diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8bf675101a..9595718bc8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -114,7 +114,10 @@ option(CP2K_USE_METIS "enable metis library support" OFF)
 option(CP2K_USE_LIBXSMM "Use libxsmm for small gemms (supports x86 platforms)"
        OFF)
 option(BUILD_SHARED_LIBS "Build cp2k shared library" ON)
-
+option(
+  CP2K_USE_FFTW3_WITH_MKL
+  "MKL has its own compatible implementation of the fftw. This option when ON will use the original implementation of the fftw library"
+  OFF)
 cmake_dependent_option(CP2K_ENABLE_ELPA_OPENMP_SUPPORT
                        "Enable elpa openmp support" ON "CP2K_USE_ELPA" OFF)
 cmake_dependent_option(CP2K_ENABLE_FFTW3_OPENMP_SUPPORT
@@ -577,27 +580,35 @@ endif()
 
 # FFTW3
 
+# we set this variable to ON when we want fftw3 support (with or without MKL).
+set(CP2K_USE_FFTW3_ OFF)
 if(CP2K_USE_FFTW3)
-  find_package(Fftw REQUIRED)
-  if(CP2K_ENABLE_FFTW3_THREADS_SUPPORT AND CP2K_ENABLE_FFTW3_OPENMP_SUPPORT)
-    message(
-      FATAL_ERROR
-        "Fftw3 threads and openmp supports can not be used at the same time")
-  endif()
+  if(NOT CP2K_BLAS_VENDOR MATCHES "MKL" OR CP2K_USE_FFTW3_WITH_MKL)
+    find_package(Fftw REQUIRED)
+    if(CP2K_ENABLE_FFTW3_THREADS_SUPPORT AND CP2K_ENABLE_FFTW3_OPENMP_SUPPORT)
+      message(
+        FATAL_ERROR
+          "Fftw3 threads and openmp supports can not be used at the same time")
+    endif()
 
-  if((CP2K_ENABLE_FFTW3_THREADS_SUPPORT) AND (NOT TARGET
-                                              cp2k::FFTW3::fftw3_threads))
-    message(
-      FATAL_ERROR
-        "fftw3 was compiled without multithreading support (--enable-threads option in the fftw build system)."
-    )
-  endif()
+    if((CP2K_ENABLE_FFTW3_THREADS_SUPPORT) AND (NOT TARGET
+                                                cp2k::FFTW3::fftw3_threads))
+      message(
+        FATAL_ERROR
+          "fftw3 was compiled without multithreading support (--enable-threads option in the fftw build system)."
+      )
+    endif()
 
-  if((CP2K_ENABLE_FFTW3_OPENMP_SUPPORT) AND (NOT TARGET cp2k::FFTW3::fftw3_omp))
-    message(
-      FATAL_ERROR
-        "fftw3 was compiled without openmp support  (--enable-openmp option in the fftw build system)."
-    )
+    if((CP2K_ENABLE_FFTW3_OPENMP_SUPPORT) AND (NOT TARGET cp2k::FFTW3::fftw3_omp
+                                              ))
+      message(
+        FATAL_ERROR
+          "fftw3 was compiled without openmp support  (--enable-openmp option in the fftw build system)."
+      )
+    endif()
+    set(CP2K_USE_FFTW3_ ON)
+  else()
+    message("-- Using the MKL implementation of FFTW3.")
   endif()
 endif()
 
diff --git a/cmake/cp2kConfig.cmake.in b/cmake/cp2kConfig.cmake.in
index a9e0eb5a58..f119c8bdfb 100644
--- a/cmake/cp2kConfig.cmake.in
+++ b/cmake/cp2kConfig.cmake.in
@@ -23,7 +23,7 @@ if(NOT TARGET cp2k::cp2k)
   set(CP2K_BLAS_LINK_LIBRARIES @CP2K_BLAS_LINK_LIBRARIES@)
   set(CP2K_LAPACK_LINK_LIBRARIES @CP2K_LAPACK_LINK_LIBRARIES@)
   set(CP2K_SCALAPACK_LINK_LIBRARIES @CP2K_SCALAPACK_LINK_LIBRARIES@)
-
+  set(CP2K_USE_FFTW3_WITH_MKL @CP2K_USE_FFTW3_WITH_MKL@)
   set(CP2K_CONFIG_PACKAGE ON)
   find_dependency(Lapack REQUIRED)
 
@@ -67,7 +67,7 @@ if(NOT TARGET cp2k::cp2k)
     find_dependency(MPI REQUIRED)
   endif()
 
-  if(@CP2K_USE_FFTW3@)
+  if(@CP2K_USE_FFTW3_@)
     find_dependency(Fftw REQUIRED)
   endif()
   # QUIP
diff --git a/cmake/modules/FindMKL.cmake b/cmake/modules/FindMKL.cmake
index 87bd80de1d..8bc6979d9c 100644
--- a/cmake/modules/FindMKL.cmake
+++ b/cmake/modules/FindMKL.cmake
@@ -456,8 +456,6 @@ if(MKL_FOUND)
   unset(__mkl_scalapack_lib)
   unset(__mkl_scalapack_inc)
   set(CP2K_BLAS_VENDOR "MKL")
-  set(CP2K_MKL_SCALAPACK_VENDOR TRUE)
   mark_as_advanced(CP2K_BLAS_VENDOR)
   mark_as_advanced(CP2K_MKL_FOUND)
-  mark_as_advanced(CP2K_MKL_SCALAPACK_VENDOR)
 endif()
diff --git a/cmake/modules/FindSCI.cmake b/cmake/modules/FindSCI.cmake
index 3a540b2024..c6c9d202c5 100644
--- a/cmake/modules/FindSCI.cmake
+++ b/cmake/modules/FindSCI.cmake
@@ -98,7 +98,6 @@ if(CP2K_LIBSCI_FOUND)
   endif()
 
   set(CP2K_BLAS_VENDOR "SCI")
-
 endif()
 
