Merge pull request #7 from CESM-Development/master

update to cime0_3_20 from CESM svn

driver_cpl/cimetest/testlist_drv.xml

@@ -52,6 +52,9 @@
         <machine compiler="intel" testtype="prebeta">yellowstone</machine>
         <machine compiler="pgi" testtype="prebeta">yellowstone</machine>
       </test>
+      <test name="PEM">
+        <machine compiler="intel" testtype="prealpha">yellowstone</machine>
+      </test>
     </grid>
     <grid name="f45_g37_rx1">
       <test name="CME_Ld3">
@@ -147,6 +150,9 @@
         <machine compiler="intel" testtype="prealpha">yellowstone</machine>
         <machine compiler="pgi" testtype="prealpha">yellowstone</machine>
       </test>
+      <test name="PET_D_E_CG">
+        <machine compiler="intel" testtype="prealpha">yellowstone</machine>
+      </test>
       <test name="PET_PT_Ld3">
         <machine compiler="pgi" testtype="prebeta">goldbach</machine>
         <machine compiler="intel" testtype="prebeta">janus</machine>
@@ -155,7 +161,6 @@
         <machine compiler="pgi" testtype="prebeta">yellowstone</machine>
       </test>
       <test name="SEQ_IOP_PFC_Ld3">
-        <machine compiler="intel" testtype="prebeta">goldbach</machine>
         <machine compiler="pgi" testtype="prebeta">goldbach</machine>
         <machine compiler="intel" testtype="prebeta">janus</machine>
         <machine compiler="gnu" testtype="prebeta">yellowstone</machine>

externals/CMake/.gitignore

@@ -0,0 +1,5 @@
+CMakeCache.txt
+CMakeFiles
+Makefile
+cmake_install.cmake
+install_manifest.txt

externals/CMake/CESM_utils.cmake

@@ -0,0 +1,73 @@
+# Module used for CESM testing.
+#
+# This module contains statements that would otherwise be boilerplate in
+# most CESM tests. It enables CTest testing, handles the USE_COLOR and
+# ENABLE_GENF90 arguments, and includes several other modules.
+
+#==========================================================================
+# Copyright (c) 2013-2014, University Corporation for Atmospheric Research
+#
+# This software is distributed under a two-clause BSD license, with no
+# warranties, express or implied. See the accompanying LICENSE file for
+# details.
+#==========================================================================
+
+#=================================================
+# Enable CTest tests.
+#=================================================
+
+enable_testing()
+
+#=================================================
+# Color output
+#=================================================
+
+option(USE_COLOR "Allow color from the build output." ON)
+
+set(CMAKE_COLOR_MAKEFILE "${USE_COLOR}")
+
+#=================================================
+# Compiler info
+#=================================================
+
+if("${CMAKE_BUILD_TYPE}" MATCHES CESM)
+  include(${CMAKE_BINARY_DIR}/CESM_Macros.cmake)
+else()
+  include(Compilers)
+endif()
+
+#=================================================
+# GenF90
+#=================================================
+
+option(ENABLE_GENF90
+  "Use genf90.pl to regenerate out-of-date Fortran files from .in files."
+  OFF)
+
+if(ENABLE_GENF90)
+  find_program(GENF90 genf90.pl)
+
+  if(NOT GENF90)
+    message(FATAL_ERROR "ENABLE_GENF90 enabled, but genf90.pl not found!")
+  endif()
+
+endif()
+
+# Preprocessing utility functions.
+include(genf90_utils)
+
+#=================================================
+# pFUnit
+#=================================================
+
+# pFUnit and its preprocessor
+find_package(pFUnit)
+
+# Preprocessor and driver handling.
+include(pFUnit_utils)
+
+#=================================================
+# Source list and path utilities.
+#=================================================
+
+include(Sourcelist_utils)

externals/CMake/ChangeLog

@@ -0,0 +1,8 @@
+This repository tracks changes using the Git log.
+
+For small changes, e.g. fixing typos, use a one line, 50 character summary.
+
+For larger changes, this summary should be followed by a blank line and a
+longer description. The following link gives good advice:
+
+http://justinhileman.info/article/changing-history/#make-the-most-of-your-commit-message

