G Ninja && cmake --build build --parallel 4 --target install
     - source env/DAMASK.sh
   script:
     - cd PRIVATE/testing
@@ -247,7 +245,7 @@ c++-linter:
   script:
     - source env/DAMASK.sh
     - ./bin/DAMASK_test
-    - find . -name '*.gcda' -not -path "**/test/*" -exec gcov {} \;
+    - find . -name '*.gcda' -not -path "**/test/*" -exec gcov {} \; | grep src/.\*.f90 -A+1 || true
     - ctest --test-dir build/src/test/cpp --output-on-failure -j"$(nproc)" --no-tests=ignore
   parallel:
     matrix:

CITATION.cff

@@ -15,22 +15,22 @@ authors:
     orcid: 'https://orcid.org/0000-0002-3738-7363'
   - given-names: Philip
     family-names: Eisenlohr
-    orcid: 'https://orcid.org/0000-0002-8220-5995'
     email: [email protected]
     affiliation: Michigan State University
+    orcid: 'https://orcid.org/0000-0002-8220-5995'
   - given-names: Sharan
     family-names: Roongta
+    email: [email protected]
     affiliation: Max-Planck-Institut für Nachhaltige Materialien GmbH
-    email: [email protected]
     orcid: 'https://orcid.org/0000-0001-5754-068X'
   - given-names: Daniel
     family-names: Otto de Mentock
-    email: d.mentock@mpie.de
+    email: d.mentock@mpi-susmat.de
     affiliation: Max-Planck-Institut für Nachhaltige Materialien GmbH
     orcid: 'https://orcid.org/0009-0005-8363-6112'
   - given-names: Yi
     family-names: Hu
-    email: y.hu@mpie.de
+    email: y.hu@mpi-susmat.de
     affiliation: Max-Planck-Institut für Nachhaltige Materialien GmbH
     orcid: 'https://orcid.org/0000-0003-2775-6169'
   - given-names: Nikhil
@@ -40,12 +40,12 @@ authors:
     orcid: 'https://orcid.org/0000-0003-0843-3903'
   - given-names: Pratheek
     family-names: Shanthraj
+    email: [email protected]
     affiliation: United Kingdom Atomic Energy Authority
     orcid: 'https://orcid.org/0000-0002-6324-0306'
-    email: [email protected]
   - given-names: Franz
     family-names: Roters
-    email: f.roters@mpie.de
+    email: f.roters@mpi-susmat.de
     affiliation: Max-Planck-Institut für Nachhaltige Materialien GmbH
     orcid: 'https://orcid.org/0000-0002-9098-9566'
 identifiers:

CMakeLists.txt

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: AGPL-3.0-or-later
 cmake_minimum_required(VERSION 3.18.0)
 set(CMAKE_CXX_STANDARD 23)
 set(CMAKE_C_STANDARD 17)

PRIVATE

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: AGPL-3.0-or-later
 ###################################################################################################
 # GNU Compiler
 ###################################################################################################
@@ -18,9 +19,9 @@ elseif(OPTIMIZATION STREQUAL "AGGRESSIVE")
 endif()
 
 if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 14)
-  set(STANDARD_CHECK "-std=f2018 -pedantic-errors" )
+  set(STANDARD_CHECK "-std=f2018 -pedantic-errors")
 else()
-  set(STANDARD_CHECK "-std=f2023 -pedantic-errors" )
+  set(STANDARD_CHECK "-std=f2023 -pedantic-errors")
 endif()
 
 if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 12)

cmake/Compiler-GNU.cmake

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: AGPL-3.0-or-later
 ###################################################################################################
 # IntelLLVM Compiler
 ###################################################################################################
@@ -15,14 +16,12 @@ elseif(OPTIMIZATION STREQUAL "AGGRESSIVE")
   set(OPTIMIZATION_FLAGS "-O3 -fp-model strict -xHost -align array64byte") # -ipo/-flto give linker error
 endif()
 
