Merge pull request #2494 from boutproject/cmake-more-fixes

CMake: option to ignore a conda environment; fix for PVODE

CMakeLists.txt

@@ -16,6 +16,27 @@ project(BOUT++
   VERSION ${BOUT_CMAKE_ACCEPTABLE_VERSION}
   LANGUAGES CXX)
 
+# Optionally ignore anything that is installed by conda
+set (BOUT_IGNORE_CONDA_ENV OFF CACHE BOOL "Ignore anything installed by conda. May introduce a slow step to the configuration, due to scanning a large number of files under $CONDA_PREFIX.")
+if (BOUT_IGNORE_CONDA_ENV)
+  if (EXISTS $ENV{CONDA_PREFIX})
+    # CMake does not allow ignoring everything under a prefix, so we have to
+    # get a list with *every* directory under CONDA_PREFIX.
+    # GLOB_RECURSE also doesn't seem to directly allow matching directories,
+    # but 'LIST_DIRECTORIES true' makes all directories traversed appear in the
+    # result, and setting the glob-pattern to [] (which does not match anything
+    # because square brackets match to any of the characters inside the
+    # brackets) means we do not actually match any files.
+    # [This may become less awful in CMake-3.23.0, where it may be possible to
+    # filter by prefix, not just directory, see
+    # https://gitlab.kitware.com/cmake/cmake/-/merge_requests/6880]
+    file(GLOB_RECURSE BOUT_IGNORE_CONDA_ENV_DIRECTORY_LIST
+         LIST_DIRECTORIES true
+         $ENV{CONDA_PREFIX}/[])
+    list (APPEND CMAKE_IGNORE_PATH ${BOUT_IGNORE_CONDA_ENV_DIRECTORY_LIST})
+  endif()
+endif()
+
 # This might not be entirely sensible, but helps CMake to find the
 # correct MPI, workaround for https://gitlab.kitware.com/cmake/cmake/issues/18895
 find_program(MPIEXEC_EXECUTABLE NAMES mpiexec mpirun)

bout++Config.cmake.in

@@ -75,6 +75,13 @@ if(EXISTS "@HDF5F_ROOT@")
 endif()
 if(EXISTS "@PVODE_ROOT@")
   set(PVODE_ROOT "@PVODE_ROOT@")
+elseif(EXISTS "@PVODE_DIR@")
+    set(PVODE_DIR "@PVODE_DIR@")
+elseif(EXISTS "@PVODE_BINARY_DIR@")
+    set(PVODE_DIR "@PVODE_BINARY_DIR@")
+endif()
+if(EXISTS "@Libuuid_ROOT@")
+  set(Libuuid_ROOT "@Libuuid_ROOT@")
 endif()
 
 if(@BOUT_USE_SYSTEM_MPARK_VARIANT@)
@@ -91,6 +98,7 @@ if (BOUT_USE_OPENMP)
   find_dependency(OpenMP)
 endif()
 if (BOUT_HAS_NETCDF)
+  find_dependency(netCDF @netCDF_VERSION@)
   find_dependency(netCDFCxx @netCDFCxx_VERSION@)
 endif()
 if (BOUT_HAS_HDF5)

cmake/FindFFTW.cmake

@@ -29,6 +29,11 @@ if (FFTW_INCLUDE_DIRS)
   set (FFTW_FIND_QUIETLY TRUE)
 endif (FFTW_INCLUDE_DIRS)
 
+if (EXISTS ${FFTW_ROOT})
+  # Make sure FFTW_ROOT is an absolute path by setting it as a 'FILEPATH'
+  set (FFTW_ROOT "" CACHE FILEPATH "Location of the FFTW library")
+endif()
+
 find_program(FFTW_WISDOM "fftw-wisdom"
   PATHS "${FFTW_ROOT}"
   PATH_SUFFIXES bin

cmake/FindnetCDF.cmake

@@ -27,13 +27,16 @@
 
 include(BOUT++functions)
 
