├── python ├── slim │ ├── __init__.py │ ├── test │ │ ├── __init__.py │ │ └── README │ ├── mksurdat │ │ └── __init__.py │ ├── modify_input_files │ │ └── __init__.py │ ├── import_hook.py │ ├── unit_testing.py │ ├── add_slim_cime_py_to_path.py │ ├── add_cime_to_path.py │ ├── git_utils.py │ ├── run_slim_py_tests.py │ ├── utils.py │ ├── slim_logging.py │ ├── path_utils.py │ └── config_utils.py ├── run_slim_py_tests ├── conda_env_slim_py.txt ├── pyproject.toml ├── conda_env_slim_py_cgd.txt ├── README.md └── Makefile ├── manage_externals ├── test │ ├── doc │ │ ├── .gitignore │ │ ├── index.rst │ │ ├── Makefile │ │ └── testing.rst │ ├── repos │ │ ├── container.git │ │ │ ├── HEAD │ │ │ ├── refs │ │ │ │ └── heads │ │ │ │ │ └── master │ │ │ ├── description │ │ │ ├── config │ │ │ ├── objects │ │ │ │ ├── 41 │ │ │ │ │ └── 1de5d96ee418c1c55f3e96e6e6e7c06bb95801 │ │ │ │ ├── 71 │ │ │ │ │ └── 5b8f3e4afe1802a178e1d603af404ba45d59de │ │ │ │ ├── b0 │ │ │ │ │ └── f87705e2b9601cb831878f3d51efa78b910d7b │ │ │ │ └── f9 │ │ │ │ │ └── e08370a737e941de6f6492e3f427c2ef4c1a03 │ │ │ └── info │ │ │ │ └── exclude │ │ ├── mixed-cont-ext.git │ │ │ ├── HEAD │ │ │ ├── refs │ │ │ │ └── heads │ │ │ │ │ ├── master │ │ │ │ │ └── new-feature │ │ │ ├── description │ │ │ ├── config │ │ │ ├── objects │ │ │ │ ├── 14 │ │ │ │ │ └── 368b701616a8c53820b610414a4b9a07540cf6 │ │ │ │ ├── 15 │ │ │ │ │ └── 2b57e1cf23721cd17ff681cb9276e3fb9fc091 │ │ │ │ ├── 37 │ │ │ │ │ └── f0e70b609adc90f4c09ee21d82ed1d79c81d69 │ │ │ │ ├── 38 │ │ │ │ │ └── 9a2b876b8965d3c91a3db8d28a483eaf019d5c │ │ │ │ ├── 41 │ │ │ │ │ └── 1de5d96ee418c1c55f3e96e6e6e7c06bb95801 │ │ │ │ ├── 93 │ │ │ │ │ └── a159deb9175bfeb2820a0006ddd92d78131332 │ │ │ │ ├── 95 │ │ │ │ │ └── 80ecc12f16334ce44e42287d5d46f927bb7b75 │ │ │ │ ├── 00 │ │ │ │ │ └── 437ac2000d5f06fb8a572a01a5bbdae98b17cb │ │ │ │ ├── 01 │ │ │ │ │ └── 97458f2dbe5fcd6bc44fa46983be0a30282379 │ │ │ │ ├── 06 │ │ │ │ │ └── ea30b03ffa2f8574705f8b9583f7ca7e2dccf7 │ │ │ │ ├── 1f │ │ │ │ │ └── 01fa46c17b1f38b37e6259f6e9d041bda3144f │ │ │ │ ├── 6e │ │ │ │ │ └── 9f4baa6e94a0af4e094836c2eb55ccedef5fc4 │ │ │ │ ├── 6f │ │ │ │ │ └── c379457ecb4e576a13c7610ae1fa73f845ee6a │ │ │ │ ├── a9 │ │ │ │ │ └── 288dcd8a719a1f4ed3cba43a2a387ae7cd60fd │ │ │ │ ├── e8 │ │ │ │ │ └── ea32a11d30ee703f6f661ae7c2376f4ab84d38 │ │ │ │ └── fd │ │ │ │ │ └── 15a5ad5204356229c60a831d2a8120a43ac901 │ │ │ └── info │ │ │ │ └── exclude │ │ ├── simple-ext.git │ │ │ ├── HEAD │ │ │ ├── refs │ │ │ │ ├── tags │ │ │ │ │ ├── tag1 │ │ │ │ │ └── tag2 │ │ │ │ └── heads │ │ │ │ │ ├── feature2 │ │ │ │ │ ├── feature3 │ │ │ │ │ └── master │ │ │ ├── description │ │ │ ├── config │ │ │ ├── objects │ │ │ │ ├── 11 │ │ │ │ │ └── a76e3d9a67313dec7ce1230852ab5c86352c5c │ │ │ │ ├── 14 │ │ │ │ │ └── 2711fdbbcb8034d7cad6bae6801887b12fe61d │ │ │ │ ├── 31 │ │ │ │ │ └── dbcd6de441e671a467ef317146539b7ffabb11 │ │ │ │ ├── 36 │ │ │ │ │ └── 418b4e5665956a90725c9a1b5a8e551c5f3d48 │ │ │ │ ├── 41 │ │ │ │ │ └── 1de5d96ee418c1c55f3e96e6e6e7c06bb95801 │ │ │ │ ├── 60 │ │ │ │ │ ├── 7ec299c17dd285c029edc41a0109e49d441380 │ │ │ │ │ └── b1cc1a38d63a4bcaa1e767262bbe23dbf9f5f5 │ │ │ │ ├── 63 │ │ │ │ │ └── a99393d1baff97ccef967af30380659867b139 │ │ │ │ ├── 95 │ │ │ │ │ └── 3256da5612fcd9263590a353bc18c6f224e74f │ │ │ │ ├── 00 │ │ │ │ │ └── fd13e76189f9134b0506b4b8ed3172723b467f │ │ │ │ ├── 09 │ │ │ │ │ └── 0e1034746b2c865f7b0280813dbf4061a700e8 │ │ │ │ ├── 0b │ │ │ │ │ └── 15e8af3d4615b42314216efeae3fff184046a8 │ │ │ │ ├── 9b │ │ │ │ │ └── 75494003deca69527bb64bcaa352e801611dd2 │ │ │ │ ├── a2 │ │ │ │ │ └── 2a5da9119328ea6d693f88861457c07e14ac04 │ │ │ │ ├── b7 │ │ │ │ │ └── 692b6d391899680da7b9b6fd8af4c413f06fe7 │ │ │ │ ├── c5 │ │ │ │ │ └── b315915742133dbdfbeed0753e481b55c1d364 │ │ │ │ ├── d1 │ │ │ │ │ └── 163870d19c3dee34fada3a76b785cfa2a8424b │ │ │ │ ├── d8 │ │ │ │ │ └── ed2f33179d751937f8fde2e33921e4827babf4 │ │ │ │ └── df │ │ │ │ │ └── 312890f93ba4d2c694208599b665c4a08afeff │ │ │ └── info │ │ │ │ └── exclude │ │ ├── simple-ext-fork.git │ │ │ ├── HEAD │ │ │ ├── refs │ │ │ │ ├── heads │ │ │ │ │ └── feature2 │ │ │ │ └── tags │ │ │ │ │ ├── abandoned-feature │ │ │ │ │ └── forked-feature-v1 │ │ │ ├── description │ │ │ ├── objects │ │ │ │ ├── 11 │ │ │ │ │ └── a76e3d9a67313dec7ce1230852ab5c86352c5c │ │ │ │ ├── 16 │ │ │ │ │ └── 5506a7408a482f50493434e13fffeb44af893f │ │ │ │ ├── 24 │ │ │ │ │ └── 4386e788c9bc608613e127a329c742450a60e4 │ │ │ │ ├── 32 │ │ │ │ │ └── 7e97d86e941047d809dba58f2804740c6c30cf │ │ │ │ ├── 36 │ │ │ │ │ └── 418b4e5665956a90725c9a1b5a8e551c5f3d48 │ │ │ │ ├── 41 │ │ │ │ │ └── 1de5d96ee418c1c55f3e96e6e6e7c06bb95801 │ │ │ │ ├── 56 │ │ │ │ │ └── 175e017ad38bf3d33d74b6bd7c74624b28466a │ │ │ │ ├── 67 │ │ │ │ │ └── 136e5ab4d5c1c65d10c8048763b96b0e53c1d6 │ │ │ │ ├── 88 │ │ │ │ │ └── cf20868e0cc445f5642a480ed034c71e0d7e9f │ │ │ │ ├── 00 │ │ │ │ │ └── fd13e76189f9134b0506b4b8ed3172723b467f │ │ │ │ ├── 0b │ │ │ │ │ ├── 15e8af3d4615b42314216efeae3fff184046a8 │ │ │ │ │ └── 67df4e7e8e6e1c6e401542738b352d18744677 │ │ │ │ ├── 3d │ │ │ │ │ ├── 7099c35404ae6c8640ce263b38bef06e98cc26 │ │ │ │ │ └── ec1fdf8e2f5edba28148c5db2fe8d7a842360b │ │ │ │ ├── 4d │ │ │ │ │ └── 837135915ed93eed6fff6b439f284ce317296f │ │ │ │ ├── 5f │ │ │ │ │ └── 1d4786d12e52d7ab28d2f2f1118c1059a9f1ae │ │ │ │ ├── 7b │ │ │ │ │ └── 0bd630ac13865735a1dff3437a137d8ab50663 │ │ │ │ ├── 8d │ │ │ │ │ └── 2b3b35126224c975d23f109aa1e3cbac452989 │ │ │ │ ├── 9b │ │ │ │ │ └── 75494003deca69527bb64bcaa352e801611dd2 │ │ │ │ ├── a2 │ │ │ │ │ └── 2a5da9119328ea6d693f88861457c07e14ac04 │ │ │ │ ├── a4 │ │ │ │ │ └── 2fe9144f5707bc1e9515ce1b44681f7aba6f95 │ │ │ │ ├── b9 │ │ │ │ │ └── 3737be3ea6b19f6255983748a0a0f4d622f936 │ │ │ │ ├── c5 │ │ │ │ │ ├── 32bc8fde96fa63103a52057f0baffcc9f00c6b │ │ │ │ │ └── b315915742133dbdfbeed0753e481b55c1d364 │ │ │ │ └── f2 │ │ │ │ │ └── 68d4e56d067da9bd1d85e55bdc40a8bd2b0bca │ │ │ ├── info │ │ │ │ └── exclude │ │ │ ├── packed-refs │ │ │ └── config │ │ └── error │ │ │ └── readme.txt │ ├── requirements.txt │ ├── .gitignore │ ├── .coveragerc │ ├── README.md │ └── Makefile ├── manic │ ├── __init__.py │ ├── global_constants.py │ ├── repository_factory.py │ └── repository.py ├── .gitignore ├── .dir_locals.el ├── .travis.yml ├── .github │ ├── ISSUE_TEMPLATE.md │ └── PULL_REQUEST_TEMPLATE.md ├── checkout_externals ├── README_FIRST └── LICENSE.txt ├── cime_config ├── testdefs │ ├── testmods_dirs │ │ └── slim │ │ │ ├── Monthly │ │ │ ├── include_user_mods │ │ │ └── user_nl_slim │ │ │ ├── g16_SOM │ │ │ ├── include_user_mods │ │ │ ├── shell_commands │ │ │ └── user_docn.streams.txt.som │ │ │ ├── global_uniform │ │ │ ├── include_user_mods │ │ │ └── shell_commands │ │ │ ├── realistic_2000 │ │ │ ├── include_user_mods │ │ │ └── shell_commands │ │ │ ├── save_cplhist │ │ │ ├── include_user_mods │ │ │ └── user_nl_cpl │ │ │ ├── g16_SOM_save_cplhist │ │ │ └── include_user_mods │ │ │ ├── default │ │ │ ├── shell_commands │ │ │ └── user_nl_slim │ │ │ ├── global_uniform_g16_SOM │ │ │ └── include_user_mods │ │ │ └── global_uniform_g16_SOMMonthly │ │ │ └── include_user_mods │ └── ExpectedTestFails.xml ├── slim_cime_py │ └── __init__.py ├── buildnml_test │ ├── run_buildnml │ ├── env_archive.xml │ ├── env_workflow.xml │ ├── env_mach_specific.xml │ ├── env_batch.xml │ ├── env_build.xml │ ├── user_nl_slim │ ├── env_run.xml │ ├── env_case.xml │ └── env_mach_pes.xml ├── user_nl_slim ├── buildnml ├── config_archive.xml ├── config_component.xml ├── namelist_definition.xsl ├── buildlib └── config_compsets.xml ├── README.rst ├── src ├── main │ ├── dtypes.h │ ├── clm_varpar.F90 │ ├── abortutils.F90 │ ├── ncdio_utils.F90 │ ├── clm_instMod.F90 │ ├── GridcellType.F90 │ ├── GetGlobalValuesMod.F90 │ └── subgridRestMod.F90 ├── utils │ ├── dtypes.h │ ├── clm_varorb.F90 │ ├── getdatetime.F90 │ ├── array_utils.F90.in │ ├── clm_nlUtilsMod.F90 │ └── spmdMod.F90 ├── cpl │ └── nuopc │ │ └── lnd_comp_shr.F90 └── init_interp │ ├── initInterpMultilevelBase.F90 │ ├── initInterpBounds.F90 │ ├── initInterp1dData.F90 │ └── initInterpMultilevelCopy.F90 ├── tools ├── modify_input_files │ ├── surdat_modifier │ ├── README.surdat_modifier │ ├── modify_surdat_defaults.cfg │ └── modify_surdat_template.cfg ├── README └── mksurdat │ └── README.mksurdat ├── README.md ├── .gitignore ├── README.testing ├── CONTRIBUTING.md ├── .config_files.xml ├── Externals.cfg ├── LICENSE ├── README ├── Copyright ├── README_EXTERNALS.rst └── py_env_create /python/slim/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /python/slim/test/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /python/slim/mksurdat/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /python/slim/modify_input_files/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /manage_externals/test/doc/.gitignore: -------------------------------------------------------------------------------- 1 | _build 2 | 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/HEAD: -------------------------------------------------------------------------------- 1 | ref: refs/heads/master 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/HEAD: -------------------------------------------------------------------------------- 1 | ref: refs/heads/master 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/HEAD: -------------------------------------------------------------------------------- 1 | ref: refs/heads/master 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/Monthly/include_user_mods: -------------------------------------------------------------------------------- 1 | ../default 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/g16_SOM/include_user_mods: -------------------------------------------------------------------------------- 1 | ../default 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/HEAD: -------------------------------------------------------------------------------- 1 | ref: refs/heads/master 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/global_uniform/include_user_mods: -------------------------------------------------------------------------------- 1 | ../default 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/realistic_2000/include_user_mods: -------------------------------------------------------------------------------- 1 | ../default 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/save_cplhist/include_user_mods: -------------------------------------------------------------------------------- 1 | ../default 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/refs/tags/tag1: -------------------------------------------------------------------------------- 1 | 11a76e3d9a67313dec7ce1230852ab5c86352c5c 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/refs/tags/tag2: -------------------------------------------------------------------------------- 1 | b7692b6d391899680da7b9b6fd8af4c413f06fe7 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/Monthly/user_nl_slim: -------------------------------------------------------------------------------- 1 | hist_nhtfrq = 0 2 | hist_mfilt = 1 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/refs/heads/master: -------------------------------------------------------------------------------- 1 | 715b8f3e4afe1802a178e1d603af404ba45d59de 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/refs/heads/feature2: -------------------------------------------------------------------------------- 1 | 36418b4e5665956a90725c9a1b5a8e551c5f3d48 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/refs/heads/feature3: -------------------------------------------------------------------------------- 1 | 090e1034746b2c865f7b0280813dbf4061a700e8 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/refs/heads/master: -------------------------------------------------------------------------------- 1 | 607ec299c17dd285c029edc41a0109e49d441380 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/g16_SOM_save_cplhist/include_user_mods: -------------------------------------------------------------------------------- 1 | ../g16_SOM 2 | ../save_cplhist 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/refs/heads/master: -------------------------------------------------------------------------------- 1 | 6fc379457ecb4e576a13c7610ae1fa73f845ee6a 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2: -------------------------------------------------------------------------------- 1 | f268d4e56d067da9bd1d85e55bdc40a8bd2b0bca 2 | -------------------------------------------------------------------------------- /cime_config/slim_cime_py/__init__.py: -------------------------------------------------------------------------------- 1 | # pylint: disable=missing-module-docstring 2 | from .buildnml import buildnml 3 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/default/shell_commands: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ./xmlchange SLIM_START_TYPE="cold" 3 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/global_uniform_g16_SOM/include_user_mods: -------------------------------------------------------------------------------- 1 | ../global_uniform 2 | ../g16_SOM 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/refs/heads/new-feature: -------------------------------------------------------------------------------- 1 | 9580ecc12f16334ce44e42287d5d46f927bb7b75 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature: -------------------------------------------------------------------------------- 1 | a42fe9144f5707bc1e9515ce1b44681f7aba6f95 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1: -------------------------------------------------------------------------------- 1 | 8d2b3b35126224c975d23f109aa1e3cbac452989 2 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/default/user_nl_slim: -------------------------------------------------------------------------------- 1 | hist_ndens = 1 2 | hist_nhtfrq =-24 3 | hist_mfilt = 5 4 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/global_uniform/shell_commands: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ./xmlchange SLIM_SCENARIO="global_uniform" 3 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/global_uniform_g16_SOMMonthly/include_user_mods: -------------------------------------------------------------------------------- 1 | ../Monthly 2 | ../global_uniform_g16_SOM 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/description: -------------------------------------------------------------------------------- 1 | Unnamed repository; edit this file 'description' to name the repository. 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/description: -------------------------------------------------------------------------------- 1 | Unnamed repository; edit this file 'description' to name the repository. 2 | -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- 1 | ================ 2 | SimpleLandModel 3 | ================ 4 | 5 | SLIM the Simple Land Interface Model coupled to CESM2 6 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/realistic_2000/shell_commands: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ./xmlchange SLIM_SCENARIO="realistic_from_2000" 3 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/description: -------------------------------------------------------------------------------- 1 | Unnamed repository; edit this file 'description' to name the repository. 2 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/description: -------------------------------------------------------------------------------- 1 | Unnamed repository; edit this file 'description' to name the repository. 2 | -------------------------------------------------------------------------------- /manage_externals/test/requirements.txt: -------------------------------------------------------------------------------- 1 | pylint>=1.7.0 2 | autopep8>=1.3.0 3 | coverage>=4.4.0 4 | coveralls>=1.2.0 5 | sphinx>=1.6.0 6 | -------------------------------------------------------------------------------- /manage_externals/test/repos/error/readme.txt: -------------------------------------------------------------------------------- 1 | Invalid or corrupted git repository (.git dir exists, but is empty) for error 2 | testing. 3 | 4 | -------------------------------------------------------------------------------- /manage_externals/test/.gitignore: -------------------------------------------------------------------------------- 1 | # virtual environments 2 | env_python* 3 | 4 | # python code coverage tool output 5 | .coverage 6 | htmlcov 7 | 8 | -------------------------------------------------------------------------------- /src/main/dtypes.h: -------------------------------------------------------------------------------- 1 | #define TYPETEXT 100 2 | #define TYPEREAL 101 3 | #define TYPEDOUBLE 102 4 | #define TYPEINT 103 5 | #define TYPELONG 104 6 | #define TYPELOGICAL 105 7 | -------------------------------------------------------------------------------- /manage_externals/test/.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | branch = True 3 | omit = test_unit_*.py 4 | test_sys_*.py 5 | /usr/* 6 | .local/* 7 | */site-packages/* -------------------------------------------------------------------------------- /src/utils/dtypes.h: -------------------------------------------------------------------------------- 1 | #define TYPEDOUBLE 102 2 | #define TYPEINT 103 3 | #define TYPETEXT 100 4 | #define TYPELONG 104 5 | #define TYPEREAL 101 6 | #define TYPELOGICAL 105 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/config: -------------------------------------------------------------------------------- 1 | [core] 2 | repositoryformatversion = 0 3 | filemode = true 4 | bare = true 5 | ignorecase = true 6 | precomposeunicode = true 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/config: -------------------------------------------------------------------------------- 1 | [core] 2 | repositoryformatversion = 0 3 | filemode = true 4 | bare = true 5 | ignorecase = true 6 | precomposeunicode = true 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/config: -------------------------------------------------------------------------------- 1 | [core] 2 | repositoryformatversion = 0 3 | filemode = true 4 | bare = true 5 | ignorecase = true 6 | precomposeunicode = true 7 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/run_buildnml: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | rm Buildconf/slimconf/lnd_in 3 | env CIMEROOT=`pwd`/../../cime ../buildnml `pwd` --verbose --debug 4 | cat Buildconf/slimconf/lnd_in 5 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/g16_SOM/shell_commands: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | CIMEROOT=`./xmlquery --value -s CIMEROOT` 3 | cp $CIMEROOT/../cime_config/testdefs/testmods_dirs/slim/g16_SOM/user_docn* . 4 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_archive.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 |
4 |
5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/save_cplhist/user_nl_cpl: -------------------------------------------------------------------------------- 1 | histaux_a2x3hr=.true. 2 | histaux_a2x3hrp = .true. 3 | histaux_a2x1hri = .true. 4 | histaux_a2x1hr = .true. 5 | histaux_a2x24hr = .true. 6 | histaux_a2x = .true. 7 | -------------------------------------------------------------------------------- /python/slim/import_hook.py: -------------------------------------------------------------------------------- 1 | # pylint: disable=missing-module-docstring 2 | import sys 3 | import os 4 | 5 | _CIMEROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "..", "cime") 6 | sys.path.append(_CIMEROOT) 7 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_workflow.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 |
