Add Albany external library support for MPASLI #340
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Updating to MPASLI commit d5ef579. This brings in a number of features that are needed for upcoming ACME development: * updates landice core to use same version of framework as ocean and cice cores - framework version 0893c55 * works with the current version of Albany - b255f2c * includes LI core fix for Intel - 5b093d2 * includes a framework fix for building MPAS C++ code in ESMs (needed on Edison) - 77b8a62 * separates the initial LI diagnostic solve into its own routine so it can be called from an ESM driver - a6395b4 Also, the initial implementation of analysis members is added - 986572f Note that also in this commit glc_comp_mct has been updated to work with the updated MPASLI code. Recent updates in MPAS require domain % ioContext as an argument to two subroutines called in glc_comp_mct. These MPAS changes were needed to support multiple MPAS cores in the same executable.
Make dt and output interval 1 day. Make restart interval 1 year. This is still in flux, but coupling interval may be this short, so switching to this for now.
And change stop time to 5 days. These are short intervals for the ice sheet model, but are adequate for confirming the model runs.
This calls a new function in MPASLI that calculates the initial ice sheet state. This is necessary for two reasons: 1. So that the initial state exported to the coupler (upperSurface, mask) is correct. 2. So that evolution on the first time step within glc_run works correctly.
This has been added in a general way, following exactly how Trilinos support occurs in ACME/CESM. In other words, any component can set a XXX_USE_ALBANY env variable, and if any of these are set, a master USE_ALBANY var is set which will add Albany libs to the linking stage. Currently only MPASLI is anticipated to use Albany. Note that Albany builds will only work on machines where ALBANY_PATH has been set in machines-acme/config_compilers.xml, which currently is nowhere, but will be added in additional commits.
This creates separate GLC component names: MPASLISIA, MPASLIALBFO to be used in compset descriptions depending on which version of MPASLI is desired. These compset definitions control a MPASLI_USE_ALBANY variable set in config_compsets.xml. In a separate commit that variable will be used to control the MPASLI build within the mpasli component.
If MPASLI_USE_ALBANY has been set by the compset system, these changes allow mpasli.buildlib to 'turn on' Albany code in MPASLI through the ALBANY=true make option.
Adding hardcoded path to Albany install for edison,intel build. [BFB]
I pulled new versions of Albany and Trilinos, and so updated the path in config_compilers to point to the install. I am installing these in a directory with the date for a way of doing micro-releases and capturing provenance. Otherwise, I could just overwrite the install directory. [BFB]
If MPASLI_USE_ALBANY xml option is TRUE, then the build-namelist script will set MPASLI namelist options appropriate for using Albany.
albany_input.xml is a required configuration file for Albany. This commit adds a copy of this file configured for MPASLI to the MPASLI namelist_files directory. When a compset with MPASLI is selected, this file will be copied to the run directory.
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Note this cannot be merged until the CIME integration branch has been merged into master. |
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This can be run on Mustang with something like: Success is the model running to completion. I have confirmed that the history file output matches BFB with a standalone MPASLI run with the same configuration. |
Within cesm_build.pl, shell commands were built up to call xmlchange to set use_trilinos and use_albany in env_build.xml. However the commands were not actually run. I confirmed that the use_albany variable is set properly in env_build.xml already, so these uncalled commands are not actually needed.
