Merge pull request #15 from ekluzek/xlffill8thpy3fixes

Bring in changes for xlf compiler, pio, and python3 update

Author: ekluzek

cime_config/buildlib

@@ -1,6 +1,10 @@
 #!/usr/bin/env python
-
-import os, shutil, sys, glob
+"""
+Build the mosart component library
+"""
+#pylint: disable=unused-wildcard-import, wildcard-import, multiple-imports
+#pylint: disable=wrong-import-position, invalid-name, too-many-locals
+import os, sys
 
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
@@ -22,25 +26,25 @@ def _build_mosart():
 
     with Case(caseroot) as case:
         casetools = case.get_value("CASETOOLS")
-        gmake_j   = case.get_value("GMAKE_J")
-        gmake     = case.get_value("GMAKE")
+        gmake_j = case.get_value("GMAKE_J")
+        gmake = case.get_value("GMAKE")
 
         # create Filepath file
         objroot = case.get_value("OBJROOT")
-        filepath_file = os.path.join(objroot,"rof","obj","Filepath")
+        filepath_file = os.path.join(objroot, "rof", "obj", "Filepath")
         if not os.path.isfile(filepath_file):
             srcroot = case.get_value("SRCROOT")
             caseroot = case.get_value("CASEROOT")
-            paths = [ os.path.join(caseroot,"SourceMods","src.mosart"), 
-                      os.path.join(srcroot,"components","mosart","src","riverroute"),
-                      os.path.join(srcroot,"components","mosart","src","cpl")]
+            paths = [os.path.join(caseroot, "SourceMods", "src.mosart"),
+                     os.path.join(srcroot, "components", "mosart", "src", "riverroute"),
+                     os.path.join(srcroot, "components", "mosart", "src", "cpl")]
 
             with open(filepath_file, "w") as filepath:
                 filepath.write("\n".join(paths))
                 filepath.write("\n")
 
         # build the library
-        complib = os.path.join(libroot,"librof.a")
+        complib = os.path.join(libroot, "librof.a")
         makefile = os.path.join(casetools, "Makefile")
 
         cmd = "%s complib -j %d MODEL=mosart COMPLIB=%s -f %s" \
@@ -49,12 +53,9 @@ def _build_mosart():
         rc, out, err = run_cmd(cmd, from_dir=bldroot)
         expect(rc == 0, "Command %s failed rc=%d\nout=%s\nerr=%s" % (cmd, rc, out, err))
 
-        logger.info("Command %s completed with output %s\nerr %s" ,cmd, out, err)
+        logger.info("Command %s completed with output %s\nerr %s", cmd, out, err)
 
 ###############################################################################
 
 if __name__ == "__main__":
     _build_mosart()
-
-
-

cime_config/buildnml

@@ -8,8 +8,8 @@
 
 # Disable these because this is our standard setup
 # pylint: disable=wildcard-import,unused-wildcard-import,wrong-import-position
-
-import os, shutil, sys, glob
+# pylint: disable=multiple-imports
+import os, shutil, sys
 
 CIMEROOT = os.environ.get("CIMEROOT")
 if CIMEROOT is None:
@@ -20,13 +20,13 @@ from standard_script_setup import *
 from CIME.case import Case
 from CIME.nmlgen import NamelistGenerator
 from CIME.utils import expect
-from CIME.buildnml import create_namelist_infile
+from CIME.buildnml import create_namelist_infile, parse_input
 
 logger = logging.getLogger(__name__)
 
 # pylint: disable=too-many-arguments,too-many-locals,too-many-branches,too-many-statements
 ####################################################################################
-def _create_namelists(case, confdir, inst_string, infile, nmlgen):
+def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path):
 ####################################################################################
     """Write out the namelist for this component.
 