6 | 7 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /manage_externals/manic/__init__.py: -------------------------------------------------------------------------------- 1 | """Public API for the manage_externals library 2 | """ 3 | 4 | from manic import checkout 5 | from manic.utils import printlog 6 | 7 | __all__ = [ 8 | 'checkout', 'printlog', 9 | ] 10 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/SimpleLand/cesm2_3_slim/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/objects/71/5b8f3e4afe1802a178e1d603af404ba45d59de: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/SimpleLand/cesm2_3_slim/manage_externals/test/repos/container.git/objects/71/5b8f3e4afe1802a178e1d603af404ba45d59de -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/objects/b0/f87705e2b9601cb831878f3d51efa78b910d7b: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ESCOMP/SimpleLand/cesm2_3_slim/manage_externals/test/repos/container.git/objects/b0/f87705e2b9601cb831878f3d51efa78b910d7b -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/objects/f9/e08370a737e941de6f6492e3f427c2ef4c1a03: -------------------------------------------------------------------------------- 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*.pyc 15 | -------------------------------------------------------------------------------- /manage_externals/test/repos/container.git/info/exclude: -------------------------------------------------------------------------------- 1 | # git ls-files --others --exclude-from=.git/info/exclude 2 | # Lines that start with '#' are comments. 3 | # For a project mostly in C, the following would be a good set of 4 | # exclude patterns (uncomment them if you want to use them): 5 | # *.[oa] 6 | # *~ 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/mixed-cont-ext.git/info/exclude: -------------------------------------------------------------------------------- 1 | # git ls-files --others --exclude-from=.git/info/exclude 2 | # Lines that start with '#' are comments. 3 | # For a project mostly in C, the following would be a good set of 4 | # exclude patterns (uncomment them if you want to use them): 5 | # *.[oa] 6 | # *~ 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext.git/info/exclude: -------------------------------------------------------------------------------- 1 | # git ls-files --others --exclude-from=.git/info/exclude 2 | # Lines that start with '#' are comments. 3 | # For a project mostly in C, the following would be a good set of 4 | # exclude patterns (uncomment them if you want to use them): 5 | # *.[oa] 6 | # *~ 7 | -------------------------------------------------------------------------------- /manage_externals/.dir_locals.el: -------------------------------------------------------------------------------- 1 | ; -*- mode: Lisp -*- 2 | 3 | ((python-mode 4 | . ( 5 | ;; fill the paragraph to 80 columns when using M-q 6 | (fill-column . 80) 7 | 8 | ;; Use 4 spaces to indent in Python 9 | (python-indent-offset . 4) 10 | (indent-tabs-mode . nil) 11 | ))) 12 | 13 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/info/exclude: -------------------------------------------------------------------------------- 1 | # git ls-files --others --exclude-from=.git/info/exclude 2 | # Lines that start with '#' are comments. 3 | # For a project mostly in C, the following would be a good set of 4 | # exclude patterns (uncomment them if you want to use them): 5 | # *.[oa] 6 | # *~ 7 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/packed-refs: -------------------------------------------------------------------------------- 1 | # pack-refs with: peeled fully-peeled sorted 2 | 36418b4e5665956a90725c9a1b5a8e551c5f3d48 refs/heads/feature2 3 | 9b75494003deca69527bb64bcaa352e801611dd2 refs/heads/master 4 | 11a76e3d9a67313dec7ce1230852ab5c86352c5c refs/tags/tag1 5 | ^9b75494003deca69527bb64bcaa352e801611dd2 6 | -------------------------------------------------------------------------------- /manage_externals/test/repos/simple-ext-fork.git/config: -------------------------------------------------------------------------------- 1 | [core] 2 | repositoryformatversion = 0 3 | filemode = true 4 | bare = true 5 | ignorecase = true 6 | precomposeunicode = true 7 | [remote "origin"] 8 | url = /Users/andreb/projects/ncar/git-conversion/checkout-model-dev/cesm-demo-externals/manage_externals/test/repos/simple-ext.git 9 | -------------------------------------------------------------------------------- /manage_externals/.travis.yml: -------------------------------------------------------------------------------- 1 | language: python 2 | os: linux 3 | python: 4 | - "2.7" 5 | - "3.4" 6 | - "3.5" 7 | - "3.6" 8 | - "3.7" 9 | - "3.8" 10 | install: 11 | - pip install -r test/requirements.txt 12 | before_script: 13 | - git --version 14 | script: 15 | - cd test; make test 16 | - cd test; make lint 17 | after_success: 18 | - cd test; make coverage 19 | - cd test; coveralls 20 | -------------------------------------------------------------------------------- /python/run_slim_py_tests: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | """Driver for running the unit tests of the python code 3 | 4 | We use this rather than simply relying on 'python -m unittest discover' so we can do some 5 | initial setup, like configuring logging, before running the unit tests. 6 | """ 7 | 8 | from slim import add_cime_to_path 9 | from slim.run_slim_py_tests import main 10 | 11 | if __name__ == "__main__": 12 | main(__doc__) 13 | -------------------------------------------------------------------------------- /manage_externals/.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | ### Summary of Issue: 2 | ### Expected behavior and actual behavior: 3 | ### Steps to reproduce the problem (should include model description file(s) or link to publi c repository): 4 | ### What is the changeset ID of the code, and the machine you are using: 5 | ### have you modified the code? If so, it must be committed and available for testing: 6 | ### Screen output or log file showing the error message and context: 7 | -------------------------------------------------------------------------------- /src/cpl/nuopc/lnd_comp_shr.F90: -------------------------------------------------------------------------------- 1 | module lnd_comp_shr 2 | 3 | ! Model mesh info is here in order to be leveraged by CDEPS in line calls 4 | 5 | use ESMF 6 | use shr_kind_mod, only : r8 => shr_kind_r8, cl=>shr_kind_cl 7 | 8 | implicit none 9 | public 10 | 11 | type(ESMF_Clock) :: model_clock ! model clock 12 | type(ESMF_Mesh) :: mesh ! model_mesh 13 | character(len=cl) :: model_meshfile ! model mesh file 14 | 15 | end module lnd_comp_shr 16 | -------------------------------------------------------------------------------- /manage_externals/manic/global_constants.py: -------------------------------------------------------------------------------- 1 | """Globals shared across modules 2 | """ 3 | 4 | from __future__ import absolute_import 5 | from __future__ import unicode_literals 6 | from __future__ import print_function 7 | 8 | import pprint 9 | 10 | EMPTY_STR = '' 11 | LOCAL_PATH_INDICATOR = '.' 12 | VERSION_SEPERATOR = '.' 13 | LOG_FILE_NAME = 'manage_externals.log' 14 | PPRINTER = pprint.PrettyPrinter(indent=4) 15 | 16 | VERBOSITY_DEFAULT = 0 17 | VERBOSITY_VERBOSE = 1 18 | VERBOSITY_DUMP = 2 19 | -------------------------------------------------------------------------------- /python/conda_env_slim_py.txt: -------------------------------------------------------------------------------- 1 | # 2 | # NOTE: Changes here should be coordinated with the cgd python environment file 3 | # 4 | # To install this on cheyenne with conda loaded in modules 5 | # use the top level bash script: 6 | # ../py_env_create # Do this each time you update your CTSM Version 7 | # conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script 8 | # 9 | python=3.7.9 10 | pylint=2.8.3 11 | black=22.6.0 12 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_mach_specific.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 8 | 9 |
10 |
11 | 12 | 13 | char 14 | executable name 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /tools/modify_input_files/surdat_modifier: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | """ 3 | For description and instructions, please see README. 4 | """ 5 | 6 | import os 7 | import sys 8 | 9 | _SLIM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), 10 | os.pardir, 11 | os.pardir, 12 | 'python') 13 | sys.path.insert(1, _SLIM_PYTHON) 14 | 15 | from slim.modify_input_files.surdat_modifier import main 16 | 17 | if __name__ == "__main__": 18 | main() 19 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SLIM: The Simple Land Interface Model 2 | Simple Land Model for CESM 3 | 4 | 5 | For instructions on how to run SLIM on it's own or coupled to CESM on Cheyenne, see the Wiki, and the README file at the top of the 6 | SLIM checkout. 7 | 8 | To cite, please use: 9 | 10 | Laguë, M. M., Bonan, G. B., & Swann, A. L. S. (2019). Separating the Impact of Individual Land Surface Properties on the Terrestrial Surface Energy Budget in both the Coupled and Uncoupled Land–Atmosphere System. Journal of Climate, 32(18), 5725–5744. https://doi.org/10.1175/jcli-d-18-0812.1 11 | 12 | -------------------------------------------------------------------------------- /python/pyproject.toml: -------------------------------------------------------------------------------- 1 | # 2 | # This is a configuration file for python projects. 3 | # Sepcifically covering build system requirements. 4 | # 5 | # Here we are just using a couple options to specify the operation 6 | # of the python formatter "black". 7 | # 8 | [tool.black] 9 | 10 | line-length = 100 # This is the black default 11 | target-version = ['py37'] 12 | include = '(run_slim_py_tests|\.py$)' # Files to include 13 | exclude = '(\.pylintrc|\.pyc)' # Files to explicitly exclude pylint file and compiled python 14 | -------------------------------------------------------------------------------- /python/slim/unit_testing.py: -------------------------------------------------------------------------------- 1 | """Functions to aid unit tests""" 2 | 3 | from slim.slim_logging import setup_logging_for_tests 4 | 5 | 6 | def setup_for_tests(enable_critical_logs=False): 7 | """Call this at the beginning of unit testing 8 | 9 | Does various setup that would normally be done by the top-level application/script 10 | 11 | Args: 12 | enable_critical_logs (bool): If True, then critical logging messages will be output; 13 | if False, then even critical messages will be suppressed 14 | """ 15 | setup_logging_for_tests(enable_critical_logs) 16 | -------------------------------------------------------------------------------- /manage_externals/.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | [ 50 character, one line summary ] 2 | 3 | [ Description of the changes in this commit. It should be enough 4 | information for someone not following this development to understand. 5 | Lines should be wrapped at about 72 characters. ] 6 | 7 | User interface changes?: [ No/Yes ] 8 | [ If yes, describe what changed, and steps taken to ensure backward compatibilty ] 9 | 10 | Fixes: [Github issue #s] And brief description of each issue. 11 | 12 | Testing: 13 | test removed: 14 | unit tests: 15 | system tests: 16 | manual testing: 17 | 18 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_batch.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 |
4 |
5 | 6 | 9 | 10 | 11 | char 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /manage_externals/test/doc/index.rst: -------------------------------------------------------------------------------- 1 | .. Manage Externals documentation master file, created by 2 | sphinx-quickstart on Wed Nov 29 10:53:25 2017. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to Manage Externals's documentation! 7 | ============================================ 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | 14 | develop.rst 15 | testing.rst 16 | 17 | Indices and tables 18 | ================== 19 | 20 | * :ref:`genindex` 21 | * :ref:`modindex` 22 | * :ref:`search` 23 | -------------------------------------------------------------------------------- /src/utils/clm_varorb.F90: -------------------------------------------------------------------------------- 1 | 2 | module clm_varorb 3 | 4 | use shr_kind_mod , only: r8 => shr_kind_r8 5 | implicit none 6 | 7 | ! Orbital information needed as input to orbit_parms 8 | 9 | real(r8) :: eccen ! Earth's eccentricity factor (unitless) (typically 0 to 0.1) 10 | 11 | ! Orbital information after processed by orbit_params 12 | 13 | real(r8) :: obliqr ! Earth's obliquity in radians 14 | real(r8) :: lambm0 ! Mean longitude of perihelion at the vernal equinox (radians) 15 | real(r8) :: mvelpp ! Earth's moving vernal equinox longitude of perihelion plus pi (radians) 16 | 17 | end module clm_varorb 18 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_build.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 |
6 | 7 | 10 | 11 | 12 | char 13 | Land (lnd) grid 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /python/conda_env_slim_py_cgd.txt: -------------------------------------------------------------------------------- 1 | # NOTE: This version is just for cgd.ucar.edu systems, where conda limits python to version 3.7.0 2 | # See issue https://github.com/ESCOMP/CTSM/issues/1792 3 | # 4 | # This should be coordinated with the main python environment file! 5 | # 6 | # To install this on cheyenne with conda loaded in modules 7 | # use the top level bash script: 8 | # ../py_env_create # Do this each time you update your CTSM Version 9 | # 10 | python=3.7.0 # The python version MUST match the python version available on CGD systems through modules exactly 11 | pylint=2.8.3 12 | black=22.6.0 13 | -------------------------------------------------------------------------------- /python/slim/add_slim_cime_py_to_path.py: -------------------------------------------------------------------------------- 1 | """Adds slim_cime_py lib to path 2 | 3 | Any file that can potentially be run as a top-level script (with an if __name__ == 4 | '__main__' block) that needs slim_cime_py should import this. This includes unit test 5 | modules. 6 | 7 | This should be the very first slim module imported. That way, slim_cime_py will be added to your 8 | path before other imports. That is, your script should have: 9 | 10 | # Standard library imports go here 11 | # Then: 12 | from slim import add_slim_cime_py_to_path 13 | """ 14 | 15 | from slim.path_utils import add_slim_cime_pylib_to_path 16 | 17 | _ = add_slim_cime_pylib_to_path() 18 | -------------------------------------------------------------------------------- /manage_externals/test/doc/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = ManageExternals 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # directories checked out by manage_externals, and other files created 2 | # by manage_externals 3 | manage_externals.log 4 | cime/ 5 | components/ 6 | ccs_config/ 7 | libraries/ 8 | share/ 9 | 10 | # ignore svn directories 11 | **/.svn/** 12 | .svn/ 13 | 14 | # binary files 15 | *.nc 16 | 17 | # editor files 18 | *.swp 19 | *~ 20 | 21 | # cime_config 22 | buildnmlc 23 | buildcppc 24 | 25 | # mac files 26 | .DS_Store 27 | 28 | # cmake generated files 29 | build/ 30 | CMakeFiles/ 31 | 32 | # build output 33 | *.o 34 | *.mod 35 | core.* 36 | *.gz 37 | *.log !run.log 38 | *.pyc 39 | 40 | # buildnml testing 41 | cime_config/buildnml_test/run 42 | cime_config/buildnml_test/Buildconf 43 | cime_config/buildnml_test/buildnml.log 44 | -------------------------------------------------------------------------------- /python/slim/test/README: -------------------------------------------------------------------------------- 1 | SLIM-specific boiler-plate needed for most unit test modules: 2 | 3 | (1) If cime stuff is invoked by these unit tests (directly or 4 | indirectly, then: the first slim import statement near the top of 5 | the module should be: 6 | 7 | from slim import add_cime_to_path # pylint: disable=unused-import 8 | 9 | (2) Import the slim-specific unit_testing module: 10 | 11 | from slim import unit_testing 12 | 13 | (3) Allow names that pylint doesn't like: 14 | 15 | # Allow names that pylint doesn't like, because otherwise I find it hard 16 | # to make readable unit test names 17 | # pylint: disable=invalid-name 18 | 19 | (4) Have a 'main' block at the bottom: 20 | 21 | if __name__ == '__main__': 22 | unit_testing.setup_for_tests() 23 | unittest.main() 24 | -------------------------------------------------------------------------------- /cime_config/user_nl_slim: -------------------------------------------------------------------------------- 1 | !---------------------------------------------------------------------------------- 2 | ! Users should add all user specific namelist changes below in the form of 3 | ! namelist_var = new_namelist_value 4 | ! 5 | ! EXCEPTIONS: 6 | ! Set dtime with L_NCPL option 7 | ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options 8 | ! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases 9 | ! (includes $inst_string for multi-ensemble cases) 10 | ! or with SLIM_START_TYPE=cold to do a cold start 11 | ! or set it with an explicit filename here. 12 | !---------------------------------------------------------------------------------- 13 | 14 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/user_nl_slim: -------------------------------------------------------------------------------- 1 | !---------------------------------------------------------------------------------- 2 | ! Users should add all user specific namelist changes below in the form of 3 | ! namelist_var = new_namelist_value 4 | ! 5 | ! EXCEPTIONS: 6 | ! Set dtime with L_NCPL option 7 | ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options 8 | ! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases 9 | ! (includes $inst_string for multi-ensemble cases) 10 | ! or with SLIM_START_TYPE=cold to do a cold start 11 | ! or set it with an explicit filename here. 12 | !---------------------------------------------------------------------------------- 13 | 14 | -------------------------------------------------------------------------------- /cime_config/testdefs/testmods_dirs/slim/g16_SOM/user_docn.streams.txt.som: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | GENERIC 5 | 6 | 7 | 8 | time time 9 | xc lon 10 | yc lat 11 | area area 12 | mask mask 13 | 14 | 15 | /gpfs/fs1/work/mlague/CESM/som/qflux 16 | 17 | 18 | pop_frc.b.e11.B1850C5CN.f09_g16.005.082914_j.nc 19 | 20 | 21 | 22 | 23 | T t 24 | U u 25 | V v 26 | dhdx dhdx 27 | dhdy dhdy 28 | hblt h 29 | qdp qbot 30 | 31 | 32 | /gpfs/fs1/work/mlague/CESM/som/qflux 33 | 34 | 35 | pop_frc.b.e11.B1850C5CN.f09_g16.005.082914_j.nc 36 | 37 | 38 | 0 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /manage_externals/checkout_externals: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """Main driver wrapper around the manic/checkout utility. 4 | 5 | Tool to assemble external respositories represented in an externals 6 | description file. 7 | 8 | """ 9 | from __future__ import absolute_import 10 | from __future__ import unicode_literals 11 | from __future__ import print_function 12 | 13 | import sys 14 | import traceback 15 | 16 | import manic 17 | 18 | if sys.hexversion < 0x02070000: 19 | print(70 * '*') 20 | print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0])) 21 | print('It appears that you are running python {0}'.format( 22 | '.'.join(str(x) for x in sys.version_info[0:3]))) 23 | print(70 * '*') 24 | sys.exit(1) 25 | 26 | 27 | if __name__ == '__main__': 28 | ARGS = manic.checkout.commandline_arguments() 29 | try: 30 | RET_STATUS, _ = manic.checkout.main(ARGS) 31 | sys.exit(RET_STATUS) 32 | except Exception as error: # pylint: disable=broad-except 33 | manic.printlog(str(error)) 34 | if ARGS.backtrace: 35 | traceback.print_exc() 36 | sys.exit(1) 37 | -------------------------------------------------------------------------------- /manage_externals/manic/repository_factory.py: -------------------------------------------------------------------------------- 1 | """Factory for creating and initializing the appropriate repository class 2 | """ 3 | 4 | from __future__ import absolute_import 5 | from __future__ import unicode_literals 6 | from __future__ import print_function 7 | 8 | from .repository_git import GitRepository 9 | from .repository_svn import SvnRepository 10 | from .externals_description import ExternalsDescription 11 | from .utils import fatal_error 12 | 13 | 14 | def create_repository(component_name, repo_info, svn_ignore_ancestry=False): 15 | """Determine what type of repository we have, i.e. git or svn, and 16 | create the appropriate object. 17 | 18 | """ 19 | protocol = repo_info[ExternalsDescription.PROTOCOL].lower() 20 | if protocol == 'git': 21 | repo = GitRepository(component_name, repo_info) 22 | elif protocol == 'svn': 23 | repo = SvnRepository(component_name, repo_info, ignore_ancestry=svn_ignore_ancestry) 24 | elif protocol == 'externals_only': 25 | repo = None 26 | else: 27 | msg = 'Unknown repo protocol "{0}"'.format(protocol) 28 | fatal_error(msg) 29 | return repo 30 | -------------------------------------------------------------------------------- /cime_config/buildnml: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | """ 4 | SLIM namelist creator executable 5 | """ 6 | import sys, os 7 | 8 | _SLIM_PYTHON = os.path.normpath( 9 | os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir, "python") 10 | ) 11 | sys.path.insert(1, _SLIM_PYTHON) 12 | 13 | from slim import add_cime_to_path 14 | from slim import add_slim_cime_py_to_path 15 | from slim.slim_logging import setup_logging 16 | 17 | from standard_script_setup import * 18 | from CIME.buildnml import parse_input 19 | from CIME.case import Case 20 | from slim_cime_py import buildnml 21 | 22 | ############################################################################### 23 | def _main_func(): 24 | 25 | caseroot = parse_input(sys.argv) 26 | level = logging.WARNING 27 | setup_logging(level) 28 | with Case(caseroot) as case: 29 | compname = case.get_value("COMP_LND") 30 | logger.warning( "WARNING: buildnml is being called as program rather than a subroutine " + 31 | "as it is expected to be in the CESM context" ) 32 | buildnml(case, caseroot, compname) 33 | 34 | 35 | if __name__ == "__main__": 36 | _main_func() 37 | -------------------------------------------------------------------------------- /python/README.md: -------------------------------------------------------------------------------- 1 | # Testing the code here 2 | 3 | ## Running everything 4 | 5 | To run all tests (unit tests, system tests and pylint), simply run `make 6 | all` from this directory. 7 | 8 | ## Python environment 9 | 10 | use the "npl" conda environment on cheyenne 11 | 12 | ## Unit and system tests 13 | 14 | Unit and system tests can be run in one of two ways; these do the same 15 | thing, but support different options: 16 | 17 | 1. via `make test` 18 | 19 | You can specify a few arguments to this: 20 | 21 | - python version: `make python=python3.9 test` (defaults to `python3`; you should expect errors if trying to run with python2) 22 | - verbose: `make verbose=true test` 23 | - debug: `make debug=true test` 24 | 25 | Note that unit tests and system tests can be run separately with 26 | `make utest` or `make stest`, or they can all be run with `make 27 | test`. 28 | 29 | 2. via `./run_slim_py_tests` 30 | 31 | You can specify various arguments to this; run `./run_slim_py_tests 32 | -h` for details 33 | 34 | ## pylint 35 | 36 | You can run pylint on everything in the slim package with `make lint`. 37 | 38 | ## black 39 | 40 | You can run black on everything in the slim package with `make black`. 