Merge pull request ESMCI#1844 from ESMCI/jgfouca/get_pfunit_working_o…

…n_melvin

Get PFUnit working on melvin.
Fix up serial settings in melvin.
Need to explicitly declare PFUNIT_PATH in cmake calls in run_tests.py
Need to load env before making env XML files, some compiler vars pull from environment
Need to not crash when CMAKE_Fortran_COMPILER_ID is empty
Test suite: scripts_regression_tests.py N_TestUnitTest
Test baseline:
Test namelist changes:
Test status: bit for bit

Fixes ESMCI#1297

User interface changes?: N

Update gh-pages html (Y/N)?: N

Code review: @billsacks @jedwards4b (confirmed N_TestUnitTest still works on cheyenne)

config/acme/machines/config_compilers.xml

@@ -673,6 +673,7 @@ for mct, etc.
   <CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
   <NETCDF_PATH>$(NETCDFROOT)</NETCDF_PATH>
   <PNETCDF_PATH>$(PNETCDFROOT)</PNETCDF_PATH>
+  <PFUNIT_PATH MPILIB="mpi-serial" compile_threaded="false">/sems-data-store/ACME/pfunit/pfunit-3.2.8</PFUNIT_PATH>
   <ADD_SLIBS> $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -lblas -llapack</ADD_SLIBS>
   <CXX_LIBS>-lstdc++ -lmpi_cxx</CXX_LIBS>
   <ALBANY_PATH>/projects/install/rhel6-x86_64/ACME/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>

config/acme/machines/config_machines.xml

@@ -546,16 +546,19 @@
         <command name="load">sems-env</command>
         <command name="load">sems-git</command>
         <command name="load">sems-python/2.7.9</command>
+        <command name="load">sems-cmake/2.8.12</command>
       </modules>
       <modules compiler="gnu">
         <command name="load">sems-gcc/5.3.0</command>
       </modules>
       <modules compiler="intel">
         <command name="load">sems-intel/16.0.3</command>
       </modules>
-      <modules>
+      <modules mpilib="mpi-serial">
+        <command name="load">sems-netcdf/4.4.1/exo</command>
+      </modules>
+      <modules mpilib="!mpi-serial">
         <command name="load">sems-openmpi/1.8.7</command>
-        <command name="load">sems-cmake/2.8.12</command>
         <command name="load">sems-netcdf/4.4.1/exo_parallel</command>
       </modules>
     </module_system>

scripts/fortran_unit_testing/run_tests.py

@@ -146,7 +146,7 @@ def parse_command_line(args):
         args.use_openmp, args.xml_test_list, args.verbose
 
 
-def cmake_stage(name, test_spec_dir, build_optimized, use_mpiserial, mpirun_command, output,
+def cmake_stage(name, test_spec_dir, build_optimized, use_mpiserial, mpirun_command, output, pfunit_path,
                 cmake_args=None, clean=False, verbose=False, enable_genf90=True, color=True):
     """Run cmake in the current working directory.
 
@@ -178,10 +178,12 @@ def cmake_stage(name, test_spec_dir, build_optimized, use_mpiserial, mpirun_comm
 
         cmake_command = [
             "cmake",
+            "-C Macros.cmake",
             test_spec_dir,
             "-DCIME_CMAKE_MODULE_DIRECTORY="+os.path.abspath(os.path.join(_CIMEROOT,"src","CMake")),
             "-DCMAKE_BUILD_TYPE="+build_type,
             "-DPFUNIT_MPIRUN='"+mpirun_command+"'",
+            "-DPFUNIT_PATH="+pfunit_path
             ]
         if use_mpiserial:
             cmake_command.append("-DUSE_MPI_SERIAL=ON")
@@ -241,6 +243,7 @@ def find_pfunit(compilerobj, mpilib, use_openmp):
            """PFUNIT_PATH not found for this machine and compiler, with MPILIB={} and compile_threaded={}.
 You must specify PFUNIT_PATH in config_compilers.xml, with attributes MPILIB and compile_threaded.""".format(mpilib, attrs['compile_threaded']))
     logger.info("Using PFUNIT_PATH: {}".format(pfunit_path.text))
+    return pfunit_path.text
 
 #=================================================
 # Iterate over input suite specs, building the tests.
@@ -306,7 +309,7 @@ def _main():
 
     compilerobj = Compilers(machobj, compiler=compiler, mpilib=mpilib)
 
-    find_pfunit(compilerobj, mpilib=mpilib, use_openmp=use_openmp)
+    pfunit_path = find_pfunit(compilerobj, mpilib=mpilib, use_openmp=use_openmp)
 
     debug = not build_optimized
     os_ = machobj.get_value("OS")
@@ -375,7 +378,7 @@ def _main():
             if not os.path.islink("Macros.cmake"):
                 os.symlink(os.path.join(build_dir,"Macros.cmake"), "Macros.cmake")
             use_mpiserial = not use_mpi
-            cmake_stage(name, directory, build_optimized, use_mpiserial, mpirun_command, output, verbose=verbose,
+            cmake_stage(name, directory, build_optimized, use_mpiserial, mpirun_command, output, pfunit_path, verbose=verbose,
                         enable_genf90=enable_genf90, cmake_args=cmake_args)
             make_stage(name, output, make_j, clean=clean, verbose=verbose)
 
@@ -399,8 +402,5 @@ def _main():
             run_cmd_no_fail(" ".join(ctest_command), from_dir=label, arg_stdout=None, arg_stderr=subprocess.STDOUT)
 