externals/CMake/Compilers.cmake

@@ -0,0 +1,138 @@
+# Flags for builds with different machines/compilers.
+#
+# This module is currently a catch-all for compiler-specific functionality
+# needed by CESM. It defines OS and compiler CPP macros and CESM build
+# types, as well as including the file containing CESM compiler flags, if
+# necessary.
+#
+# There is also one function intended for CTest test writers, described
+# below.
+#
+#==========================================================================
+#
+# define_Fortran_stop_failure
+#
+# Arguments:
+#    test_name - Name of a CTest test.
+#
+# Ensures that if the named test uses "STOP 1" to signal failure, that this
+# is detected by CTest. Currently this is only necessary for NAG, which
+# prints the stop code rather than using it as an error code.
+#
+#==========================================================================
+
+#==========================================================================
+# Copyright (c) 2013-2014, University Corporation for Atmospheric Research
+#
+# This software is distributed under a two-clause BSD license, with no
+# warranties, express or implied. See the accompanying LICENSE file for
+# details.
+#==========================================================================
+
+#=================================================
+# Define OS and compiler macros.
+#=================================================
+
+# Define OS.
+string(TOUPPER ${CMAKE_SYSTEM_NAME} os)
+add_definitions(-D${os})
+
+# Define CESM-compatible compiler names.
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL NAG)
+  set(compiler_name nag)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL GNU)
+  set(compiler_name gnu)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL XL)
+  set(compiler_name ibm)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL Intel)
+  set(compiler_name intel)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL PGI)
+  set(compiler_name pgi)
+endif()
+
+# Define CPP macro for the compiler.
+string(TOUPPER -DCPR${compiler_name} compiler_cppdef)
+add_definitions(${compiler_cppdef})
+
+#=================================================
+# Utility functions.
+#=================================================
+
+# Add flags to space-separated list rather than normal CMake list.
+function(add_flags list)
+  string(REPLACE ";" " " flags "${ARGN}")
+  set(${list} "${${list}} ${flags}" PARENT_SCOPE)
+endfunction()
+
+
+# Add configuration-specific preprocessor definitions.
+function(add_config_definitions configuration)
+  get_directory_property(cppdefs COMPILE_DEFINITIONS_${configuration})
+  foreach(flag IN LISTS ARGN)
+    string(REPLACE "-D" "" def "${flag}")
+    list(APPEND cppdefs ${def})
+  endforeach()
+  set_directory_properties(PROPERTIES COMPILE_DEFINITIONS_${configuration}
+    "${cppdefs}")
+endfunction()
+
+
+#=================================================
+# Build flags required to use pFUnit.
+#=================================================
+
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL Intel)
+  add_flags(CMAKE_Fortran_FLAGS -assume realloc_lhs)
+endif()
+
+#=================================================
+# Add flags for debugging output.
+#=================================================
+
+# Define Fortran compiler flags.
+
+# Add pretty output and extra warnings regardless of build type. However,
+# don't set any options in the generic flags that would affect the
+# generated binary, because we want to be able to get binaries that
+# resemble what you get from the CESM flags.
+
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL NAG)
+  add_flags(CMAKE_Fortran_FLAGS -strict95)
+  if(USE_COLOR)
+    add_flags(CMAKE_Fortran_FLAGS -colour)
+  endif()
+
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL GNU)
+  # Turn on warnings, but leave out uninitialized check as it was producing
+  # a lot of false positives.
+  add_flags(CMAKE_Fortran_FLAGS -Wall -Wextra -Wno-uninitialized)
+
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL XL)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL Intel)
+elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL PGI)
+endif()
+
+# Define C flags, analogous to the above Fortran block.
+if(CMAKE_C_COMPILER_LOADED)
+  if(${CMAKE_C_COMPILER_ID} STREQUAL GNU)
+    add_flags(CMAKE_C_FLAGS -Wall -Wextra -pedantic)
+  endif()
+endif()
+
+#=================================================
+# Help CTest tests recognize when "stop X" is called with non-zero X.
+#=================================================
+
+# Detect "STOP" for CTest.
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL NAG)
+  # NAG prints the stop code instead of yielding a non-zero return, so we
+  # have to use a regex to catch that.
+  function(define_Fortran_stop_failure test_name)
+    set_tests_properties(${test_name} PROPERTIES
+      FAIL_REGULAR_EXPRESSION "STOP: [1-9]")
+  endfunction(define_Fortran_stop_failure)
+else()
+  # Usually, stop /= 0 is already detected with the return code.
+  function(define_Fortran_stop_failure test_name)
+  endfunction(define_Fortran_stop_failure)
+endif()