-# set(STANDARD_CHECK "-stand f23 -standard-semantics -assume nostd_mod_proc_name")
-# -assume std_mod_proc_name (included in -standard-semantics) causes problems if other modules
-#  (PETSc, HDF5) are not compiled with this option
-#  https://community.intel.com/t5/Intel-Fortran-Compiler/building-and-linking-against-a-Fortran-dynamic-library-on-Linux/td-p/1178514
-# -standard-semantics causes a bizzare increase in runtime on matesting (Intel(R) Xeon(R) CPU X5670)
-#  so use only -fpscomp logicals.
-#  https://fortran-lang.discourse.group/t/performance-drop-when-using-intel-oneapi-with-standard-sematics-option/9944/5
-set(STANDARD_CHECK "-stand f23 -fpscomp logicals")
+set(STANDARD_CHECK "-stand f23 -fpscomp logicals -assume noold_unit_star")
+# -standard-semantics causes a bizzare increase in runtime on matesting (Intel(R) Xeon(R) CPU
+# X5670), o only enforce a logical representation that is compatible with C and enable to close the
+# output unit.
+# https://fortran-lang.discourse.group/t/performance-drop-when-using-intel-oneapi-with-standard-sematics-option/9944/5
+# https://community.intel.com/t5/Intel-Fortran-Compiler/Redirecting-File-STDOUT-and-STDERR-in-Intel-Fortran-Without/m-p/1550590
 
 # Link against shared Intel libraries instead of static ones:
 set(LINKER_FLAGS   "${LINKER_FLAGS} -shared-intel")

cmake/Compiler-IntelLLVM.cmake

@@ -1,10 +1,28 @@
+# SPDX-License-Identifier: AGPL-3.0-or-later
 ###################################################################################################
 # LLVM Compiler
 ###################################################################################################
-set(Fortran_COMPILER_VERSION_MIN 20)
+set(Fortran_COMPILER_VERSION_MIN 22)
 
 if(OPENMP)
   set(OPENMP_FLAGS "-fopenmp")
 endif()
 
-set(STANDARD_CHECK "-std=f2018 -pedantic" )
+if(OPTIMIZATION STREQUAL "DEBUG")
+  set(OPTIMIZATION_FLAGS "-O0")
+elseif(OPTIMIZATION STREQUAL "OFF")
+  set(OPTIMIZATION_FLAGS "-O0")
+elseif(OPTIMIZATION STREQUAL "DEFENSIVE")
+  set(OPTIMIZATION_FLAGS "-O2 -mtune=native")
+elseif(OPTIMIZATION STREQUAL "AGGRESSIVE")
+  set(OPTIMIZATION_FLAGS "-O3 -march=native -funroll-loops -ftree-vectorize -flto")
+endif()
+
+set(STANDARD_CHECK "-std=f2018 -pedantic")
+
+#------------------------------------------------------------------------------------------------
+# Fine tuning compilation options
+#------------------------------------------------------------------------------------------------
+
+# position independent code:
+set(COMPILE_FLAGS "${COMPILE_FLAGS} -fPIE")

cmake/Compiler-LLVMFlang.cmake

@@ -1,4 +1,5 @@
-# sets up an environment for DAMASK on bash
+# SPDX-License-Identifier: AGPL-3.0-or-later
+# set up an environment for DAMASK on bash
 # usage:  source DAMASK.sh
 
 function canonicalPath {

env/DAMASK.sh

@@ -1,4 +1,5 @@
-# sets up an environment for DAMASK on zsh
+# SPDX-License-Identifier: AGPL-3.0-or-later
+# set up an environment for DAMASK on zsh
 # usage:  source DAMASK.zsh
 
 function canonicalPath {

env/DAMASK.zsh

@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+# SPDX-License-Identifier: AGPL-3.0-or-later
 
 import os
 import sys