Merge branch 'origin/release-2021' into merge-2021-into-master

Resolved Conflicts:
	src/gromacs/gmxpreprocess/readir.cpp
        admin/gitlab/archive.gitlab-ci-yml

diff --cc admin/gitlab-ci/archive.gitlab-ci.yml
Simple merge

diff --cc admin/gitlab-ci/gromacs.gitlab-ci.yml
index a7ec874ed8a2cc6808fd309c80573f39377cfb59,a4deaa01e7824371a03246d4d203951992b9756a..8ddef2991554c48400995b30a1dd2fe3b725577e
--- 1/admin/gitlab-ci/gromacs.gitlab-ci.yml
--- 2/admin/gitlab-ci/gromacs.gitlab-ci.yml
+++ b/admin/gitlab-ci/gromacs.gitlab-ci.yml
@@@ -222,12 -226,27 +226,27 @@@ gromacs:gcc-7:configure
      - .use-gcc:base
      - .use-opencl
      - .rules:merge-and-post-merge-acceptance
-   image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
+   image: gromacs/ci-ubuntu-18.04-gcc-7
    variables:
+     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
      CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
 -    CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
 +    CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON -DGMX_INSTALL_LEGACY_API=ON"
      COMPILER_MAJOR_VERSION: 7
  
+ gromacs:clang-8-cuda-10.0:configure:
+   extends:
+     - .gromacs:base:configure
+     - .use-clang:base
+     - .use-cuda
+     - .rules:merge-and-post-merge-acceptance
+   image: gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0
+   variables:
+     CMAKE: /usr/local/cmake-3.13.0/bin/cmake
+     CMAKE_SIMD_OPTIONS: "-DGMX_USE_SIMD_KERNELS=off"
+     CMAKE_EXTRA_OPTIONS: "-DGMX_CLANG_CUDA=ON"
+     CMAKE_BUILD_TYPE_OPTIONS: "-DCMAKE_BUILD_TYPE=RelWithDebInfo"
+     COMPILER_MAJOR_VERSION: 8
+ 
  gromacs:gcc-8-cuda-11.0:configure:
    extends:
      - .gromacs:base:configure

diff --cc admin/gitlab-ci/lint.gitlab-ci.yml
Simple merge

diff --cc admin/gitlab-ci/python-gmxapi.gitlab-ci.yml
Simple merge

diff --cc admin/gitlab-ci/sample_restraint.gitlab-ci.yml
Simple merge

diff --cc api/legacy/include/gromacs/fileio/filetypes.h
Simple merge

diff --cc api/nblib/CMakeLists.txt
Simple merge

diff --cc src/gromacs/CMakeLists.txt
Simple merge

diff --cc src/gromacs/fileio/filetypes.cpp
Simple merge

diff --cc src/programs/CMakeLists.txt
index 29da4ea35f3ae885aa435570e9f38cc895632c5a,d41ca70478fda8a79dd18a52e64f920a321137d6..5797b1de820b9d43dcc56fe9c1bd9d7208793d8c
--- 1/src/programs/CMakeLists.txt
--- 2/src/programs/CMakeLists.txt
+++ b/src/programs/CMakeLists.txt
@@@ -75,10 -74,9 +75,11 @@@ else(
      gmx_target_compile_options(view_objlib)
      target_compile_definitions(view_objlib PRIVATE HAVE_CONFIG_H)
      target_include_directories(view_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
 +    target_link_libraries(view_objlib PRIVATE legacy_api)
      add_library(gmx_objlib OBJECT ${GMX_MAIN_SOURCES})
 +    target_link_libraries(gmx_objlib PRIVATE legacy_api)
      target_include_directories(gmx_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+     target_include_directories(gmx_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
      add_executable(gmx
          $<TARGET_OBJECTS:gmx_objlib>
          $<TARGET_OBJECTS:mdrun_objlib>

diff --cc src/testutils/CMakeLists.txt
Simple merge