41 | 42 | -------------------------------------------------------------------------------- /python/slim/add_cime_to_path.py: -------------------------------------------------------------------------------- 1 | """Adds cime lib to path 2 | 3 | Any file that can potentially be run as a top-level script (with an if __name__ == 4 | '__main__' block) that needs cime should import this. This includes unit test 5 | modules. However: see the NOTE at the bottom of this documentation. 6 | 7 | This should be the very first slim module imported. That way, cime will be added to your 8 | path before other imports. That is, your script should have: 9 | 10 | # Standard library imports go here 11 | # Then something like this: 12 | _SLIM_PYTHON = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'python') 13 | sys.path.insert(1, _SLIM_PYTHON) 14 | # Then: 15 | from slim import add_cime_to_path 16 | 17 | NOTE: For top-level scripts that either (a) want to pass some argument(s) to 18 | add_cime_lib_to_path, or (b) want to store the returned value from add_cime_lib_to_path: 19 | they should include copies of what's in this module (adding the appropriate argument(s)), 20 | rather than actually importing this module. So this module should be viewed as a 21 | convenience that can be used by scripts with simple needs, but does not need to be used. 22 | """ 23 | 24 | from slim.path_utils import add_cime_lib_to_path 25 | 26 | _ = add_cime_lib_to_path() 27 | -------------------------------------------------------------------------------- /tools/modify_input_files/README.surdat_modifier: -------------------------------------------------------------------------------- 1 | surdat_modifier is a tool that modifies SLIM surdat files. It reads a surface 2 | dataset (surdat file) and outputs a modified copy of the same file. 3 | 4 | SLIM's surdat_modifier used CTSM's fsurdat_modifier as a design template. 5 | 6 | Files involved 7 | -------------- 8 | python/slim/modify_input_files/surdat_modifier.py 9 | python/slim/modify_input_files/modify_surdat.py 10 | tools/modify_input_files/surdat_modifier 11 | tools/modify_input_files/modify_surdat_template.cfg 12 | 13 | Instructions 14 | ------------ 15 | To run on Cheyenne/Casper/Izumi 16 | 1) (Un)load, execute, and activate the following: 17 | module unload python 18 | module load conda 19 | ./py_env_create 20 | conda activate slim_pylib # conda activate ctsm_pylib UNTIL slim separates from ctsm 21 | (Use "deactivate" to reverse the latter.) 22 | 2) Copy, then modify the configure file named modify_surdat_template.cfg, which 23 | contains all the arguments needed by the script. 24 | 3) Run the script ./surdat_modifier pointing to the copied/modified .cfg file, 25 | e.g. modify_users_copy.cfg 26 | ./surdat_modifier modify_users_copy.cfg 27 | See modify_surdat_template.cfg for required and optional settings. 28 | 4) Use the --verbose option to see progress output on your screen 29 | -------------------------------------------------------------------------------- /tools/README: -------------------------------------------------------------------------------- 1 | $SLIMROOT/tools/README Feb/28/2023 2 | 3 | SLIM tools for analysis of SLIM history files or 4 | for creation or modification of SLIM input files. 5 | 6 | I. General directory structure: 7 | 8 | $SLIMROOT/tools 9 | mksurdat Create SLIM surface dataset (surdat file) from CTSM 10 | history output files. TOOL NOT AVAILABLE 11 | 12 | modify_input_files Scripts to modify SLIM input files. Currently 13 | there is one available tool and it can modify 14 | SLIM surdat files. 15 | 16 | cime-tools ($CIMEROOT/tools/) (CIMEROOT is ../cime for a SLIM checkout and ../../../cime for a CESM checkout) 17 | $CIMEROOT/mapping/gen_domain_files 18 | gen_domain ------- Create data model domain datasets from SCRIP mapping datasets. 19 | 20 | II. Notes on building/running for each of the above tools: 21 | 22 | Refer to each tool's README for more information. 23 | 24 | III. Create input datasets needed to run SLIM 25 | 26 | 1.) Create surface dataset with mksurdat.ipynb. Detailed instructions here: 27 | /glade/work/slevis/git_slim/surdat_modifier/tools/mksurdat/README.mksurdat 28 | 29 | 2.) Add the new file to XML data or using user_nl_clm (optional) 30 | -------------------------------------------------------------------------------- /cime_config/config_archive.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | r 4 | rh\d? 5 | h\d*.*\.nc$ 6 | e 7 | locfnh 8 | 9 | rpointer.lnd$NINST_STRING 10 | ./$CASE.slim$NINST_STRING.r.$DATENAME.nc 11 | 12 | 13 | rpointer.lnd 14 | rpointer.lnd_9999 15 | casename.slim.r.1976-01-01-00000.nc 16 | casename.slim.rh4.1976-01-01-00000.nc 17 | casename.slim.h0.1976-01-01-00000.nc 18 | casename.slim.h0.1976-01-01-00000.nc.base 19 | casename.slim_0002.e.postassim.1976-01-01-00000.nc 20 | casename.slim_0002.e.preassim.1976-01-01-00000.nc 21 | anothercasename.slim.i.1976-01-01-00000.nc 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /tools/modify_input_files/modify_surdat_defaults.cfg: -------------------------------------------------------------------------------- 1 | [modify_input] 2 | 3 | # ------------------------------------------------------------------------ 4 | # .cfg file with defaults for surdat_modifier. 5 | # ------------------------------------------------------------------------ 6 | 7 | glc_mask = 0 0 0 0 0 0 0 0 0 0 0 0 8 | alb_gvd = 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 9 | alb_svd = 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 10 | alb_gnd = 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 11 | alb_snd = 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 12 | alb_gvf = 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 13 | alb_svf = 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 14 | alb_gnf = 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 15 | alb_snf = 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 16 | bucketdepth = 200 200 200 200 200 200 200 200 200 200 200 200 17 | emissivity = 1 1 1 1 1 1 1 1 1 1 1 1 18 | snowmask = 50 50 50 50 50 50 50 50 50 50 50 50 19 | roughness = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 20 | evap_res = 100 100 100 100 100 100 100 100 100 100 100 100 21 | soil_type = 0 0 0 0 0 0 0 0 0 0 0 0 22 | soil_tk_1d = 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 23 | soil_cv_1d = 2e6 2e6 2e6 2e6 2e6 2e6 2e6 2e6 2e6 2e6 2e6 2e6 24 | glc_tk_1d = 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 25 | glc_cv_1d = 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 1.9e6 26 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_run.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 |
6 | 7 | 8 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | -------------------------------------------------------------------------------- /python/slim/git_utils.py: -------------------------------------------------------------------------------- 1 | """General-purpose git utility functions""" 2 | 3 | import logging 4 | import subprocess 5 | 6 | from slim.path_utils import path_to_slim_root 7 | 8 | logger = logging.getLogger(__name__) 9 | 10 | 11 | def get_slim_git_short_hash(): 12 | """ 13 | Returns Git short SHA for the SLIM repository. 14 | 15 | Args: 16 | 17 | Raises: 18 | 19 | Returns: 20 | sha (str) : git short hash for slim repository 21 | """ 22 | sha = ( 23 | subprocess.check_output(["git", "-C", path_to_slim_root(), "rev-parse", "--short", "HEAD"]) 24 | .strip() 25 | .decode() 26 | ) 27 | return sha 28 | 29 | 30 | def get_slim_git_long_hash(): 31 | """ 32 | Returns Git long SHA for the SLIM repository. 33 | 34 | Args: 35 | 36 | Raises: 37 | 38 | Returns: 39 | sha (str) : git long hash for slim repository 40 | """ 41 | sha = ( 42 | subprocess.check_output(["git", "-C", path_to_slim_root(), "rev-parse", "HEAD"]) 43 | .strip() 44 | .decode() 45 | ) 46 | return sha 47 | 48 | 49 | def get_slim_git_describe(): 50 | """ 51 | Function for giving the recent tag of the SLIM repository 52 | 53 | Args: 54 | 55 | Raises: 56 | 57 | Returns: 58 | label (str) : ouput of running 'git describe' for the SLIM repository 59 | """ 60 | label = subprocess.check_output(["git", "-C", path_to_slim_root(), "describe"]).strip().decode() 61 | return label 62 | -------------------------------------------------------------------------------- /README.testing: -------------------------------------------------------------------------------- 1 | # README.testing 2 | # 3 | # The test list "aux_slim" is run as a test suite with the "create_test" script under cime/scripts 4 | # as follows. 5 | # NOTE: There are also tests for prealpha, prebeta for use with CESM testing 6 | # And slim_sci to run a few standard tests for SLIM science 7 | # 8 | # Tests on cheyenne 9 | 10 | 11 | cd cime/scripts 12 | qcmd -l walltime=08:00:00 -q premium -- ./create_test --compare \ 13 | --queue premium --machine cheyenne -r cases --baseline-root /glade/p/cgd/tss/ctsm_baselines \ 14 | --generate --xml-category aux_slim --xml-machine cheyenne \ 15 | --xml-compiler intel --compiler intel 16 | qcmd -l walltime=08:00:00 -q premium -- ./create_test --compare \ 17 | --queue premium --machine cheyenne -r cases --baseline-root /glade/p/cgd/tss/ctsm_baselines \ 18 | --generate --xml-category aux_slim --xml-machine cheyenne \ 19 | --xml-compiler gnu --compiler gnu 20 | 21 | # Tests on izumi 22 | # 23 | cd cime/scripts 24 | nohup ./create_test --compare --generate machine izumi -r cases \ 25 | --xml-category aux_slim --xml-machine izumi --xml-compiler nag & 26 | nohup ./create_test --compare --generate machine izumi -r cases \ 27 | --xml-category aux_slim --xml-machine izumi --xml-compiler gnu & 28 | nohup ./create_test --compare --generate machine izumi -r cases \ 29 | --xml-category aux_slim --xml-machine izumi --xml-compiler intel & 30 | -------------------------------------------------------------------------------- /tools/mksurdat/README.mksurdat: -------------------------------------------------------------------------------- 1 | mksurdat is a jupyter notebook tool that generates SLIM surdat files. 2 | It reads pre-averaged ctsm and cpl history files and outputs a SLIM 3 | surdat file. 4 | 5 | Files involved 6 | -------------- 7 | python/slim/mksurdat/mksurdat.ipynb 8 | 9 | Instructions 10 | ------------ 11 | To run on Cheyenne/Casper 12 | 1) Before starting the jupyter session for the first time, set up your 13 | conda environment: 14 | 15 | > cd /path/to/your_checked_out_ctsm_directory 16 | > ./py_env_create # needed the first time & periodically for environment updates 17 | > conda activate ctsm_pylib 18 | > pip install ipykernel 19 | 20 | Also you need the next line to use nco (netcdf operators) a bit later: 21 | > module load nco 22 | 23 | 2) On your browser go here: 24 | https://jupyterhub.hpc.ucar.edu/ 25 | 26 | a) Start default server 27 | b) Launch server 28 | c) Use jupyter's file navigation to get to 29 | your_checked_out_ctsm_directory/python/slim/mksurdat 30 | d) Open mksurdat.ipynb 31 | e) Use the menu to select Kernel --> Change Kernel --> ctsm_pylib 32 | f) In the notebook's second cell, modify the following settings: 33 | - casename 34 | - start_yr 35 | - surfdat_file (not required; tool will work without this file) 36 | g) In the notebook's third cell, find a suggestion for generating 37 | concatenated ctsm and cpl history files using nco 38 | 39 | 9) Using the menu, select Run, Run all cells 40 | 41 | 10) You should have a new surdat file in the same directory as the .ipynb 42 | file (see Files involved above) in less than a minute 43 | -------------------------------------------------------------------------------- /src/utils/getdatetime.F90: -------------------------------------------------------------------------------- 1 | !----------------------------------------------------------------------- 2 | !BOP 3 | ! 4 | ! !ROUTINE: getdatetime 5 | ! 6 | ! !INTERFACE: 7 | subroutine getdatetime (cdate, ctime) 8 | ! 9 | ! !DESCRIPTION: 10 | ! A generic Date and Time routine 11 | ! 12 | ! !USES: 13 | use spmdMod , only : mpicom, masterproc, MPI_CHARACTER 14 | ! !ARGUMENTS: 15 | implicit none 16 | character(len=8), intent(out) :: cdate !current date 17 | character(len=8), intent(out) :: ctime !current time 18 | ! 19 | ! !REVISION HISTORY: 20 | ! Created by Mariana Vertenstein 21 | ! 22 | ! 23 | ! !LOCAL VARIABLES: 24 | !EOP 25 | character(len=8) :: date !current date 26 | character(len=10) :: time !current time 27 | character(len=5) :: zone !zone 28 | integer, dimension(8) :: values !temporary 29 | integer :: ier !MPI error code 30 | !----------------------------------------------------------------------- 31 | if (masterproc) then 32 | 33 | call date_and_time (date, time, zone, values) 34 | 35 | cdate(1:2) = date(5:6) 36 | cdate(3:3) = '/' 37 | cdate(4:5) = date(7:8) 38 | cdate(6:6) = '/' 39 | cdate(7:8) = date(3:4) 40 | 41 | ctime(1:2) = time(1:2) 42 | ctime(3:3) = ':' 43 | ctime(4:5) = time(3:4) 44 | ctime(6:6) = ':' 45 | ctime(7:8) = time(5:6) 46 | 47 | endif 48 | 49 | call mpi_bcast (cdate,len(cdate),MPI_CHARACTER, 0, mpicom, ier) 50 | call mpi_bcast (ctime,len(ctime),MPI_CHARACTER, 0, mpicom, ier) 51 | 52 | return 53 | end subroutine getdatetime 54 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | ## How to contribute: 2 | 3 | We recommend that you first open an issue (https://github.com/escomp/ctsm/issues/) to 4 | discuss the changes or additions that you propose. You should also contact some of the responsible 5 | individuals for SLIM and run by the changes with them. 6 | 7 | Erik Kluzek -- Software Engineering (erik@ucar.edu) 8 | Marysa Lague -- Originator (marysa.lague@usask.ca) 9 | Isla Simpson -- Principal Investigator (simpson@ucar.edu) 10 | 11 | Use the help from the wiki below to setup a fork and personal branch in GitHub to put your developments 12 | on and keep up to date with the master branch of SLIM. Once the changes are sufficiently advanced you 13 | can form a Pull Request on GitHub. Either from your fork on GitHub, or from the main ESCOMP GitHub page 14 | for SLIM (be sure to hit the "compare across forks" link at the top of the page when you first create 15 | the pull request). 16 | 17 | https://github.com/ESCOMP/SimpleLand/pulls 18 | 19 | This allows you to show your proposed changes and start getting feedback on them (even if they aren't finished). 20 | This also allows your changes to be planned for and slated for a time to come into SLIM master. In most 21 | cases you won't merge the Pull Request yourself, but a software engineer responsible for SLIM will do 22 | additional testing and bring the changes to SLIM master. 23 | 24 | #### SLIM Wiki: 25 | 26 | https://github.com/ESCOMP/SimpleLand/wiki 27 | 28 | #### Code of Conduct: 29 | 30 | See the `CODE_OF_CONDUCT.md` file for expectations of how to work in the community. 31 | -------------------------------------------------------------------------------- /.config_files.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 16 | 17 | char 18 | unset 19 | 20 | $SRCROOT 21 | $SRCROOT/components/cpl7/components/data_comps_mct/dlnd 22 | $SRCROOT/components/cdeps/dlnd 23 | $SRCROOT/components/cpl7/components/stub_comps_mct/slnd 24 | $SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd 25 | $CIMEROOT/src/components/stub_comps_nuopc/slnd 26 | $CIMEROOT/src/components/xcpl_comps_nuopc/xlnd 27 | 28 | case_comps 29 | env_case.xml 30 | Root directory of the case land model component 31 | $CIMEROOT/config/xml_schemas/config_compsets.xsd 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /python/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for running tests on the python code here 2 | 3 | # These variables can be overridden from the command-line 4 | python = not-set 5 | verbose = not-set 6 | debug = not-set 7 | 8 | ifneq ($(python), not-set) 9 | PYTHON=$(python) 10 | else 11 | PYTHON=python3 12 | endif 13 | 14 | ifneq ($(debug), not-set) 15 | TEST_ARGS+=--debug 16 | endif 17 | ifneq ($(verbose), not-set) 18 | TEST_ARGS+=--verbose 19 | endif 20 | 21 | PYLINT=pylint 22 | PYLINT_ARGS=-j 4 --rcfile=slim/.pylintrc 23 | DIR_SRC = \ 24 | slim \ 25 | ../cime_config/slim_cime_py 26 | 27 | all: lint black test 28 | test: utest stest 29 | 30 | .PHONY: utest 31 | utest: FORCE 32 | $(PYTHON) ./run_slim_py_tests $(TEST_ARGS) --unit 33 | 34 | .PHONY: stest 35 | stest: FORCE 36 | $(PYTHON) ./run_slim_py_tests $(TEST_ARGS) --sys 37 | 38 | .PHONY: lint 39 | lint: FORCE 40 | $(PYLINT) $(PYLINT_ARGS) $(DIR_SRC) 41 | 42 | .PHONY: black 43 | # Run black check on all of the python files here and undeneath. 44 | # Should be identical to run_black option below, other than the --check option added in 45 | # Use the black configure file to explicitly set a few things and specifiy the exact files. 46 | black: FORCE 47 | black --check --config pyproject.toml $(DIR_SRC) 48 | 49 | .PHONY: run_black 50 | # Run black on all of the python files here and undeneath -- CHANGING THE FILES! 51 | # Should be identical to above, other than the "--check" option is removed. 52 | # Use the black configure file to explicitly set a few things and specifiy the exact files. 53 | run_black: FORCE 54 | black --config pyproject.toml $(DIR_SRC) 55 | 56 | 57 | .PHONY: clean 58 | clean: FORCE 59 | find . -name '*.pyc' -exec rm {} \; 60 | 61 | FORCE: 62 | 63 | -------------------------------------------------------------------------------- /src/main/clm_varpar.F90: -------------------------------------------------------------------------------- 1 | module clm_varpar 2 | 3 | !----------------------------------------------------------------------- 4 | ! !DESCRIPTION: 5 | ! Module containing CLM parameters 6 | ! 7 | ! !USES: 8 | use shr_kind_mod , only: r8 => shr_kind_r8 9 | use spmdMod , only: masterproc 10 | use clm_varctl , only: iulog 11 | 12 | ! !PUBLIC TYPES: 13 | implicit none 14 | save 15 | 16 | ! Note - model resolution is read in from the surface dataset 17 | 18 | integer :: nlevgrnd ! number of ground layers 19 | ! (includes lower layers that are hydrologically inactive) 20 | ! (includes lower layers that are biogeochemically inactive) 21 | !ED variables 22 | integer, parameter :: numrad = 2 ! number of solar radiation bands: vis, nir 23 | integer, parameter :: ndst = 4 ! number of dust size classes (BGC only) 24 | 25 | ! !PUBLIC MEMBER FUNCTIONS: 26 | public clm_varpar_init ! set parameters 27 | ! 28 | !----------------------------------------------------------------------- 29 | 30 | contains 31 | 32 | !------------------------------------------------------------------------------ 33 | subroutine clm_varpar_init() 34 | ! 35 | ! !DESCRIPTION: 36 | ! Initialize module variables 37 | ! 38 | ! !ARGUMENTS: 39 | implicit none 40 | ! 41 | ! !LOCAL VARIABLES: 42 | ! 43 | character(len=32) :: subname = 'clm_varpar_init' ! subroutine name 44 | !------------------------------------------------------------------------------ 45 | 46 | nlevgrnd = 15 47 | 48 | if ( masterproc )then 49 | write(iulog, *) 'CLM varpar subsurface discretization levels ' 50 | write(iulog, '(a, i3)') ' nlevgrnd = ', nlevgrnd 51 | write(iulog, *) 52 | end if 53 | 54 | end subroutine clm_varpar_init 55 | 56 | end module clm_varpar 57 | -------------------------------------------------------------------------------- /Externals.cfg: -------------------------------------------------------------------------------- 1 | [slm] 2 | local_path = . 3 | protocol = externals_only 4 | required = True 5 | 6 | [cam] 7 | tag = cam6_3_116 8 | protocol = git 9 | repo_url = https://github.com/ESCOMP/CAM 10 | local_path = components/cam 11 | externals = Externals_CAM.cfg 12 | required = True 13 | 14 | [cice6] 15 | tag = cesm_cice6_4_1_9 16 | protocol = git 17 | repo_url = https://github.com/ESCOMP/CESM_CICE 18 | local_path = components/cice 19 | externals = Externals.cfg 20 | required = True 21 | 22 | [cice5] 23 | tag = cice5_20220204 24 | protocol = git 25 | repo_url = https://github.com/ESCOMP/CESM_CICE5 26 | local_path = components/cice5 27 | required = True 28 | 29 | [ccs_config] 30 | tag = ccs_config_cesm0.0.71 31 | protocol = git 32 | repo_url = https://github.com/ESMCI/ccs_config_cesm.git 33 | local_path = ccs_config 34 | required = True 35 | 36 | [cdeps] 37 | tag = cdeps1.0.14 38 | protocol = git 39 | repo_url = https://github.com/ESCOMP/CDEPS 40 | local_path = components/cdeps 41 | externals = Externals_CDEPS.cfg 42 | required = True 43 | 44 | [cmeps] 45 | tag = cmeps0.14.34 46 | protocol = git 47 | repo_url = https://github.com/ESCOMP/CMEPS 48 | local_path = components/cmeps 49 | required = True 50 | 51 | [cpl7] 52 | tag = cpl77.0.5 53 | protocol = git 54 | repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps 55 | local_path = components/cpl7 56 | required = True 57 | 58 | [share] 59 | tag = share1.0.17 60 | protocol = git 61 | repo_url = https://github.com/ESCOMP/CESM_share 62 | local_path = share 63 | required = True 64 | 65 | [mct] 66 | tag = MCT_2.11.0 67 | protocol = git 68 | repo_url = https://github.com/MCSclimate/MCT 69 | local_path = libraries/mct 70 | required = True 71 | 72 | [parallelio] 73 | tag = pio2_5_10 74 | protocol = git 75 | repo_url = https://github.com/NCAR/ParallelIO 76 | local_path = libraries/parallelio 77 | required = True 78 | 79 | [cime] 80 | local_path = cime 81 | protocol = git 82 | repo_url = https://github.com/ESMCI/cime 83 | tag = cime6.0.140 84 | required = True 85 | 86 | [externals_description] 87 | schema_version = 1.0.01 88 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_case.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 |
