Merge branch 'master' into jedwards/solar_zenith_angle_correction

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,7 +4,7 @@
 
 Contributors other than yourself, if any:
 
-CMEPS Issues Fixed (include github issue #):
+CDEPS Issues Fixed (include github issue #):
 
 Are there dependencies on other component PRs
  - [ ] CIME (list)

cime_config/buildlib

@@ -15,18 +15,51 @@ _LIBDIR = os.path.join(_CIMEROOT, "scripts", "lib")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup import *
-from CIME.buildlib import parse_input
 from CIME.case import Case
 from CIME.utils import run_cmd, symlink_force, expect
 from CIME.build import get_standard_cmake_args
-from CIME.XML.machines import Machines
-from CIME.XML.compilers import Compilers
 
 logger = logging.getLogger(__name__)
 
-def buildlib(bldroot, libroot, case, compname=None):
-    if bldroot.endswith("obj") and not compname:
-        compname = os.path.basename(os.path.abspath(os.path.join(bldroot,os.pardir)))
+def parse_command_line(args, description):
+###############################################################################
+    parser = argparse.ArgumentParser(
+        usage="""\n{0} [--debug]
+OR
+{0} --verbose
+OR
+{0} --help
+
+\033[1mEXAMPLES:\033[0m
+    \033[1;32m# Run \033[0m
+    > {0}
+""" .format (os.path.basename(args[0])),
+
+description=description,
+
+formatter_class=argparse.ArgumentDefaultsHelpFormatter
+)
+
+    CIME.utils.setup_standard_logging_options(parser)
+
+    parser.add_argument("buildroot",
+                        help="build path root")
+
+    parser.add_argument("installpath",
+                        help="install path ")
+
+    parser.add_argument("caseroot", nargs="?", default=os.getcwd(),
+                        help="Case directory to build")
+
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
+
+    return args.buildroot, args.installpath, args.caseroot
+
+
+def buildlib(bldroot, libroot, case):
+    expect(not bldroot.endswith("obj"),
+           "It appears that the main CDEPS buildlib is being called for a specific component\n"
+           "(specific data model components should use buildlib_comps)")
 
     if case.get_value("DEBUG"):
         strdebug = "debug"
@@ -41,88 +74,76 @@ def buildlib(bldroot, libroot, case, compname=None):
     sharedpath = os.path.join(case.get_value("COMPILER"),mpilib,
                               strdebug, strthread, "nuopc")
 