-find_package(netCDF QUIET CONFIG)
-if (netCDF_FOUND)
-  set(netCDF_FOUND TRUE)
-  if (NOT TARGET netCDF::netcdf)
-    bout_add_library_alias(netCDF::netcdf netcdf)
+if (NOT EXISTS ${NC_CONFIG})
+  # Only search if NC_CONFIG was not set explicitly
+  find_package(netCDF QUIET CONFIG)
+  if (netCDF_FOUND)
+    set(netCDF_FOUND TRUE)
+    if (NOT TARGET netCDF::netcdf)
+      bout_add_library_alias(netCDF::netcdf netcdf)
+    endif()
+    return()
   endif()
-  return()
 endif()
 
 find_program(NC_CONFIG "nc-config"

cmake/FindnetCDFCxx.cmake

@@ -27,13 +27,16 @@
 
 include(BOUT++functions)
 
-find_package(netCDFCxx QUIET CONFIG)
-if (netCDFCxx_FOUND)
-  set(netCDFCxx_FOUND TRUE)
-  if (NOT TARGET netCDF::netcdf-cxx4)
-    bout_add_library_alias(netCDF::netcdf-cxx4 netcdf-cxx4)
+if (NOT EXISTS ${NCXX4_CONFIG})
+  # Only search if NCXX4_CONFIG was not set explicitly
+  find_package(netCDFCxx QUIET CONFIG)
+  if (netCDFCxx_FOUND)
+    set(netCDFCxx_FOUND TRUE)
+    if (NOT TARGET netCDF::netcdf-cxx4)
+      bout_add_library_alias(netCDF::netcdf-cxx4 netcdf-cxx4)
+    endif()
+    return()
   endif()
-  return()
 endif()
 
 find_package(netCDF REQUIRED)

manual/sphinx/user_docs/advanced_install.rst

@@ -64,7 +64,10 @@ Machine-specific installation
 -----------------------------
 
 These are some configurations which have been found to work on
-particular machines.
+particular machines. There is also the repo
+https://github.com/boutproject/BOUT-configs which provides scripts for one or
+two line compilation, with dependencies, of known-good versions on several
+machines (different machines are in different branches).
 
 Archer
 ~~~~~~

manual/sphinx/user_docs/installing.rst

@@ -373,7 +373,7 @@ time as your project, therefore there is no option to use an external
 installation for that.
 
 Using CMake with your physics model
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 You can write a CMake configuration file (``CMakeLists.txt``) for your
 physics model in only four lines:
@@ -406,6 +406,28 @@ source. Doing this has the advantage that any changes you make to
 BOUT++ source files will trigger a rebuild of both the BOUT++ library
 and your model when you next build your code.
 
+Working with an active `conda` environment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+When `conda` is used, it installs separate versions of several libraries. These
+can cause warnings or even failures when linking BOUT++ executables. There are
+several alternatives to deal with this problem:
+* The simplest but least convenient option is to use `conda deactivate` before
+  configuring, compiling, or running any BOUT++ program.
+* You might sometimes want to link to the conda-installed libraries. This is
+  probably not ideal for production runs on an HPC system (as conda downloads
+  binary packages that will not be optimized for specific hardware), but can be
+  a simple way to get packages for testing or on a personal computer. In this
+  case just keep your `conda` environment active, and with luck the libraries
+  should be picked up by the standard search mechanisms.
+* In case you do want a fully optimized and as-stable-as-possible build for
+  production runs, it is probably best not to depend on any conda packages for
+  compiling or running BOUT++ executables (restrict `conda` to providing Python
+  packages for post-processing, and their dependencies). Passing
+  `-DBOUT_IGNORE_CONDA_ENV=ON` (default `OFF`) excludes anything in the conda
+  environment from CMake search paths. This should totally separate BOUT++ from
+  the `conda` environment.
+
 .. _sec-config-nls:
 
 Natural Language Support