6 | 7 | 10 | 11 | 12 | 13 | 14 | char 15 | file containing specification of component specific definitions and values(for documentation only - DO NOT EDIT) 16 | $CIMEROOT/config/xml_schemas/entry_id.xsd 17 | $CIMEROOT/config/xml_schemas/entry_id_version3.xsd 18 | 19 | 20 | 21 | char 22 | Component set long name (for documentation only - DO NOT EDIT) 23 | 24 | 25 | 26 | char 27 | Root directory of the case land model component 28 | $CIMEROOT/config/xml_schemas/config_compsets.xsd 29 | 30 | 31 | 32 | char 33 | slim 34 | Name of land component 35 | 36 | 37 | 38 | char 39 | full pathname of source root directory 40 | 41 | 42 | 43 | char 44 | case name 45 | 46 | 47 | 48 | char 49 | model system name 50 | 51 | 52 | 53 | char 54 | full pathname of case 55 | 56 | 57 | 58 | char 59 | Land grid 60 | 61 | 62 | 63 | 64 | -------------------------------------------------------------------------------- /manage_externals/README_FIRST: -------------------------------------------------------------------------------- 1 | CESM is comprised of a number of different components that are 2 | developed and managed independently. Each component may have 3 | additional 'external' dependancies and optional parts that are also 4 | developed and managed independently. 5 | 6 | The checkout_externals.py tool manages retreiving and updating the 7 | components and their externals so you have a complete set of source 8 | files for the model. 9 | 10 | checkout_externals.py relies on a model description file that 11 | describes what components are needed, where to find them and where to 12 | put them in the source tree. The default file is called "CESM.xml" 13 | regardless of whether you are checking out CESM or a standalone 14 | component. 15 | 16 | checkout_externals requires access to git and svn repositories that 17 | require authentication. checkout_externals may pass through 18 | authentication requests, but it will not cache them for you. For the 19 | best and most robust user experience, you should have svn and git 20 | working without password authentication. See: 21 | 22 | https://help.github.com/articles/connecting-to-github-with-ssh/ 23 | 24 | ?svn ref? 25 | 26 | NOTE: checkout_externals.py *MUST* be run from the root of the source 27 | tree it is managing. For example, if you cloned CLM with: 28 | 29 | $ git clone git@github.com/ncar/clm clm-dev 30 | 31 | Then the root of the source tree is /path/to/cesm-dev. If you obtained 32 | CLM via an svn checkout of CESM and you need to checkout the CLM 33 | externals, then the root of the source tree for CLM is: 34 | 35 | /path/to/cesm-dev/components/clm 36 | 37 | The root of the source tree will be referred to as ${SRC_ROOT} below. 38 | 39 | To get started quickly, checkout all required components from the 40 | default model description file: 41 | 42 | $ cd ${SRC_ROOT} 43 | $ ./checkout_cesm/checkout_externals.py 44 | 45 | For additional information about using checkout model, please see: 46 | 47 | ${SRC_ROOT}/checkout_cesm/README 48 | 49 | or run: 50 | 51 | $ cd ${SRC_ROOT} 52 | $ ./checkout_cesm/checkout_externals.py --help 53 | 54 | 55 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2005-2022, University Corporation for Atmospheric Research (UCAR) 2 | All rights reserved. 3 | 4 | Developed by: 5 | University Corporation for Atmospheric Research - National Center for Atmospheric Research 6 | https://www2.cesm.ucar.edu/working-groups/sewg 7 | 8 | Permission is hereby granted, free of charge, to any person obtaining 9 | a copy of this software and associated documentation files (the "Software"), 10 | to deal with the Software without restriction, including without limitation 11 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 12 | and/or sell copies of the Software, and to permit persons to whom 13 | the Software is furnished to do so, subject to the following conditions: 14 | 15 | - Redistributions of source code must retain the above copyright notice, 16 | this list of conditions and the following disclaimers. 17 | - Redistributions in binary form must reproduce the above copyright notice, 18 | this list of conditions and the following disclaimers in the documentation 19 | and/or other materials provided with the distribution. 20 | - Neither the names of [Name of Development Group, UCAR], 21 | nor the names of its contributors may be used to endorse or promote 22 | products derived from this Software without specific prior written permission. 23 | 24 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 25 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 26 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 27 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 28 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 29 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 30 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 31 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 32 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 33 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 34 | POSSIBILITY OF SUCH DAMAGE. 35 | -------------------------------------------------------------------------------- /manage_externals/LICENSE.txt: -------------------------------------------------------------------------------- 1 | Copyright (c) 2017-2018, University Corporation for Atmospheric Research (UCAR) 2 | All rights reserved. 3 | 4 | Developed by: 5 | University Corporation for Atmospheric Research - National Center for Atmospheric Research 6 | https://www2.cesm.ucar.edu/working-groups/sewg 7 | 8 | Permission is hereby granted, free of charge, to any person obtaining 9 | a copy of this software and associated documentation files (the "Software"), 10 | to deal with the Software without restriction, including without limitation 11 | the rights to use, copy, modify, merge, publish, distribute, sublicense, 12 | and/or sell copies of the Software, and to permit persons to whom 13 | the Software is furnished to do so, subject to the following conditions: 14 | 15 | - Redistributions of source code must retain the above copyright notice, 16 | this list of conditions and the following disclaimers. 17 | - Redistributions in binary form must reproduce the above copyright notice, 18 | this list of conditions and the following disclaimers in the documentation 19 | and/or other materials provided with the distribution. 20 | - Neither the names of [Name of Development Group, UCAR], 21 | nor the names of its contributors may be used to endorse or promote 22 | products derived from this Software without specific prior written permission. 23 | 24 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 25 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 26 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 27 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 28 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 29 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 30 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 31 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 32 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 33 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 34 | POSSIBILITY OF SUCH DAMAGE. 35 | -------------------------------------------------------------------------------- /manage_externals/test/README.md: -------------------------------------------------------------------------------- 1 | # Testing for checkout_externals 2 | 3 | NOTE: Python2 is the supported runtime environment. Python3 compatibility is 4 | in progress, complicated by the different proposed input methods 5 | (yaml, xml, cfg/ini, json) and their different handling of strings 6 | (unicode vs byte) in python2. Full python3 compatibility will be 7 | possible once the number of possible input formats has been narrowed. 8 | 9 | ## Setup development environment 10 | 11 | Development environments should be setup for python2 and python3: 12 | 13 | ```SH 14 | cd checkout_externals/test 15 | make python=python2 env 16 | make python=python3 env 17 | ``` 18 | 19 | ## Unit tests 20 | 21 | Tests should be run for both python2 and python3. It is recommended 22 | that you have seperate terminal windows open python2 and python3 23 | testing to avoid errors activating and deactivating environments. 24 | 25 | ```SH 26 | cd checkout_externals/test 27 | . env_python2/bin/activate 28 | make utest 29 | deactivate 30 | ``` 31 | 32 | ```SH 33 | cd checkout_externals/test 34 | . env_python2/bin/activate 35 | make utest 36 | deactivate 37 | ``` 38 | 39 | ## System tests 40 | 41 | Not yet implemented. 42 | 43 | ## Static analysis 44 | 45 | checkout_externals is difficult to test thoroughly because it relies 46 | on git and svn, and svn requires a live network connection and 47 | repository. Static analysis will help catch bugs in code paths that 48 | are not being executed, but it requires conforming to community 49 | standards and best practices. autopep8 and pylint should be run 50 | regularly for automatic code formatting and linting. 51 | 52 | ```SH 53 | cd checkout_externals/test 54 | . env_python2/bin/activate 55 | make lint 56 | deactivate 57 | ``` 58 | 59 | The canonical formatting for the code is whatever autopep8 60 | generates. All issues identified by pylint should be addressed. 61 | 62 | 63 | ## Code coverage 64 | 65 | All changes to the code should include maintaining existing tests and 66 | writing new tests for new or changed functionality. To ensure test 67 | coverage, run the code coverage tool: 68 | 69 | ```SH 70 | cd checkout_externals/test 71 | . env_python2/bin/activate 72 | make coverage 73 | open -a Firefox.app htmlcov/index.html 74 | deactivate 75 | ``` 76 | 77 | 78 | -------------------------------------------------------------------------------- /cime_config/buildnml_test/env_mach_pes.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 |
5 |
6 | 7 | 8 | 9 | 12 | 13 | 14 | integer 15 | 16 | 17 | 18 | integer 19 | 20 | 21 | 22 | integer 23 | 24 | 25 | 26 | integer 27 | 28 | 29 | 30 | integer 31 | Force this exact number of spare nodes to be allocated 32 | 33 | 34 | 35 | integer 36 | 37 | 1 38 | 1 39 | 1 40 | 1 41 | 42 | 43 | 44 | 45 | 46 | integer 47 | 48 | -2 49 | -2 50 | -2 51 | -2 52 | 53 | 54 | 55 | 56 | 57 | integer 58 | 59 | 0 60 | 0 61 | 0 62 | 0 63 | 64 | 65 | 66 | 67 | 68 | integer 69 | 70 | 1 71 | 1 72 | 1 73 | 74 | 75 | 76 | 77 | 78 | integer 79 | 80 | 1 81 | 1 82 | 1 83 | 1 84 | 85 | 86 | 87 | 88 | 89 | 90 | -------------------------------------------------------------------------------- /src/main/abortutils.F90: -------------------------------------------------------------------------------- 1 | module abortutils 2 | 3 | !----------------------------------------------------------------------- 4 | ! !MODULE: abortutils 5 | ! 6 | ! !DESCRIPTION: 7 | ! Abort the model for abnormal termination 8 | !----------------------------------------------------------------------- 9 | 10 | private 11 | save 12 | 13 | public :: endrun 14 | 15 | interface endrun 16 | module procedure endrun_vanilla 17 | module procedure endrun_globalindex 18 | end interface 19 | 20 | CONTAINS 21 | 22 | !----------------------------------------------------------------------- 23 | subroutine endrun_vanilla(msg) 24 | 25 | !----------------------------------------------------------------------- 26 | ! !DESCRIPTION: 27 | ! Abort the model for abnormal termination 28 | ! 29 | use shr_sys_mod , only: shr_sys_abort 30 | use clm_varctl , only: iulog 31 | ! 32 | ! !ARGUMENTS: 33 | implicit none 34 | character(len=*), intent(in), optional :: msg ! string to be printed 35 | !----------------------------------------------------------------------- 36 | 37 | if (present (msg)) then 38 | write(iulog,*)'ENDRUN:', msg 39 | else 40 | write(iulog,*)'ENDRUN: called without a message string' 41 | end if 42 | 43 | call shr_sys_abort() 44 | 45 | end subroutine endrun_vanilla 46 | 47 | !----------------------------------------------------------------------- 48 | subroutine endrun_globalindex(decomp_index, clmlevel, msg) 49 | 50 | !----------------------------------------------------------------------- 51 | ! Description: 52 | ! Abort the model for abnormal termination 53 | ! 54 | use shr_sys_mod , only: shr_sys_abort 55 | use clm_varctl , only: iulog 56 | use GetGlobalValuesMod, only: GetGlobalWrite 57 | ! 58 | ! Arguments: 59 | implicit none 60 | integer , intent(in) :: decomp_index 61 | character(len=*) , intent(in) :: clmlevel 62 | character(len=*) , intent(in), optional :: msg ! string to be printed 63 | ! 64 | ! Local Variables: 65 | integer :: igrc 66 | !----------------------------------------------------------------------- 67 | 68 | write(6,*)'calling getglobalwrite with decomp_index= ',decomp_index,' and clmlevel= ',trim(clmlevel) 69 | call GetGlobalWrite(decomp_index, clmlevel) 70 | 71 | if (present (msg)) then 72 | write(iulog,*)'ENDRUN:', msg 73 | else 74 | write(iulog,*)'ENDRUN: called without a message string' 75 | end if 76 | 77 | call shr_sys_abort() 78 | 79 | end subroutine endrun_globalindex 80 | 81 | end module abortutils 82 | -------------------------------------------------------------------------------- /src/main/ncdio_utils.F90: -------------------------------------------------------------------------------- 1 | module ncdio_utils 2 | 3 | !----------------------------------------------------------------------- 4 | ! This module provides higher-level netcdf i/o utilities, which build on ncdio_pio. 5 | ! 6 | ! The main reason for putting these utilities in a separate module (rather than putting 7 | ! them in ncdio_pio) is to enhance testability: These routines can be unit tested with 8 | ! a stub version of ncdio_pio. 9 | use ncdio_pio 10 | ! 11 | implicit none 12 | save 13 | private 14 | 15 | public :: find_var_on_file ! given a list of possible variables, find the one that exists on the file 16 | 17 | contains 18 | 19 | !----------------------------------------------------------------------- 20 | subroutine find_var_on_file(ncid, varname_list, varname_on_file) 21 | ! 22 | ! !DESCRIPTION: 23 | ! Given a colon-delimited list of possible variable names, return the first one that 24 | ! was found on the file. 25 | ! 26 | ! If none are found, arbitrarily return the first variable in the list. (Doing this 27 | ! rather than returning a special flag simplifies the logic elsewhere - allowing the 28 | ! ncd_io call to fail rather than requiring extra error-checking logic.) 29 | ! 30 | ! !USES: 31 | use shr_string_mod, only : shr_string_listGetNum, shr_string_listGetName 32 | ! 33 | ! !ARGUMENTS: 34 | type(file_desc_t) , intent(inout) :: ncid ! netcdf file id 35 | character(len=*) , intent(in) :: varname_list ! colon-delimited list of possible variable names 36 | character(len=*) , intent(out) :: varname_on_file ! first variable from the list that was found on file 37 | ! 38 | ! !LOCAL VARIABLES: 39 | integer :: num_vars 40 | integer :: n 41 | logical :: found 42 | logical :: readvar 43 | character(len=len(varname_on_file)) :: cur_varname 44 | integer :: varid 45 | type(var_desc_t) :: vardesc 46 | 47 | character(len=*), parameter :: subname = 'find_var_on_file' 48 | !----------------------------------------------------------------------- 49 | 50 | num_vars = shr_string_listGetNum(varname_list) 51 | 52 | found = .false. 53 | n = 1 54 | do while ((.not. found) .and. (n <= num_vars)) 55 | call shr_string_listGetName(varname_list, n, cur_varname) 56 | call ncd_inqvid(ncid, cur_varname, varid, vardesc, readvar=readvar) 57 | found = readvar 58 | n = n + 1 59 | end do 60 | 61 | if (found) then 62 | varname_on_file = cur_varname 63 | else 64 | ! If none are found, arbitrarily return the first variable in the list 65 | call shr_string_listGetName(varname_list, 1, varname_on_file) 66 | end if 67 | 68 | end subroutine find_var_on_file 69 | 70 | end module ncdio_utils 71 | -------------------------------------------------------------------------------- /python/slim/run_slim_py_tests.py: -------------------------------------------------------------------------------- 1 | """Runner for the python unit tests defined here 2 | 3 | This is the main implementation of the run_slim_py_tests script contained in the 4 | parent directory 5 | """ 6 | 7 | import unittest 8 | import os 9 | import argparse 10 | import logging 11 | from slim import unit_testing 12 | 13 | logger = logging.getLogger(__name__) 14 | 15 | 16 | def main(description): 17 | """Main function called when run_tests is run from the command-line 18 | 19 | Args: 20 | description (str): description printed to usage message 21 | """ 22 | args = _commandline_args(description) 23 | verbosity = _get_verbosity_level(args) 24 | 25 | if args.pattern is not None: 26 | pattern = args.pattern 27 | elif args.unit: 28 | pattern = "test_unit*.py" 29 | elif args.sys: 30 | pattern = "test_sys*.py" 31 | else: 32 | pattern = "test*.py" 33 | 34 | # This setup_for_tests call is the main motivation for having this wrapper script to 35 | # run the tests rather than just using 'python -m unittest discover' 36 | unit_testing.setup_for_tests(enable_critical_logs=args.debug) 37 | 38 | mydir = os.path.dirname(os.path.abspath(__file__)) 39 | testsuite = unittest.defaultTestLoader.discover(start_dir=mydir, pattern=pattern) 40 | # NOTE(wjs, 2018-08-29) We may want to change the meaning of '--debug' 41 | # vs. '--verbose': I could imagine having --verbose set buffer=False, and --debug 42 | # additionally sets the logging level to much higher - e.g., debug level. 43 | testrunner = unittest.TextTestRunner(buffer=(not args.debug), verbosity=verbosity) 44 | testrunner.run(testsuite) 45 | 46 | 47 | def _commandline_args(description): 48 | """Parse and return command-line arguments""" 49 | parser = argparse.ArgumentParser( 50 | description=description, formatter_class=argparse.RawTextHelpFormatter 51 | ) 52 | 53 | output_level = parser.add_mutually_exclusive_group() 54 | 55 | output_level.add_argument( 56 | "-v", "--verbose", action="store_true", help="Run tests with more verbosity" 57 | ) 58 | 59 | output_level.add_argument( 60 | "-d", "--debug", action="store_true", help="Run tests with even more verbosity" 61 | ) 62 | 63 | test_subset = parser.add_mutually_exclusive_group() 64 | 65 | test_subset.add_argument("-u", "--unit", action="store_true", help="Only run unit tests") 66 | 67 | test_subset.add_argument("-s", "--sys", action="store_true", help="Only run system tests") 68 | 69 | test_subset.add_argument( 70 | "-p", "--pattern", help="File name pattern to match\n" "Default is test*.py" 71 | ) 72 | 73 | args = parser.parse_args() 74 | 75 | return args 76 | 77 | 78 | def _get_verbosity_level(args): 79 | if args.debug or args.verbose: 80 | verbosity = 2 81 | else: 82 | verbosity = 1 83 | return verbosity 84 | -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | ============================================================================================= 2 | Important files in main directories: 3 | ============================================================================================= 4 | 5 | Externals.cfg --------------- File for management of the main high level externals 6 | 7 | ============================================================================================= 8 | Important main subdirectories 9 | ============================================================================================= 10 | 11 | src --------------- SLIM Source code. 12 | tools ------------- SLIM Offline tools to prepare input datasets and process output. 13 | cime_config ------- Configuration files of cime for compsets and SLIM settings 14 | manage_externals -- Script to manage the external source directories 15 | py_env_create ----- Script to setup the python environment for SLIM python tools using conda 16 | python ------------ Some python modules 17 | components -------- Other active sub-components needed for SLIM to run (CAM and CICE) 18 | libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO 19 | share ------------- CESM shared code 20 | 21 | cime/scripts --------------- cesm/cime driver scripts 22 | 23 | ============================================================================================= 24 | SLIM XML variables: 25 | ============================================================================================= 26 | 27 | SLIM_SCENARIO: Scenario to use, usually set by the compset 28 | SLIM_START_TYPE: The start type to use, usually set by the RUN_TYPE 29 | 30 | ============================================================================================= 31 | SLIM important namelist items: 32 | ============================================================================================= 33 | 34 | mml_surdat -- Dataset of surface characteristics to use (usually set by the compset/grid) 35 | finidat ----- Initial conditions to startup with 36 | hist_nhtfrq - History file frequency of output 37 | 38 | ============================================================================================= 39 | QUICKSTART: using the CPL7 scripts: 40 | ============================================================================================= 41 | 42 | cd cime/scripts 43 | ./create_newcase # get help on how to run create_newcase 44 | ./create_newcase --case testI --res f19_f19_mg17 --compset I2000SlimRsGs 45 | # create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res 46 | # "I2000SlimRsGs" case is SLIM active, datm8, and inactive ice/ocn/glc/rof 47 | cd testI 48 | ./case.setup # create the $CASE.run file 49 | ./case.build # build model and create namelists 50 | ./case.submit # submit script 51 | # (NOTE: ./xmlchange RESUBMIT=10 to set RESUBMIT to number 52 | # # of times to automatically resubmit -- 10 in this example) 53 | 54 | -------------------------------------------------------------------------------- /cime_config/config_component.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 14 | 15 | 16 | 17 | Simple Land Model: 18 | 19 | 20 | 21 | char 22 | slim 23 | slim 24 | case_comp 25 | env_case.xml 26 | Name of land component 27 | 28 | 29 | 30 | char 31 | global_uniform 32 | global_uniform,realistic_from_1850,realistic_from_2000,user_defined 33 | 34 | realistic_from_2000 35 | realistic_from_1850 36 | realistic_from_1850 37 | 38 | run_component_slim 39 | env_run.xml 40 | SLIM namelist use_case scenario. 