@@ -40,36 +40,29 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen):
     #----------------------------------------------------
     config = {}
     config['mosart_mode'] = case.get_value("MOSART_MODE")
-    config['mosart_flood_mode']  = case.get_value("MOSART_FLOOD_MODE")
+    config['mosart_flood_mode'] = case.get_value("MOSART_FLOOD_MODE")
     config['clm_accel'] = case.get_value("CLM_ACCELERATED_SPINUP")
     config['rof_grid'] = case.get_value("ROF_GRID")
     config['lnd_grid'] = case.get_value("LND_GRID")
     config['rof_ncpl'] = case.get_value("ROF_NCPL")
     config['simyr'] = case.get_value("MOSART_SIM_YEAR")
 
-    logger.debug ("River Transport Model (MOSART) mode is %s " %(config['mosart_mode']))
-    logger.debug ("  MOSART lnd grid is %s " %(config['lnd_grid']))
-    logger.debug ("  MOSART rof grid is %s " %(config['rof_grid']))
+    logger.debug("River Transport Model (MOSART) mode is %s ", config['mosart_mode'])
+    logger.debug("  MOSART lnd grid is %s ", config['lnd_grid'])
+    logger.debug("  MOSART rof grid is %s ", config['rof_grid'])
 
     #----------------------------------------------------
     # Check for incompatible options.
     #----------------------------------------------------
 
     if config["rof_grid"] == "null" and config["mosart_mode"] != "NULL":
-        expect (False, "ROF_GRID is null MOSART_MODE not NULL")
-
-    #----------------------------------------------------
-    # Clear out old data.
-    #----------------------------------------------------
-    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "mosart.input_data_list")
-    if os.path.exists(data_list_path):
-        os.remove(data_list_path)
+        expect(False, "ROF_GRID is null MOSART_MODE not NULL")
 
     #----------------------------------------------------
     # Initialize namelist defaults
     #----------------------------------------------------
     nmlgen.init_defaults(infile, config)
-        
+
     #----------------------------------------------------
     # Set values not obtained in the default settings
     #----------------------------------------------------
@@ -78,10 +71,10 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen):
     if run_type == 'branch' or run_type == 'hybrid':
         run_refcase = case.get_value("RUN_REFCASE")
         run_refdate = case.get_value("RUN_REFDATE")
-        run_tod     = case.get_value("RUN_REFTOD")
-        rundir      = case.get_value("RUNDIR")
+        run_tod = case.get_value("RUN_REFTOD")
+        rundir = case.get_value("RUNDIR")
         filename = "%s.mosart%s.r.%s-%s.nc" %(run_refcase, inst_string, run_refdate, run_tod)
-        if not os.path.exists(os.path.join(rundir, filename ) ):
+        if not os.path.exists(os.path.join(rundir, filename)):
             filename = "%s.mosart.r.%s-%s.nc" %(run_refcase, run_refdate, run_tod)
 
         if run_type == "hybrid":
@@ -95,7 +88,7 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen):
         else:
             nmlgen.add_default("finidat_rtm")
 
-    ncpl_base_period  = case.get_value('NCPL_BASE_PERIOD')
+    ncpl_base_period = case.get_value('NCPL_BASE_PERIOD')
     if ncpl_base_period == 'hour':
         basedt = 3600
     elif ncpl_base_period == 'day':
@@ -118,7 +111,7 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen):
 
     mosart_ncpl = case.get_value("ROF_NCPL")
     if basedt % mosart_ncpl != 0:
-        expect(False, "mosart_ncpl %s doesn't divide evenly into basedt \n" 
+        expect(False, "mosart_ncpl %s doesn't divide evenly into basedt %s\n"
                %(mosart_ncpl, basedt))
     else:
         coupling_period = basedt / mosart_ncpl
@@ -135,26 +128,26 @@ def buildnml(case, caseroot, compname):
 ###############################################################################
     """Build the mosart namelist """
 
-    # Build the component namelist 
+    # Build the component namelist
     if compname != "mosart":
         raise AttributeError
 