externals/CMake/FindNETCDF.cmake

@@ -0,0 +1,63 @@
+# - Try to find Netcdf
+# Once done this will define
+#  NETCDF_FOUND - System has Netcdf
+#  NETCDF_INCLUDE_DIRS - The Netcdf include directories
+# NETCDF_C_LIBRARIES - The C libraries needed to use Netcdf
+# NETCDF_Fortran_LIBRARIES - The Fortran libraries needed to use Netcdf
+#  NETCDF_LIBRARIES - All the libraries needed to use Netcdf
+#  NETCDF_DEFINITIONS - Compiler switches required for using Netcdf
+
+find_path(NETCDF_INCLUDE_DIR netcdf.h
+          HINTS ${NETCDF_DIR}/include )
+
+find_path(NETCDF_LIB_DIR NAMES libnetcdf.a libnetcdf.so
+          HINTS ${NETCDF_DIR}/lib ${NETCDF_DIR}/lib64 )
+
+find_path(NETCDF_FORTRAN_LIB_DIR NAMES libnetcdff.a libnetcdff.so
+          HINTS ${NETCDF_DIR}/lib ${NETCDF_DIR}/lib64 )
+
+
+find_file(NETCDF4_PAR_H netcdf_par.h 
+          HINTS ${NETCDF_INCLUDE_DIR}
+          NO_DEFAULT_PATH )
+
+#MESSAGE("PAR_H: ${NETCDF4_PAR_H}")
+find_library(NETCDF_C_LIBRARY NAMES libnetcdf.a netcdf HINTS ${NETCDF_LIB_DIR})
+
+if(NOT NETCDF_FORTRAN_LIB_DIR)
+  MESSAGE("WARNING: did not find netcdf fortran library")
+else()
+  find_library(NETCDF_Fortran_LIBRARY NAMES libnetcdff.a netcdff HINTS ${NETCDF_FORTRAN_LIB_DIR})
+endif()
+set(NETCDF_LIBRARIES ${NETCDF_Fortran_LIBRARY} ${NETCDF_C_LIBRARY})
+if(NOT NETCDF4_PAR_H)
+  set(NETCDF4_PARALLEL "no")
+  MESSAGE("NETCDF built without MPIIO")
+else()
+  set(NETCDF4_PARALLEL "yes")
+  MESSAGE("NETCDF built with hdf5 MPIIO support")
+endif()
+
+set(NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR} )
+
+FIND_PACKAGE(HDF5 COMPONENTS C HL)
+
+if(${HDF5_FOUND}) 
+  MESSAGE(STATUS "Adding hdf5 libraries ")
+ set(NETCDF_C_LIBRARY ${NETCDF_C_LIBRARY} ${HDF5_LIBRARIES})  
+endif()
+
+# Export variables so other projects can use them as well
+#  ie. if pio is added with add_subdirectory
+SET(NETCDF_INCLUDE_DIR ${NETCDF_INCLUDE_DIR} CACHE STRING "Location of NetCDF include files.")
+SET(NETCDF_LIBRARIES ${NETCDF_LIBRARIES} CACHE STRING "Link line for NetCDF.")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE
+# if all listed variables are TRUE
+# (Note that the Fortran interface is not always a separate library, so
+# don't require it to be found.)
+find_package_handle_standard_args(NETCDF  DEFAULT_MSG NETCDF_LIBRARIES
+                                  NETCDF_C_LIBRARY NETCDF_INCLUDE_DIR)
+
+mark_as_advanced(NETCDF_INCLUDE_DIR NETCDF_LIBRARIES NETCDF_C_LIBRARY NETCDF_Fortran_LIBRARY NETCDF4_PARALLEL )

