def configure(machobj, output_dir, macros_format, compiler, mpilib, debug, sysos, unit_testing=False): """Add Macros, Depends, and env_mach_specific files to a directory. Arguments: machobj - Machines argument for this machine. output_dir - Directory in which to place output. macros_format - Container containing the string 'Makefile' to produce Makefile Macros output, and/or 'CMake' for CMake output. compiler - String containing the compiler vendor to configure for. mpilib - String containing the MPI implementation to configure for. debug - Boolean specifying whether debugging options are enabled. unit_testing - Boolean specifying whether we're running unit tests (as opposed to a system run) """ # Macros generation. suffixes = {'Makefile': 'make', 'CMake': 'cmake'} macro_maker = Compilers(machobj, compiler=compiler, mpilib=mpilib) for form in macros_format: out_file_name = os.path.join(output_dir,"Macros."+suffixes[form]) macro_maker.write_macros_file(macros_file=out_file_name, output_format=suffixes[form]) _copy_depends_files(machobj.get_machine_name(), machobj.machines_dir, output_dir, compiler) _generate_env_mach_specific(output_dir, machobj, compiler, mpilib, debug, sysos, unit_testing)
def configure(machobj, output_dir, macros_format, compiler, mpilib, debug, sysos, unit_testing=False): """Add Macros, Depends, and env_mach_specific files to a directory. Arguments: machobj - Machines argument for this machine. output_dir - Directory in which to place output. macros_format - Container containing the string 'Makefile' to produce Makefile Macros output, and/or 'CMake' for CMake output. compiler - String containing the compiler vendor to configure for. mpilib - String containing the MPI implementation to configure for. debug - Boolean specifying whether debugging options are enabled. unit_testing - Boolean specifying whether we're running unit tests (as opposed to a system run) """ # Macros generation. suffixes = {'Makefile': 'make', 'CMake': 'cmake'} macro_maker = Compilers(machobj, compiler=compiler, mpilib=mpilib) for form in macros_format: out_file_name = os.path.join(output_dir, "Macros." + suffixes[form]) macro_maker.write_macros_file(macros_file=out_file_name, output_format=suffixes[form]) _copy_depends_files(machobj.get_machine_name(), machobj.machines_dir, output_dir, compiler) _generate_env_mach_specific(output_dir, machobj, compiler, mpilib, debug, sysos, unit_testing)
def _has_unit_test_support(self): if self.TEST_COMPILER is None: default_compiler = self.MACHINE.get_default_compiler() compiler = Compilers(self.MACHINE, compiler=default_compiler) else: compiler = Compilers(self.MACHINE, compiler=self.TEST_COMPILER) attrs = {"MPILIB": "mpi-serial", "compile_threaded": "FALSE"} pfunit_path = compiler.get_optional_compiler_node("PFUNIT_PATH", attributes=attrs) if pfunit_path is None: return False else: return True
def test_script_is_callable(self): """The test script can be called on valid output without dying.""" # This is really more a smoke test of this script than anything else. maker = Compilers(test_utils.MockMachines("mymachine", "SomeOS"), version=2.0) test_xml = test_utils._wrap_config_compilers_xml( "<compiler><SUPPORTS_CXX>FALSE</SUPPORTS_CXX></compiler>") test_utils.get_macros(maker, test_xml, "Makefile")
def test_script_rejects_bad_build_system(self): """The macro writer rejects a bad build system string.""" maker = Compilers(test_utils.MockMachines("mymachine", "SomeOS"), version=2.0) bad_string = "argle-bargle." with self.assertRaisesRegex( utils.CIMEError, "Unrecognized build system provided to write_macros: " + bad_string, ): test_utils.get_macros(maker, "This string is irrelevant.", bad_string)