41 | Determines the use-case scenario that will be used in the SLIM buildnml utility. 42 | This is normally set by the component set. 43 | 'global_uniform' is for surface conditions are globally constant 44 | 'realistic_from_1850' are surface conditions taken from a 1850 control simulation with CTSM 45 | 'realistic_from_2000' are surface conditions taken from a 2000 control simulation with CTSM 46 | 'user_defined' means the user will provide their own surface condition file (mml_surdat) 47 | 48 | 49 | 50 | 51 | char 52 | cold,any,required 53 | any 54 | 55 | required 56 | required 57 | any 58 | 59 | run_component_slim 60 | env_run.xml 61 | 62 | SLIM run type. 63 | 'cold' is a cold start from arbitrary initial conditions, it will fail if you do provide initial conditions 64 | 'any' is a run using initial conditions if provided, OR arbitrary initial conditions if no files can be found 65 | 'required' is a run where starting from provided initial conditions is required, it will fail if they aren't 66 | 67 | 68 | 69 | 70 | ========================================= 71 | SLIM naming conventions 72 | ========================================= 73 | note: [^_]* means match zero or more of any character BUT an underbar. 74 | (in other words make sure there is NOT a underbar before the string afterwards) 75 | 76 | 77 | 78 | -------------------------------------------------------------------------------- /src/main/clm_instMod.F90: -------------------------------------------------------------------------------- 1 | module clm_instMod 2 | 3 | !------------------------------------------------------------------------------ 4 | ! !DESCRIPTION: 5 | ! Instances and definitions of all data types 6 | ! 7 | ! !USES: 8 | use shr_kind_mod , only : r8 => shr_kind_r8 9 | use decompMod , only : bounds_type 10 | use clm_varcon , only : bdsno 11 | use clm_varctl , only : iulog 12 | use perf_mod , only : t_startf, t_stopf 13 | 14 | !----------------------------------------- 15 | ! Constants 16 | !----------------------------------------- 17 | 18 | !----------------------------------------- 19 | ! Definition of component types 20 | !----------------------------------------- 21 | 22 | use atm2lndType , only : atm2lnd_type 23 | use lnd2atmType , only : lnd2atm_type 24 | use GridcellType , only : grc 25 | ! 26 | implicit none 27 | public ! By default everything is public 28 | ! 29 | !----------------------------------------- 30 | ! Instances of component types 31 | !----------------------------------------- 32 | 33 | ! Physics types 34 | type(atm2lnd_type) :: atm2lnd_inst 35 | type(lnd2atm_type) :: lnd2atm_inst 36 | 37 | public :: clm_instInit ! Initialize 38 | public :: clm_instRest ! Setup restart 39 | !----------------------------------------------------------------------- 40 | 41 | contains 42 | 43 | !----------------------------------------------------------------------- 44 | subroutine clm_instInit(bounds) 45 | ! 46 | ! !ARGUMENTS 47 | type(bounds_type), intent(in) :: bounds ! processor bounds 48 | ! 49 | ! !LOCAL VARIABLES: 50 | !---------------------------------------------------------------------- 51 | 52 | ! Initialize clm->drv and drv->clm data structures 53 | 54 | call atm2lnd_inst%Init(bounds) 55 | call lnd2atm_inst%Init(bounds) 56 | 57 | ! Initialization of public data types 58 | 59 | ! TODO SLIM: slevis keeping an example of an accumulated field as template 60 | ! ! ------------------------------------------------------------------------ 61 | ! ! Initialize accumulated fields 62 | ! ! ------------------------------------------------------------------------ 63 | 64 | ! ! The time manager needs to be initialized before this called is made, since 65 | ! ! the step size is needed. 66 | 67 | ! call t_startf('init_accflds') 68 | ! call atm2lnd_inst%InitAccBuffer(bounds) 69 | ! call t_stopf('init_accflds') 70 | 71 | end subroutine clm_instInit 72 | 73 | !----------------------------------------------------------------------- 74 | subroutine clm_instRest(bounds, ncid, flag) 75 | ! 76 | ! !USES: 77 | use ncdio_pio , only : file_desc_t 78 | ! 79 | ! !DESCRIPTION: 80 | ! Define/write/read CLM restart file. 81 | ! 82 | ! !ARGUMENTS: 83 | type(bounds_type) , intent(in) :: bounds 84 | type(file_desc_t) , intent(inout) :: ncid ! netcdf id 85 | character(len=*) , intent(in) :: flag ! 'define', 'write', 'read' 86 | !----------------------------------------------------------------------- 87 | 88 | call atm2lnd_inst%restart (bounds, ncid, flag=flag) 89 | 90 | end subroutine clm_instRest 91 | 92 | end module clm_instMod 93 | 94 | -------------------------------------------------------------------------------- /Copyright: -------------------------------------------------------------------------------- 1 | CESM1.5: Copyright Notice and Disclaimer 2 | 3 | The Community Earth System Model (CESM was developed in cooperation with 4 | the National Science Foundation, the Department of Energy, 5 | the National Aeronautics and Space Administration, and 6 | the University Corporation for Atmospheric Research National Center for Atmospheric Research. 7 | 8 | Except for the segregable components listed below, CESM is public domain software. 9 | There may be other third party tools and libraries that are embedded, and 10 | they may have their own copyright notices and terms. 11 | 12 | The following components are copyrighted and may only be used, modified, 13 | or redistributed under the terms indicated below. 14 | 15 | Code Institution Copyright Terms of Use/Disclaimer 16 | ---- ----------- --------- ----------------------- 17 | ESMF University of Copyright University of Illinois/NCSA Open Source License 18 | Illinois/NCSA 2002-2009, 19 | University of 20 | Illinois/NCSA 21 | Open Source 22 | License 23 | 24 | POP,SCRIP,CICE Los Alamos National Copyright 2008 Los Alamos National Security, LLC 25 | Laboratory Los Alamos 26 | National 27 | Security, LLC 28 | 29 | Glimmer-CISM LANL/U. Copyright GNU General Public License 30 | Bristol/U. 2004-2010, 31 | Edinburgh/U. GNU General 32 | Montana/U. Public License 33 | Swansea 34 | 35 | AER RRTMG Atmospheric Copyright AER RRTMG Copyright 36 | and 2002-2010, 37 | Environmental Atmospheric 38 | Research, Inc. and 39 | Environmental 40 | Research, Inc. 41 | 42 | MCT Argonne Copyright 2000, MCT Copyright 43 | National 2010, 44 | Laboratory University of 45 | Chicago. 46 | 47 | ICSSP N/A Copyright 2003, ISCCP Simulator Software 48 | 2010, Steve 49 | Klein and Mark 50 | Webb 51 | 52 | XML/Lite Wadsack-Allen Copyright 2001, The documentation for the Perl XML-Lite 53 | Digital Group 2010 module is no longer available on-line. 54 | Wadsack-Allen 55 | Digital Group 56 | 57 | Inf_NaN Lahey Copyright(c) Copies of this source code, or standalone compiled 58 | _Detection Computer 2003, Lahey files derived from this source may not be sold 59 | module Systems, Inc. Computer without permission from Lahey Computers Systems. 60 | Systems, Inc. All or part of this module may be freely incorporated 61 | into executable programs which are offered for sale. 62 | Otherwise, distribution of all or part of this file is 63 | permitted, provided this copyright notice and header 64 | are included. 65 | 66 | 67 | THIS SOFTWARE IS PROVIDED BY UCAR AND ANY CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 68 | INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 69 | DISCLAIMED. IN NO EVENT SHALL UCAR OR ANY CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 70 | EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 71 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER 72 | IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF 73 | THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 74 | 75 | -------------------------------------------------------------------------------- /manage_externals/test/Makefile: -------------------------------------------------------------------------------- 1 | python = not-set 2 | verbose = not-set 3 | debug = not-set 4 | 5 | ifneq ($(python), not-set) 6 | PYTHON=$(python) 7 | else 8 | PYTHON=python 9 | endif 10 | 11 | # we need the python path to point one level up to access the package 12 | # and executables 13 | PYPATH=PYTHONPATH=..: 14 | 15 | # common args for running tests 16 | TEST_ARGS=-m unittest discover 17 | 18 | ifeq ($(debug), not-set) 19 | ifeq ($(verbose), not-set) 20 | # summary only output 21 | TEST_ARGS+=--buffer 22 | else 23 | # show individual test summary 24 | TEST_ARGS+=--buffer --verbose 25 | endif 26 | else 27 | # show detailed test output 28 | TEST_ARGS+=--verbose 29 | endif 30 | 31 | 32 | # auto reformat the code 33 | AUTOPEP8=autopep8 34 | AUTOPEP8_ARGS=--aggressive --in-place 35 | 36 | # run lint 37 | PYLINT=pylint 38 | PYLINT_ARGS=-j 2 --rcfile=.pylint.rc 39 | 40 | # code coverage 41 | COVERAGE=coverage 42 | COVERAGE_ARGS=--rcfile=.coveragerc 43 | 44 | # source files 45 | SRC = \ 46 | ../checkout_externals \ 47 | ../manic/*.py 48 | 49 | CHECKOUT_EXE = ../checkout_externals 50 | 51 | TEST_DIR = . 52 | 53 | README = ../README.md 54 | 55 | # 56 | # testing 57 | # 58 | .PHONY : utest 59 | utest : FORCE 60 | $(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_unit_*.py' 61 | 62 | .PHONY : stest 63 | stest : FORCE 64 | $(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_sys_*.py' 65 | 66 | .PHONY : test 67 | test : utest stest 68 | 69 | # 70 | # documentation 71 | # 72 | .PHONY : readme 73 | readme : $(CHECKOUT_EXE) 74 | printf "%s\n\n" "-- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --" > $(README) 75 | printf "%s" '[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)' >> $(README) 76 | printf "%s" '[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)' >> $(README) 77 | printf "\n%s\n" '```' >> $(README) 78 | $(CHECKOUT_EXE) --help >> $(README) 79 | 80 | # 81 | # coding standards 82 | # 83 | .PHONY : style 84 | style : FORCE 85 | $(AUTOPEP8) $(AUTOPEP8_ARGS) --recursive $(SRC) $(TEST_DIR)/test_*.py 86 | 87 | .PHONY : lint 88 | lint : FORCE 89 | $(PYLINT) $(PYLINT_ARGS) $(SRC) $(TEST_DIR)/test_*.py 90 | 91 | .PHONY : stylint 92 | stylint : style lint 93 | 94 | .PHONY : coverage 95 | # Need to use a single coverage run with a single pattern rather than 96 | # using two separate commands with separate patterns for test_unit_*.py 97 | # and test_sys_*.py: The latter clobbers some results from the first 98 | # run, even if we use the --append flag to 'coverage run'. 99 | coverage : FORCE 100 | $(PYPATH) $(COVERAGE) erase 101 | $(PYPATH) $(COVERAGE) run $(COVERAGE_ARGS) $(TEST_ARGS) --pattern 'test_*.py' 102 | $(PYPATH) $(COVERAGE) html 103 | 104 | # 105 | # virtual environment creation 106 | # 107 | .PHONY : env 108 | env : FORCE 109 | $(PYPATH) virtualenv --python $(PYTHON) $@_$(PYTHON) 110 | . $@_$(PYTHON)/bin/activate; pip install -r requirements.txt 111 | 112 | # 113 | # utilites 114 | # 115 | .PHONY : clean 116 | clean : FORCE 117 | -rm -rf *~ *.pyc tmp fake htmlcov 118 | 119 | .PHONY : clobber 120 | clobber : clean 121 | -rm -rf env_* 122 | 123 | FORCE : 124 | 125 | -------------------------------------------------------------------------------- /python/slim/utils.py: -------------------------------------------------------------------------------- 1 | """General-purpose utility functions""" 2 | 3 | import logging 4 | import os 5 | import sys 6 | import pdb 7 | 8 | from datetime import date 9 | from getpass import getuser 10 | 11 | from slim.git_utils import get_slim_git_short_hash 12 | 13 | logger = logging.getLogger(__name__) 14 | 15 | 16 | def abort(errmsg): 17 | """Abort the program with the given error message 18 | 19 | No traceback is given, but if the logging level is DEBUG, then we'll enter pdb 20 | """ 21 | if logger.isEnabledFor(logging.DEBUG): 22 | pdb.set_trace() 23 | 24 | sys.exit("ERROR: {}".format(errmsg)) 25 | 26 | 27 | def update_metadata(file, title, summary, contact, data_script, description): 28 | """ 29 | Description 30 | ----------- 31 | Update netcdf file's metadata 32 | Arguments 33 | --------- 34 | title: No more than short one-sentence explanation. 35 | summary: No more than two-sentence explanation. 36 | contact: E.g. CAM bulletin board at https://bb.cgd.ucar.edu 37 | data_script: Script or instructions used to generate the dataset. 38 | description: Anything else that's relevant. Capturing the command-line 39 | would be good (sys.argv) here or in data_script. 40 | """ 41 | 42 | # update attributes 43 | today = date.today() 44 | today_string = today.strftime("%Y-%m-%d") 45 | 46 | # This is the required metadata for inputdata files 47 | file.attrs["title"] = title 48 | file.attrs["summary"] = summary 49 | file.attrs["creator"] = getuser() 50 | file.attrs["contact"] = contact 51 | file.attrs["creation_date"] = today_string 52 | file.attrs["data_script"] = data_script 53 | file.attrs["description"] = description 54 | 55 | # delete unrelated attributes if they exist 56 | del_attrs = [ 57 | "source_code", 58 | "SVN_url", 59 | "hostname", 60 | "history", 61 | "History_Log", 62 | "Logname", 63 | "Host", 64 | "Version", 65 | "Compiler_Optimized", 66 | ] 67 | attr_list = file.attrs 68 | 69 | for attr in del_attrs: 70 | if attr in attr_list: 71 | del file.attrs[attr] 72 | 73 | 74 | def write_output(file, file_in, file_out, file_type): 75 | """ 76 | Description 77 | ----------- 78 | Write output file 79 | Arguments 80 | --------- 81 | file_in: 82 | (str) User-defined entry of input file 83 | file_out: 84 | (str) User-defined entry of output file 85 | file_type: 86 | (str) examples: mesh, surdat 87 | """ 88 | 89 | # update attributes 90 | title = "Modified " + file_type + " file" 91 | summary = "Modified " + file_type + " file" 92 | contact = "N/A" 93 | data_script = os.path.abspath(__file__) + " -- " + get_slim_git_short_hash() 94 | description = "Modified this file: " + file_in 95 | update_metadata( 96 | file, 97 | title=title, 98 | summary=summary, 99 | contact=contact, 100 | data_script=data_script, 101 | description=description, 102 | ) 103 | 104 | # mode 'w' overwrites file if it exists 105 | file.to_netcdf(path=file_out, mode="w", format="NETCDF3_64BIT") 106 | logger.info("Successfully created: %s", file_out) 107 | file.close() 108 | -------------------------------------------------------------------------------- /cime_config/testdefs/ExpectedTestFails.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 29 | 30 | 31 | 32 | 33 | 34 | FAIL 35 | ESCOMP/SimpleLand#85 36 | 37 | 38 | 39 | 40 | FAIL 41 | ESCOMP/SimpleLand#85 42 | 43 | 44 | 45 | 46 | FAIL 47 | ESCOMP/SimpleLand#85 48 | 49 | 50 | 51 | 52 | FAIL 53 | ESCOMP/SimpleLand#85 54 | 55 | 56 | 57 | 58 | FAIL 59 | ESCOMP/SimpleLand#17 60 | 61 | 62 | 63 | 64 | FAIL 65 | ESCOMP/SimpleLand#17 66 | 67 | 68 | 69 | 70 | FAIL 71 | ESCOMP/SimpleLand#75 72 | 73 | 74 | 75 | 76 | FAIL 77 | ESCOMP/SimpleLand#79 78 | 79 | 80 | 81 | 82 | FAIL 83 | ESCOMP/SimpleLand#79 84 | 85 | 86 | 87 | 88 | FAIL 89 | ESCOMP/SimpleLand#79 90 | 91 | 92 | 93 | 94 | -------------------------------------------------------------------------------- /python/slim/slim_logging.py: -------------------------------------------------------------------------------- 1 | """Utilities to facilitate logging 2 | 3 | A guide to logging in slim python scripts: 4 | 5 | - At the top of each module, you should have: 6 | logger = logging.getLogger(__name__) 7 | 8 | - Logging should be done via that logger, NOT via logging.[whatever] 9 | 10 | - If you want to allow the user to control logging via command-line arguments, you should: 11 | 12 | (1) At the very start of a script / application, call setup_logging_pre_config(). (We 13 | need to initialize logging to avoid errors from logging calls made very early in the 14 | script.) 15 | 16 | (2) When setting up the argument parser, call add_logging_args(parser) 17 | 18 | (3) After parsing arguments, call process_logging_args(args) 19 | 20 | - If you don't want to allow the user to control logging via command-line arguments, then 21 | simply: 22 | 23 | (1) At the very start of a script / application, call setup_logging() with the desired 24 | arguments 25 | 26 | - In unit tests, to avoid messages about loggers not being set up, you should call 27 | setup_logging_for_tests (this is typically done via unit_testing.setup_for_tests) 28 | """ 29 | 30 | import logging 31 | 32 | logger = logging.getLogger(__name__) 33 | 34 | 35 | def setup_logging_pre_config(): 36 | """Setup logging for a script / application 37 | 38 | This function should be called at the very start of a script / application where you 39 | intend to allow the user to control logging preferences via command-line arguments. 40 | 41 | This sets initial options that may be changed later by process_logging_args. 42 | """ 43 | setup_logging(level=logging.WARNING) 44 | 45 | 46 | def setup_logging_for_tests(enable_critical=False): 47 | """Setup logging as appropriate for unit tests""" 48 | setup_logging(level=logging.CRITICAL) 49 | if not enable_critical: 50 | logging.disable(logging.CRITICAL) 51 | 52 | 53 | def setup_logging(level=logging.WARNING): 54 | """Setup logging for a script / application 55 | 56 | This function should be called at the very start of a script / application where you 57 | do NOT intend to allow the user to control logging preferences via command-line 58 | arguments, so that all of the final logging options are set here. 59 | """ 60 | logging.basicConfig(format="%(levelname)s: %(message)s", level=level) 61 | 62 | 63 | def add_logging_args(parser): 64 | """Add common logging-related options to the argument parser""" 65 | 66 | logging_level = parser.add_mutually_exclusive_group() 67 | 68 | logging_level.add_argument( 69 | "-v", "--verbose", action="store_true", help="Output extra logging info" 70 | ) 71 | 72 | logging_level.add_argument( 73 | "--debug", 74 | action="store_true", 75 | help="Output even more logging info for debugging", 76 | ) 77 | 78 | 79 | def process_logging_args(args): 80 | """Configure logging based on the logging-related args added by add_logging_args""" 81 | root_logger = logging.getLogger() 82 | 83 | if args.debug: 84 | root_logger.setLevel(logging.DEBUG) 85 | elif args.verbose: 86 | root_logger.setLevel(logging.INFO) 87 | else: 88 | root_logger.setLevel(logging.WARNING) 89 | 90 | 91 | def output_to_file(file_path, message, log_to_logger=False): 92 | """ 93 | helper function to write to log file. 94 | """ 95 | with open(file_path, "a") as log_file: 96 | log_file.write(message) 97 | if log_to_logger: 98 | logger.info(message) 99 | -------------------------------------------------------------------------------- /manage_externals/manic/repository.py: -------------------------------------------------------------------------------- 1 | """Base class representation of a repository 2 | """ 3 | 4 | from .externals_description import ExternalsDescription 5 | from .utils import fatal_error 6 | from .global_constants import EMPTY_STR 7 | 8 | 9 | class Repository(object): 10 | """ 11 | Class to represent and operate on a repository description. 12 | """ 13 | 14 | def __init__(self, component_name, repo): 15 | """ 16 | Parse repo externals description 17 | """ 18 | self._name = component_name 19 | self._protocol = repo[ExternalsDescription.PROTOCOL] 20 | self._tag = repo[ExternalsDescription.TAG] 21 | self._branch = repo[ExternalsDescription.BRANCH] 22 | self._hash = repo[ExternalsDescription.HASH] 23 | self._url = repo[ExternalsDescription.REPO_URL] 24 | self._sparse = repo[ExternalsDescription.SPARSE] 25 | 26 | if self._url is EMPTY_STR: 27 | fatal_error('repo must have a URL') 28 | 29 | if ((self._tag is EMPTY_STR) and (self._branch is EMPTY_STR) and 30 | (self._hash is EMPTY_STR)): 31 | fatal_error('{0} repo must have a branch, tag or hash element') 32 | 33 | ref_count = 0 34 | if self._tag is not EMPTY_STR: 35 | ref_count += 1 36 | if self._branch is not EMPTY_STR: 37 | ref_count += 1 38 | if self._hash is not EMPTY_STR: 39 | ref_count += 1 40 | if ref_count != 1: 41 | fatal_error('repo {0} must have exactly one of ' 42 | 'tag, branch or hash.'.format(self._name)) 43 | 44 | def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive): # pylint: disable=unused-argument 45 | """ 46 | If the repo destination directory exists, ensure it is correct (from 47 | correct URL, correct branch or tag), and possibly update the source. 48 | If the repo destination directory does not exist, checkout the correce 49 | branch or tag. 50 | NB: is include as an argument for compatibility with 51 | git functionality (repository_git.py) 52 | """ 53 | msg = ('DEV_ERROR: checkout method must be implemented in all ' 54 | 'repository classes! {0}'.format(self.__class__.__name__)) 55 | fatal_error(msg) 56 | 57 | def status(self, stat, repo_dir_path): # pylint: disable=unused-argument 58 | """Report the status of the repo 59 | 60 | """ 61 | msg = ('DEV_ERROR: status method must be implemented in all ' 62 | 'repository classes! {0}'.format(self.__class__.__name__)) 63 | fatal_error(msg) 64 | 65 | def submodules_file(self, repo_path=None): 66 | # pylint: disable=no-self-use,unused-argument 67 | """Stub for use by non-git VC systems""" 68 | return None 69 | 70 | def url(self): 71 | """Public access of repo url. 72 | """ 73 | return self._url 74 | 75 | def tag(self): 76 | """Public access of repo tag 77 | """ 78 | return self._tag 79 | 80 | def branch(self): 81 | """Public access of repo branch. 82 | """ 83 | return self._branch 84 | 85 | def hash(self): 86 | """Public access of repo hash. 87 | """ 88 | return self._hash 89 | 90 | def name(self): 91 | """Public access of repo name. 92 | """ 93 | return self._name 94 | 95 | def protocol(self): 96 | """Public access of repo protocol. 97 | """ 98 | return self._protocol 99 | -------------------------------------------------------------------------------- /cime_config/namelist_definition.xsl: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | SLIM Namelist Definition 14 | 15 | 16 |

