Merging in changes from release/public-v1 (NOAA-EMC#141)

* Initial spack/cmake version

* updated for umbrella build

* tweak to findnetcdf

* added include directory

* updated cmake

* changed to https for cmake submodule

* updated cmake submodule

* updated install directory

* added build for libnceppost.a

* modifications for macOS clang/gfortran build

* updated for gnu build

* udpated cmake submodule

* Add RST file for UPP v4.0

* Modifying introduction

* merged develop in and separated library from executable in build

* Update CMakeLists.txt files to support GNU compilers

* applied patch from Dusan

* Add conf.py for upp documentation

* Add index.rst for upp documentation

* Add readthedocs config file

* Modify name of main rst doc in index for readthedocs build test

* Change master file to index

* Edits for UFS documentation to remove WRF and grib1 references

* Add a readthedocs config file

* Mods to config and index files for use in readthedocs

* Update submodule pointer for cmake

* Remove old GNU makefiles with problematic names (only differing in case from existing files)

* Add files for GRIB2 table of fields

* Update .gitmodules, add branch = ufs_release_1.0 for cmake

* Update .gitmodules for testing, code review and merging

* Update include/lib flags for sigio, sfcio, nemsio

* Add REQUIRED attribute to find_package calls in CMakeLists.txt

* Comment out LAPACK dependency in CMakeLists.txt

* Revert change to .gitmodules, update submodule pointer for cmake

* sorc/ncep_post.fd/CMakeLists.txt: change GFSIO_INC to GFSIO_INC4

* Add capacity of detecting scaning mode north2south vs south2north in gaussian grid from Dusan.

* Re-factor CMake

* Fix library linking

* small fix to kyles refactor

* Add capacity of detecting scaning mode north2south vs south2north in gaussian grid from Dusan.

* Fix typo in sorc/ncep_post.fd/CMakeLists.txt

* Fix how Intel compile options with spaces in them are handled

* Update branch name for cmake submodule, update submodule pointer

* Update submodule pointer for cmake

* Update .gitmodules and submodule pointer for cmake, bugfixes for CMakeLists.txt

* Update submodule pointer for cmake

* fixes problem linking ncep_post with gnu/openmpi

* Update submodule pointer for cmake

* Revert .gitmodules change

* Bugfix: comment out debug print statement that can lead to out-of-bounds access; update submodule pointer for cmake

* Update submodule pointer for cmake

* OpenMP bugfix, use lowercase in find_package(CRTM)

* Fix post crash on macOS: use allocatable array

* Update submodule pointer for cmake

* Add UFS UPP rst documentation

* Update submodule pointer for cmake

* Rename g2tmpl_d to g2tmpl (NOAA-EMC#89)

* Update submodule pointer for cmake

* cleanup post

Change-Id: Ie52af5ff79ac4122e79d7a46e89ee2077188b0a4

* we dont depend on C HDF5 library. remove.

Change-Id: I26aa7c0bf7ed2783de1a9967d961d0260dee8b54

* use transitive properties. apply OpenMP flags if OpenMP is found. Formatting using cmake-format

Change-Id: Ic08ce6bc85a7d949c779ec597241c8cb4c20db86

* add debug gnu flags. compile_definitions does not like the quotes around long long, remove

Change-Id: Iccd5bb496944f75a79500729051dd571303cb50f

* Update CMakeLists.txt

* Update submodule pointer for cmake

* Update submodule pointer for cmake

* Add LGPL license to repository

* EMC_post is a Fortran only project. blockIO.c is not used, so do not include in building

* Update submodule pointer for cmake

* Bug fix for unary operator in INITPOST_GFS_NEMS_MPIIO.f. (NOAA-EMC#92)

* Remove old unused makefiles

* CMakeLists.txt: install postxconfig-NT-GFS-F00.txt and postxconfig-NT-GFS.txt in share directory

* Update version

@fossell says post is at version 8.0.0

* Update submodule pointer for cmake

* Fix Out of Bound Exception in GFSPOST.F (NOAA-EMC#100)

* Fix out-of-bound error in tpause routine in GFSPOST.F

* Fix use of undefined variables.

* Feature/cleanup (NOAA-EMC#95)

* cleanup post

Change-Id: Ie52af5ff79ac4122e79d7a46e89ee2077188b0a4

* we dont depend on C HDF5 library. remove.