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) This merge adds Albany external library support for the MPASLI GLC component. Albany is a C++ library built on the Trilinos framework and is used as an external library for the "First Order" solver in MPASLI (which will be used for Antarctic Ice Sheet simulations in ACME v1). Albany library support has been added to ACME in a general way, following exactly how Trilinos support occurs in ACME/CESM, meaning other components could use it with minimal additional changes. Additionally, a compset has been added that runs MPASLI+Albany, and when this compset is selected, there is logic in the scripts that build the MPASLI library and namelist that adjusts the build and run-time configuration accordingly. For ACME to build with Albany, the location of the Albany installation has to be specified for each machine for which support is desired. This merge adds that support for Mustang and Wolf, as well as partial support for Edison. Additional machines will be added in the future in separate branches. It has been confirmed that a simulation using MPASLI+Albany within ACME is BFB with standalone MPASLI+Albany. OG-418 OG-422 OG-423 * matthewhoffman/mpasli/add_albany_build_postcime2: Remove uncalled sysmod calls for Trilinos & Albany from cesm_build.pl Have mpasli.buildnml copy albany_input.xml to run dir Have build-namelist set MPASLI nl opts for Albany use Updated path to installed Albany on Edision machines: added ALBANY_PATH to edison config Modify mpasli.buildlib to enable build w/Albany Add compset for Albany solver for MPASLI Add Albany path for mustang and wolf machines Add ability for ACME to use Albany library
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12d2135 Merge pull request #388 from ESMCI/jgfouca/need_to_report_build_exceptions 8f677cd Add test to ensure build fails report info to teststatus.log 7095ef0 Need to report build exception contents 7c9cc94 Merge pull request #387 from ESMCI/jgfouca/fix_case_build_return_code bf941ed case.build needs to check success in order to return a sane error code df432e8 update ChangeLog 154d5f8 Merge pull request #378 from ESMCI/rljacob/update-config-files 6b8fc76 Merge pull request #382 from ESMCI/sarich/fix-taskmaker-counter 5df46a2 Merge pull request #381 from jedwards4b/test_fixes e58d624 component_compare_test was not properly reporting failures 0e0e577 Update acme config_files for mpas 84122dd Merge pull request #376 from ESMCI/jgfouca/changes_from_acme 38e2f8a More stuff from ACME c86398e Merge pull request #375 from ESMCI/jgfouca/portable_run_cmd_utest daaf621 Merge pull request #373 from ESMCI/jgfouca/enhance_bisect e61ba96 Change MPAS compset for test c77a64e Add homme python test 3031f00 Better support for 'none' module system 3ceef7b Make run_cmd_no_fail unit test more portable bbd20fb Merge branch 'jgfouca/fix_module_list' (PR #374) 6eb8143 Reactivate creation of software_environment.txt 4dd30c6 Ensure module setup is sourced before list c8bd20e fix bug in translation from perl 20a3412 cime_bisect: Add better support for modifying create_test run 77871de update changelog e74906b comment out code until it works for tcsh users 4a13413 fix issue with module list 6ad4b2d update changelog cef688d update changelog 835b511 Merge pull request #367 from jedwards4b/user_mod_0len_fix b280b55 Merge pull request #362 from ESMCI/jgfouca/remove_perl_taskmaker 12a30ee Merge pull request #356 from ESMCI/jgfouca/minor_timing_chg 3fb0b80 Merge pull request #355 from ESMCI/jgfouca/wait_for_test_refactor d083933 user_nl_ file was being removed if a user_nl file in any mods directory was missing 39de940 Fix comment 5d38420 Revert "Merge pull request #343 from ESMCI/wilke/scripts/xmlchange" 8dc2354 Merge pull request #363 from ESMCI/rljacob/machines/fix-acme 0773aac Increase default walltime for blues c4dce0f Remove last uses of taskmaker.pl 76eb1bc Remove -A directive from edison d67b267 Merge pull request #361 from billsacks/cism_nag bf02e3e Merge pull request #357 from ekluzek/fixpionml c9b8910 Seperate out modelio namelist definition since it uses the same names, but defines them differently 805ad7f Add -mismatch_all when compiling cism with nag fff9a9b Set CHECK_TIMING to true in addition to SAVE_TIMING if --save-timing given to create_test f25a518 wait_for_tests will now always specifically wait for the RUN phase e19e72c Update drv buildnamelist test to work with cime5 db1538e Merge branch 'douglasjacobsen/add_lanl_machines' (PR #353) 893c6c6 