Update to GEOS-Chem 12.6.3 (to keep pace with GCHP 12.6.3)

(1) Update Github issue templates to include links to our videos, as well as a checklist of what people should do before submitting an issue. (2) Changed version numbers to 12.6.3 in gc_classic_version.H and in the main CMakeLists.txt. Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Nov 25, 2019 · 5f25c0f · 5f25c0f
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diff --git a/.github/ISSUE_TEMPLATE/ask-a-question-about-geos-chem.md b/.github/ISSUE_TEMPLATE/ask-a-question-about-geos-chem.md
@@ -9,10 +9,23 @@ assignees: ''
 
 # Ask a question about GEOS-Chem
 
-To report a GEOS-Chem bug or technical issue, please use [this issue template](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=report-a-bug-or-technical-issue.md&title=%5BBUG%2FISSUE%5D) instead.
+## STOP!  Before you submit an issue, please follow these steps
 
-Please keep in mind that the [GEOS-Chem Support Team](http://wiki.geos-chem.org/GEOS-Chem_Support_Team) focuses primarily on software development and user support rather than on scientific research. If your question is more scientific in nature (e.g. "What happens if I change this reaction rate from X to Y?", or "Is emissions inventory A better than inventory B?", etc.), then we recommend that you contact the relevant [GEOS-Chem Working Group(s)](http://www.geos-chem.org/geos_working_groups.html) for assistance. 
+### Please see our Github tutorial videos
+If this is the first time you are submitting a GEOS-Chem issue via Github, we recommend that you first view our tutorial videos on [youtube.geos-chem.org](http://youtube.geos-chem.org).  These videos will demonstrate how to use the Github issue trackers and how to receive notifications about issues that have been posted:
 
-## Type your question:
+  * [*Submitting GEOS-Chem issues on Github*](https://www.youtube.com/watch?v=dFBhdotYVf8&t=1103s)
+  * [*Subscribing to Github notifications*](https://www.youtube.com/watch?v=RuH6zeYuzuY)
+  * [*Searching for GEOS-Chem issues and pull requests*](https://www.youtube.com/watch?v=EiZC2vaXNnU&t=35s)
 
-Feel free to delete all of the text above this line...
+### Use the bug/issue template to report GEOS-Chem bugs or technical issues
+
+This issue template is designed for asking general questions about GEOS-Chem. To report a GEOS-Chem bug or technical issue, please use [this issue template](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=report-a-bug-or-technical-issue.md&title=%5BBUG%2FISSUE%5D) instead.
+
+### Contact the GEOS-Chem Working Groups directly for assistance with scientific questions
+
+Please keep in mind that the [GEOS-Chem Support Team](http://wiki.geos-chem.org/GEOS-Chem_Support_Team) focuses primarily on software development and user support rather than on scientific research. If your question is more scientific in nature (e.g. "What happens if I change this reaction rate from X to Y?", or "Is emissions inventory A better than inventory B?", etc.), then we recommend that you contact the relevant [GEOS-Chem Working Group(s)](http://www.geos-chem.org/geos_working_groups.html) for assistance.
+
+^^^^^^ YOU MAY DELETE ALL TEXT ABOVE THIS LINE WHEN CREATING YOUR ISSUE ^^^^^^
+
+## Ask your question here!
diff --git a/.github/ISSUE_TEMPLATE/report-a-bug-or-technical-issue.md b/.github/ISSUE_TEMPLATE/report-a-bug-or-technical-issue.md
@@ -9,13 +9,41 @@ assignees: ''
 
 # Report a GEOS-Chem bug or technical issue
 
-## First check to see if your issue has already been resolved
+## STOP!  Before you submit an issue, please follow these steps
+
+### Please see our Github tutorial videos
+If this is the first time you are submitting a GEOS-Chem issue via Github, we recommend that you first view our tutorial videos on [youtube.geos-chem.org](http://youtube.geos-chem.org).  These videos will demonstrate how to use the Github issue trackers and how to receive notifications about issues that have been posted:
+
+  * [*Submitting GEOS-Chem issues on Github*](https://www.youtube.com/watch?v=dFBhdotYVf8&t=1103s)
+  * [*Subscribing to Github notifications*](https://www.youtube.com/watch?v=RuH6zeYuzuY)
+  * [*Searching for GEOS-Chem issues and pull requests*](https://www.youtube.com/watch?v=EiZC2vaXNnU&t=35s)
+
+### Check to see if your issue has already been resolved
+
 Before submitting a GEOS-Chem bug/issue report, please take a moment to check if a solution for your issue has already been reported at:
 
 1. [The issue tracker attached to this Github repository](https://github.com/geoschem/geos-chem/issues);
 2. Our [Guide to GEOS-Chem error messages](http://wiki.geos-chem.org/Guide_to_GEOS-Chem_error_messages) on the GEOS-Chem wiki; and/or
 3. Our [list of GEOS-Chem bugs and fixes](http://wiki.geos-chem.org/Bugs_and_fixes) on the GEOS-Chem wiki.
 