Change-Id: I26aa7c0bf7ed2783de1a9967d961d0260dee8b54

* use transitive properties. apply OpenMP flags if OpenMP is found. Formatting using cmake-format

Change-Id: Ic08ce6bc85a7d949c779ec597241c8cb4c20db86

* add debug gnu flags. compile_definitions does not like the quotes around long long, remove

Change-Id: Iccd5bb496944f75a79500729051dd571303cb50f

* Update CMakeLists.txt

* EMC_post is a Fortran only project. blockIO.c is not used, so do not include in building

* Update version

@fossell says post is at version 8.0.0

* Revert "Feature/cleanup (NOAA-EMC#95)"

This reverts commit 7e9797b355d2b86ea9e274534f86adc42e866b95.

* remove unused compile definitions and update cmake pointer

Change-Id: Ie47cf16ebc25928bf30bfd05d4f25678219571a6

* Fix ID index in WRF-CHEM SMOKE block, which currently causes failed build in debug mode

* remove unnecessary commented line

* NetCDF static fix (#1)

* CMakeLists.txt: add MODULE to find_package calls

* Cleanup of NetCDF in CMakeLists.txt

* update cmake submodule pointer

Change-Id: I763882fd6ecc4b8cc64a60eddabccfdb7046040d

* Add MODULE to find_package(NetCDF) call (NOAA-EMC#3)

* update cmake submodule pointer

Change-Id: I69015efa425658645567e9d9f22d5e51301c1a0b

* Change version from 8.0.0 to 1.0.0

* fix the install path of compiled Fortran module files

Co-authored-by: Mark A Potts <mark.potts@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com>
Co-authored-by: Tracy <hertneky@ucar.edu>
Co-authored-by: Kate Fossell <fossell@ucar.edu>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
Co-authored-by: Wen Meng <wen.meng@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
Co-authored-by: Kyle Gerheiser <kgerheiser@icloud.com>
Co-authored-by: Mark Potts <mpotts@redlineperf.com>
Co-authored-by: Kyle Gerheiser <3209794+kgerheiser@users.noreply.github.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>
Co-authored-by: Tracy <tracy.hertneky@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>

.gitignore

@@ -9,8 +9,15 @@
 # USE CAUTION WHEN ADDING WILDCARDS, as some builds use different filename   #
 # conventions than others                                                    #
 ##############################################################################
-*.exe
-*.o
+build/
+install/
+
+*.[ao]
 *.mod
-*.a
+*.so
+*.exe
+*.x
+
+*.swp
 configure.upp*
+*.a

.gitmodules

@@ -1,3 +1,7 @@
 [submodule "comupp/src/lib/crtm2"]
 	path = sorc/comlibs/crtm2
 	url = https://github.com/NCAR/UPP_CRTM
+[submodule "cmake"]
+	path = cmake
+	url = https://github.com/NOAA-EMC/CMakeModules
+	branch = release/public-v1

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+#python:
+#  version: 3.7
+#  install:
+
+#    - requirements: docs/requirements.txt