-    exe_root = case.get_value("EXEROOT")
-
-    if compname:
-        s, o, e = run_cmd("make d{}".format(compname), from_dir=bldroot, verbose=True)
-        libname = "lib{}.a".format(compname)
-        dlibname = "libd{}.a".format(compname)
-        dlibpath = os.path.join(bldroot, dlibname)
-        if os.path.exists(dlibpath):
-            symlink_force(os.path.join(bldroot,dlibname), os.path.join(libroot,libname))
-        else:
-            expect(False, "ERROR in {} build {} {}".format(compname,o,e))
+    logger.info("Running cmake for CDEPS")
+    srcpath = os.path.abspath(os.path.join(os.path.dirname(__file__),os.pardir))
+    cmake_flags = get_standard_cmake_args(case, os.path.join(sharedpath,"cdeps"), shared_lib=True)
+    # base path of install to be completed by setting DESTDIR in make install
+    cmake_flags += " -DCMAKE_INSTALL_PREFIX:PATH=/"
+    cmake_flags += " -DLIBROOT={} ".format(libroot)
+    cmake_flags += " -DMPILIB={} ".format(mpilib)
+    cmake_flags += " -DPIO_C_LIBRARY={path}/lib -DPIO_C_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
+    cmake_flags += " -DPIO_Fortran_LIBRARY={path}/lib -DPIO_Fortran_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
+    cmake_flags += srcpath
+    all_src_files = list(all_files_under(srcpath, ignoredirs=[".git","cmake","test",".github","cime_config","fox"]))
+    # Search SourceMods path for CDEPS files. We only look in the data component directories for these, files in cdeps share
+    # directories should be added to one of the data component directories
+    srcmodsdir = os.path.join(case.get_value("CASEROOT"),"SourceMods")
+    all_files_in_srcmods = []
+    for comp_class in case.get_values("COMP_CLASSES"):
+        if comp_class == "CPL":
+            continue
+        comp = case.get_value("COMP_{}".format(comp_class))
+        cdeps_comp_name = "d"+comp_class.lower()
+        if comp == cdeps_comp_name:
+            all_files_in_srcmods.extend(list(all_files_under(os.path.join(srcmodsdir,"src."+cdeps_comp_name))))
+
+    basenames1 = [os.path.basename(f) for f in all_src_files]
+    basenames2 = [os.path.basename(f) for f in all_files_in_srcmods]
+    srcmods = list(set(basenames1).intersection(set(basenames2)))
+    if srcmods:
+        logger.info("Found SourceMods {}".format(srcmods))
+        for i, v in enumerate(all_src_files):
+            for sfile in all_files_in_srcmods:
+                if os.path.basename(sfile) == os.path.basename(v):
+                    all_src_files[i] = v.replace(os.path.dirname(v), os.path.dirname(sfile))
+    logger.debug("all_src_files: {}".format(all_src_files))
+    latest_src_file = max(all_src_files, key=os.path.getmtime)
+
+    src_time = os.path.getmtime(latest_src_file)
+    if os.path.exists(os.path.join(bldroot,"CMakeFiles")):
+        bld_time = os.path.getmtime(os.path.join(bldroot,"CMakeFiles"))
+    else:
+        bld_time = src_time - 1
+
+    # if any file in src is newer than CmakeFiles in the build directory, rerun cmake
+
+    if src_time > bld_time:
+        logger.info("cmake_flags {}".format(cmake_flags))
+        s,o,e = run_cmd("cmake {} ".format(cmake_flags), from_dir=bldroot, verbose=True)
+        expect(not s,"ERROR from cmake output={}, error={}".format(o,e))
     else:
-        logger.info("Running cmake for CDEPS")
-        srcpath = os.path.abspath(os.path.join(os.path.dirname(__file__),os.pardir))
-        cmake_flags = get_standard_cmake_args(case, os.path.join(sharedpath,"cdeps"), shared_lib=True)
-        # base path of install to be completed by setting DESTDIR in make install
-        cmake_flags += " -DCMAKE_INSTALL_PREFIX:PATH=/"
-        cmake_flags += " -DLIBROOT={} ".format(libroot)
-        cmake_flags += " -DMPILIB={} ".format(mpilib)
-        cmake_flags += " -DPIO_C_LIBRARY={path}/lib -DPIO_C_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
-        cmake_flags += " -DPIO_Fortran_LIBRARY={path}/lib -DPIO_Fortran_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
-        cmake_flags += srcpath
-        all_src_files = list(all_files_under(srcpath, ignoredirs=[".git","cmake","test",".github","cime_config","fox"]))
-        # Search SourceMods path for CDEPS files. We only look in the data component directories for these, files in cdeps share
-        # directories should be added to one of the data component directories
-        srcmodsdir = os.path.join(case.get_value("CASEROOT"),"SourceMods")
-        all_files_in_srcmods = []
-        for comp_class in case.get_values("COMP_CLASSES"):
-            if comp_class == "CPL":
-                continue
-            comp = case.get_value("COMP_{}".format(comp_class))
-            cdeps_comp_name = "d"+comp_class.lower()
-            if comp == cdeps_comp_name:
-                all_files_in_srcmods.extend(list(all_files_under(os.path.join(srcmodsdir,"src."+cdeps_comp_name))))
-
-        basenames1 = [os.path.basename(f) for f in all_src_files]
-        basenames2 = [os.path.basename(f) for f in all_files_in_srcmods]
-        srcmods = list(set(basenames1).intersection(set(basenames2)))
-        if srcmods:
-            logger.info("Found SourceMods {}".format(srcmods))
-            for i, v in enumerate(all_src_files):
-                for sfile in all_files_in_srcmods:
-                    if os.path.basename(sfile) == os.path.basename(v):
-                        all_src_files[i] = v.replace(os.path.dirname(v), os.path.dirname(sfile))
-        logger.debug("all_src_files: {}".format(all_src_files))
-        latest_src_file = max(all_src_files, key=os.path.getmtime)
-
-        src_time = os.path.getmtime(latest_src_file)
-        if os.path.exists(os.path.join(bldroot,"CMakeFiles")):
-            bld_time = os.path.getmtime(os.path.join(bldroot,"CMakeFiles"))
-        else:
-            bld_time = src_time - 1
-
-        # if any file in src is newer than CmakeFiles in the build directory, rerun cmake
-
-        if src_time > bld_time:
-            logger.info("cmake_flags {}".format(cmake_flags))
-            s,o,e = run_cmd("cmake {} ".format(cmake_flags), from_dir=bldroot, verbose=True)
-            expect(not s,"ERROR from cmake output={}, error={}".format(o,e))
-        else:
-            # The dwav_lib is the last file built in cdeps, wait for it to be built
-            dwav_lib = os.path.join(bldroot,"dwav","libdwav.a")
-            time_to_wait = 300
-            time_counter = 0
-            while not os.path.exists(dwav_lib):
-                time.sleep(1)
-                time_counter += 1
-                if time_counter > time_to_wait:
-                    break
-            expect(time_counter <= time_to_wait," Timeout waiting for {}".format(dwav_lib))
-
-        s,o,e = run_cmd("make install VERBOSE=1 DESTDIR={}".format(libroot), from_dir=bldroot, verbose=True)
-        expect(not s,"ERROR from make output={}, error={}".format(o,e))
-
-        # Link the CDEPS component directories to the location expected by cime
-        for comp in ("atm", "lnd", "ice", "ocn", "rof", "wav"):
-            compname = case.get_value("COMP_{}".format(comp.upper()))
-            comppath = os.path.join(case.get_value("EXEROOT"),comp,"obj")
-            if compname == "d"+comp:
-                if not os.path.islink(comppath):
-                    os.rmdir(comppath)
-                symlink_force(os.path.join(bldroot,compname), comppath)
+        # The dwav_lib is the last file built in cdeps, wait for it to be built
+        dwav_lib = os.path.join(bldroot,"dwav","libdwav.a")
+        time_to_wait = 300
+        time_counter = 0
+        while not os.path.exists(dwav_lib):
+            time.sleep(1)
+            time_counter += 1
+            if time_counter > time_to_wait:
+                break
+        expect(time_counter <= time_to_wait," Timeout waiting for {}".format(dwav_lib))
+
+    s,o,e = run_cmd("make install VERBOSE=1 DESTDIR={}".format(libroot), from_dir=bldroot, verbose=True)
+    expect(not s,"ERROR from make output={}, error={}".format(o,e))
+
+    # Link the CDEPS component directories to the location expected by cime
+    for comp in ("atm", "lnd", "ice", "ocn", "rof", "wav"):
+        compname = case.get_value("COMP_{}".format(comp.upper()))
+        comppath = os.path.join(case.get_value("EXEROOT"),comp,"obj")
+        if compname == "d"+comp:
+            if not os.path.islink(comppath):
+                os.rmdir(comppath)
+            symlink_force(os.path.join(bldroot,compname), comppath)
 
