CMAKE example with HDF5 and PETSC

examples/buildsystems/cmake/.gitignore

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+build

examples/buildsystems/cmake/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.10)
+
+# set the project name
+project(HELLO VERSION 1.0)
+
+
+set(CMAKE_MODULE_PATH "${HELLO_SOURCE_DIR}/Modules")
+message(${CMAKE_MODULE_PATH})
+
+# find PETSc
+find_package(PETSc REQUIRED)
+message(STATUS "Found PETSc version ${PETSC_VERSION}")
+include_directories(${PETSC_INCLUDES})
+
+# use HDF5 macro
+include(MyFindHDF5)
+# define include directories
+include_directories(${HDF5_INCLUDE_DIRS})
+
+# add the executable
+add_executable(hello_project src/hello_project.cpp)
+
+# enable GSl library linkage
+target_link_libraries(hello_project ${HDF5_LIBRARIES} ${PETSC_LIBRARIES})
+
+

examples/buildsystems/cmake/Modules/CorrectWindowsPaths.cmake

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+# CorrectWindowsPaths - this module defines one macro
+#
+# CONVERT_CYGWIN_PATH( PATH )
+#  This uses the command cygpath (provided by cygwin) to convert
+#  unix-style paths into paths useable by cmake on windows
+
+macro (CONVERT_CYGWIN_PATH _path)
+  if (WIN32)
+    EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+      OUTPUT_VARIABLE ${_path})
+    string (STRIP ${${_path}} ${_path})
+  endif (WIN32)
+endmacro (CONVERT_CYGWIN_PATH)
+

examples/buildsystems/cmake/Modules/FindPackageMultipass.cmake

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+# PackageMultipass - this module defines two macros
+#
+# FIND_PACKAGE_MULTIPASS (Name CURRENT
+#  STATES VAR0 VAR1 ...
+#  DEPENDENTS DEP0 DEP1 ...)
+#
+#  This function creates a cache entry <UPPERCASED-Name>_CURRENT which
+#  the user can set to "NO" to trigger a reconfiguration of the package.
+#  The first time this function is called, the values of
+#  <UPPERCASED-Name>_VAR0, ... are saved.  If <UPPERCASED-Name>_CURRENT
+#  is false or if any STATE has changed since the last time
+#  FIND_PACKAGE_MULTIPASS() was called, then CURRENT will be set to "NO",
+#  otherwise CURRENT will be "YES".  IF not CURRENT, then
+#  <UPPERCASED-Name>_DEP0, ... will be FORCED to NOTFOUND.
+#  Example:
+#    find_path (FOO_DIR include/foo.h)
+#    FIND_PACKAGE_MULTIPASS (Foo foo_current
+#      STATES DIR
+#      DEPENDENTS INCLUDES LIBRARIES)
+#    if (NOT foo_current)
+#      # Make temporary files, run programs, etc, to determine FOO_INCLUDES and FOO_LIBRARIES
+#    endif (NOT foo_current)
+#
+# MULTIPASS_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS LANGUAGE)
+#  Always runs the given test, use this when you need to re-run tests
+#  because parent variables have made old cache entries stale. The LANGUAGE
+#  variable is either C or CXX indicating which compiler the test should
+#  use.
+# MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
+#  DEPRECATED! This is only included for backwards compatability. Use
+#  the more general MULTIPASS_SOURCE_RUNS instead.
+#  Always runs the given test, use this when you need to re-run tests
+#  because parent variables have made old cache entries stale.
+
+macro (FIND_PACKAGE_MULTIPASS _name _current)
+  string (TOUPPER ${_name} _NAME)
+  set (_args ${ARGV})
+  list (REMOVE_AT _args 0 1)
+
+  set (_states_current "YES")
+  list (GET _args 0 _cmd)
+  if (_cmd STREQUAL "STATES")
+    list (REMOVE_AT _args 0)
+    list (GET _args 0 _state)
+    while (_state AND NOT _state STREQUAL "DEPENDENTS")
+      # The name of the stored value for the given state
+      set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+      if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+        set (_states_current "NO")
+      endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+      set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
+      list (REMOVE_AT _args 0)
+      list (GET _args 0 _state)
+    endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
+  endif (_cmd STREQUAL "STATES")
+
+  set (_stored ${_NAME}_CURRENT)
+  if (NOT ${_stored})
+    set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current?  Set to \"NO\" to reconfigure." FORCE)
+    set (_states_current "NO")
+  endif (NOT ${_stored})
+
+  set (${_current} ${_states_current})
+  if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+    message (STATUS "Clearing ${_name} dependent variables")
+    # Clear all the dependent variables so that the module can reset them
+    list (GET _args 0 _cmd)
+    if (_cmd STREQUAL "DEPENDENTS")
+      list (REMOVE_AT _args 0)
+      foreach (dep ${_args})
+        set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+      endforeach (dep)
+    endif (_cmd STREQUAL "DEPENDENTS")
+    set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+  endif ()
+  set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
+endmacro (FIND_PACKAGE_MULTIPASS)
+
+
+macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language)
+  include (Check${language}SourceRuns)
+  # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
+  # *name* of the return variable doesn't change, then the test does
+  # not need to be re-run.  We keep an internal count which we
+  # increment to guarantee that every test name is unique.  If we've
+  # gotten here, then the configuration has changed enough that the
+  # test *needs* to be rerun.
+  if (NOT MULTIPASS_TEST_COUNT)
+    set (MULTIPASS_TEST_COUNT 00)
+  endif (NOT MULTIPASS_TEST_COUNT)
+  math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+  set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+  set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+  set (CMAKE_REQUIRED_INCLUDES ${includes})
+  set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+  if(${language} STREQUAL "C")
+    check_c_source_runs ("${source}" ${testname})
+  elseif(${language} STREQUAL "CXX")
+    check_cxx_source_runs ("${source}" ${testname})
+  endif()
+  set (${runs} "${${testname}}")
+endmacro (MULTIPASS_SOURCE_RUNS)
+
+macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+  multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
+endmacro (MULTIPASS_C_SOURCE_RUNS)