CMakeLists.txt

@@ -0,0 +1,95 @@
+cmake_minimum_required(VERSION 3.15)
+
+file(STRINGS "VERSION" pVersion)
+
+project(
+  ncep_post
+  VERSION ${pVersion}
+  LANGUAGES Fortran)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/")
+
+if(POLICY CMP0054)
+  cmake_policy(SET CMP0054 NEW)
+endif()
+if(POLICY CMP0012)
+  cmake_policy(SET CMP0012 NEW)
+endif()
+
+option(OPENMP "use OpenMP threading" OFF)
+
+if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
+  message(STATUS "Setting build type to 'Release' as none was specified.")
+  set(CMAKE_BUILD_TYPE
+      "Release"
+      CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+                                               "MinSizeRel" "RelWithDebInfo")
+endif()
+
+if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|GNU|Clang|AppleClang)$")
+  message(WARNING "Compiler not officially supported: ${CMAKE_Fortran_COMPILER_ID}")
+endif()
+
+find_package(MPI REQUIRED)
+find_package(PNG REQUIRED)
+find_package(Jasper REQUIRED)
+find_package(NetCDF MODULE REQUIRED)
+
+if(OPENMP)
+  find_package(OpenMP REQUIRED COMPONENTS Fortran)
+endif()
+
+set(CMAKE_FIND_PACKAGE_PREFER_CONFIG true)
+
+if(NOT TARGET sigio_4)
+  find_package(sigio REQUIRED)
+endif()
+
+if(NOT TARGET w3nco_4)
+  find_package(w3nco REQUIRED)
+endif()
+
+if(NOT TARGET g2_4)
+  find_package(g2 REQUIRED)
+endif()
+
+if(NOT TARGET g2tmpl)
+  find_package(g2tmpl REQUIRED)
+endif()
+
+if(NOT TARGET bacio_4)
+  find_package(bacio REQUIRED)
+endif()
+
+if(NOT TARGET ip_4)
+  find_package(ip REQUIRED)
+endif()
+
+if(NOT TARGET sp_4)
+  find_package(sp REQUIRED)
+endif()
+
+if(NOT TARGET sfcio_4)
+  find_package(sfcio REQUIRED)
+endif()
+
+if(NOT TARGET nemsio)
+  find_package(nemsio REQUIRED)
+endif()
+
+if(NOT TARGET gfsio_4)
+  find_package(gfsio REQUIRED)
+endif()
+
+if(NOT TARGET w3emc_4)
+  find_package(w3emc REQUIRED)
+endif()
+
+if(NOT TARGET crtm)
+  find_package(crtm REQUIRED)
+endif()
+
+add_subdirectory(sorc)
+
+install(FILES parm/postxconfig-NT-GFS.txt parm/postxconfig-NT-GFS-F00.txt DESTINATION share)

LICENSE.md

@@ -0,0 +1,157 @@
+### GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+This version of the GNU Lesser General Public License incorporates the
+terms and conditions of version 3 of the GNU General Public License,
+supplemented by the additional permissions listed below.
+
+#### 0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the
+GNU General Public License.
+
+"The Library" refers to a covered work governed by this License, other
+than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+#### 1. Exception to Section 3 of the GNU GPL.
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+#### 2. Conveying Modified Versions.
+
+If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+-   a) under this License, provided that you make a good faith effort
+    to ensure that, in the event an Application does not supply the
+    function or data, the facility still operates, and performs
+    whatever part of its purpose remains meaningful, or
+-   b) under the GNU GPL, with none of the additional permissions of
+    this License applicable to that copy.
+
+#### 3. Object Code Incorporating Material from Library Header Files.
+
+The object code form of an Application may incorporate material from a
+header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+-   a) Give prominent notice with each copy of the object code that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the object code with a copy of the GNU GPL and this
+    license document.
+
+#### 4. Combined Works.
+
+You may convey a Combined Work under terms of your choice that, taken
+together, effectively do not restrict modification of the portions of
+the Library contained in the Combined Work and reverse engineering for
+debugging such modifications, if you also do each of the following:
+
+-   a) Give prominent notice with each copy of the Combined Work that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the Combined Work with a copy of the GNU GPL and this
+    license document.
+-   c) For a Combined Work that displays copyright notices during
+    execution, include the copyright notice for the Library among
+    these notices, as well as a reference directing the user to the
+    copies of the GNU GPL and this license document.
+-   d) Do one of the following:
+    -   0) Convey the Minimal Corresponding Source under the terms of
+        this License, and the Corresponding Application Code in a form
+        suitable for, and under terms that permit, the user to
+        recombine or relink the Application with a modified version of
+        the Linked Version to produce a modified Combined Work, in the
+        manner specified by section 6 of the GNU GPL for conveying
+        Corresponding Source.
+    -   1) Use a suitable shared library mechanism for linking with
+        the Library. A suitable mechanism is one that (a) uses at run
+        time a copy of the Library already present on the user's
+        computer system, and (b) will operate properly with a modified
+        version of the Library that is interface-compatible with the
+        Linked Version.
+-   e) Provide Installation Information, but only if you would
+    otherwise be required to provide such information under section 6
+    of the GNU GPL, and only to the extent that such information is
+    necessary to install and execute a modified version of the
+    Combined Work produced by recombining or relinking the Application
+    with a modified version of the Linked Version. (If you use option
+    4d0, the Installation Information must accompany the Minimal
+    Corresponding Source and Corresponding Application Code. If you
+    use option 4d1, you must provide the Installation Information in
+    the manner specified by section 6 of the GNU GPL for conveying
+    Corresponding Source.)
+
+#### 5. Combined Libraries.
+
+You may place library facilities that are a work based on the Library
+side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+-   a) Accompany the combined library with a copy of the same work
+    based on the Library, uncombined with any other library
+    facilities, conveyed under the terms of this License.
+-   b) Give prominent notice with the combined library that part of it
+    is a work based on the Library, and explaining where to find the
+    accompanying uncombined form of the same work.
+
+#### 6. Revised Versions of the GNU Lesser General Public License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+as you received it specifies that a certain numbered version of the
+GNU Lesser General Public License "or any later version" applies to
+it, you have the option of following the terms and conditions either
+of that published version or of any later version published by the
+Free Software Foundation. If the Library as you received it does not
+specify a version number of the GNU Lesser General Public License, you
+may choose any version of the GNU Lesser General Public License ever
+published by the Free Software Foundation.
+
+If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