 def all_files_under(path, ignoredirs=[]):
     """Iterates through all files that are under the given path."""
@@ -131,27 +152,10 @@ def all_files_under(path, ignoredirs=[]):
         for filename in filenames:
             yield os.path.join(cur_path, filename)
 
-def get_compiler_names(case):
-    machine=case.get_value("MACH")
-    machobj = Machines(machine=machine)
-    compobj = Compilers(machobj)
-    compiler = case.get_value("COMPILER")
-    if case.get_value("MPILIB") == 'mpi-serial':
-        ccomp = compobj.get_value("SCC",{"COMPILER":compiler,"MACH":machine}).strip()
-        cxxcomp = compobj.get_value("SCXX",{"COMPILER":compiler}).strip()
-        fcomp = compobj.get_value("SFC",{"COMPILER":compiler}).strip()
-    else:
-        ccomp = compobj.get_value("MPICC",{"COMPILER":compiler}).strip()
-        cxxcomp = compobj.get_value("MPICXX",{"COMPILER":compiler}).strip()
-        fcomp = compobj.get_value("MPIFC",{"COMPILER":compiler}).strip()
-
-    return ccomp, cxxcomp, fcomp
-
-
 def _main_func(args):
-    caseroot, libroot, bldroot = parse_input(args)
+    bldroot, installpath, caseroot = parse_command_line(args, __doc__)
     with Case(caseroot) as case:
-        buildlib(bldroot, libroot, case)
+        buildlib(bldroot, installpath, case)
 
