Merge branch 'master' of https://github.com/altMITgcm/MITgcm into manual_edits

Author: jrscott

.travis.yml

@@ -10,7 +10,43 @@ before_install:
  - docker exec -i fc11-testreport ls -altr /MITgcm
  - docker exec -i fc11-testreport yum install python-pip
  - docker exec -i fc11-testreport yum install gcc-gfortran
+ - docker exec -i fc11-testreport yum install python-argparse
 
 script: 
  - echo `pwd`
- - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_barotropic_gyre"
+ # aim.5l_cs
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t aim.5l_cs | tee aim.5l_cs/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'aim.5l_cs/testreport_out.txt' -threshold 14 16"
+ # global_ocean.cs32x15
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t global_ocean.cs32x15 | tee global_ocean.cs32x15/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'global_ocean.cs32x15/testreport_out.txt' -threshold 16 16 16 16 16"
+ # global_ocean.90x40x15
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t global_ocean.90x40x15 | tee global_ocean.90x40x15/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'global_ocean.90x40x15/testreport_out.txt' -threshold 16 16 16"
+ # hs94.cs-32x32x5
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t hs94.cs-32x32x5 | tee hs94.cs-32x32x5/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'hs94.cs-32x32x5/testreport_out.txt' -threshold 13 16" 
+ # isomip
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t isomip | tee isomip/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'isomip/testreport_out.txt' -threshold 16 16 16"
+ # offline_exf_seaice
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t offline_exf_seaice | tee offline_exf_seaice/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'offline_exf_seaice/testreport_out.txt' -threshold 16 16 16 16 16"
+ # tutorial advection in gyre
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_advection_in_gyre | tee tutorial_advection_in_gyre/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_advection_in_gyre/testreport_out.txt' -threshold 16"
+ # tutorial cfc offline
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_cfc_offline | tee tutorial_cfc_offline/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_cfc_offline/testreport_out.txt' -threshold 16"
+ # tutorial deep convection
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_deep_convection | tee tutorial_deep_convection/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_deep_convection/testreport_out.txt' -threshold 16 16"
+ # tutorial global oce biogeo
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_global_oce_biogeo | tee tutorial_global_oce_biogeo/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_global_oce_biogeo/testreport_out.txt' -threshold 16"
+ # tutorial global oce in p
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_global_oce_in_p | tee tutorial_global_oce_in_p/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_global_oce_in_p/testreport_out.txt' -threshold 16"
+ # tutorial_plume_on_slope
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; ./testreport -t tutorial_plume_on_slope | tee tutorial_plume_on_slope/testreport_out.txt"
+ - docker exec -i fc11-testreport bash -c "cd /MITgcm/verification; python verification_parser.py -filename 'tutorial_plume_on_slope/testreport_out.txt' -threshold 16"

README.md

@@ -1,4 +1,4 @@
 [![Build Status](https://travis-ci.org/altMITgcm/MITgcm.svg?branch=master)](https://travis-ci.org/altMITgcm/MITgcm)
 
-# MITgcm66h
-M.I.T general circulation model as of checkpoint66h with author emails
+# MITgcm
+The M.I.T general circulation model

doc/_extensions/mitgcm.py

@@ -0,0 +1,12 @@
+from docutils import nodes
+
+def setup(app):
+    app.add_role('filelink', autolink('https://github.com/altMITgcm/MITgcm/blob/master/%s'))
+    app.add_role('varlink', autolink('http://mitgcm.org/lxr/ident/MITgcm?_i=%s'))
+
+def autolink(pattern):
+    def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+        url = pattern % (text,)
+        node = nodes.reference(rawtext, text, refuri=url, **options)
+        return [node], []
+    return role

doc/conf.py

@@ -16,9 +16,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.join(os.path.abspath('.'), '_extensions'))
 
 
 # -- General configuration ------------------------------------------------
@@ -33,7 +33,8 @@
 extensions = ['sphinx.ext.autodoc',
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
-    'sphinxcontrib.bibtex']
+    'sphinxcontrib.bibtex',
+    'mitgcm']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

verification/verification_parser.py

@@ -0,0 +1,90 @@
+"""Parse verification outputs."""
+
+import re
+import glob
+import os
+
+def verification_parser(filename, threshold):
+
+    # function should be given a threshold value for each sub test
+    (directory, _) = os.path.split(filename)
+    # how many additional tests are run with tweaks to this configuration
+    num_exps = len(glob.glob(directory+'/input.*'))+1
+
+    # check that the correct number of values for `threshold` have been given
+    if len(threshold) != num_exps:
+        # some if statements to deal with grammar
+        if len(threshold)==1:
+            error_message = '{0} value given for threshold, '.format(len(threshold))
+        else:
+            error_message = '{0} values given for threshold, '.format(len(threshold))
+        
+        if num_exps==1:
+            error_message = error_message + 'but {0} subtest found.'.format(num_exps)        
+        else:
+            error_message = error_message + 'but {0} subtests found.'.format(num_exps)
+
+        raise ValueError(error_message)
+        
+    # open the testreport output to assess pass/fail            
+    with open(filename) as f:
+        lines = f.readlines()
+
+        first_match = True
+
+        # extract lines from output
+        for i, line in enumerate(lines):
+            if line[:5] == '2 d e':
+                if first_match:
+                    # skip the first match, since it doesn't contain output,
+                    # but set to false to catch next matches.
+                    first_match = False
+                else:
+                    # save the line number where the output is found
+                    output_line = i
+                    break
+
+        # loop through each of the subexperiments:
+        for j in xrange(len(threshold)):
+            test_results = lines[output_line+2+j]
+
+            # split test_results into a list with values for each number. 
+            # this uses spaces and the < > characters to separate the numbers.
+            test_results = re.split('[ ><]',test_results)
+            # ignore the Genmake, depend, make, and run checks, as well as
+            # the "pass" or "fail" and test name at the end of the line
+            test_results = test_results[4:-3]
+            # convert to floats
+            dp_similarity = []
+            for i, x in enumerate(test_results):
+                try:
+                    dp_similarity.append(float(x))
+                except ValueError:
+                    pass
+
+
+            if len(dp_similarity) >= 17:
+                # this means that the test wasn't an offline advection test.
+                # Remove the means of u and v since they are constrained 
+                # to ~0 by domain geometry and can cause the test to fail 
+                # when it shouldn't.
+                del dp_similarity[15]
+                del dp_similarity[11]
+
+            assert all(elements >= threshold[j] for elements in dp_similarity)
+
+if __name__ == '__main__':
+
+    import argparse
+
+    parser = argparse.ArgumentParser(description='Check that verification simulation passed the test.')
+
+    parser.add_argument('-filename', type=str, 
+                        help='path to output file from the verification test')
+
+    parser.add_argument('-threshold',nargs='+', type=int, default=15, 
+                        help='number of decimal places of similarity required for test to pass. Requires a value for each sub test. Separate values with a space.')
+
+    args = parser.parse_args()
+
+    verification_parser(**vars(args))