17 |

18 |
19 |

20 |

21 |

Definition of SLIM namelist variables

22 |

We list all of the relevant namelist variables for SLIM cases. This includes 23 | SLIM Namelist items.

24 |
25 |

Definition of SLIM namelist variables

26 |

Note, these all would go into the user_nl_slim file

27 |

Included in the table are the following pieces of information:

28 |
    29 |
  • Variable name.
    • 30 |
  • Variable type (char, integer, 31 | real, or logical). The type 32 | char has the length appended 33 | following an asterisk, e.g., char*256. Variables that are 34 | arrays have their dimension specifier appended inside parentheses. For 35 | example char*1(6) denotes a array of six 36 | char*1 values. 37 |
    • 38 |
  • Variable description (includes information on defaults).
    • 39 |
  • Valid values (if restricted).
    • 40 |
41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 |
SLIM Namelist Physics Options
NameTypeDescription
Valid values
54 | 55 | 56 | 57 | 58 | 59 | 60 | 62 | 63 | 64 | 65 | 66 | 67 |
SLIM Namelist Datasets
NameTypeDescription 61 |
Valid values
68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 |
SLIM Namelist History output settings
NameTypeDescription
Valid values
81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 |
SLIM Namelist Performance Tuning
NameTypeDescription
Valid values
94 | 95 |