Add support for LANL's mustang and wolf to cime dea8a3a Merge pull request #350 from ESMCI/rerun_test_functionality 9b4488b Changes based on github feedback c103e08 Add SAVE_TIMING_DIR for edison 98f95bb Merge pull request #341 from ESMCI/santos/fix-env-leakage 1b775e4 Fixes post-upstream-merge ea97b56 Merge branch 'master' into rerun_test_functionality 1ca1b83 Merge pull request #348 from ESMCI/jayeshkrishna/machinefiles/get_acme_cime_dev_working_on_mira 252aea7 Merge pull request #343 from ESMCI/wilke/scripts/xmlchange 2db894f Add missing files 622b7d0 Complete ba69385 progress 84000ee Fixing the runjob command for ACME on Mira 1a55232 Adding config for ERS_Ld3.ne30_g16_rx1.A test d1df346 Error handling; check for correct length of key-value pair array after split fa1cb49 listofsettings allways an array, test for length of array a6a3d33 Changed number of expected positional arguments to 0 or 1 , warnings and debug statements 74d2100 checking for missing values in settings string from command line cd350da Remove `GenericXML` check for env variables. 6ca6b59 progress e7b334e Merge pull request #340 from ESMCI/douglasjacobsen/fix_test_template 43807a5 Add white space after batch directives in script templates e061505 Merge pull request #337 from ESMCI/jgfouca/autosave_env_info edc1671 Autosave environment information in case_setup. 33ce89b Merge pull request #336 from ESMCI/jgfouca/fix_create_test_not_catching_missing_project c3f8f84 create_test was not failing the create_newcase phase when project info was missing fef81df Merge pull request #335 from ESMCI/jgfouca/add_queue_option_to_create_test 731f8a0 Add ability to select queue to create_test and create_newcase 6f9613f Merge pull request #333 from ESMCI/jgfouca/even_more_sky_env_fixes 11877a2 Fix mismatch between MPI_PATH and the mpi module being loaded d37e177 Merge pull request #322 from ESMCI/jgfouca/restore_good_python_version_error ad18c34 Merge pull request #331 from ESMCI/jgfouca/reduce_output_from_check_input_data 0268cb7 Only report present files in debug mode 47b4216 Fix spelling mistake dddd7f0 Merge pull request #327 from ESMCI/jgfouca/fix_more_sky_env_issues 07aeb52 Get cime_developer building again on skybridge. 0aceb94 Merge branch 'wilke/template/directives' (PR #324) d8f331c moved batchdirectives to top of the template dbbd3a1 Users should get a nice error when their python is too old 5eea798 Merge pull request #320 from ESMCI/jgfouca/fix_skybridge_env_issues ca3e004 Fix skybridge environment problems, port to new SEMS modules 1a82a57 Merge pull request #318 from ESMCI/jgfouca/remove_sentinel_concept e266dd9 Remove sentinel concept from jenkins_generic_job aae8e30 comments for cime5.0.5 e20f807 Merge pull request #317 from billsacks/restore_lii 1967bb3 Restore LII test c404dfa Merge remote-tracking branch 'origin/master' 0406b7d updates for cime5.0.4 7930cd7 Merge pull request #316 from ESMCI/jgfouca/update_code_checker 009f7a1 code_checker: Leverage .gitignore by using git ls-files instead of find to get list of ifles to check c5555c7 Merge pull request #315 from Katetc/master c4817d7 fix issue 314 7a493a0 remove multiple run lines from test file c269ab9 Merge pull request #313 from ESMCI/jgfouca/correctly_report_problem_in_test 734e4b4 Rolling the Intel compiler back to v15.0.2 9a46a99 On batch systems, be sure to report that the problem is with wait_for_tests, not create_test 0e95d19 add some more info to README file e9586c1 Changes required to support the new Hobart cluster configuration cdb7805 update documentation for --xml options 98a0380 Merge pull request #307 from ESMCI/rljacob/tests/add-readme 46ff3c6 work on test rerunability c5f2ae9 Merge pull request #308 from ESMCI/jgfouca/fix_check_input_bug bddea72 document ERR test 8639ba1 create ability to run tests in same case more than once b18580b Fix minor erroneous output bug in check_input_data 6f3e448 Add README back to Testcases fd001a7 Add README back to SystemTests 929f05a Merge pull request #305 from ESMCI/jgfouca/advanced_profiling_tool 20c2e22 Make prof tools a bit more user friendly 1f9b49b Merge pull request #304 from jedwards4b/dynamic_system_test_dirs 0ba7f50 handle so that we dont have a list of test names to maintain 92a266e handle so that we dont have a list of test names to maintain 99f3d35 New tool 'advanced-py-prof' 4e6f7f5 initialize contents 3703d94 machine specific fixes for edison/cori/slurm systems f6dc40a fixes git issue 303 7bacf48 repeat change for acme 503d5ad load system test