 # prevent clutter in cache
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8ee82a8579..bec6eff26e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1550,9 +1550,9 @@ target_link_libraries(
     $<$<BOOL:${CP2K_USE_SPGLIB}>:cp2k::LIBSPG::libspg>
     $<$<BOOL:${CP2K_USE_LIBXC}>:cp2k::Libxc::xc>
     $<$<BOOL:${CP2K_USE_ELPA}>:cp2k::ELPA::elpa>
-    $<$<BOOL:${CP2K_USE_FFTW3}>:cp2k::FFTW3::fftw3>
-    $<$<BOOL:${CP2K_ENABLE_FFTW3_THREADS_SUPPORT}>:cp2k::FFTW3::fftw3_threads>
-    $<$<BOOL:${CP2K_ENABLE_FFTW3_OPENMP_SUPPORT}>:cp2k::FFTW3::fftw3_omp>
+    $<$<BOOL:${CP2K_USE_FFTW3_}>:cp2k::FFTW3::fftw3>
+    $<$<AND:$<BOOL:${CP2K_USE_FFTW3_}>,$<BOOL:${CP2K_ENABLE_FFTW3_THREADS_SUPPORT}>>:cp2k::FFTW3::fftw3_threads>
+    $<$<AND:$<BOOL:${CP2K_USE_FFTW3_}>,$<BOOL:${CP2K_ENABLE_FFTW3_OPENMP_SUPPORT}>>:cp2k::FFTW3::fftw3_omp>
     $<$<BOOL:${CP2K_USE_SPLA}>:SPLA::spla>
     $<$<BOOL:${CP2K_USE_LIBINT2}>:cp2k::Libint2::int2>
     $<$<BOOL:${CP2K_USE_TORCH}>:${TORCH_LIBRARIES}>
@@ -1560,7 +1560,8 @@ target_link_libraries(
     $<$<BOOL:${CP2K_USE_COSMA}>:cosma::cosma>
     DBCSR::dbcsr
     $<$<BOOL:${CP2K_USE_MPI}>:cp2k::SCALAPACK::scalapack>
-    cp2k_linalg_libs)
+    cp2k_linalg_libs
+    $<$<AND:$<CONFIG:COVERAGE>,$<Fortran_COMPILER_ID:GNU>>:gcov>)
 
 string(TIMESTAMP CP2K_TIMESTAMP "%Y-%m-%d %H:%M:%S")
 
@@ -1569,7 +1570,7 @@ target_compile_definitions(
   cp2k
   PUBLIC $<$<BOOL:${CP2K_USE_MPI}>:__parallel>
          $<$<BOOL:${CP2K_USE_MPI}>:__SCALAPACK>
-         $<$<BOOL:${CP2K_USE_F08_MPI}>:__MPI_F08>
+         $<$<BOOL:${CP2K_USE_MPI_F08}>:__MPI_F08>
          __COMPILE_DATE=\"${CP2K_TIMESTAMP}\"
          __COMPILE_HOST=\"${CP2K_HOST_NAME}\"
          __COMPILE_REVISION=\"${CP2K_GIT_HASH}\"
@@ -1591,7 +1592,7 @@ target_compile_definitions(
          $<$<BOOL:${CP2K_USE_SPLA_GEMM_OFFLOADING}>:__OFFLOAD_GEMM>
          $<$<BOOL:${CP2K_USE_ELPA}>:__ELPA>
          $<$<BOOL:${CP2K_USE_LIBXC}>:__LIBXC>
-         $<$<BOOL:${CP2K_USE_FFTW3}>:__FFTW3>
+         $<$<BOOL:${CP2K_USE_FFTW3_}>:__FFTW3>
          $<$<BOOL:${CP2K_USE_LIBINT2}>:__LIBINT>
          $<$<BOOL:${CP2K_USE_PEXSI}>:__LIBPEXSI>
          $<$<BOOL:${CP2K_USE_LIBTORCH}>:__LIBTORCH>
@@ -1752,7 +1753,10 @@ foreach(__app grid_miniapp grid_unittest dbm_miniapp)
            $<$<BOOL:${CP2K_USE_CUDA}>:${CMAKE_CUDA_INCLUDE_DIRECTORIES}>
            $<$<BOOL:${CP2K_USE_HIP}>:${CMAKE_HIP_INCLUDE_DIRECTORIES}>)
 
-  target_link_libraries(${__app} PUBLIC cp2k_linalg_libs m)
+  target_link_libraries(
+    ${__app}
+    PUBLIC cp2k_linalg_libs
+           $<$<AND:$<CONFIG:COVERAGE>,$<Fortran_COMPILER_ID:GNU>>:gcov> m)
 endforeach()
 
 # ##############################################################################
diff --git a/tools/docker/scripts/test_regtest_cmake.sh b/tools/docker/scripts/test_regtest_cmake.sh
index d042d5d19d..9a89787052 100755
--- a/tools/docker/scripts/test_regtest_cmake.sh
+++ b/tools/docker/scripts/test_regtest_cmake.sh
@@ -28,7 +28,6 @@ if ! cmake \
   -DCP2K_USE_LIBXC=ON \
   -DCP2K_USE_LIBTORCH=OFF \
   -DCP2K_USE_MPI=ON \
-  -DCP2K_USE_MPI_F08=ON \
   -DCP2K_ENABLE_REGTESTS=ON \
   .. &> ./cmake.log; then
   tail -n 100 cmake.log