Merge pull request mom-ocean#508 from bensonr/zhi_nest_merge_nofms2io

test of nest updates for 2019.01.03

.travis.yml

@@ -32,7 +32,6 @@ before_script:
   - export CPPFLAGS="-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500 ${CPPFLAGS_ADD}"
   - export FCFLAGS="-fcray-pointer -Waliasing -ffree-line-length-none -fno-range-check ${FCFLAGS_REAL_KIND} ${OPENMP}"
   - export LDFLAGS='-L/usr/lib'
-  - export LOG_DRIVER_FLAGS="--comments"
 
 script:
   - autoreconf -i

CHANGELOG.md

@@ -0,0 +1,28 @@
+# ChangeLog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0),
+and this project uses `yyyy.rr[.pp]`, where `yyyy` is the year a patch is released,
+`rr` is a sequential release number (starting from `01`), and an optional two-digit
+sequential patch number (starting from `01`).
+
+## [Unreleased]
+### Added
+### Changed
+### Deprecated
+### Removed
+### Fixed
+
+## [2019.01] - 2019-11-26
+### Added
+- switch from "city" versioning style to `yyyy.<2_digit_version_number>[.<2-digit-patch number>]` style
+- main development branch is `master` instead of `dev/master`
+- affinity handling moved to the affinity directory
+- support for building with autotools
+- [fms_platform.h](include/fms_platform.h) contains directives that support building on macOS
+- unit and build tests are available in the [test_fms](test_fms) directory
+- updated [fv3gfs/makefile](fv3gfs/makefile) for use with current EMC build system
+### Fixed
+- Fixed `time_interp_missing` parameter in [time_interp/time_interp_external.F90](time_interp/time_interp_external.F90) to be within range when compiled in mixed-mode.
+- reverted `QUAD_PRECISION` cpp macro behavior to pre-Xanadu behavior in [include/fms_platform.h](include/fms_platform.h)
+- Fixed a GNU compiler issue with the logical check to set the netCDF fill value in `mpp_io_write` by separating the logical `.AND.` into nested `if` statements.

affinity/affinity.c

@@ -27,7 +27,7 @@
 #include <sys/resource.h>
 #include <sys/syscall.h>
 
-#ifndef __APPLE__
+#ifndef HAVE_GETTID
 static pid_t gettid(void)
 {
   return syscall(__NR_gettid);

configure.ac

@@ -53,15 +53,12 @@ AC_PROG_F77
 # Find the install program.
 AC_PROG_INSTALL
 
-# Is bats installed? It is required for testing.
-AC_CHECK_PROGS([FMS_BATS], [bats])
-if test -z "$FMS_BATS"; then
-   AC_MSG_ERROR([Cannot find bats utility. Install bats and try again.])
-fi
-
 # Check to see if any macros must be set to enable large (>2GB) files.
 AC_SYS_LARGEFILE
 
+# Check if Linux gettid is avaiable
+AC_CHECK_FUNCS([gettid], [], [])
+
 # Require MPI.
 AC_CHECK_FUNC([MPI_Init], [], [AC_MSG_ERROR([MPI C library required to build FMS])])
 
@@ -139,6 +136,7 @@ AC_CONFIG_FILES([Makefile
         sat_vapor_pres/Makefile
         random_numbers/Makefile
         libFMS/Makefile
+        test_fms/test_common.sh
         test_fms/Makefile
         test_fms/diag_manager/Makefile
         test_fms/data_override/Makefile

diag_integral/diag_integral.F90

@@ -117,11 +117,9 @@ module diag_integral_mod
 private
 
 !-------------------------------------------------------------------------------
-!----------- version number for this module -------------------
-
-character(len=128) :: version = '$Id$'
-character(len=128) :: tagname = '$Name$'
-
+! version number of this module
+! Include variable "version" to be written to log file.
+#include<file_version.h>
 
 !-------------------------------------------------------------------------------
 !------ interfaces ------
@@ -394,7 +392,7 @@ subroutine diag_integral_init (Time_init, Time, blon, blat, area_in)
 !-------------------------------------------------------------------------------
 !    write version number and namelist to logfile.
 !-------------------------------------------------------------------------------
-      call write_version_number (version, tagname)
+      call write_version_number ('DIAG_INTEGRAL_MOD', version)
       logunit = stdlog()
       if (mpp_pe() == mpp_root_pe() ) &
                        write (logunit, nml=diag_integral_nml)

monin_obukhov/monin_obukhov.F90

@@ -74,11 +74,10 @@ module monin_obukhov_mod
                       stable_mix_2d, stable_mix_3d
 end interface
 
-
-!--------------------- version number ---------------------------------
-
-character(len=128) :: version = '$Id$'
-character(len=128) :: tagname = '$Name$'
+!-----------------------------------------------------------------------
+! version number of this module
+! Include variable "version" to be written to log file.
+#include<file_version.h>
 
 !=======================================================================
 
@@ -135,7 +134,7 @@ subroutine monin_obukhov_init
 !---------- output namelist to log-------------------------------------
 
       if ( mpp_pe() == mpp_root_pe() ) then
-           call write_version_number(version, tagname)
+           call write_version_number('MONIN_OBUKOV_MOD', version)
            logunit = stdlog()
            write (logunit, nml=monin_obukhov_nml)
       endif

mpp/Makefile.am

@@ -44,7 +44,7 @@ mpp.$(OBJEXT): mpp_data_mod.mod
 mpp_utilities.$(OBJEXT): mpp_mod.mod mpp_efp_mod.mod
 mpp_memutils.$(OBJEXT): mpp_mod.mod
 mpp_pset.$(OBJEXT): mpp_mod.mod
-mpp_efp.$(OBJEXT): mpp_efp_mod.mod mpp_parameter_mod.mod mpp_mod.mod
+mpp_efp.$(OBJEXT): mpp_parameter_mod.mod mpp_mod.mod
 mpp_domains.$(OBJEXT): mpp_data_mod.mod mpp_parameter_mod.mod \
   mpp_mod.mod mpp_memutils_mod.mod mpp_pset_mod.mod mpp_efp_mod.mod
 mpp_io.$(OBJEXT): mpp_parameter_mod.mod mpp_mod.mod mpp_domains_mod.mod

mpp/include/mpp_comm_mpi.inc

@@ -1382,31 +1382,49 @@ end subroutine mpp_gsm_free
 !                                                                             !
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_int4
 #define MPP_TYPE_ integer(INT_KIND)
 #define MPI_TYPE_ MPI_INTEGER4
 #include <mpp_type_mpi.h>
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_int8
 #define MPP_TYPE_ integer(LONG_KIND)
 #define MPI_TYPE_ MPI_INTEGER8
 #include <mpp_type_mpi.h>
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_real4
 #define MPP_TYPE_ real(FLOAT_KIND)
 #define MPI_TYPE_ MPI_REAL4
 #include <mpp_type_mpi.h>
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_real8
 #define MPP_TYPE_ real(DOUBLE_KIND)
 #define MPI_TYPE_ MPI_REAL8
 #include <mpp_type_mpi.h>
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_logical4
 #define MPP_TYPE_ logical(INT_KIND)
 #define MPI_TYPE_ MPI_INTEGER4
 #include <mpp_type_mpi.h>
 
+#undef MPP_TYPE_CREATE_
+#undef MPP_TYPE_
+#undef MPI_TYPE_
 #define MPP_TYPE_CREATE_ mpp_type_create_logical8
 #define MPP_TYPE_ logical(LONG_KIND)
 #define MPI_TYPE_ MPI_INTEGER8