externals/CMake/FindNETCDF_C.cmake

@@ -0,0 +1,38 @@
+# - Try to find Netcdf
+# Once done this will define
+#  NETCDF_C_FOUND - System has Netcdf
+#  NETCDF_C_INCLUDE_DIRS - The Netcdf include directories
+#  NETCDF_C_LIBRARY - The C libraries needed to use Netcdf
+#  NETCDF_C_LIBRARIES - All the libraries needed to use Netcdf
+#  NETCDF_C_DEFINITIONS - Compiler switches required for using Netcdf
+#
+include(LibFindMacros)
+set(NETCDF_C_PARALLEL FALSE)
+find_path(NETCDF_C_INCLUDE_DIR
+          NAMES netcdf.h
+          PATHS ${NETCDF_C_PKGCONF_INCLUDE_DIRS}
+          HINTS ${NETCDF_DIR}/include ${NETCDF_C_DIR}/include)
+
+# See if netcdf includes parallel support 
+find_path(NETCDF_C_PAR_INCLUDE_DIR
+          NAMES netcdf_par.h
+          PATHS ${NETCDF_C_PKGCONF_INCLUDE_DIRS}
+          HINTS ${NETCDF_DIR}/include ${NETCDF_C_DIR}/include)        
+
+set(NETCDF_C_DEFINITIONS "-D_NETCDF")
+if(${NETCDF_C_PAR_INCLUDE_DIR} STREQUAL "NETCDF_C_PAR_INCLUDE_DIR-NOTFOUND")
+  MESSAGE("Netcdf library does not appear to have parallel IO support")
+else()
+  MESSAGE("Netcdf library includes HDF5 parallel support")
+  LIST(APPEND NETCDF_C_DEFINITIONS "-D_NETCDF4")
+endif()
+find_library(NETCDF_C_LIBRARY
+             NAMES libnetcdf.a netcdf
+             PATHS ${NETCDF_C_PKGCONF_LIBRARY_DIRS}
+	     HINTS ${NETCDF_DIR}/lib ${NETCDF_C_DIR}/lib)        
+
+set(NETCDF_C_PROCESS_INCLUDES NETCDF_C_INCLUDE_DIR)
+
+set(NETCDF_C_PROCESS_LIBS NETCDF_C_LIBRARY)
+
+libfind_process(NETCDF_C)

externals/CMake/FindNETCDF_Fortran.cmake

@@ -0,0 +1,25 @@
+# - Try to find Netcdf
+# Once done this will define
+#  NETCDF_Fortran_FOUND - System has Netcdf
+#  NETCDF_Fortran_INCLUDE_DIRS - The Netcdf include directories
+#  NETCDF_Fortran_LIBRARY - The C libraries needed to use Netcdf
+#  NETCDF_Fortran_LIBRARIES - All the libraries needed to use Netcdf
+#  NETCDF_Fortran_DEFINITIONS - Compiler switches required for using Netcdf
+#
+include(LibFindMacros)
+
+find_path(NETCDF_Fortran_INCLUDE_DIR
+          NAMES netcdf.inc
+          PATHS ${NETCDF_Fortran_PKGCONF_INCLUDE_DIRS}
+          HINTS ${NETCDF_DIR}/include ${NETCDF_Fortran_DIR}/include)
+libfind_package(NETCDF_Fortran NETCDF_C)
+find_library(NETCDF_Fortran_LIBRARY
+             NAMES libnetcdff.a netcdff
+             PATHS ${NETCDF_Fortran_PKGCONF_LIBRARY_DIRS}
+	     HINTS ${NETCDF_DIR}/lib ${NETCDF_Fortran_DIR}/lib)        
+
+set(NETCDF_Fortran_PROCESS_INCLUDES NETCDF_Fortran_INCLUDE_DIR)
+
+set(NETCDF_Fortran_PROCESS_LIBS NETCDF_Fortran_LIBRARY)
+
+libfind_process(NETCDF_Fortran)