96 |

97 | 98 |

99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | Valid Values: 110 | 111 | 112 | 113 | 114 | 115 | -------------------------------------------------------------------------------- /src/main/GridcellType.F90: -------------------------------------------------------------------------------- 1 | module GridcellType 2 | 3 | !----------------------------------------------------------------------- 4 | ! !DESCRIPTION: 5 | ! Gridcell data type allocation 6 | ! -------------------------------------------------------- 7 | ! gridcell types can have values of 8 | ! -------------------------------------------------------- 9 | ! 1 => default 10 | ! 11 | use shr_kind_mod , only : r8 => shr_kind_r8 12 | use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) 13 | use clm_varcon , only : ispval 14 | ! 15 | ! !PUBLIC TYPES: 16 | implicit none 17 | save 18 | private 19 | ! 20 | type, public :: gridcell_type 21 | 22 | ! topological mapping functionality, local 1d gdc arrays 23 | integer , pointer :: gindex (:) ! global index 24 | real(r8), pointer :: area (:) ! total land area, gridcell (km^2) 25 | real(r8), pointer :: lat (:) ! latitude (radians) 26 | real(r8), pointer :: lon (:) ! longitude (radians) 27 | real(r8), pointer :: latdeg (:) ! latitude (degrees) 28 | real(r8), pointer :: londeg (:) ! longitude (degrees) 29 | logical , pointer :: active (:) ! just needed for symmetry with other subgrid types 30 | 31 | ! Daylength 32 | real(r8) , pointer :: max_dayl (:) ! maximum daylength for this grid cell (s) 33 | real(r8) , pointer :: dayl (:) ! daylength (seconds) 34 | real(r8) , pointer :: prev_dayl (:) ! daylength from previous timestep (seconds) 35 | 36 | contains 37 | 38 | procedure, public :: Init 39 | procedure, public :: Clean 40 | 41 | end type gridcell_type 42 | type(gridcell_type), public, target :: grc !gridcell data structure 43 | !------------------------------------------------------------------------ 44 | 45 | contains 46 | 47 | !------------------------------------------------------------------------ 48 | subroutine Init(this, begg, endg) 49 | ! 50 | ! !ARGUMENTS: 51 | class(gridcell_type) :: this 52 | integer, intent(in) :: begg, endg 53 | !------------------------------------------------------------------------ 54 | 55 | ! The following is set in InitGridCells 56 | allocate(this%gindex (begg:endg)) ; this%gindex (:) = ispval 57 | allocate(this%area (begg:endg)) ; this%area (:) = nan 58 | allocate(this%lat (begg:endg)) ; this%lat (:) = nan 59 | allocate(this%lon (begg:endg)) ; this%lon (:) = nan 60 | allocate(this%latdeg (begg:endg)) ; this%latdeg (:) = nan 61 | allocate(this%londeg (begg:endg)) ; this%londeg (:) = nan 62 | allocate(this%active (begg:endg)) ; this%active (:) = .true. 63 | 64 | ! This is initiailized in module DayLength 65 | allocate(this%max_dayl (begg:endg)) ; this%max_dayl (:) = nan 66 | allocate(this%dayl (begg:endg)) ; this%dayl (:) = nan 67 | allocate(this%prev_dayl (begg:endg)) ; this%prev_dayl (:) = nan 68 | 69 | end subroutine Init 70 | 71 | !------------------------------------------------------------------------ 72 | subroutine Clean(this) 73 | ! 74 | ! !ARGUMENTS: 75 | class(gridcell_type) :: this 76 | !------------------------------------------------------------------------ 77 | 78 | deallocate(this%gindex ) 79 | deallocate(this%area ) 80 | deallocate(this%lat ) 81 | deallocate(this%lon ) 82 | deallocate(this%latdeg ) 83 | deallocate(this%londeg ) 84 | deallocate(this%active ) 85 | deallocate(this%max_dayl ) 86 | deallocate(this%dayl ) 87 | deallocate(this%prev_dayl ) 88 | 89 | end subroutine Clean 90 | 91 | end module GridcellType 92 | -------------------------------------------------------------------------------- /src/utils/array_utils.F90.in: -------------------------------------------------------------------------------- 1 | module array_utils 2 | 3 | ! ------------------------------------------------------------------------ 4 | ! !DESCRIPTION: 5 | ! This module contains routines for working with arrays. 6 | ! 7 | ! NOTE(wjs, 2015-10-21) These routines could be moved to csm_share. However, I'm not 8 | ! sure if these routines will stick around for long, since they are just here to work 9 | ! around the fact that we don't specify -Mallocatable=03 with pgi (which in turn is 10 | ! because that flag led to bugs with pgi14). 11 | ! 12 | ! !USES: 13 | 14 | use shr_kind_mod, only : r8 => shr_kind_r8, i4=>shr_kind_i4 15 | 16 | implicit none 17 | private 18 | save 19 | 20 | ! Public routines 21 | 22 | public :: transpose_wrapper ! wrap the intrinsic transpose function, first allocating the destination array 23 | public :: pack_wrapper ! wrap the intrinsic pack function, first allocating the destination array 24 | 25 | interface transpose_wrapper 26 | !TYPE int,double 27 | module procedure transpose_wrapper_{TYPE} 28 | end interface transpose_wrapper 29 | 30 | contains 31 | 32 | !----------------------------------------------------------------------- 33 | !TYPE int,double 34 | subroutine transpose_wrapper_{TYPE}(arr_out, arr_in) 35 | ! 36 | ! !DESCRIPTION: 37 | ! Wrap the intrinsic transpose function, doing the necessary allocation of the 38 | ! destination array 39 | ! 40 | ! NOTE(wjs, 2015-10-21) This is supposed to be handled for you in Fortran2003. Within 41 | ! CESM, it currently appears to be handled for all compilers except pgi: It is 42 | ! handled with intel through the use of '-assume realloc_lhs'. It could be handled 43 | ! with pgi through the use of '-Mallocatable=03', but we currently don't use that 44 | ! flag, because it triggered bugs with pgi14. 45 | ! 46 | ! !USES: 47 | ! 48 | ! !ARGUMENTS: 49 | {VTYPE}, allocatable, intent(out) :: arr_out(:,:) 50 | {VTYPE}, intent(in) :: arr_in(:,:) 51 | ! 52 | ! !LOCAL VARIABLES: 53 | integer :: size1, size2 54 | 55 | character(len=*), parameter :: subname = 'transpose_wrapper_{TYPE}' 56 | !----------------------------------------------------------------------- 57 | 58 | size1 = size(arr_in, 1) 59 | size2 = size(arr_in, 2) 60 | allocate(arr_out(size2, size1)) 61 | 62 | arr_out = transpose(arr_in) 63 | 64 | end subroutine transpose_wrapper_{TYPE} 65 | 66 | !----------------------------------------------------------------------- 67 | subroutine pack_wrapper(arr_packed, arr, mask) 68 | ! 69 | ! !DESCRIPTION: 70 | ! Wrap the intrinsic pack function, doing the necessary allocation of the destination 71 | ! array. 72 | ! 73 | ! NOTE(wjs, 2015-10-21) This is supposed to be handled for you in Fortran2003. Within 74 | ! CESM, it currently appears to be handled for all compilers except pgi: It is 75 | ! handled with intel through the use of '-assume realloc_lhs'. It could be handled 76 | ! with pgi through the use of '-Mallocatable=03', but we currently don't use that 77 | ! flag, because it triggered bugs with pgi14. 78 | ! 79 | ! !USES: 80 | ! 81 | ! !ARGUMENTS: 82 | real(r8), allocatable, intent(out) :: arr_packed(:) 83 | real(r8), intent(in) :: arr(:) 84 | logical , intent(in) :: mask(:) 85 | ! 86 | ! !LOCAL VARIABLES: 87 | integer :: packed_size 88 | 89 | character(len=*), parameter :: subname = 'pack_wrapper' 90 | !----------------------------------------------------------------------- 91 | 92 | packed_size = count(mask) 93 | allocate(arr_packed(packed_size)) 94 | arr_packed = pack(arr, mask) 95 | 96 | end subroutine pack_wrapper 97 | 98 | end module array_utils 99 | 100 | -------------------------------------------------------------------------------- /cime_config/buildlib: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | 3 | """ 4 | build slim ibrary 5 | """ 6 | import sys, os, time, filecmp 7 | 8 | _CIMEROOT = os.environ.get("CIMEROOT") 9 | if _CIMEROOT is None: 10 | raise SystemExit("ERROR: must set CIMEROOT environment variable") 11 | 12 | _LIBDIR = os.path.join(_CIMEROOT, "CIME", "Tools") 13 | sys.path.append(_LIBDIR) 14 | 15 | from standard_script_setup import * 16 | from CIME.buildlib import parse_input 17 | from CIME.build import get_standard_makefile_args 18 | from CIME.case import Case 19 | from CIME.utils import run_cmd, expect 20 | 21 | logger = logging.getLogger(__name__) 22 | 23 | ############################################################################### 24 | def _main_func(): 25 | ############################################################################### 26 | 27 | caseroot, libroot, bldroot = parse_input(sys.argv) 28 | 29 | with Case(caseroot) as case: 30 | 31 | casetools = case.get_value("CASETOOLS") 32 | makefile = os.path.join(casetools, "Makefile") 33 | lnd_root = case.get_value("COMP_ROOT_DIR_LND") 34 | gmake_j = case.get_value("GMAKE_J") 35 | gmake = case.get_value("GMAKE") 36 | gmake_opts = get_standard_makefile_args(case) 37 | driver = case.get_value("COMP_INTERFACE").lower() 38 | nthrds = case.get_value("LND_NTHRDS") 39 | 40 | if nthrds > 1: 41 | expect( 42 | False, 43 | "LND_NTHRDS must be 1 as threading isn't implemented (see issue #14)", 44 | ) 45 | 46 | # ------------------------------------------------------- 47 | # create Filepath file 48 | #------------------------------------------------------- 49 | compname = case.get_value("COMP_LND") 50 | filepath_file = os.path.join(bldroot,"Filepath") 51 | if not os.path.isfile(filepath_file): 52 | caseroot = case.get_value("CASEROOT") 53 | expect( (compname == "slim"), "Unexpected COMP_LND name: %s" % (compname)) 54 | paths = [os.path.join(caseroot,"SourceMods","src."+compname), 55 | os.path.join(lnd_root,"src","cpl",driver), 56 | os.path.join(lnd_root,"src","main"), 57 | os.path.join(lnd_root,"src","init_interp"), 58 | os.path.join(lnd_root,"src","utils"), 59 | os.path.join(lnd_root,"src","cpl")] 60 | 61 | # Paths needed to build the current system, but won't be long term 62 | paths.append(os.path.join(lnd_root, "src", "biogeophys")) 63 | paths.append(os.path.join(lnd_root, "src", "biogeochem")) 64 | paths.append(os.path.join(lnd_root, "src", "soilbiogeochem")) 65 | 66 | with open(filepath_file, "w") as filepath: 67 | filepath.write("\n".join(paths)) 68 | filepath.write("\n") 69 | 70 | # ------------------------------------------------------- 71 | # create the library in libroot 72 | # ------------------------------------------------------- 73 | 74 | complib = os.path.join(libroot, "liblnd.a") 75 | makefile = os.path.join(casetools, "Makefile") 76 | 77 | cmd = "{} complib -j {} COMP_NAME={} COMPLIB={} -f {} {}" \ 78 | .format(gmake, gmake_j, compname, complib, makefile, gmake_opts ) 79 | 80 | rc, out, err = run_cmd(cmd) 81 | logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n" % (cmd, out, err)) 82 | expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc)) 83 | 84 | 85 | ############################################################################### 86 | 87 | if __name__ == "__main__": 88 | logger.warning( "WARNING: buildlib is being called as a program rather than a subroutine as " + 89 | "it is expected to be in the CESM context" ) 90 | _main_func() 91 | -------------------------------------------------------------------------------- /src/init_interp/initInterpMultilevelBase.F90: -------------------------------------------------------------------------------- 1 | module initInterpMultilevelBase 2 | 3 | ! ------------------------------------------------------------------------ 4 | ! !DESCRIPTION: 5 | ! This module defines a base class for handling multi-level fields 6 | ! 7 | ! Usage: For a given variable: 8 | ! 9 | ! First call check_npts with the number of destination points, to ensure that this 10 | ! interpolator is appropriate for this variable. 11 | ! 12 | ! Then call interp_multilevel once for each destination point 13 | ! 14 | ! Note that these interpolators only care about the destination point, not the source 15 | ! point. Any information on the source grid is expected to have already been 16 | ! interpolated to the destination grid. (This is needed for the sake of memory 17 | ! scalability: Information on the source grid is not decomposed across processors, so 18 | ! results in large amounts of memory usage.) 19 | ! 20 | ! !USES: 21 | 22 | implicit none 23 | private 24 | save 25 | 26 | ! Public types 27 | 28 | public :: interp_multilevel_type 29 | 30 | type, abstract :: interp_multilevel_type 31 | contains 32 | procedure(check_npts_interface), deferred :: check_npts 33 | procedure(interp_multilevel_interface), deferred :: interp_multilevel 34 | procedure(get_description_interface), deferred :: get_description ! get text description of interpolator 35 | end type interp_multilevel_type 36 | 37 | abstract interface 38 | 39 | subroutine check_npts_interface(this, npts, varname) 40 | ! !DESCRIPTION: 41 | ! Checks the number of destination points, to ensure that this interpolator is 42 | ! appropriate for this variable. This should be called once for each variable. 43 | ! 44 | ! Aborts if there is a mismatch. 45 | ! 46 | ! !USES: 47 | import:: interp_multilevel_type 48 | ! 49 | ! !ARGUMENTS: 50 | class(interp_multilevel_type), intent(in) :: this 51 | integer, intent(in) :: npts ! number of dest points (on this processor) 52 | character(len=*), intent(in) :: varname ! variable name (for diagnostic output) 53 | end subroutine check_npts_interface 54 | 55 | subroutine interp_multilevel_interface(this, & 56 | data_dest, data_source, index_dest) 57 | ! !DESCRIPTION: 58 | ! Interpolates a multi-level field from source to dest, for a single point. 59 | ! 60 | ! data_dest and data_source give values for all levels, for one destination or 61 | ! source point. index_dest gives the spatial index (e.g., column index) of the dest 62 | ! point; this is needed for some types of interpolation (to find the appropriate 63 | ! metadata), but is ignored by others. This index should be 1-based (i.e., if the 64 | ! lower bounds in the caller are not 1, they should be adjusted so that the first 65 | ! index is 1). 66 | ! 67 | ! !USES: 68 | use shr_kind_mod, only : r8 => shr_kind_r8 69 | import :: interp_multilevel_type 70 | ! 71 | ! !ARGUMENTS: 72 | class(interp_multilevel_type), intent(in) :: this 73 | real(r8) , intent(inout) :: data_dest(:) 74 | real(r8) , intent(in) :: data_source(:) 75 | integer , intent(in) :: index_dest 76 | end subroutine interp_multilevel_interface 77 | 78 | pure function get_description_interface(this) result(description) 79 | ! !DESCRIPTION 80 | ! Returns a text description of this interpolator 81 | ! 82 | ! !USES: 83 | import :: interp_multilevel_type 84 | ! 85 | ! !ARGUMENTS: 86 | character(len=:), allocatable :: description ! function result 87 | class(interp_multilevel_type), intent(in) :: this 88 | end function get_description_interface 89 | end interface 90 | 91 | end module initInterpMultilevelBase 92 | -------------------------------------------------------------------------------- /src/utils/clm_nlUtilsMod.F90: -------------------------------------------------------------------------------- 1 | module clm_nlUtilsMod 2 | !----------------------------------------------------------------------- 3 | !BOP 4 | ! 5 | ! !MODULE: clm_nltUtilsMod 6 | ! 7 | ! !DESCRIPTION: 8 | ! Utilities to handle namelists. 9 | ! 10 | ! !USES: 11 | 12 | ! !PUBLIC TYPES: 13 | implicit none 14 | save 15 | 16 | private ! By default everything is private 17 | 18 | ! !PUBLIC MEMBER FUNCTIONS: 19 | public :: find_nlgroup_name ! find a specified namelist group in a file 20 | ! 21 | ! !REVISION HISTORY: 22 | ! Created by B. Eaton 23 | ! Move to CLM by E. Kluzek 24 | ! 25 | ! !PRIVATE MEMBER FUNCTIONS: None 26 | !----------------------------------------------------------------------- 27 | ! !PRIVATE DATA MEMBERS: None 28 | 29 | !EOP 30 | !----------------------------------------------------------------------- 31 | contains 32 | 33 | !----------------------------------------------------------------------- 34 | 35 | !----------------------------------------------------------------------- 36 | !BOP 37 | ! 38 | ! !IROUTINE: find_nlgroup_name 39 | ! 40 | ! !INTERFACE: 41 | subroutine find_nlgroup_name(unit, group, status) 42 | ! 43 | ! !DESCRIPTION: 44 | ! Search a file that contains namelist input for the specified namelist group name. 45 | ! Leave the file positioned so that the current record is the first record of the 46 | ! input for the specified group. 47 | ! 48 | ! METHOD: 49 | ! Read the file line by line. Each line is searched for an '&' which may only 50 | ! be preceded by blanks, immediately followed by the group name which is case 51 | ! insensitive. If found then backspace the file so the current record is the 52 | ! one containing the group name and return success. Otherwise return -1. 53 | ! 54 | ! !USES: 55 | use shr_kind_mod , only : CS => shr_kind_cs 56 | use shr_string_mod, only : shr_string_toLower 57 | ! 58 | ! !ARGUMENTS: 59 | integer, intent(in) :: unit ! fortran unit attached to file 60 | character(len=*), intent(in) :: group ! namelist group name 61 | integer, intent(out) :: status ! 0 for success, -1 if group name not found 62 | ! 63 | ! !REVISION HISTORY: 64 | ! Created by B. Eaton, August 2007 65 | ! Move to CLM E. Kluzek, August 2012 66 | ! 67 | ! 68 | ! !LOCAL VARIABLES: 69 | !EOP 70 | integer :: len_grp ! length of the groupname 71 | integer :: ios ! io status 72 | character(len=CS) :: inrec ! first shr_kind_CS characters of input record 73 | character(len=CS) :: inrec2 ! left adjusted input record 74 | character(len=len(group)) :: lc_group ! lower-case group name 75 | character(len=32) :: subname = 'find_nlgroup_name' ! subroutine name 76 | !----------------------------------------------------------------------- 77 | len_grp = len_trim(group) 78 | lc_group = shr_string_toLower(group) 79 | 80 | ios = 0 81 | do while (ios <= 0) 82 | 83 | read(unit, '(a)', iostat=ios, end=100) inrec 84 | 85 | if (ios <= 0) then ! ios < 0 indicates an end of record condition 86 | 87 | ! look for group name in this record 88 | 89 | ! remove leading blanks 90 | inrec2 = adjustl(inrec) 91 | 92 | ! check for leading '&' 93 | if (inrec2(1:1) == '&') then 94 | 95 | ! check for case insensitive group name 96 | if (trim(lc_group) == shr_string_toLower(inrec2(2:len_grp+1))) then 97 | 98 | ! found group name. backspace to leave file position at this record 99 | backspace(unit) 100 | status = 0 101 | return 102 | 103 | end if 104 | end if 105 | end if 106 | 107 | end do 108 | 109 | 100 continue ! end of file processing 110 | status = -1 111 | 112 | end subroutine find_nlgroup_name 113 | 114 | !----------------------------------------------------------------------- 115 | 116 | end module clm_nlUtilsMod 117 | -------------------------------------------------------------------------------- /src/main/GetGlobalValuesMod.F90: -------------------------------------------------------------------------------- 1 | module GetGlobalValuesMod 2 | 3 | !----------------------------------------------------------------------- 4 | ! Obtain and Write Global Index information 5 | !----------------------------------------------------------------------- 6 | implicit none 7 | private 8 | 9 | ! PUBLIC MEMBER FUNCTIONS: 10 | 11 | public :: GetGlobalIndex 12 | public :: GetGlobalWrite 13 | 14 | character(len=*), parameter, private :: sourcefile = & 15 | __FILE__ 16 | !----------------------------------------------------------------------- 17 | 18 | contains 19 | 20 | !----------------------------------------------------------------------- 21 | integer function GetGlobalIndex(decomp_index, clmlevel) 22 | 23 | !---------------------------------------------------------------- 24 | ! Description 25 | ! Determine global index space value for target point at given clmlevel 26 | ! 27 | ! Uses: 28 | use shr_log_mod, only: errMsg => shr_log_errMsg 29 | use decompMod , only: bounds_type, get_clmlevel_gsmap, get_proc_bounds 30 | use spmdMod , only: iam 31 | use clm_varcon , only: nameg 32 | use clm_varctl , only: iulog 33 | use mct_mod , only: mct_gsMap, mct_gsMap_orderedPoints 34 | use shr_sys_mod, only: shr_sys_abort 35 | ! 36 | ! Arguments 37 | integer , intent(in) :: decomp_index 38 | character(len=*) , intent(in) :: clmlevel 39 | ! 40 | ! Local Variables: 41 | type(bounds_type) :: bounds_proc ! processor bounds 42 | type(mct_gsMap),pointer :: gsmap ! global seg map 43 | integer, pointer,dimension(:) :: gsmap_ordered ! gsmap ordered points 44 | integer :: beg_index ! beginning proc index for clmlevel 45 | !---------------------------------------------------------------- 46 | 47 | call get_proc_bounds(bounds_proc) 48 | 49 | if (trim(clmlevel) == nameg) then 50 | beg_index = bounds_proc%begg 51 | else 52 | call shr_sys_abort('clmlevel of '//trim(clmlevel)//' not supported' // & 53 | errmsg(sourcefile, __LINE__)) 54 | end if 55 | 56 | call get_clmlevel_gsmap(clmlevel=trim(clmlevel), gsmap=gsmap) 57 | call mct_gsMap_orderedPoints(gsmap, iam, gsmap_ordered) 58 | GetGlobalIndex = gsmap_ordered(decomp_index - beg_index + 1) 59 | deallocate(gsmap_ordered) 60 | 61 | end function GetGlobalIndex 62 | 63 | !----------------------------------------------------------------------- 64 | subroutine GetGlobalWrite(decomp_index, clmlevel) 65 | 66 | !----------------------------------------------------------------------- 67 | ! Description: 68 | ! Write global index information for input local indices 69 | ! 70 | use shr_sys_mod , only : shr_sys_flush 71 | use shr_sys_mod , only : shr_sys_abort 72 | use shr_log_mod , only : errMsg => shr_log_errMsg 73 | use clm_varctl , only : iulog 74 | use clm_varcon , only : nameg 75 | use GridcellType , only : grc 76 | ! 77 | ! Arguments: 78 | integer , intent(in) :: decomp_index 79 | character(len=*) , intent(in) :: clmlevel 80 | ! 81 | ! Local Variables: 82 | integer :: igrc 83 | !----------------------------------------------------------------------- 84 | 85 | if (trim(clmlevel) == nameg) then 86 | 87 | igrc = decomp_index 88 | write(iulog,*)'local gridcell index = ',igrc 89 | write(iulog,*)'global gridcell index = ',GetGlobalIndex(decomp_index=igrc, clmlevel=nameg) 90 | write(iulog,*)'gridcell longitude = ',grc%londeg(igrc) 91 | write(iulog,*)'gridcell latitude = ',grc%latdeg(igrc) 92 | 93 | else 94 | call shr_sys_abort('clmlevel '//trim(clmlevel)//'not supported '//errmsg(sourcefile, __LINE__)) 95 | 96 | end if 97 | 98 | call shr_sys_flush(iulog) 99 | 100 | end subroutine GetGlobalWrite 101 | 102 | end module GetGlobalValuesMod 103 | -------------------------------------------------------------------------------- /src/utils/spmdMod.F90: -------------------------------------------------------------------------------- 1 | 2 | module spmdMod 3 | 4 | !----------------------------------------------------------------------- 5 | !BOP 6 | ! 7 | ! !MODULE: spmdMod 8 | ! 9 | ! !DESCRIPTION: 10 | ! SPMD initialization 11 | ! 12 | ! !REVISION HISTORY: 13 | ! Author: Mariana Vertenstein 14 | ! 15 | !EOP 16 | !----------------------------------------------------------------------- 17 | 18 | use shr_kind_mod, only: r8 => shr_kind_r8 19 | use clm_varctl , only: iulog 20 | implicit none 21 | 22 | private 23 | 24 | #include 25 | 26 | save 27 | 28 | ! Default settings valid even if there is no spmd 29 | 30 | logical, public :: masterproc ! proc 0 logical for printing msgs 31 | integer, public :: iam ! processor number 32 | integer, public :: npes ! number of processors for clm 33 | integer, public :: mpicom ! communicator group for clm 34 | integer, public :: comp_id ! component id 35 | 36 | ! 37 | ! Public methods 38 | ! 39 | public :: spmd_init ! Initialization 40 | 41 | ! 42 | ! Values from mpif.h that can be used 43 | ! 44 | public :: MPI_INTEGER 45 | public :: MPI_REAL8 46 | public :: MPI_LOGICAL 47 | public :: MPI_SUM 48 | public :: MPI_MIN 49 | public :: MPI_MAX 50 | public :: MPI_LOR 51 | public :: MPI_STATUS_SIZE 52 | public :: MPI_ANY_SOURCE 53 | public :: MPI_CHARACTER 54 | public :: MPI_COMM_WORLD 55 | public :: MPI_MAX_PROCESSOR_NAME 56 | 57 | contains 58 | 59 | !----------------------------------------------------------------------- 60 | !BOP 61 | ! 62 | ! !IROUTINE: spmd_init( clm_mpicom ) 63 | ! 64 | ! !INTERFACE: 65 | subroutine spmd_init( clm_mpicom, LNDID ) 66 | ! 67 | ! !DESCRIPTION: 68 | ! MPI initialization (number of cpus, processes, tids, etc) 69 | ! 70 | ! !USES 71 | ! 