examples/buildsystems/cmake/Modules/MyFindHDF5.cmake

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+# Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+# Defines the following variables:
+#   - HDF5_FOUND - If HDF5 was found
+#   - HDF5_LIBRARIES - The HDF5 libraries
+#   - HDF5_INCLUDE_DIRS - The HDF5 include directories
+
+# First Check for HDF5_DIR
+if(NOT HDF5_DIR)
+    MESSAGE(FATAL_ERROR "Could not find HDF5. HDF5 support needs explicit HDF5_DIR")
+endif()
+
+# Find includes
+find_path( HDF5_INCLUDE_DIRS hdf5.h
+           PATHS  ${HDF5_DIR}/include/
+           NO_DEFAULT_PATH
+           NO_CMAKE_ENVIRONMENT_PATH
+           NO_CMAKE_PATH
+           NO_SYSTEM_ENVIRONMENT_PATH
+           NO_CMAKE_SYSTEM_PATH)
+
+find_library( __HDF5_LIBRARY NAMES hdf5 libhdf5 libhdf5_D libhdf5_debug
+              PATHS ${HDF5_DIR}/lib
+              NO_DEFAULT_PATH
+              NO_CMAKE_ENVIRONMENT_PATH
+              NO_CMAKE_PATH
+              NO_SYSTEM_ENVIRONMENT_PATH
+              NO_CMAKE_SYSTEM_PATH)
+
+find_library( __HDF5_HL_LIBRARY NAMES hdf5_hl libhdf5_hl libhdf5_hl_D libhdf5_hl_debug
+              PATHS ${HDF5_DIR}/lib
+              NO_DEFAULT_PATH
+              NO_CMAKE_ENVIRONMENT_PATH
+              NO_CMAKE_PATH
+              NO_SYSTEM_ENVIRONMENT_PATH
+              NO_CMAKE_SYSTEM_PATH)
+
+set(HDF5_LIBRARIES ${__HDF5_HL_LIBRARY} ${__HDF5_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+
+# Handle the QUIETLY and REQUIRED arguments and set HDF5_FOUND to TRUE if all
+# listed variables are TRUE
+find_package_handle_standard_args(HDF5  DEFAULT_MSG
+                                  HDF5_INCLUDE_DIRS
+                                  __HDF5_LIBRARY
+                                  __HDF5_HL_LIBRARY
+                                  HDF5_LIBRARIES )

