Update Thompson MP from gsl/develop, minor CCPP updates, minor regres…

…sion test script updates (NOAA-EMC#498)

- Updates to auto-rt in PR ufs-community/ufs-weather-model#491 from @BrianCurtis-NOAA 
- Fixes to the regression testing scripts in branch https://github.com/DusanJovic-NOAA/ufs-weather-model/tree/rt_log_dir_fix from @DusanJovic-NOAA 
- Change baseline location on gaea to where emc.nemspara can write
- Update of submodule pointers for fv3atm, ccpp-framework and ccpp-physics, and new Thompson MP lookup tables for the changes described in the associated PRs below
- Remove tests fv3_gfs_v15p2_RRTMGP and fv3_gfs_v15p2_RRTMGP_debug from `tests/rt_gnu.conf` (same errors as with other GFS v15p2 tests previously, `compute_qs: saturation vapor pressure table overflow`)

tests/auto/.gitignore

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+accesstoken
+rt_auto_*.log

tests/auto/jobs/bl.py

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+# Imports
+import datetime
+import logging
+import os
+import sys
+from . import rt
+
+def run(job_obj):
+    logger = logging.getLogger('BL/RUN')
+    workdir, rtbldir, blstore = set_directories(job_obj)
+    pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
+    bldate = get_bl_date(job_obj, pr_repo_loc)
+    bldir = f'{blstore}/develop-{bldate}/{job_obj.compiler.upper()}'
+    run_regression_test(job_obj, pr_repo_loc)
+    post_process(job_obj, pr_repo_loc, repo_dir_str, rtbldir, bldir)
+
+
+def set_directories(job_obj):
+    logger = logging.getLogger('BL/SET_DIRECTORIES')
+    if job_obj.machine == 'hera':
+        workdir = '/scratch1/NCEPDEV/nems/emc.nemspara/autort/pr'
+        blstore = '/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs'
+        rtbldir = '/scratch1/NCEPDEV/stmp4/emc.nemspara/FV3_RT/'\
+                 f'REGRESSION_TEST_{job_obj.compiler.upper()}'
+    elif job_obj.machine == 'jet':
+        workdir = '/lfs4/HFIP/h-nems/emc.nemspara/autort/pr'
+        blstore = '/lfs4/HFIP/hfv3gfs/RT/NEMSfv3gfs/'
+        rtbldir = '/lfs4/HFIP/hfv3gfs/emc.nemspara/RT_BASELINE/'\
+                 f'emc.nemspara/FV3_RT/REGRESSION_TEST_{job_obj.compiler.upper()}'
+    elif job_obj.machine == 'gaea':
+        workdir = '/lustre/f2/pdata/ncep/emc.nemspara/autort/pr'
+        blstore = '/lustre/f2/pdata/ncep_shared/emc.nemspara/RT/NEMSfv3gfs'
+        rtbldir = '/lustre/f2/scratch/emc.nemspara/FV3_RT/'\
+                 f'REGRESSION_TEST_{job_obj.compiler.upper()}'
+    elif job_obj.machine == 'orion':
+        workdir = '/work/noaa/nems/emc.nemspara/autort/pr'
+        blstore = '/work/noaa/nems/emc.nemspara/RT/NEMSfv3gfs'
+        rtbldir = '/work/noaa/stmp/bcurtis/stmp/bcurtis/FV3_RT/'\
+                 f'REGRESSION_TEST_{job_obj.compiler.upper()}'
+    elif job_obj.machine == 'cheyenne':
+        workdir = '/glade/work/heinzell/fv3/ufs-weather-model/auto-rt'
+        blstore = '/glade/p/ral/jntp/GMTB/ufs-weather-model/RT'
+        rtbldir = '/glade/work/heinzell/FV3_RT/'\
+                 f'REGRESSION_TEST_{job_obj.compiler.upper()}'
+    else:
+        logger.critical(f'Machine {job_obj.machine} is not supported for this job')
+        raise KeyError
+
+    logger.info(f'machine: {job_obj.machine}')
+    logger.info(f'workdir: {workdir}')
+    logger.info(f'blstore: {blstore}')
+    logger.info(f'rtbldir: {rtbldir}')
+
+    return workdir, rtbldir, blstore
+
+
+def check_for_bl_dir(bldir):