72 | ! !ARGUMENTS: 73 | implicit none 74 | integer, intent(in) :: clm_mpicom 75 | integer, intent(in) :: LNDID 76 | ! 77 | ! !REVISION HISTORY: 78 | ! Author: Mariana Vertenstein 79 | ! 80 | ! 81 | ! !LOCAL VARIABLES: 82 | !EOP 83 | integer :: i,j ! indices 84 | integer :: ier ! return error status 85 | integer :: mylength ! my processor length 86 | logical :: mpi_running ! temporary 87 | integer, allocatable :: length(:) 88 | integer, allocatable :: displ(:) 89 | character*(MPI_MAX_PROCESSOR_NAME), allocatable :: procname(:) 90 | character*(MPI_MAX_PROCESSOR_NAME) :: myprocname 91 | !----------------------------------------------------------------------- 92 | 93 | ! Initialize mpi communicator group 94 | 95 | mpicom = clm_mpicom 96 | 97 | comp_id = LNDID 98 | 99 | ! Get my processor id 100 | 101 | call mpi_comm_rank(mpicom, iam, ier) 102 | if (iam==0) then 103 | masterproc = .true. 104 | else 105 | masterproc = .false. 106 | end if 107 | 108 | ! Get number of processors 109 | 110 | call mpi_comm_size(mpicom, npes, ier) 111 | 112 | ! Get my processor names 113 | 114 | allocate (length(0:npes-1), displ(0:npes-1), procname(0:npes-1)) 115 | 116 | call mpi_get_processor_name (myprocname, mylength, ier) 117 | call mpi_allgather(mylength,1,MPI_INTEGER,length,1,MPI_INTEGER,mpicom,ier) 118 | 119 | do i = 0,npes-1 120 | displ(i)=i*MPI_MAX_PROCESSOR_NAME 121 | end do 122 | call mpi_gatherv (myprocname,mylength,MPI_CHARACTER, & 123 | procname,length,displ,MPI_CHARACTER,0,mpicom,ier) 124 | if (masterproc) then 125 | write(iulog,100)npes 126 | write(iulog,200) 127 | write(iulog,220) 128 | do i=0,npes-1 129 | write(iulog,250)i,(procname((i))(j:j),j=1,length(i)) 130 | end do 131 | endif 132 | 133 | deallocate (length, displ, procname) 134 | 135 | 100 format(//,i3," pes participating in computation for CLM") 136 | 200 format(/,35('-')) 137 | 220 format(/,"NODE#",2x,"NAME") 138 | 250 format("(",i5,")",2x,100a1,//) 139 | 140 | end subroutine spmd_init 141 | 142 | end module spmdMod 143 | -------------------------------------------------------------------------------- /README_EXTERNALS.rst: -------------------------------------------------------------------------------- 1 | Obtaining the full model code and associated scripting infrastructure 2 | ===================================================================== 3 | 4 | #. Clone the repository. :: 5 | 6 | 7 | #. Run the script **manage_externals/checkout_externals**. :: 8 | 9 | ./manage_externals/checkout_externals 10 | 11 | The **checkout_externals** script is a package manager that will 12 | populate the directory with the relevant versions of each of the 13 | components along with the CIME infrastructure code. 14 | 15 | At this point you have a working version. 16 | 17 | To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ . 18 | 19 | More details on checkout_externals 20 | ---------------------------------- 21 | 22 | The file **Externals.cfg** in your top-level directory tells 23 | **checkout_externals** which tag/branch of each component should be 24 | brought in to generate your sandbox. 25 | 26 | **You need to rerun checkout_externals whenever Externals.cfg has 27 | changed** (unless you have already manually updated the relevant 28 | external(s) to have the correct branch/tag checked out). Common times 29 | when this is needed are: 30 | 31 | * After checking out a new branch/tag 32 | 33 | * After merging some other branch/tag into your currently 34 | checked-out branch 35 | 36 | **checkout_externals** must be run from the root of the source 37 | tree. For example, if you cloned with:: 38 | 39 | git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox 40 | 41 | then you must run **checkout_externals** from 42 | ``/path/to/my_ctsm_sandbox``. 43 | 44 | To see more details of **checkout_externals**, issue :: 45 | 46 | ./manage_externals/checkout_externals --help 47 | 48 | Customizing your sandbox 49 | ============================= 50 | 51 | There are several use cases to consider when you want to customize or modify your sandbox. 52 | 53 | Switching to a different branch or tag 54 | ------------------------------------------- 55 | 56 | If you have already checked out a branch or tag and **HAVE NOT MADE ANY 57 | MODIFICATIONS** it is simple to change your sandbox. Say that you 58 | checked out ctsm1.0.0 but really wanted to have ctsm1.1.0; 59 | you would simply do the following:: 60 | 61 | git checkout ctsm1.1.0 62 | ./manage_externals/checkout_externals 63 | 64 | You should **not** use this method if you have made any source code 65 | changes, or if you have any ongoing cases that were created from 66 | this sandbox. In these cases, it is often easiest to do a second **git 67 | clone**. 68 | 69 | Pointing to a different version of a component 70 | ---------------------------------------------- 71 | 72 | Each entry in **Externals.cfg** has the following form (we use CIME as an 73 | example below):: 74 | 75 | [cime] 76 | local_path = cime 77 | protocol = git 78 | repo_url = https://github.com/CESM-Development/cime 79 | tag = cime5.4.0-alpha.20 80 | required = True 81 | 82 | Each entry specifies either a tag or a branch. To point to a new tag: 83 | 84 | #. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing 85 | ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above) 86 | 87 | #. Checkout the new component(s):: 88 | 89 | ./manage_externals/checkout_externals 90 | 91 | Keep in mind that changing individual components from a tag may result 92 | in an invalid model (won't compile, won't run, not scientifically 93 | meaningful) and is unsupported. 94 | 95 | Committing your change to Externals.cfg 96 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 | 98 | After making this change, it's a good idea to commit the change in your 99 | local git repository. First create a branch in your local 100 | repository, then commit it. (Unlike with subversion, branches are stored 101 | locally unless you explicitly push them up to github. Feel free to 102 | create whatever local branches you'd like.) For example:: 103 | 104 | git checkout -b my_ctsm_branch 105 | git add Externals.cfg 106 | git commit -m "Update CIME to cime5.4.0-alpha.20" 107 | 108 | -------------------------------------------------------------------------------- /manage_externals/test/doc/testing.rst: -------------------------------------------------------------------------------- 1 | Testing 2 | ======= 3 | 4 | The manage_externals package has an automated test suite. All pull 5 | requests are expected to pass 100% of the automated tests, as well as 6 | be pep8 and lint 'clean' and maintain approximately constant (at a 7 | minimum) level of code coverage. 8 | 9 | Quick Start 10 | ----------- 11 | 12 | Do nothing approach 13 | ~~~~~~~~~~~~~~~~~~~ 14 | 15 | When you create a pull request on GitHub, Travis-CI continuous 16 | integration testing will run the test suite in both python2 and 17 | python3. Test results, lint results, and code coverage results are 18 | available online. 19 | 20 | Do something approach 21 | ~~~~~~~~~~~~~~~~~~~~~ 22 | 23 | In the test directory, run: 24 | 25 | .. code-block:: shell 26 | 27 | make env 28 | make lint 29 | make test 30 | make coverage 31 | 32 | 33 | Automated Testing 34 | ----------------- 35 | 36 | The manage_externals manic library and executables are developed to be 37 | python2 and python3 compatible using only the standard library. The 38 | test suites meet the same requirements. But additional tools are 39 | required to provide lint and code coverage metrics and generate 40 | documentation. The requirements are maintained in the requirements.txt 41 | file, and can be automatically installed into an isolated environment 42 | via Makefile. 43 | 44 | Bootstrap requirements: 45 | 46 | * python2 - version 2.7.x or later 47 | 48 | * python3 - version 3.6 tested other versions may work 49 | 50 | * pip and virtualenv for python2 and python3 51 | 52 | Note: all make rules can be of the form ``make python=pythonX rule`` 53 | or ``make rule`` depending if you want to use the default system 54 | python or specify a specific version. 55 | 56 | The Makefile in the test directory has the following rules: 57 | 58 | * ``make python=pythonX env`` - create a python virtual environment 59 | for python2 or python3 and install all required packages. These 60 | packages are required to run lint or coverage. 61 | 62 | * ``make style`` - runs autopep8 63 | 64 | * ``make lint`` - runs autopep8 and pylint 65 | 66 | * ``make test`` - run the full test suite 67 | 68 | * ``make utest`` - run jus the unit tests 69 | 70 | * ``make stest`` - run jus the system integration tests 71 | 72 | * ``make coverage`` - run the full test suite through the code 73 | coverage tool and generate an html report. 74 | 75 | * ``make readme`` - automatically generate the README files. 76 | 77 | * ``make clean`` - remove editor and pyc files 78 | 79 | * ``make clobber`` - remove all generated test files, including 80 | virtual environments, coverage reports, and temporary test 81 | repository directories. 82 | 83 | Unit Tests 84 | ---------- 85 | 86 | Unit tests are probably not 'true unit tests' for the pedantic, but 87 | are pragmatic unit tests. They cover small practicle code blocks: 88 | functions, class methods, and groups of functions and class methods. 89 | 90 | System Integration Tests 91 | ------------------------ 92 | 93 | NOTE(bja, 2017-11) The systems integration tests currently do not include svn repositories. 94 | 95 | The manage_externals package is extremely tedious and error prone to test manually. 96 | 97 | Combinations that must be tested to ensure basic functionality are: 98 | 99 | * container repository pulling in simple externals 100 | 101 | * container repository pulling in mixed externals with sub-externals. 102 | 103 | * mixed repository acting as a container, pulling in simple externals and sub-externals 104 | 105 | Automatic system tests are handled the same way manual testing is done: 106 | 107 | * clone a test repository 108 | 109 | * create an externals description file for the test 110 | 111 | * run the executable with the desired args 112 | 113 | * check the results 114 | 115 | * potentially modify the repo (checkout a different branch) 116 | 117 | * rerun and test 118 | 119 | * etc 120 | 121 | The automated system stores small test repositories in the main repo 122 | by adding them as bare repositories. These repos are cloned via a 123 | subprocess call to git and manipulated during the tests. 124 | -------------------------------------------------------------------------------- /tools/modify_input_files/modify_surdat_template.cfg: -------------------------------------------------------------------------------- 1 | [modify_input] 2 | 3 | # ------------------------------------------------------------------------ 4 | # .cfg file with inputs for surdat_modifier. 5 | # 6 | # We advise users to make a copy of this file that they can change freely, 7 | # rather than changing this "template" file. 8 | # 9 | # Variables with FILL_THIS_IN must be specified. 10 | # Variables with UNSET may be specified; if not and 11 | # - defaults = False, they will remain unused 12 | # - defaults = True, they will take on default values hardwired in the 13 | # code. Details in comments below. 14 | # Variables with values already set, may be changed to other values. If 15 | # they get omitted, they will obtain the same default values found here. 16 | # ------------------------------------------------------------------------ 17 | 18 | # Path and name of input surface dataset (str) 19 | surdat_in = FILL_THIS_IN 20 | 21 | # Path and name of output surface dataset (str) 22 | surdat_out = FILL_THIS_IN 23 | 24 | # defaults (bool) 25 | # When user wants existing values in surdat to persist in all except the 26 | # variables that they explicitly request to change, then set this to False. 27 | # When user wants default representation of the land by resetting all 28 | # surdat variables, some through this file and others by using hardwired 29 | # defaults, then set this to True. Hardwired values are as follows: 30 | # glc_mask = [0] * self.months 31 | # alb_gvd = [0.2] * self.months 32 | # alb_svd = [0.8] * self.months 33 | # alb_gnd = [0.3] * self.months 34 | # alb_snd = [0.6] * self.months 35 | # alb_gvf = [0.2] * self.months 36 | # alb_svf = [0.8] * self.months 37 | # alb_gnf = [0.3] * self.months 38 | # alb_snf = [0.6] * self.months 39 | # bucketdepth = [200] * self.months 40 | # emissivity = [1] * self.months 41 | # snowmask = [50] * self.months 42 | # roughness = [0.1] * self.months 43 | # evap_res = [100] * self.months 44 | # soil_type = [0] * self.months 45 | # soil_tk_1d = [1.5] * self.months 46 | # soil_cv_1d = [2e6] * self.months 47 | # glc_tk_1d = [2.4] * self.months 48 | # glc_cv_1d = [1.9e6] * self.months 49 | defaults = False 50 | 51 | # Boundaries of user-defined rectangle (float) 52 | # If lat_1 > lat_2, the code creates two rectangles, one in the north and 53 | # one in the south. 54 | # If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. 55 | # Alternatively, user may specify a custom area in a .nc landmask_file 56 | # below. If set, this will override the lat/lon settings. 57 | # ----------------------------------- 58 | # southernmost latitude for rectangle 59 | lnd_lat_1 = -90 60 | # northernmost latitude for rectangle 61 | lnd_lat_2 = 90 62 | # westernmost longitude for rectangle 63 | lnd_lon_1 = 0 64 | # easternmost longitude for rectangle 65 | lnd_lon_2 = 360 66 | # User-defined mask in a file, as alternative to setting lat/lon values. 67 | # If set, lat_dimname and lon_dimname should likely also be set. IMPORTANT: 68 | # - lat_dimname and lon_dimname may be left UNSET if they match the expected 69 | # default values 'lsmlat' and 'lsmlon' 70 | landmask_file = UNSET 71 | lat_dimname = UNSET 72 | lon_dimname = UNSET 73 | 74 | # Monthly values over the user-defined mask. 75 | # Space-delimited list of 12 floats or int without brackets 76 | # e.g., glc_mask = 1 1 1 1 1 1 1 1 1 1 1 1 77 | # Any of the variables updated below by the user will be 78 | # updated in the surdat_out file in the user-defined mask. 79 | # if defaults = True and some of the following variables are UNSET, then they 80 | # will default to the corresponding values listed above in the "defaults" 81 | # comments, again only in the user-defined mask. 82 | # if defaults = False and some of the following variables are UNSET, then they 83 | # will remain unchanged from the surdat_in file. 84 | # SOIL_TYPE accepts integer values from ? to ?. 85 | glc_mask = UNSET 86 | alb_gvd = UNSET 87 | alb_svd = UNSET 88 | alb_gnd = UNSET 89 | alb_snd = UNSET 90 | alb_gvf = UNSET 91 | alb_svf = UNSET 92 | alb_gnf = UNSET 93 | alb_snf = UNSET 94 | bucketdepth = UNSET 95 | emissivity = UNSET 96 | snowmask = UNSET 97 | roughness = UNSET 98 | evap_res = UNSET 99 | soil_type = UNSET 100 | soil_tk_1d = UNSET 101 | soil_cv_1d = UNSET 102 | glc_tk_1d = UNSET 103 | glc_cv_1d = UNSET 104 | -------------------------------------------------------------------------------- /src/init_interp/initInterpBounds.F90: -------------------------------------------------------------------------------- 1 | module initInterpBounds 2 | 3 | ! ------------------------------------------------------------------------ 4 | ! !DESCRIPTION: 5 | ! This module defines a class for storing and querying bounds information for initInterp 6 | ! 7 | ! !USES: 8 | use shr_log_mod , only : errMsg => shr_log_errMsg 9 | use abortutils , only : endrun 10 | 11 | implicit none 12 | private 13 | save 14 | 15 | ! Public types 16 | 17 | public :: interp_bounds_type 18 | 19 | type :: interp_bounds_type 20 | private 21 | integer :: begg ! beginning gridcell-level index 22 | integer :: endg ! ending gridcell-level index 23 | contains 24 | procedure :: get_begg 25 | procedure :: get_endg 26 | procedure :: get_beg ! get beginning index for a given subgrid level 27 | procedure :: get_end ! get ending index for a given subgrid level 28 | end type interp_bounds_type 29 | 30 | interface interp_bounds_type 31 | module procedure constructor 32 | end interface interp_bounds_type 33 | 34 | character(len=*), parameter, private :: sourcefile = & 35 | __FILE__ 36 | 37 | contains 38 | 39 | ! ======================================================================== 40 | ! Constructors 41 | ! ======================================================================== 42 | 43 | !----------------------------------------------------------------------- 44 | function constructor(begg, endg) result(this) 45 | ! 46 | ! !DESCRIPTION: 47 | ! Create an interp_bounds_type instance 48 | ! 49 | ! !USES: 50 | ! 51 | ! !ARGUMENTS: 52 | type(interp_bounds_type) :: this ! function result 53 | integer, intent(in) :: begg, endg 54 | ! 55 | ! !LOCAL VARIABLES: 56 | 57 | character(len=*), parameter :: subname = 'constructor' 58 | !----------------------------------------------------------------------- 59 | 60 | this%begg = begg 61 | this%endg = endg 62 | 63 | end function constructor 64 | 65 | ! ======================================================================== 66 | ! Public methods 67 | ! ======================================================================== 68 | 69 | integer function get_begg(this) 70 | class(interp_bounds_type), intent(in) :: this 71 | get_begg = this%begg 72 | end function get_begg 73 | 74 | integer function get_endg(this) 75 | class(interp_bounds_type), intent(in) :: this 76 | get_endg = this%endg 77 | end function get_endg 78 | 79 | !----------------------------------------------------------------------- 80 | function get_beg(this, subgrid_level) result(beg_index) 81 | ! 82 | ! !DESCRIPTION: 83 | ! Get beginning index for a given subgrid level 84 | ! 85 | ! !USES: 86 | ! 87 | ! !ARGUMENTS: 88 | integer :: beg_index ! function result 89 | class(interp_bounds_type), intent(in) :: this 90 | character(len=*), intent(in) :: subgrid_level ! 'gridcell' 91 | ! 92 | ! !LOCAL VARIABLES: 93 | 94 | character(len=*), parameter :: subname = 'get_beg' 95 | !----------------------------------------------------------------------- 96 | 97 | select case (subgrid_level) 98 | case('gridcell') 99 | beg_index = this%begg 100 | case default 101 | call endrun(msg=subname//' ERROR: Unknown subgrid level: '//trim(subgrid_level)// & 102 | errMsg(sourcefile, __LINE__)) 103 | end select 104 | 105 | end function get_beg 106 | 107 | !----------------------------------------------------------------------- 108 | function get_end(this, subgrid_level) result(end_index) 109 | ! 110 | ! !DESCRIPTION: 111 | ! Get ending index for a given subgrid level 112 | ! 113 | ! !USES: 114 | ! 115 | ! !ARGUMENTS: 116 | integer :: end_index ! function result 117 | class(interp_bounds_type), intent(in) :: this 118 | character(len=*), intent(in) :: subgrid_level ! 'gridcell' 119 | ! 120 | ! !LOCAL VARIABLES: 121 | 122 | character(len=*), parameter :: subname = 'get_end' 123 | !----------------------------------------------------------------------- 124 | 125 | select case (subgrid_level) 126 | case('gridcell') 127 | end_index = this%endg 128 | case default 129 | call endrun(msg=subname//' ERROR: Unknown subgrid level: '//trim(subgrid_level)// & 130 | errMsg(sourcefile, __LINE__)) 131 | end select 132 | 133 | end function get_end 134 | 135 | end module initInterpBounds 136 | -------------------------------------------------------------------------------- /cime_config/config_compsets.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | ========================================= 7 | compset naming convention 8 | ========================================= 9 | The compset longname below has the specified order 10 | atm, lnd, ice, ocn, river, glc wave cesm-options 11 | 12 | The notation for the compset longname is 13 | TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_BGC%phys] 14 | Where for the CAM specific compsets below the following is supported 15 | TIME = Time period (e.g. 2000, HIST, RCP8...) 16 | ATM = [CAM40, CAM50, CAM60] 17 | LND = [SLIM, SLND] 18 | ICE = [CICE, CICE5, DICE, SICE] 19 | OCN = [DOCN, ,AQUAP, SOCN] 20 | ROF = [RTM, SROF] 21 | GLC = [SGLC] 22 | WAV = [SWAV] 23 | BGC = optional BGC scenario 24 | 25 | The OPTIONAL %phys attributes specify submodes of the given system 26 | For example DOCN%DOM is the data ocean model for DOCN 27 | ALL the possible %phys choices for each component are listed 28 | with the -list command for create_newcase 29 | ALL data models must have a %phys option that corresponds to the data model mode 30 | 31 | Each compset node is associated with the following elements 32 | - lname 33 | - alias 34 | - science_support (if this compset is supported scientifically with control simulations) 35 | 36 | 37 | 40 | 41 | 42 | 43 | ELT2000ClimoTESTC6I5Slim 44 | 2000_CAM60_SLIM_CICE5_DOCN%SOM_SROF_SGLC_SWAV 45 | 46 | 47 | 48 | ELT2000ClimoTESTC6I6Slim 49 | 2000_CAM60_SLIM_CICE_DOCN%SOM_SROF_SGLC_SWAV 50 | 51 | 52 | 53 | 54 | 55 | ELT1850TESTC6I5Slim 56 | 1850_CAM60_SLIM_CICE5_DOCN%SOM_SROF_SGLC_SWAV 57 | 58 | 59 | ELT1850TESTC6I6Slim 60 | 1850_CAM60_SLIM_CICE_DOCN%SOM_SROF_SGLC_SWAV 61 | 62 | 63 | 64 | 65 | FLT2000ClimoC6I5Slim 66 | 2000_CAM60_SLIM_CICE5%PRES_DOCN%DOM_SROF_SGLC_SWAV 67 | 68 | 69 | FLT2000ClimoC6I6Slim 70 | 2000_CAM60_SLIM_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV 71 | 72 | 73 | 74 | 75 | ELT2000ClimoTESTC5I5Slim 76 | 2000_CAM50_SLIM_CICE5_DOCN%SOM_SROF_SGLC_SWAV 77 | 78 | 79 | 80 | 81 | FLTHISTC5I5Slim 82 | HIST_CAM50_SLIM_CICE5%PRES_DOCN%DOM_SROF_SGLC_SWAV 83 | 84 | 85 | 88 | 89 | 90 | 91 | IHistSlimRsGs 92 | HIST_DATM%GSWP3v1_SLIM_SICE_SOCN_SROF_SGLC_SWAV 93 | 94 | 96 | 97 | IHistSlimQianRsGs 98 | HIST_DATM%QIA_SLIM_SICE_SOCN_SROF_SGLC_SWAV 99 | 100 | 101 | 102 | I2000SlimRsGs 103 | 2000_DATM%GSWP3v1_SLIM_SICE_SOCN_SROF_SGLC_SWAV 104 | 105 | 106 | 107 | 108 | I1850SlimRsGs 109 | 1850_DATM%GSWP3v1_SLIM_SICE_SOCN_SROF_SGLC_SWAV 110 | 111 | 112 | 113 | 114 | I1850SlimCruRsGs 115 | 1850_DATM%CRUv7_SLIM_SICE_SOCN_SROF_SGLC_SWAV 116 | 117 | 118 | 119 | 120 | I1850SlimCplhistRsGs 121 | 1850_DATM%CPLHIST_SLIM_SICE_SOCN_SROF_SGLC_SWAV 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 1850-01-01 131 | 132 | 133 | 134 | 135 | 136 | 137 | -------------------------------------------------------------------------------- /py_env_create: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # 3 | # py_env_create -- setup the python environment in order to use SLIM python tools 4 | # 5 | # Simple bash script to setup the python environment for the user so they can run the SLIM 6 | # python tools using "conda". 7 | # 8 | dir=${0%/*} 9 | if [ "$dir" = "$0" ];then 10 | dir="." 11 | fi 12 | 13 | # Check if conda is in your path 14 | conda --help >& condahelp.txt 15 | error=$? 16 | if [ $error != 0 ]; then 17 | echo "conda is NOT in your path for the bash shell add it with modules or whatever is required on your system to get it in your path" 18 | echo "on cheyenne/capser/etc use -- module load conda" 19 | echo "on izumi/CGD systems use -- module load lang/python" 20 | echo "For notes on installing on a user system see: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html" 21 | echo "Error code was $error" 22 | cat condahelp.txt 23 | exit -1 24 | fi 25 | rm condahelp.txt 26 | python_env=slim_pylib 27 | 28 | 29 | condadir="$dir/python" 30 | 31 | domain=`domainname` 32 | if [[ $domain =~ cgd.* ]]; then 33 | condafile="conda_env_slim_py_cgd.txt" 34 | else 35 | condafile="conda_env_slim_py.txt" 36 | fi 37 | #---------------------------------------------------------------------- 38 | # Usage subroutine 39 | usage() { 40 | echo "" 41 | echo "***********************************************************************" 42 | echo "usage:" 43 | echo "./py_env_create" 44 | echo "" 45 | echo "valid arguments: " 46 | echo "[-h|--help] " 47 | echo " Displays this help message" 48 | echo "[-v|--verbose] " 49 | echo " Run with verbose mode for the install so you see the progress bar" 50 | echo "[-f|--file ] " 51 | echo " Conda environment file to use (can be a text format or YAML format)" 52 | echo " Assumed to be under the directory: $condadir" 53 | echo " Default is: $condafile" 54 | echo "[--option