examples/buildsystems/cmake/Modules/ResolveCompilerPaths.cmake

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+# ResolveCompilerPaths - this module defines two macros
+#
+# RESOLVE_LIBRARIES (XXX_LIBRARIES LINK_LINE)
+#  This macro is intended to be used by FindXXX.cmake modules.
+#  It parses a compiler link line and resolves all libraries
+#  (-lfoo) using the library path contexts (-L/path) in scope.
+#  The result in XXX_LIBRARIES is the list of fully resolved libs.
+#  Example:
+#
+#    RESOLVE_LIBRARIES (FOO_LIBRARIES "-L/A -la -L/B -lb -lc -ld")
+#
+#  will be resolved to
+#
+#    FOO_LIBRARIES:STRING="/A/liba.so;/B/libb.so;/A/libc.so;/usr/lib/libd.so"
+#
+#  if the filesystem looks like
+#
+#    /A:       liba.so         libc.so
+#    /B:       liba.so libb.so
+#    /usr/lib: liba.so libb.so libc.so libd.so
+#
+#  and /usr/lib is a system directory.
+#
+#  Note: If RESOLVE_LIBRARIES() resolves a link line differently from
+#  the native linker, there is a bug in this macro (please report it).
+#
+# RESOLVE_INCLUDES (XXX_INCLUDES INCLUDE_LINE)
+#  This macro is intended to be used by FindXXX.cmake modules.
+#  It parses a compile line and resolves all includes
+#  (-I/path/to/include) to a list of directories.  Other flags are ignored.
+#  Example:
+#
+#    RESOLVE_INCLUDES (FOO_INCLUDES "-I/A -DBAR='\"irrelevant -I/string here\"' -I/B")
+#
+#  will be resolved to
+#
+#    FOO_INCLUDES:STRING="/A;/B"
+#
+#  assuming both directories exist.
+#  Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
+include (CorrectWindowsPaths)
+
+macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
+  string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))" _all_tokens "${LINK_LINE}")
+  set (_libs_found "")
+  set (_directory_list "")
+  foreach (token ${_all_tokens})
+    if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+      # If it's a library path, add it to the list
+      string (REGEX REPLACE "^-L" "" token ${token})
+      string (REGEX REPLACE "//" "/" token ${token})
+      convert_cygwin_path(token)
+      list (APPEND _directory_list ${token})
+    elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
+      # It's a library, resolve the path by looking in the list and then (by default) in system directories
+      if (WIN32) #windows expects "libfoo", linux expects "foo"
+        string (REGEX REPLACE "^-l" "lib" token ${token})
+      else (WIN32)
+        string (REGEX REPLACE "^-l" "" token ${token})
+      endif (WIN32)
+      set (_root "")
+      if (token MATCHES "^/")	# We have an absolute path
+        #separate into a path and a library name:
+        string (REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
+        string (REGEX MATCH ".*[^${libname}$]" libpath ${token})
+        convert_cygwin_path(libpath)
+        set (_directory_list ${_directory_list} ${libpath})
+        set (token ${libname})
+      endif (token MATCHES "^/")
+      set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+      find_library (_lib ${token} HINTS ${_directory_list} ${_root})
+      if (_lib)
+	string (REPLACE "//" "/" _lib ${_lib})
+        list (APPEND _libs_found ${_lib})
+      else (_lib)
+        message (STATUS "Unable to find library ${token}")
+      endif (_lib)
+    endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+  endforeach (token)
+  set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+  # only the LAST occurence of each library is required since there should be no circular dependencies
+  if (_libs_found)
+    list (REVERSE _libs_found)
+    list (REMOVE_DUPLICATES _libs_found)
+    list (REVERSE _libs_found)
+  endif (_libs_found)
+  set (${LIBS} "${_libs_found}")
+endmacro (RESOLVE_LIBRARIES)
+
+macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
+  string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+  set (_incs_found "")
+  foreach (token ${_all_tokens})
+    string (REGEX REPLACE "^-I" "" token ${token})
+    string (REGEX REPLACE "//" "/" token ${token})
+    convert_cygwin_path(token)
+    if (EXISTS ${token})
+      list (APPEND _incs_found ${token})
+    else (EXISTS ${token})
+      message (STATUS "Include directory ${token} does not exist")
+    endif (EXISTS ${token})
+  endforeach (token)
+  list (REMOVE_DUPLICATES _incs_found)
+  set (${INCS} "${_incs_found}")
+endmacro (RESOLVE_INCLUDES)

examples/buildsystems/cmake/README.md

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+## Load the following modules
+
+```
+module load  gcc/7.1.0 
+module load impi/17.0.3
+module load cmake/3.20.2
+module load petsc/3.9
+module load phdf5/1.8.16
+```
+
+
+## Run cmake with the following commad line
+```
+cmake -DHDF5_DIR=$TACC_HDF5_DIR -DCMAKE_CXX_COMPILER=mpicxx -DPETSC_DIR=$PETSC_DIR -DPETSC_ARCH=$PETSC_ARCH ../
+```