+    logger = logging.getLogger('BL/CHECK_FOR_BL_DIR')
+    logger.info('Checking if baseline directory exists')
+    if os.path.exists(bldir):
+        logger.critical(f'Baseline dir: {bldir} exists. It should not, yet.')
+        raise FileExistsError
+    return False
+
+
+def create_bl_dir(bldir):
+    logger = logging.getLogger('BL/CREATE_BL_DIR')
+    if not check_for_bl_dir(bldir):
+        os.makedirs(bldir)
+        if not os.path.exists(bldir):
+            logger.critical(f'Someting went wrong creating {bldir}')
+            raise FileNotFoundError
+
+
+#def get_bl_date(job_obj):
+#    logger = logging.getLogger('BL/GET_BL_DATE')
+#    for line in job_obj.preq_dict['preq'].body.splitlines():
+#        if 'BL_DATE:' in line:
+#            bldate = line
+#            bldate = bldate.replace('BL_DATE:', '')
+#            bldate = bldate.replace(' ', '')
+#            if len(bldate) != 8:
+#                print(f'Date: {bldate} is not formatted YYYYMMDD')
+#                raise ValueError
+#            logger.info(f'BL_DATE: {bldate}')
+#            bl_format = '%Y%m%d'
+#            try:
+#                datetime.datetime.strptime(bldate, bl_format)
+#            except ValueError:
+#                logger.info(f'Date {bldate} is not formatted YYYYMMDD')
+#                raise ValueError
+#            return bldate
+#    logger.critical('"BL_DATE:YYYYMMDD" needs to be in the PR body.'\
+#                    'On its own line. Stopping')
+#    raise ValueError
+
+
+def run_regression_test(job_obj, pr_repo_loc):
+    logger = logging.getLogger('BL/RUN_REGRESSION_TEST')
+    if job_obj.compiler == 'gnu':
+        rt_command = [[f'export RT_COMPILER="{job_obj.compiler}" && cd tests '
+                       '&& /bin/bash --login ./rt.sh -e -c -l rt_gnu.conf',
+                       pr_repo_loc]]
+    elif job_obj.compiler == 'intel':
+        rt_command = [[f'export RT_COMPILER="{job_obj.compiler}" && cd tests '
+                       '&& /bin/bash --login ./rt.sh -e -c', pr_repo_loc]]
+    job_obj.run_commands(logger, rt_command)
+
+
+def remove_pr_data(job_obj, pr_repo_loc, repo_dir_str, rt_dir):
+    logger = logging.getLogger('BL/REMOVE_PR_DATA')
+    rm_command = [
+                 [f'rm -rf {rt_dir}', pr_repo_loc],
+                 [f'rm -rf {repo_dir_str}', pr_repo_loc]
+                 ]
+    job_obj.run_commands(logger, rm_command)
+
+
+def clone_pr_repo(job_obj, workdir):
+    ''' clone the GitHub pull request repo, via command line '''
+    logger = logging.getLogger('BL/CLONE_PR_REPO')
+    repo_name = job_obj.preq_dict['preq'].head.repo.name
+    branch = job_obj.preq_dict['preq'].head.ref
+    git_url = job_obj.preq_dict['preq'].head.repo.html_url.split('//')
+    git_url = f'{git_url[0]}//${{ghapitoken}}@{git_url[1]}'
+    logger.debug(f'GIT URL: {git_url}')
+    logger.info('Starting repo clone')
+    repo_dir_str = f'{workdir}/'\
+                   f'{str(job_obj.preq_dict["preq"].id)}/'\
+                   f'{datetime.datetime.now().strftime("%Y%m%d%H%M%S")}'
+    pr_repo_loc = f'{repo_dir_str}/{repo_name}'
+    job_obj.comment_text_append(f'Repo location: {pr_repo_loc}')
+    create_repo_commands = [
+        [f'mkdir -p "{repo_dir_str}"', os.getcwd()],
+        [f'git clone -b {branch} {git_url}', repo_dir_str],
+        ['git submodule update --init --recursive',
+         f'{repo_dir_str}/{repo_name}'],
+        ['git config user.email "brian.curtis@noaa.gov"',