 if __name__ == "__main__":
     _main_func(sys.argv)

cime_config/buildlib_comps

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+"""
+build cime component model library.   This buildlib script is used by all CDEPS components.
+"""
+
+import sys, os
+
+_CIMEROOT = os.environ.get("CIMEROOT")
+if _CIMEROOT is None:
+    raise SystemExit("ERROR: must set CIMEROOT environment variable")
+sys.path.append(os.path.join(_CIMEROOT, "scripts", "Tools"))
+
+_LIBDIR = os.path.join(_CIMEROOT, "scripts", "lib")
+sys.path.append(_LIBDIR)
+
+from standard_script_setup import *
+from CIME.buildlib import parse_input
+from CIME.case import Case
+from CIME.utils import run_cmd, symlink_force, expect
+
+logger = logging.getLogger(__name__)
+
+def buildlib(bldroot, libroot, case, compname=None):
+    if not compname:
+        expect(bldroot.endswith("obj"),
+               "It appears that buildlib_comps is being called for the main CDEPS build\n"
+               "(the main CDEPS build should use buildlib, not buildlib_comps)")
+        compname = os.path.basename(os.path.abspath(os.path.join(bldroot,os.pardir)))
+
+    _, o, e = run_cmd("make d{}".format(compname), from_dir=bldroot, verbose=True)
+    libname = "lib{}.a".format(compname)
+    dlibname = "libd{}.a".format(compname)
+    dlibpath = os.path.join(bldroot, dlibname)
+    if os.path.exists(dlibpath):
+        symlink_force(os.path.join(bldroot,dlibname), os.path.join(libroot,libname))
+    else:
+        expect(False, "ERROR in {} build {} {}".format(compname,o,e))
+
+def _main_func(args):
+    caseroot, libroot, bldroot = parse_input(args)
+    with Case(caseroot) as case:
+        buildlib(bldroot, libroot, case)
+
+if __name__ == "__main__":
+    _main_func(sys.argv)

cime_config/stream_cdeps.py

@@ -44,7 +44,7 @@
 """
 
 valid_values = {}
-valid_values["mapalgo"]  = ["bilinear", "nn", "redist", "mapconsd", "mapconf"]
+valid_values["mapalgo"]  = ["bilinear", "nn", "redist", "mapconsd", "mapconf", "none"]
 valid_values["tintalgo"] = ["lower", "upper", "nearest", "linear", "coszen"]
 valid_values["taxmode"]  = ["cycle", "extend", "limit"]
 
@@ -94,7 +94,7 @@ def create_stream_xml(self, stream_names, case, streams_xml_file, data_list_file
                     break
                 # endif
             # end while
-            index += 1 
+            index += 1
             lines_input_new.append(line)
         #end while
 
@@ -104,9 +104,9 @@ def create_stream_xml(self, stream_names, case, streams_xml_file, data_list_file
             expect(len(stream_mods) == 2,
                    "input stream mod can only be of the form streamname:var=value(s)")
             stream,varmod = stream_mods
-            expect (stream in stream_names, 
+            expect (stream in stream_names,
                     "{} contains a streamname \'{}\' that is not part of valid streamnames {}".
-                    format(user_mods_file,stream,stream_names)) 
+                    format(user_mods_file,stream,stream_names))
             if stream  not in stream_mod_dict:
                 stream_mod_dict[stream] = {}
             # var=value and check the validity

datm/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

dice/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

dlnd/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

docn/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

drof/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

dwav/cime_config/buildlib

@@ -1 +1 @@
-../../cime_config/buildlib
+../../cime_config/buildlib_comps

streams/dshr_stream_mod.F90

@@ -698,6 +698,7 @@ subroutine shr_stream_init_from_esmfconfig(streamfilename, streamdat, logunit,
           streamdat(i)%varlist(n)%nameinfile = strm_tmpstrings(n)(1:index(trim(strm_tmpstrings(n)), " "))
           streamdat(i)%varlist(n)%nameinmodel = strm_tmpstrings(n)(index(trim(strm_tmpstrings(n)), " ", .true.)+1:)
         enddo
+        deallocate(strm_tmpstrings)
       else
         call shr_sys_abort("stream data variables must be provided")
       endif