-    srcroot = case.get_value("SRCROOT") 
+    srcroot = case.get_value("SRCROOT")
     rundir = case.get_value("RUNDIR")
     ninst = case.get_value("NINST_ROF")
 
     # Determine configuration directory
-    confdir = os.path.join(caseroot,"Buildconf","mosartconf")
+    confdir = os.path.join(caseroot, "Buildconf", "mosartconf")
     if not os.path.isdir(confdir):
         os.makedirs(confdir)
 
     #----------------------------------------------------
-    # Construct the namelist generator 
+    # Construct the namelist generator
     #----------------------------------------------------
     # Determine directory for user modified namelist_definitions.xml and namelist_defaults.xml
     user_xml_dir = os.path.join(caseroot, "SourceMods", "src.mosart")
-    expect (os.path.isdir(user_xml_dir),
-            "user_xml_dir %s does not exist " %user_xml_dir)
+    expect(os.path.isdir(user_xml_dir),
+           "user_xml_dir %s does not exist "%user_xml_dir)
 
     # NOTE: User definition *replaces* existing definition.
     namelist_xml_dir = os.path.join(srcroot, "components", "mosart", "cime_config")
@@ -168,6 +161,12 @@ def buildnml(case, caseroot, compname):
     # Create the namelist generator object - independent of instance
     nmlgen = NamelistGenerator(case, definition_file)
 
+    #----------------------------------------------------
+    # Clear out old data.
+    #----------------------------------------------------
+    data_list_path = os.path.join(case.get_case_root(), "Buildconf", "mosart.input_data_list")
+    if os.path.exists(data_list_path):
+        os.remove(data_list_path)
     #----------------------------------------------------
     # Loop over instances
     #----------------------------------------------------
@@ -180,9 +179,9 @@ def buildnml(case, caseroot, compname):
 
         # If multi-instance case does not have restart file, use
         # single-case restart for each instance
-        rpointer = "rpointer.rof" 
-        if (os.path.isfile(os.path.join(rundir,rpointer)) and
-            (not os.path.isfile(os.path.join(rundir,rpointer + inst_string)))):
+        rpointer = "rpointer.rof"
+        if (os.path.isfile(os.path.join(rundir, rpointer)) and
+                (not os.path.isfile(os.path.join(rundir, rpointer + inst_string)))):
             shutil.copy(os.path.join(rundir, rpointer),
                         os.path.join(rundir, rpointer + inst_string))
 
@@ -199,16 +198,16 @@ def buildnml(case, caseroot, compname):
         namelist_infile = [infile]
 
         # create namelist and stream file(s) data component
-        _create_namelists(case, confdir, inst_string, namelist_infile, nmlgen)
+        _create_namelists(case, confdir, inst_string, namelist_infile, nmlgen, data_list_path)
 
         # copy namelist files and stream text files, to rundir
         if os.path.isdir(rundir):
-            file_src  = os.path.join(confdir, 'mosart_in')
+            file_src = os.path.join(confdir, 'mosart_in')
             file_dest = os.path.join(rundir, 'mosart_in')
             if inst_string:
                 file_dest += inst_string
             shutil.copy(file_src, file_dest)
-            
+
 ###############################################################################
 def _main_func():
 

cime_config/namelist_definition_mosart.xml

@@ -165,7 +165,8 @@
     <input_pathname>abs</input_pathname>
     <group>mosart_inparm</group> 
     <values>
-      <value rof_grid="r05">$DIN_LOC_ROOT/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc</value>
+      <value rof_grid="r05" >$DIN_LOC_ROOT/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc</value>
+      <value rof_grid="r8th">$DIN_LOC_ROOT/rof/mosart/MOSART_Global_8th_20160716a.nc</value>
     </values>
     <desc>
       Full pathname of input datafile for RTM.