+         f'{repo_dir_str}/{repo_name}'],
+        ['git config user.name "Brian Curtis"',
+         f'{repo_dir_str}/{repo_name}']
+    ]
+
+    job_obj.run_commands(logger, create_repo_commands)
+
+    logger.info('Finished repo clone')
+    return pr_repo_loc, repo_dir_str
+
+
+def post_process(job_obj, pr_repo_loc, repo_dir_str, rtbldir, bldir):
+    logger = logging.getLogger('BL/MOVE_RT_LOGS')
+    rt_log = f'tests/RegressionTests_{job_obj.machine}'\
+             f'.{job_obj.compiler}.log'
+    filepath = f'{pr_repo_loc}/{rt_log}'
+    rt_dir, logfile_pass = process_logfile(job_obj, filepath)
+    if logfile_pass:
+        create_bl_dir(bldir)
+        move_bl_command = [[f'mv {rtbldir}/* {bldir}/', pr_repo_loc]]
+        job_obj.run_commands(logger, move_bl_command)
+        logger.info('Starting RT Job')
+        rt.run(job_obj)
+        logger.info('Finished with RT Job')
+        remove_pr_data(job_obj, pr_repo_loc, repo_dir_str, rt_dir)
+
+
+def get_bl_date(job_obj, pr_repo_loc):
+    logger = logging.getLogger('BL/UPDATE_RT_SH')
+    BLDATEFOUND = False
+    with open(f'{pr_repo_loc}/tests/rt.sh', 'r') as f:
+        for line in f:
+            if 'BL_DATE=' in line:
+                logger.info('Found BL_DATE in line')
+                BLDATEFOUND = True
+                bldate = line
+                bldate = bldate.rstrip('\n')
+                bldate = bldate.replace('BL_DATE=', '')
+                bldate = bldate.strip(' ')
+                logger.info(f'bldate is "{bldate}"')
+                logger.info(f'Type bldate: {type(bldate)}')
+                bl_format = '%Y%m%d'
+                try:
+                    datetime.datetime.strptime(bldate, '%Y%m%d')
+                except ValueError:
+                    logger.info(f'Date {bldate} is not formatted YYYYMMDD')
+                    raise ValueError
+    if not BLDATEFOUND:
+        job_obj.comment_text_append('BL_DATE not found in rt.sh.'
+                                    'Please manually edit rt.sh '
+                                    'with BL_DATE={bldate}')
+        job_obj.job_failed(logger, 'get_bl_date()')
+    logger.info('Finished get_bl_date')
+
+    return bldate
+
+
+def process_logfile(job_obj, logfile):
+    logger = logging.getLogger('BL/PROCESS_LOGFILE')
+    rt_dir = []
+    if os.path.exists(logfile):
+        with open(logfile) as f:
+            for line in f:
+                if 'FAIL' in line and 'Test' in line:
+                    job_obj.comment_text_append(f'{line.rstrip(chr(10))}')
+                elif 'working dir' in line and not rt_dir:
+                    logger.info(f'Found "working dir" in line: {line}')
+                    rt_dir = os.path.split(line.split()[-1])[0]
+                    logger.info(f'It is: {rt_dir}')
+                    job_obj.comment_text_append(f'Please manually delete: '
+                                                f'{rt_dir}')
+                elif 'SUCCESSFUL' in line:
+                    logger.info('RT Successful')
+                    return rt_dir, True
+        logger.critical(f'Log file exists but is not complete')
+        job_obj.job_failed(logger, f'{job_obj.preq_dict["action"]}')
+    else:
+        logger.critical(f'Could not find {job_obj.machine}'
+                        f'.{job_obj.compiler} '
+                        f'{job_obj.preq_dict["action"]} log')
+        raise FileNotFoundError