directories dynamically based on paths in config_files.xml b28ddff Merge pull request #302 from ESMCI/jgfouca/profiling_tool_etc 0e1553f Add a new tool for very simple python profiling 1eb2a56 Merge pull request #301 from jedwards4b/shell_commands_delete 2f78ec7 remove any existing shell_commands files from case before writing new ones 5f85c05 update changelog for tag 4ef656d pylint fixes 8624ece fix needed for scripts_regression_tests following PR298 6cc9110 These were supposed to be in PR296 d19afa9 Merge remote-tracking branch 'jedwards/testing_fixes' (PR #296) b302243 Merge pull request #298 from ESMCI/jgfouca/restore_verbose 0a95b04 component_compare_test should fail if one of the components to be compared is not found" 9aa8683 Reintroduce verbose option into the refactored logging system a796384 fix for lii test and response to review d8c9b2e Merge pull request #286 from jedwards4b/buildnml_output_fix 1894e28 improve documetation of debug option, remove incorrect documentation of verbose option 21ef9ae remove whitespace surrounding test names f6fdbb7 fix erp test update ChangeLog b8b4723 Fix LII test daa0c63 rename bisect unit test from acme to cime 4f1a079 move pecount code from create_test to create_newcase 24eb48f move clm include directory to prevent build confusion 1ee4449 add support for ascii testfile, allow multiple compilers in tests d6c28b4 fix memleak test giving error if baseline not found 8ff5f19 Merge pull request #287 from ESMCI/nag_mismatch a57e410 Remove `-mismatch_all` from NAG options in CESM. 5040500 output from buildnml scripts now prints git-subtree-dir: cime git-subtree-split: 12d2135
jgfouca
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) This merge adds Albany external library support for the MPASLI GLC component. Albany is a C++ library built on the Trilinos framework and is used as an external library for the "First Order" solver in MPASLI (which will be used for Antarctic Ice Sheet simulations in ACME v1). Albany library support has been added to ACME in a general way, following exactly how Trilinos support occurs in ACME/CESM, meaning other components could use it with minimal additional changes. Additionally, a compset has been added that runs MPASLI+Albany, and when this compset is selected, there is logic in the scripts that build the MPASLI library and namelist that adjusts the build and run-time configuration accordingly. For ACME to build with Albany, the location of the Albany installation has to be specified for each machine for which support is desired. This merge adds that support for Mustang and Wolf, as well as partial support for Edison. Additional machines will be added in the future in separate branches. It has been confirmed that a simulation using MPASLI+Albany within ACME is BFB with standalone MPASLI+Albany. OG-418 OG-422 OG-423 * matthewhoffman/mpasli/add_albany_build_postcime2: Remove uncalled sysmod calls for Trilinos & Albany from cesm_build.pl Have mpasli.buildnml copy albany_input.xml to run dir Have build-namelist set MPASLI nl opts for Albany use Updated path to installed Albany on Edision machines: added ALBANY_PATH to edison config Modify mpasli.buildlib to enable build w/Albany Add compset for Albany solver for MPASLI Add Albany path for mustang and wolf machines Add ability for ACME to use Albany library
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This merge adds Albany external library support for the MPASLI GLC component. Albany is a C++ library built on the Trilinos framework and is used as an external library for the "First Order" solver in MPASLI (which will be used for Antarctic Ice Sheet simulations in ACME v1).
Albany library support has been added to ACME in a general way, following exactly how Trilinos support occurs in ACME/CESM, meaning other components could use it with minimal additional changes.
Additionally, a compset has been added that runs MPASLI+Albany, and when this compset is selected, there is logic in the scripts that build the MPASLI library and namelist that adjusts the build and run-time configuration accordingly.
For ACME to build with Albany, the location of the Albany installation has to be specified for each machine for which support is desired. This merge adds that support for Mustang and Wolf, as well as partial support for Edison. Additional machines will be added in the future in separate branches.
It has been confirmed that a simulation using MPASLI+Albany within ACME is BFB with standalone MPASLI+Albany.
OG-418
OG-422
OG-423