def setUp(self): self.test_os = "SomeOS" self.test_machine = "mymachine" self.test_compiler = (self.MACHINE.get_default_compiler() if self.TEST_COMPILER is None else self.TEST_COMPILER) self.test_mpilib = (self.MACHINE.get_default_MPIlib( attributes={"compiler": self.test_compiler}) if self.TEST_MPILIB is None else self.TEST_MPILIB) self._maker = Compilers(test_utils.MockMachines( self.test_machine, self.test_os), version=2.0) super().setUp()
def setUp(self): super().setUp() if "CIME_NO_CMAKE_MACRO" not in os.environ: self.skipTest("Skipping test of old macro system") self.test_os = "SomeOS" self.test_machine = "mymachine" self.test_compiler = (self.MACHINE.get_default_compiler() if self.TEST_COMPILER is None else self.TEST_COMPILER) self.test_mpilib = (self.MACHINE.get_default_MPIlib( attributes={"compiler": self.test_compiler}) if self.TEST_MPILIB is None else self.TEST_MPILIB) self._maker = Compilers(test_utils.MockMachines( self.test_machine, self.test_os), version=2.0)
def _main(): output, build_dir, build_optimized, clean,\ cmake_args, compiler, enable_genf90, machine, machines_dir,\ make_j, use_mpi, mpilib, mpirun_command, test_spec_dir, ctest_args,\ use_openmp, xml_test_list, verbose \ = parse_command_line(sys.argv) #================================================= # Find directory and file paths. #================================================= suite_specs = [] # TODO: this violates cime policy of direct access to xml # should be moved to CIME/XML if xml_test_list is not None: test_xml_tree = ElementTree() test_xml_tree.parse(xml_test_list) known_paths = { "here": os.path.abspath(os.path.dirname(xml_test_list)), } suite_specs.extend(suites_from_xml(test_xml_tree, known_paths)) if test_spec_dir is not None: suite_specs.append( TestSuiteSpec("__command_line_test__", ["__command_line_test__"], [os.path.abspath(test_spec_dir)])) if machines_dir is not None: machines_file = os.path.join(machines_dir, "config_machines.xml") machobj = Machines(infile=machines_file, machine=machine) else: machobj = Machines(machine=machine) # Create build directory if necessary. build_dir = os.path.abspath(build_dir) if not os.path.isdir(build_dir): os.mkdir(build_dir) # Switch to the build directory. os.chdir(build_dir) if clean: pwd_contents = os.listdir(os.getcwd()) # Clear CMake cache. for file_ in pwd_contents: if file_ in ("Macros.cmake", "env_mach_specific.xml") \ or file_.startswith('Depends') or file_.startswith(".env_mach_specific"): os.remove(file_) #================================================= # Functions to perform various stages of build. #================================================= if not use_mpi: mpilib = "mpi-serial" elif mpilib is None: mpilib = machobj.get_default_MPIlib() logger.info("Using mpilib: {}".format(mpilib)) if compiler is None: compiler = machobj.get_default_compiler() logger.info("Compiler is {}".format(compiler)) compilerobj = Compilers(machobj, compiler=compiler, mpilib=mpilib) pfunit_path = find_pfunit(compilerobj, mpilib=mpilib, use_openmp=use_openmp) debug = not build_optimized os_ = machobj.get_value("OS") # Create the environment, and the Macros.cmake file # # configure(machobj, build_dir, ["CMake"], compiler, mpilib, debug, os_, unit_testing=True) machspecific = EnvMachSpecific(build_dir, unit_testing=True) fake_case = FakeCase(compiler, mpilib, debug) machspecific.load_env(fake_case) os.environ["OS"] = os_ os.environ["COMPILER"] = compiler os.environ["DEBUG"] = stringify_bool(debug) os.environ["MPILIB"] = mpilib if use_openmp: os.environ["compile_threaded"] = "true" else: os.environ["compile_threaded"] = "false" os.environ["UNIT_TEST_HOST"] = socket.gethostname() if "NETCDF_PATH" in os.environ and not "NETCDF" in os.environ: # The CMake Netcdf find utility that we use (from pio2) seems to key off # of the environment variable NETCDF, but not NETCDF_PATH logger.info("Setting NETCDF environment variable: {}".format( os.environ["NETCDF_PATH"])) os.environ["NETCDF"] = os.environ["NETCDF_PATH"] if