add fixer test and post proc script

Author: oksanaguba

cime_config/tests.py

@@ -346,7 +346,7 @@
             "ERS_Ld5.TL319_oQU240wLI_ais8to30.MPAS_LISIO_JRA1p5.mpaso-ocn_glcshelf",
             "SMS_P12x2.ne4pg2_oQU480.WCYCL1850NS.allactive-mach_mods",
             "ERS_Ln9.ne4pg2_ne4pg2.F2010-MMF1.eam-mmf_crmout",
-            "SMS_Lh4.ne4_ne4.F2010-SCREAMv1.eamxx-output-preset-1",
+            "SMS_Lh4.ne4_ne4.F2010-SCREAMv1.eamxx-output-preset-1--eamxx-fixer_debug_output",
             "SMS_Lh4.ne4pg2_ne4pg2.F2010-SCREAMv1.eamxx-output-preset-1--eamxx-prod",
             )
         },

components/eamxx/cime_config/testdefs/testmods_dirs/eamxx/fixer_debug_output/shell_commands

@@ -0,0 +1,2 @@
+$CIMEROOT/../components/eamxx/scripts/atmchange homme::enable_energy_fixer_debug_info=true -b
+./xmlchange POSTRUN_SCRIPT="$CIMEROOT/../components/eamxx/scripts/check-fixer-output"

components/eamxx/scripts/check-fixer-output

@@ -0,0 +1,156 @@
+#!/usr/bin/env python3
+
+#"""
+#aaa
+#"""
+
+import sys, re, glob, pathlib, argparse, gzip
+
+from utils import run_cmd_no_fail, expect, GoodFormatter
+
+###############################################################################
+def parse_command_line(args, description):
+###############################################################################
+    parser = argparse.ArgumentParser(
+        usage="""\n{0} <CASE_DIR> [<param>=<val>] ...
+OR
+{0} --help
+
+\033[1mEXAMPLES:\033[0m
+    \033[1;32m# Run hash checker on /my/case/dir \033[0m
+    > {0} /my/case/dir
+""".format(pathlib.Path(args[0]).name),
+        description=description,
+        formatter_class=GoodFormatter
+    )
+
+    parser.add_argument(
+        "case_dir",
+        help="The test case you want to check"
+    )
+
+    return parser.parse_args(args[1:])
+
+###############################################################################
+def readall(fn):
+###############################################################################
+    with open(fn,'r') as f:
+        txt = f.read()
+    return txt
+
+###############################################################################
+def greptxt(pattern, txt):
+###############################################################################
+    return re.findall('(?:' + pattern + ').*', txt, flags=re.MULTILINE)
+
+###############################################################################
+def grep(pattern, fn):
+###############################################################################
+    txt = readall(fn)
+    return greptxt(pattern, txt)
+
+###############################################################################
+def get_log_glob_from_atm_modelio(case_dir):
+###############################################################################
+    filename = case_dir / 'CaseDocs' / 'atm_modelio.nml'
+    ln = grep('diro = ', filename)[0]
+    run_dir = pathlib.Path(ln.split()[2].split('"')[1])
+    ln = grep('logfile = ', filename)[0]
+    atm_log_fn = ln.split()[2].split('"')[1]
+    return str(run_dir / '**' / f'atm.log.*')
+
+###############################################################################
+
+# EAMxx:: energy fixer: T tend added to each physics midlevel 0.000222
+# EAMxx:: energy fixer: total energy before fix 32486509719.486938
+# EAMxx:: energy fixer: rel energy error after fix -7.63290383866757e-18
+
+def get_fixer_lines(fn,start_from_line):
+###############################################################################
+    fixer_lines = []
+    error_vals = []
+
+    lines = []
+    with gzip.open(fn,'rt') as file:
+        start_line_found = False
+        for line in file:
+            if start_line_found:
+                lines.append(line)
+            elif start_from_line in line:
+                start_line_found = True
+
+    i = 0
+    while i < len(lines):
+        line = lines[i]
+        i = i+1
+        # eamxx hash line has the form "eamxx hash> date=YYYY-MM-DD-XXXXX (STRING), naccum=INT
+        # The INT at the end says how many of the following line contain hashes for this proc-step
+        if "EAMxx:: energy fixer: rel energy error" in line:
+            fixer_lines.append(line)
+            lline = (line.strip('\n'))
+            errr = float(lline.split()[8])
+            error_vals.append(errr)
+
+    return fixer_lines,error_vals
+
+###############################################################################
+def get_model_start_of_step_lines (atm_log):
+###############################################################################
+    lines = []
+    with gzip.open(atm_log,'rt') as file:
+        for line in file:
+            if "model beg-of-step time" in line:
+                lines.append(line)
+    return lines
+
+###############################################################################
+def check_fixer_output(case_dir):
+###############################################################################
+
+    ####################### TOLERANCE
+    TOL = 1e-12
+
+    case_dir_p = pathlib.Path(case_dir)
+    expect(case_dir_p.is_dir(), f"{case_dir} is not a dir")
+
+    # Look for the two atm.log files.
+    glob_pat = get_log_glob_from_atm_modelio(case_dir_p)
+    atm_fns = glob.glob(glob_pat, recursive=True)
+    if len(atm_fns) == 0:
+        print('Could not find atm.log files with glob string {}'.format(glob_pat))
+        return False
+    if len(atm_fns) == 1:
+        print('Found output file {}'.format(atm_fns[0]))
+
+    start_line = get_model_start_of_step_lines(atm_fns[0])[0]
+
+    print (start_line)
+
+    # Extract hash lines, along with their timestamps, but ignore anything
+    # before the line $start_line
+    f = atm_fns[0]
+    fixer_lines,errs = get_fixer_lines(f,start_line)
+    print('Array of rel. energy errors after energy fixer:',errs)
+    errsa = [abs(ele) for ele in errs]
+    mmax = max(errs)
+    print('Abs. max. for the rel. energy errors:',mmax)
+
+    if mmax < TOL:
+        print('SUCCESS')
+        return True
+    else:
+        print('FAIL, abs. max is less than tolerance, which is ', TOL)
+        return False
+
+
+
+###############################################################################
+def _main_func(description):
+###############################################################################
+    success = check_fixer_output(**vars(parse_command_line(sys.argv, description)))
+    sys.exit(0 if success else 1)
+
+###############################################################################
+
+if (__name__ == "__main__"):
+    _main_func(__doc__)