docs/ChangeLog

@@ -1,3 +1,92 @@
+===============================================================
+Tag name:  release-cesm2.0.01
+Originator(s): erik/jedwards4b
+Date: Oct 09, 2018
+One-line Summary:  New r8th routing file, pylint and py3 checking, fill value needed for pio2
+
+Add in 8th degree routine file. Run pylint and check for py3 compatability.
+There's explict setting of fill type. And also explicit use of shr_kind_r4 for 
+kind rather than real(4), which is a better mechanism. Also ncd_getiodesc 
+will read in PIO_DOUBLE for input xtype= PIO_DOUBLE or PIO_REAL. Most of this
+is direct from jedwards4b (other than r8th addition).
+
+MOSART Master Tag This Corresponds To: Identical to mosart1_0_31
+
+Science  changes since: release-cesm2.0.00
+   Added in 8th degree routing file (r8th)
+Software changes since: release-cesm2.0.00
+   Run pylint on python buildlib and buildnml scripts, check for py3 compatibility.
+   Corrects the integer fill value. Needed for pio2.
+
+Pull Requests that document the changes (include PR ids):
+
+  #15 -- Bring in changes for xlf compiler, pio, and python3 update 
+         (#13 and #6 moved to release-cesm2.0)
+  #14 -- fix type issue with xlf
+
+Testing:
+    mosart testlist on hobart and cheyenne (PASS)
+
+===============================================================
+Tag name:  release-cesm2.0.00
+Originator(s): erik
+Date: May 21, 2018
+One-line Summary: First CESM2.0 release tag, identical to mosart1_0_31
+
+MOSART Master Tag This Corresponds To: Identical to mosart1_0_31
+
+Science changes since: mosart1_0_00
+
+  * Changes from Sean Swenson to add minimum value to rlen
+  * Update areas on routing file
+  * Answer changing improvements to channel storage from HongYi Li for faster spinup.
+  * Bugfix from Tony Craig to use correct delta time for qgwl flux.
+  * Treat irrigation as a seperate flux
+  * bugfix for budget diagnostic output
+  * bugfix: calculation of qgwl_volume must be multiplied by ar
+  * Update default routing file.
+  * New method of handeling runoff terms to avoid negative runoff.
+  * switch to input dataset MOSART_Global_half_20151130a.nc
+  * update direct sparse matrix to include non basin points in order
+  * to pass data from any grid cell directly to the ocean.
+  * modify the direct term and push all direct water to outlet points
+  * set all tracer 2 water (frozen water) to be a direct term
+  * add ability to skip some tracers in the euler solver via euler_calc flag
+  * add a budget accumulator term
+  * Fix exact restart in atan slope calc
+  * Swenson bugfix for mosart direction file
+  * Swenson river volume normalization bugf
+
+Software changes since: mosart1_0_00
+
+  * Add config_archive for mosart
+  * delete rof_comp_esmf
+  * add model_doi_url,
+  * change some instances of RTM/CLM in documentation to MOSART
+  * Update testlist to version 2 format, remove ys tests
+  * Upgrade config_component to version 3
+  * allow output file format to change
+  * If NINST_ROF > 1, check if instance number in name for REFCASE
+  * Update testlist and use Clm5 compset names
+  * Update routing file
+  * Update to cime5 python namelist infrastructure
+  * Fix an issue with nag, lower amount of log output
+  * Add output frequency to history files
+  * Turn off for CLM_ACCELERATED_SPINUP="on"
+  * Add new namelist options bypass_routing_option,
+  * qgwl_runoff_option
+  * Error checking on max length of history filenames.
+  * Add testdefs dir, testmods and testlist for integration to cime
+  * test system.
+  * remove rofdto from coupler interface fields.
+  * Changes to get Mosart to build with Nag on Hobart
+  * merge ACME fixes to decomp and performance
+  * cime compatible infrastructure
+  * Add direct to ocean runoff flux
+  * PIO2 updates
+
+Changes to User Interface since: mo
+
 ===============================================================
 Tag name:  mosart1_0_31
 Originator(s): erik