not use_mpi: mpirun_command = "" elif mpirun_command is None: mpi_attribs = { "compiler": compiler, "mpilib": mpilib, "threaded": use_openmp, "unit_testing": True } # We can get away with specifying case=None since we're using exe_only=True mpirun_command, _ = machspecific.get_mpirun(None, mpi_attribs, None, exe_only=True) mpirun_command = machspecific.get_resolved_value(mpirun_command) logger.info("mpirun command is '{}'".format(mpirun_command)) #================================================= # Run tests. #================================================= for spec in suite_specs: os.chdir(build_dir) if os.path.isdir(spec.name): if clean: rmtree(spec.name) if not os.path.isdir(spec.name): os.mkdir(spec.name) for label, directory in spec: os.chdir(os.path.join(build_dir, spec.name)) if not os.path.isdir(label): os.mkdir(label) os.chdir(label) name = spec.name + "/" + label 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, pfunit_path, verbose=verbose, enable_genf90=enable_genf90, cmake_args=cmake_args) make_stage(name, output, make_j, clean=clean, verbose=verbose) for spec in suite_specs: os.chdir(os.path.join(build_dir, spec.name)) for label, directory in spec: name = spec.name + "/" + label output.print_header("Running CTest tests for " + name + ".") ctest_command = ["ctest", "--output-on-failure"] if verbose: ctest_command.append("-VV") if ctest_args is not None: ctest_command.extend(ctest_args.split(" ")) run_cmd_no_fail(" ".join(ctest_command), from_dir=label, arg_stdout=None, arg_stderr=subprocess.STDOUT)
msg = "case.setup clean complete" append_status(msg, caseroot=caseroot, sfile="CaseStatus") if not clean: models = case.get_values("COMP_CLASSES") mach, compiler, debug, mpilib = \ case.get_value("MACH"), case.get_value("COMPILER"), case.get_value("DEBUG"), case.get_value("MPILIB") expect(mach is not None, "xml variable MACH is not set") # Create Macros file only if it does not exist if not os.path.exists("Macros"): logger.debug("Creating Macros file for %s" % mach) compilers = Compilers(compiler=compiler, machine=mach, os_=case.get_value("OS"), mpilib=mpilib) compilers.write_macros_file() else: logger.debug("Macros script already created ...skipping") # Set tasks to 1 if mpi-serial library if mpilib == "mpi-serial": for vid, value in case: if vid.startswith("NTASKS_") and value != 1: case.set_value(vid, 1) # Check ninst. # In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component. # Save ninst in a dict to use later in apply_user_mods
def test_script_rejects_bad_xml(self): """The macro writer rejects input that's not valid XML.""" maker = Compilers(test_utils.MockMachines("mymachine", "SomeOS"), version=2.0) with self.assertRaises(ParseError): test_utils.get_macros(maker, "This is not valid XML.", "Makefile")
def configure(machobj, output_dir, macros_format, compiler, mpilib, debug, comp_interface, sysos, unit_testing=False, noenv=False, threaded=False, extra_machines_dir=None): """Add Macros, Depends, and env_mach_specific files to a directory. Arguments: machobj - Machines argument for this machine. output_dir - Directory in which to place output. macros_format - Container containing the string 'Makefile' to produce Makefile Macros output, and/or 'CMake' for CMake output. compiler - String containing the compiler vendor to configure for. mpilib - String containing the MPI implementation to configure for. debug - Boolean specifying whether debugging options are enabled. unit_testing - Boolean specifying whether we're running unit tests (as opposed to a system run) extra_machines_dir - String giving path to an additional directory that will be searched for a config_compilers.xml file. """ # Macros generation. suffixes = {'Makefile': 'make', 'CMake': 'cmake'} new_cmake_macros_dir = Files( comp_interface=comp_interface).get_value("CMAKE_MACROS_DIR") macro_maker = None for form in macros_format: if form == "CMake" and new_cmake_macros_dir is not None and os.path.exists( new_cmake_macros_dir ) and not "CIME_NO_CMAKE_MACRO" in os.environ: if not os.path.isfile(os.path.join(output_dir, "Macros.cmake")): safe_copy(os.path.join(new_cmake_macros_dir, "Macros.cmake"), output_dir) if not os.path.exists(os.path.join(output_dir, "cmake_macros")): shutil.copytree(new_cmake_macros_dir, os.path.join(output_dir, "cmake_macros")) else: logger.warning("Using deprecated CIME makefile generators") if macro_maker is None: macro_maker = Compilers(machobj, compiler=compiler, mpilib=mpilib, extra_machines_dir=extra_machines_dir) out_file_name = os.path.join(output_dir, "Macros." + suffixes[form]) macro_maker.write_macros_file(macros_file=out_file_name, output_format=suffixes[form]) copy_depends_files(machobj.get_machine_name(), machobj.machines_dir, output_dir, compiler) generate_env_mach_specific(output_dir, machobj, compiler, mpilib, debug, comp_interface, sysos, unit_testing, threaded, noenv=noenv)
def _case_setup_impl(case, caseroot, casebaseid, clean=False, test_mode=False, reset=False): ############################################################################### os.chdir(caseroot) msg = "case.setup starting" append_status(msg, caseroot=caseroot, sfile="CaseStatus") cimeroot = os.environ["CIMEROOT"] # Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests din_loc_root = case.get_value("DIN_LOC_ROOT") testcase = case.get_value("TESTCASE") expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"), "inputdata root is not a directory: \"$din_loc_root\" ") # Check that userdefine settings are specified before expanding variable for vid, value in case: expect(not (type(value) is str and "USERDEFINED_required_build" in value), "Parameter '%s' must be defined" % vid) # Create batch script if reset or clean: # Clean batch script backup_dir = "PESetupHist/b.%s" % time.strftime("%y%m%d-%H%M%S") if not os.path.isdir(backup_dir): os.makedirs(backup_dir) # back up relevant files for fileglob in ["case.run", "env_build.xml", "env_mach_pes.xml", "Macros*"]: for filename in glob.glob(fileglob): shutil.copy(filename, backup_dir) if os.path.exists("case.run"): os.remove("case.run") # only do the following if are NOT in testmode if not test_mode: # rebuild the models (even on restart) case.set_value("BUILD_COMPLETE", False) # backup and then clean test script if os.path.exists("case.test"): shutil.copy("case.test", backup_dir) os.remove("case.test") logger.info("Successfully cleaned test script case.test") if os.path.exists("case.testdriver"): shutil.copy("case.testdriver", backup_dir) os.remove("case.testdriver") logger.info("Successfully cleaned test script case.testdriver") logger.info("Successfully cleaned batch script case.run") logger.info("Successfully cleaned batch script case.run") logger.info("Some files have been saved to %s" % backup_dir) msg = "case.setup clean complete" append_status(msg, caseroot=caseroot, sfile="CaseStatus") if not clean: drv_comp = Component() models = drv_comp.get_valid_model_components() models.remove("DRV") mach, compiler, debug, mpilib = \ case.get_value("MACH"), case.get_value("COMPILER"), case.get_value("DEBUG"), case.get_value("MPILIB") expect(mach is not None, "xml variable MACH is not set") # Create Macros file only if it does not exist if not os.path.exists("Macros"): logger.debug("Creating Macros file for %s" % mach) compilers = Compilers(compiler=compiler, machine=mach, os_=case.get_value("OS"), mpilib=mpilib) compilers.write_macros_file() else: logger.debug("Macros script already created ...skipping") # Set tasks to 1 if mpi-serial library if mpilib == "mpi-serial": for vid, value in case: if vid.startswith("NTASKS_") and value != 1: case.set_value(vid, 1) # Check ninst. # In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component. # Save ninst in a dict to use later in apply_user_mods ninst = dict() for comp in models: comp_model = case.get_value("COMP_%s" % comp) ninst[comp_model] = case.get_value("NINST_%s" % comp) ntasks = case.get_value("NTASKS_%s" % comp) if ninst[comp_model] > ntasks: if ntasks == 1: case.set_value("NTASKS_%s" % comp, ninst[comp_model]) else: expect(False, "NINST_%s value %d greater than NTASKS_%s %d" % (comp, ninst[comp_model], comp, ntasks)) expect(not (case.get_value("BUILD_THREADED") and compiler == "nag"), "it is not possible to run with OpenMP if using the NAG Fortran compiler") if os.path.exists("case.run"): logger.info("Machine/Decomp/Pes configuration has already been done ...skipping") else: _check_pelayouts_require_rebuild(case, models) if os.path.exists("LockedFiles/env_build.xml"): os.remove("LockedFiles/env_build.xml") case.flush() check_lockedfiles() tm = TaskMaker(case) mtpn = case.get_value("MAX_TASKS_PER_NODE") pespn = case.get_value("PES_PER_NODE") # This is hardcoded because on yellowstone by default we # run with 15 pes per node # but pay for 16 pes per node. See github issue #518 if case.get_value("MACH") == "yellowstone": pespn = 16 pestot = tm.totaltasks if mtpn > pespn: pestot = pestot * (mtpn // pespn) case.set_value("COST_PES", tm.num_nodes*pespn) else: # reset cost_pes to totalpes case.set_value("COST_PES", 0) case.set_value("TOTALPES", pestot) # Compute cost based on PE count pval = 1 pcnt = 0 while pval < pestot: pval *= 2 pcnt += 6 # (scaling like sqrt(6/10)) pcost = 3 - pcnt / 10 # (3 is 64 with 6) # Compute cost based on DEBUG dcost = 3 if debug else 0 # Compute cost based on run length # For simplicity, we use a heuristic just based on STOP_OPTION (not considering # STOP_N), and only deal with options longer than ndays lcost = 0 if "nmonth" in case.get_value("STOP_OPTION"): # N months costs 30x as much as N days; since cost is based on log-base-2, add 5 lcost = 5 elif "nyear" in case.get_value("STOP_OPTION"): # N years costs 365x as much as N days; since cost is based on log-base-2, add 9 lcost = 9 estcost = pcost + dcost + lcost for cost in ["CCSM_CCOST", "CCSM_GCOST", "CCSM_TCOST", "CCSM_CCOST"]: estcost += case.get_value(cost) case.set_value("CCSM_PCOST", pcost) case.set_value("CCSM_ESTCOST", estcost) # create batch file logger.info("Creating batch script case.run") # Use BatchFactory to get the appropriate instance of a BatchMaker, # use it to create our batch scripts env_batch = case.get_env("batch") for job in env_batch.get_jobs(): input_batch_script = os.path.join(case.get_value("MACHDIR"), env_batch.get_value('template', subgroup=job)) if job == "case.test" and testcase is not None and not test_mode: logger.info("Writing %s script" % job) testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase) # Short term fix to be removed when csh tests are removed if not os.path.exists(testscript): env_batch.make_batch_script(input_batch_script, job, case) elif job != "case.test": logger.info("Writing %s script" % job) env_batch.make_batch_script(input_batch_script, job, case) # Make a copy of env_mach_pes.xml in order to be able # to check that it does not change once case.setup is invoked logger.info("Locking file env_mach_pes.xml") case.flush() shutil.copy("env_mach_pes.xml", "LockedFiles") # Create user_nl files for the required number of instances if not os.path.exists("user_nl_cpl"): logger.info("Creating user_nl_xxx files for components and cpl") # loop over models for model in models: comp = case.get_value("COMP_%s" % model) logger.info("Building %s usernl files"%model) _build_usernl_files(case, model, comp) if comp == "cism": run_cmd_no_fail("%s/../components/cism/cime_config/cism.template %s" % (cimeroot, caseroot)) _build_usernl_files(case, "drv", "cpl") user_mods_path = case.get_value("USER_MODS_FULLPATH") if user_mods_path is not None: apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst) elif case.get_value("TEST"): test_mods = parse_test_name(casebaseid)[6] if test_mods is not None: user_mods_path = os.path.join(case.get_value("TESTS_MODS_DIR"), test_mods) apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst) # Run preview namelists for scripts logger.info("preview_namelists") preview_namelists(case) logger.info("See ./CaseDoc for component namelists") logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building") # Create test script if appropriate # Short term fix to be removed when csh tests are removed if os.path.exists("env_test.xml"): if not os.path.exists("case.test"): logger.info("Starting testcase.setup") run_cmd_no_fail("./testcase.setup -caseroot %s" % caseroot) logger.info("Finished testcase.setup") msg = "case.setup complete" append_status(msg, caseroot=caseroot, sfile="CaseStatus") # Record env information env_module = case.get_env("mach_specific") env_module.make_env_mach_specific_file(compiler, debug, mpilib, "sh") env_module.make_env_mach_specific_file(compiler, debug, mpilib, "csh") with open("software_environment.txt", "w") as f: f.write(env_module.list_modules()) run_cmd_no_fail("echo -e '\n' >> software_environment.txt && \ env >> software_environment.txt")
def configure( machobj, output_dir, macros_format, compiler, mpilib, debug, comp_interface, sysos, unit_testing=False, noenv=False, threaded=False, extra_machines_dir=None, ): """Add Macros, Depends, and env_mach_specific files to a directory. Arguments: machobj - Machines argument for this machine. output_dir - Directory in which to place output. macros_format - Container containing the string 'Makefile' to produce Makefile Macros output, and/or 'CMake' for CMake output. compiler - String containing the compiler vendor to configure for. mpilib - String containing the MPI implementation to configure for. debug - Boolean specifying whether debugging options are enabled. unit_testing - Boolean specifying whether we're running unit tests (as opposed to a system run) extra_machines_dir - String giving path to an additional directory that will be searched for a config_compilers.xml file. """ # Macros generation. suffixes = {"Makefile": "make", "CMake": "cmake"} new_cmake_macros_dir = Files( comp_interface=comp_interface).get_value("CMAKE_MACROS_DIR") macro_maker = None for form in macros_format: if (new_cmake_macros_dir is not None and os.path.exists(new_cmake_macros_dir) and not "CIME_NO_CMAKE_MACRO" in os.environ): if not os.path.isfile(os.path.join(output_dir, "Macros.cmake")): safe_copy(os.path.join(new_cmake_macros_dir, "Macros.cmake"), output_dir) if not os.path.exists(os.path.join(output_dir, "cmake_macros")): shutil.copytree(new_cmake_macros_dir, os.path.join(output_dir, "cmake_macros")) # Grab macros from extra machine dir if it was provided if extra_machines_dir: extra_cmake_macros = glob.glob( "{}/cmake_macros/*.cmake".format(extra_machines_dir)) for extra_cmake_macro in extra_cmake_macros: safe_copy(extra_cmake_macro, new_cmake_macros_dir) if form == "Makefile": # Use the cmake macros to generate the make macros cmake_args = " -DOS={} -DMACH={} -DCOMPILER={} -DDEBUG={} -DMPILIB={} -Dcompile_threaded={} -DCASEROOT={}".format( sysos, machobj.get_machine_name(), compiler, stringify_bool(debug), mpilib, stringify_bool(threaded), output_dir, ) with CmakeTmpBuildDir(macroloc=output_dir) as cmaketmp: output = cmaketmp.get_makefile_vars(cmake_args=cmake_args) with open(os.path.join(output_dir, "Macros.make"), "w") as fd: fd.write(output) else: logger.warning("Using deprecated CIME makefile generators") if macro_maker is None: macro_maker = Compilers( machobj, compiler=compiler, mpilib=mpilib, extra_machines_dir=extra_machines_dir, ) out_file_name = os.path.join(output_dir, "Macros." + suffixes[form]) macro_maker.write_macros_file(macros_file=out_file_name, output_format=suffixes[form]) copy_depends_files(machobj.get_machine_name(), machobj.machines_dir, output_dir, compiler) generate_env_mach_specific( output_dir, machobj, compiler, mpilib, debug, comp_interface, sysos, unit_testing, threaded, noenv=noenv, )