VERSION

@@ -0,0 +1 @@
+1.0.0

docs/Acknowledgments.rst

@@ -0,0 +1,27 @@
+***************
+Acknowledgments
+***************
+
+The adaptation of the original WRF Post Processor package and Users
+Guide (by Mike Baldwin of NSSL/CIMMS and Hui-Ya Chuang of NCEP/EMC) was
+done by Lígia Bernardet (NOAA/ESRL/DTC) in collaboration with Dusan
+Jovic (NCEP/EMC), Robert Rozumalski (COMET), Wesley Ebisuzaki
+(NWS/HQTR), and Louisa Nance (NCAR/RAL/DTC). Upgrades to WRF Post
+Processor versions 2.2 and higher were performed by Hui-Ya Chuang, Dusan
+Jovic and Mathew Pyle (NCEP/EMC). Transitioning of the documentation
+from the WRF Post Processor to the Unified Post Processor was performed
+by Nicole McKee (NCEP/EMC), Hui-ya Chuang (NCEP/EMC), and Jamie Wolff
+(NCAR/RAL/DTC). Implementation of the Community Unified Post Processor
+was performed by Tricia Slovacek and Kate Fossell (NCAR/RAL/DTC).
+
+Acknowledgement
+
+
+If significant help was provided via the UPP helpdesk for work resulting
+in a publication, please acknowledge the Developmental Testbed Center
+UPP Team.
+
+For referencing this document please use:
+
+UPP Users Guide V4, 24 pp. [available online at
+https://dtcenter.org/sites/default/files/community-code/upp-users-guide-v4.pdf]

docs/BuildRunWithoutApp.rst

@@ -0,0 +1,7 @@
+***********************************************
+Building and Running UPP without an Application
+***********************************************
+
+Currently the UPP within the UFS application cannot be built as a standolone application. Please visit
+the `UPP community code website <https://dtcenter.org/community-code/unified-post-processor-upp>`_ for
+instructions on obtaining, building and running the UPP as a stand-alone application.

docs/CodeOverview.rst

@@ -0,0 +1,21 @@
+*************
+Code Overview
+*************
+
+The UPP can be used to post-process WRF-ARW, WRF-NMM, NMMB, GFS, CFS, and FV3 forecasts with current support within UFS available for FV3 only. It can ingest FV3 history files (dyn*/phy*) in netCDF and binarynemsiompiio format.
+
+Unipost Functionalities:
+
+   -  Interpolates the forecasts from the models native vertical
+      coordinate to NWS standard output levels (e.g., pressure, height)
+      and computes mean sea level pressure. If the requested parameter
+      is on a models native level, then no vertical interpolation is
+      performed.
+
+   -  Computes diagnostic output quantities (e.g., convective available
+      potential energy, helicity, relative humidity). A full list of
+      fields that can be generated by *unipost* is provided in
+      https://dtcenter.org/sites/default/files/community-code/upp-grib2-table_0.pdf.
+
+   -  Outputs the results in NWS and WMO standard GRIB2 format (for GRIB
+      documentation, see http://www.nco.ncep.noaa.gov/pmb/docs/).