 
-
-
-
 if __name__ == "__main__":
     _main()

scripts/lib/CIME/BuildTools/configure.py

@@ -66,7 +66,6 @@ def _copy_depends_files(machine_name, machines_dir, output_dir, compiler):
             if os.path.isfile(dfile) and not os.path.isfile(outputdfile):
                 shutil.copyfile(dfile, outputdfile)
 
-
 def _generate_env_mach_specific(output_dir, machobj, compiler, mpilib, debug,
                                 sysos, unit_testing):
     """
@@ -79,6 +78,7 @@ def _generate_env_mach_specific(output_dir, machobj, compiler, mpilib, debug,
     ems_file = EnvMachSpecific(output_dir, unit_testing=unit_testing)
     ems_file.populate(machobj)
     ems_file.write()
+    ems_file.load_env(compiler, debug, mpilib)
     for shell in ('sh', 'csh'):
         ems_file.make_env_mach_specific_file(compiler, debug, mpilib, shell)
         shell_path = os.path.join(output_dir, ".env_mach_specific." + shell)

scripts/lib/CIME/BuildTools/macrowriterbase.py

@@ -13,6 +13,7 @@
 import os
 from abc import ABCMeta, abstractmethod
 from CIME.XML.standard_module_setup import *
+from CIME.utils import get_cime_root
 logger = logging.getLogger(__name__)
 
 def _get_components(value):
@@ -234,14 +235,15 @@ def write_macros_file_v1(macros, compiler, os_, machine, macros_file="Macros", o
 '''#
 # cmake Macros generated from $compiler_file
 #
+set(CMAKE_MODULE_PATH %s)
 include(Compilers)
 set(CMAKE_C_FLAGS_RELEASE "" CACHE STRING "Flags used by c compiler." FORCE)
 set(CMAKE_C_FLAGS_DEBUG "" CACHE STRING "Flags used by c compiler." FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "" CACHE STRING "Flags used by Fortran compiler." FORCE)
 set(CMAKE_Fortran_FLAGS_DEBUG "" CACHE STRING "Flags used by Fortran compiler." FORCE)
 set(all_build_types "None Debug Release RelWithDebInfo MinSizeRel")
 set(CMAKE_BUILD_TYPE "${CMAKE_BUILD_TYPE}" CACHE STRING "Choose the type of build, options are: ${all_build_types}." FORCE)
-''')
+''' % os.path.join(get_cime_root(), "src", "CMake"))
 
             # print the settings out to the Macros file, do it in
             # two passes so that path values appear first in the
@@ -254,7 +256,10 @@ def write_macros_file_v1(macros, compiler, os_, machine, macros_file="Macros", o
                     if key.endswith("_PATH"):
                         if value.startswith("$"):
                             value = "$ENV{}".format(value[1:])
-                        fd.write("set({} {})\n".format(key, value))
+
+
+                        cmake_var = key.replace("NETCDF_PATH", "NetCDF_PATH").replace("PNETCDF_PATH", "Pnetcdf_PATH")
+                        fd.write("set({} {})\n".format(cmake_var, value))
                         fd.write("list(APPEND CMAKE_PREFIX_PATH {})\n\n".format(value))
 
             for key, value in sorted(macros.iteritems()):
@@ -268,6 +273,7 @@ def write_macros_file_v1(macros, compiler, os_, machine, macros_file="Macros", o
 
                             idx = 0
                             for is_shell, component in components:
+                                component = component.replace("NETCDF", "NetCDF").replace("PNETCDF_PATH", "Pnetcdf_PATH")
                                 if is_shell:
                                     fd.write('execute_process(COMMAND {} OUTPUT_VARIABLE TEMP{:d})\n'.format(component, idx))
                                     fd.write('string(REGEX REPLACE "\\n$" "" TEMP{:d} "${{TEMP{:d}}}")\n'.format(idx, idx))
@@ -281,13 +287,13 @@ def write_macros_file_v1(macros, compiler, os_, machine, macros_file="Macros", o
                             fd.write('set(TEMP "{}")\n'.format(value))
 
                         if "CFLAGS" in key:
-                            fd.write("add_flags(CMAKE_C_FLAGS ${TEMP})\n\n")
+                            fd.write("add_flags(CFLAGS ${TEMP})\n\n")
                         elif "FFLAGS" in key:
-                            fd.write("add_flags(CMAKE_Fortran_FLAGS ${TEMP})\n\n")
+                            fd.write("add_flags(FFLAGS ${TEMP})\n\n")
                         elif "CPPDEFS" in key:
-                            fd.write("list(APPEND COMPILE_DEFINITIONS ${TEMP})\n\n")
+                            fd.write("list(APPEND CPPDEFS ${TEMP})\n\n")
                         elif "SLIBS" in key or "LDFLAGS" in key:
-                            fd.write("add_flags(CMAKE_EXE_LINKER_FLAGS ${TEMP})\n\n")
+                            fd.write("add_flags(LDFLAGS ${TEMP})\n\n")
 
         # Recursively print the conditionals, combining tests to avoid repetition
         _parse_hash(macros["_COND_"], fd, 0, output_format)

src/CMake/Compilers.cmake

@@ -57,7 +57,7 @@ endfunction()
 #=================================================
 
 # Detect "STOP" for CTest.
-if(${CMAKE_Fortran_COMPILER_ID} STREQUAL NAG)
+if("${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)