def _case_setup_impl(case, caseroot, casebaseid, clean=False, test_mode=False, reset=False): ############################################################################### os.chdir(caseroot) msg = "case.setup starting" append_status(msg, caseroot=caseroot, sfile="CaseStatus") cimeroot = get_cime_root(case) # Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests din_loc_root = case.get_value("DIN_LOC_ROOT") testcase = case.get_value("TESTCASE") expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"), "inputdata root is not a directory: \"$din_loc_root\" ") # Check that userdefine settings are specified before expanding variable for vid, value in case: expect(not (type(value) is str and "USERDEFINED_required_build" in value), "Parameter '%s' must be defined" % vid) # Create batch script if reset or clean: # Clean batch script backup_dir = "PESetupHist/b.%s" % time.strftime("%y%m%d-%H%M%S") if not os.path.isdir(backup_dir): os.makedirs(backup_dir) # back up relevant files for fileglob in ["case.run", "env_build.xml", "env_mach_pes.xml", "Macros*"]: for filename in glob.glob(fileglob): shutil.copy(filename, backup_dir) if os.path.exists("case.run"): os.remove("case.run") # only do the following if are NOT in testmode if not test_mode: # rebuild the models (even on restart) case.set_value("BUILD_COMPLETE", False) # backup and then clean test script if os.path.exists("case.test"): shutil.copy("case.test", backup_dir) os.remove("case.test") logger.info("Successfully cleaned test script case.test") if os.path.exists("case.testdriver"): shutil.copy("case.testdriver", backup_dir) os.remove("case.testdriver") logger.info("Successfully cleaned test script case.testdriver") logger.info("Successfully cleaned batch script case.run") logger.info("Successfully cleaned batch script case.run") logger.info("Some files have been saved to %s" % backup_dir) msg = "case.setup clean complete" append_status(msg, caseroot=caseroot, sfile="CaseStatus") if not clean: models = case.get_values("COMP_CLASSES") mach, compiler, debug, mpilib = \ case.get_value("MACH"), case.get_value("COMPILER"), case.get_value("DEBUG"), case.get_value("MPILIB") expect(mach is not None, "xml variable MACH is not set") # Create Macros file only if it does not exist if not os.path.exists("Macros"): logger.debug("Creating Macros file for %s" % mach) compilers = Compilers(compiler=compiler, machine=mach, os_=case.get_value("OS"), mpilib=mpilib) compilers.write_macros_file() else: logger.debug("Macros script already created ...skipping") # Set tasks to 1 if mpi-serial library if mpilib == "mpi-serial": for vid, value in case: if vid.startswith("NTASKS_") and value != 1: case.set_value(vid, 1) # Check ninst. # In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component. # Save ninst in a dict to use later in apply_user_mods ninst = dict() for comp in models: if comp == "DRV": continue comp_model = case.get_value("COMP_%s" % comp) ninst[comp_model] = case.get_value("NINST_%s" % comp) ntasks = case.get_value("NTASKS_%s" % comp) if ninst[comp_model] > ntasks: if ntasks == 1: case.set_value("NTASKS_%s" % comp, ninst[comp_model]) else: expect(False, "NINST_%s value %d greater than NTASKS_%s %d" % (comp, ninst[comp_model], comp, ntasks)) if os.path.exists("case.run"): logger.info("Machine/Decomp/Pes configuration has already been done ...skipping") else: _check_pelayouts_require_rebuild(case, models) if os.path.exists("LockedFiles/env_build.xml"): os.remove("LockedFiles/env_build.xml") case.flush() check_lockedfiles() env_mach_pes = case.get_env("mach_pes") pestot = env_mach_pes.get_total_tasks(models) logger.debug("at update TOTALPES = %s"%pestot) case.set_value("TOTALPES", pestot) thread_count = env_mach_pes.get_max_thread_count(models) if thread_count > 1: case.set_value("BUILD_THREADED", True) expect(not (case.get_value("BUILD_THREADED") and compiler == "nag"), "it is not possible to run with OpenMP if using the NAG Fortran compiler") cost_pes = env_mach_pes.get_cost_pes(pestot, thread_count, machine=case.get_value("MACH")) case.set_value("COST_PES", cost_pes) # create batch file logger.info("Creating batch script case.run") # Use BatchFactory to get the appropriate instance of a BatchMaker, # use it to create our batch scripts env_batch = case.get_env("batch") num_nodes = env_mach_pes.get_total_nodes(pestot, thread_count) tasks_per_node = env_mach_pes.get_tasks_per_node(pestot, thread_count) for job in env_batch.get_jobs(): input_batch_script = os.path.join(case.get_value("MACHDIR"), env_batch.get_value('template', subgroup=job)) if job == "case.test" and testcase is not None and not test_mode: logger.info("Writing %s script" % job) testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase) # Short term fix to be removed when csh tests are removed if not os.path.exists(testscript): env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count) elif job != "case.test": logger.info("Writing %s script from input template %s" % (job, input_batch_script)) env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count) # Make a copy of env_mach_pes.xml in order to be able # to check that it does not change once case.setup is invoked logger.info("Locking file env_mach_pes.xml") case.flush() logger.debug("at copy TOTALPES = %s"%case.get_value("TOTALPES")) shutil.copy("env_mach_pes.xml", "LockedFiles") # Create user_nl files for the required number of instances if not os.path.exists("user_nl_cpl"): logger.info("Creating user_nl_xxx files for components and cpl") # loop over models for model in models: comp = case.get_value("COMP_%s" % model) logger.info("Building %s usernl files"%model) _build_usernl_files(case, model, comp) if comp == "cism": run_cmd_no_fail("%s/../components/cism/cime_config/cism.template %s" % (cimeroot, caseroot)) _build_usernl_files(case, "drv", "cpl") user_mods_path = case.get_value("USER_MODS_FULLPATH") if user_mods_path is not None: apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst) elif case.get_value("TEST"): test_mods = parse_test_name(casebaseid)[6] if test_mods is not None: user_mods_path = os.path.join(case.get_value("TESTS_MODS_DIR"), test_mods) apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst) # Run preview namelists for scripts logger.info("preview_namelists") preview_namelists(case) logger.info("See ./CaseDoc for component namelists") logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building") # Create test script if appropriate # Short term fix to be removed when csh tests are removed if os.path.exists("env_test.xml"): if not os.path.exists("case.test"): logger.info("Starting testcase.setup") run_cmd_no_fail("./testcase.setup -caseroot %s" % caseroot) logger.info("Finished testcase.setup") msg = "case.setup complete" append_status(msg, caseroot=caseroot, sfile="CaseStatus") # Record env information env_module = case.get_env("mach_specific") env_module.make_env_mach_specific_file(compiler, debug, mpilib, "sh") env_module.make_env_mach_specific_file(compiler, debug, mpilib, "csh") with open("software_environment.txt", "w") as f: f.write(env_module.list_modules()) run_cmd_no_fail("echo -e '\n' >> software_environment.txt && \ env >> software_environment.txt")