tests/auto/jobs/rt.py

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+# Imports
+import datetime
+import logging
+import os
+
+
+def run(job_obj):
+    logger = logging.getLogger('RT/RUN')
+    workdir = set_directories(job_obj)
+    branch, pr_repo_loc, repo_dir_str = clone_pr_repo(job_obj, workdir)
+    run_regression_test(job_obj, pr_repo_loc)
+    post_process(job_obj, pr_repo_loc, repo_dir_str, branch)
+
+
+def set_directories(job_obj):
+    logger = logging.getLogger('RT/SET_DIRECTORIES')
+    if job_obj.machine == 'hera':
+        workdir = '/scratch1/NCEPDEV/nems/emc.nemspara/autort/pr'
+    elif job_obj.machine == 'jet':
+        workdir = '/lfs4/HFIP/h-nems/emc.nemspara/autort/pr'
+    elif job_obj.machine == 'gaea':
+        workdir = '/lustre/f2/pdata/ncep/emc.nemspara/autort/pr'
+    elif job_obj.machine == 'orion':
+        workdir = '/work/noaa/nems/emc.nemspara/autort/pr'
+    elif job_obj.machine == 'cheyenne':
+        workdir = '/glade/work/heinzell/fv3/ufs-weather-model/auto-rt'
+    else:
+        print(f'Machine {job_obj.machine} is not supported for this job')
+        raise KeyError
+
+    logger.info(f'machine: {job_obj.machine}')
+    logger.info(f'workdir: {workdir}')
+
+    return workdir
+
+
+def run_regression_test(job_obj, pr_repo_loc):
+    logger = logging.getLogger('RT/RUN_REGRESSION_TEST')
+    if job_obj.compiler == 'gnu':
+        rt_command = [[f'export RT_COMPILER="{job_obj.compiler}" && cd tests '
+                       '&& /bin/bash --login ./rt.sh -e -l rt_gnu.conf',
+                       pr_repo_loc]]
+    elif job_obj.compiler == 'intel':
+        rt_command = [[f'export RT_COMPILER="{job_obj.compiler}" && cd tests '
+                       '&& /bin/bash --login ./rt.sh -e', pr_repo_loc]]
+    job_obj.run_commands(logger, rt_command)
+
+
+def remove_pr_data(job_obj, pr_repo_loc, repo_dir_str, rt_dir):
+    logger = logging.getLogger('RT/REMOVE_PR_DATA')
+    rm_command = [
+                 [f'rm -rf {rt_dir}', pr_repo_loc],
+                 [f'rm -rf {repo_dir_str}', pr_repo_loc]
+                 ]
+    job_obj.run_commands(logger, rm_command)
+
+
+def clone_pr_repo(job_obj, workdir):
+    ''' clone the GitHub pull request repo, via command line '''
+    logger = logging.getLogger('RT/CLONE_PR_REPO')
+    repo_name = job_obj.preq_dict['preq'].head.repo.name
+    branch = job_obj.preq_dict['preq'].head.ref
+    git_url = job_obj.preq_dict['preq'].head.repo.html_url.split('//')
+    git_url = f'{git_url[0]}//${{ghapitoken}}@{git_url[1]}'
+    logger.debug(f'GIT URL: {git_url}')
+    logger.info('Starting repo clone')
+    repo_dir_str = f'{workdir}/'\
+                   f'{str(job_obj.preq_dict["preq"].id)}/'\
+                   f'{datetime.datetime.now().strftime("%Y%m%d%H%M%S")}'
+    pr_repo_loc = f'{repo_dir_str}/{repo_name}'
+    job_obj.comment_text_append(f'Repo location: {pr_repo_loc}')
+    create_repo_commands = [
+        [f'mkdir -p "{repo_dir_str}"', os.getcwd()],
+        [f'git clone -b {branch} {git_url}', repo_dir_str],
+        ['git submodule update --init --recursive',
+         f'{repo_dir_str}/{repo_name}'],
+        ['git config user.email "brian.curtis@noaa.gov"',
+         f'{repo_dir_str}/{repo_name}'],
+        ['git config user.name "Brian Curtis"',
+         f'{repo_dir_str}/{repo_name}']
+    ]
+
+    job_obj.run_commands(logger, create_repo_commands)
+
+    logger.info('Finished repo clone')
+    return branch, pr_repo_loc, repo_dir_str
+
+
+def post_process(job_obj, pr_repo_loc, repo_dir_str, branch):
+    ''' This is the callback function associated with the "RT" command '''
+    logger = logging.getLogger('RT/MOVE_RT_LOGS')
+    rt_log = f'tests/RegressionTests_{job_obj.machine}'\
+             f'.{job_obj.compiler}.log'
+    filepath = f'{pr_repo_loc}/{rt_log}'
+    rt_dir, logfile_pass = process_logfile(job_obj, filepath)
+    if logfile_pass:
+        move_rt_commands = [
+            [f'git pull --ff-only origin {branch}', pr_repo_loc],
+            [f'git add {rt_log}', pr_repo_loc],
+            [f'git commit -m "RT JOBS PASSED: {job_obj.machine}'
+             f'.{job_obj.compiler}. Log file uploaded."',
+             pr_repo_loc],
+            ['sleep 10', pr_repo_loc],
+            [f'git push origin {branch}', pr_repo_loc]
+        ]
+        job_obj.run_commands(logger, move_rt_commands)
+        remove_pr_data(job_obj, pr_repo_loc, repo_dir_str, rt_dir)
+
+
+def process_logfile(job_obj, logfile):
+    logger = logging.getLogger('RT/PROCESS_LOGFILE')
+    rt_dir = []
+    if os.path.exists(logfile):
+        with open(logfile) as f:
+            for line in f:
+                if 'FAIL' in line and 'Test' in line:
+                    job_obj.comment_text_append(f'{line.rstrip(chr(10))}')
+                elif 'working dir' in line and not rt_dir:
+                    rt_dir = os.path.split(line.split()[-1])[0]
+                    job_obj.comment_text_append(f'Please manually delete: '
+                                                f'{rt_dir}')
+                elif 'SUCCESSFUL' in line:
+                    return rt_dir, True
+        job_obj.job_failed(logger, f'{job_obj.preq_dict["action"]}')
+    else:
+        logger.critical(f'Could not find {job_obj.machine}'
+                        f'.{job_obj.compiler} '
+                        f'{job_obj.preq_dict["action"]} log')
+        print(f'Could not find {job_obj.machine}.{job_obj.compiler} '
+              f'{job_obj.preq_dict["action"]} log')
+        raise FileNotFoundError