+### Try to resolve the issue yourself
+Please see our [Debugging GEOS-Chem wiki page](http://wiki.geos-chem.org/Debugging_GEOS-Chem), which contains a checklist of things that you can do to try to solve your problem yourself.  In particular:
+
+1. Make sure that your [Unix environment](http://wiki.seas.harvard.edu/geos-chem/index.php/Setting_Unix_environment_variables_for_GEOS-Chem) is set up properly;
+2. Make sure that all of the [required libraries](http://wiki.geos-chem.org/Guide_to_netCDF_in_GEOS-Chem) have been installed;
+3. Look at the error output (GEOS-Chem log, HEMCO.log, etc.) and error messages
+4. Recompile GEOS-Chem with [debugging flags](http://wiki.seas.harvard.edu/geos-chem/index.php/Debugging_GEOS-Chem#Recompile_GEOS-Chem_with_debug_options_turned_on) and re-run your simulation;
+5. [Use a debugger](http://wiki.geos-chem.org/Debugging_GEOS-Chem#Run_GEOS-Chem_in_a_debugger_to_find_the_source_of_error) to find more information about where the run is crashing;
+6. Identify if the error happens at the same date & time on every run, or seems to happen at random;
+7. Identify if the error happens in a clean, "out-of-the-box" version of GEOS-Chem, or if it happens in code that you added/modified yourself.
+8. Try to isolate the issue to a particular operation (i.e. turn off chemistry, dry-depostion, transport one at a time)
+9. Add print statements to your code to try to determine the source of the error.
+
+### Provide all requested information
+Please see our [Submitting GEOS-Chem Support Requests](http://wiki.geos-chem.org/Submitting_GEOS-Chem_Support_Requests) wiki page for a checklist of required configuration files and log files to attach to this issue.  The more information you provide, the better able we will be to help you diagnose and fix your issue.
+
+^^^^^^ YOU MAY DELETE ALL TEXT ABOVE THIS LINE WHEN CREATING YOUR ISSUE ^^^^^^
+
 ## Describe the bug
 Include a clear and concise description of the bug or issue that you have encountered.
 
@@ -43,7 +71,7 @@ Cut and paste any error output here.
 ## Required information
 Please include the following:
  - GEOS-Chem version you are using [e.g. 12.3.2]
- - Compiler version that you are using [e.g. gfortran 8.2.0, ifort 17.0.4] 
+ - Compiler version that you are using [e.g. gfortran 8.2.0, ifort 17.0.4]
  - netCDF and netCDF-Fortran library version
  - Computational environment [e.g. a cluster, or the AWS cloud]
  - The Amazon Machine Image (AMI) ID that you used (if you ran on the AWS cloud)

diff --git a/.github/ISSUE_TEMPLATE/request-a-new-feature.md b/.github/ISSUE_TEMPLATE/request-a-new-feature.md
@@ -7,4 +7,25 @@ assignees: ''
 
 ---
 
-## Add your feature request below:
+# Request a new GEOS-Chem feature
+
+## STOP!  Before you submit an issue, please follow these steps
+
+### Please see our Github tutorial videos
+If this is the first time you are submitting a GEOS-Chem issue via Github, we recommend that you first view our tutorial videos on [youtube.geos-chem.org](http://youtube.geos-chem.org).  These videos will demonstrate how to use the Github issue trackers and how to receive notifications about issues that have been posted:
+
+  * [*Submitting GEOS-Chem issues on Github*](https://www.youtube.com/watch?v=dFBhdotYVf8&t=1103s)
+  * [*Subscribing to Github notifications*](https://www.youtube.com/watch?v=RuH6zeYuzuY)
+  * [*Searching for GEOS-Chem issues and pull requests*](https://www.youtube.com/watch?v=EiZC2vaXNnU&t=35s)
+
+### Use our other issue templates for non-feature-request items
+
+This issue template is intended for requesting new GEOS-Chem features and functionality.  Please use one of the other issue templates for:
+
+* [Submitting a GEOS-Chem bug or technical issue](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=report-a-bug-or-technical-issue.md&title=%5BBUG%2FISSUE%5D);
+* [Asking a question about GEOS-Chem](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=ask-a-question-about-geos-chem.md&title=%5BQUESTION%5D); and/or
+* [Starting an extended GEOS-Chem discussion thread](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=discussion&template=start-a-geos-chem-discussion.md&title=%5BDISCUSSION%5D)
+
+^^^^^^ YOU MAY DELETE ALL TEXT ABOVE THIS LINE WHEN CREATING YOUR ISSUE ^^^^^^
+
+## Add your feature request here:
diff --git a/.github/ISSUE_TEMPLATE/start-a-geos-chem-discussion.md b/.github/ISSUE_TEMPLATE/start-a-geos-chem-discussion.md
@@ -9,15 +9,24 @@ assignees: ''
 
 # Start a discussion about a GEOS-Chem topic
 
+## STOP!  Before you submit an issue, please follow these steps
+
+### Please see our Github tutorial videos
+If this is the first time you are submitting a GEOS-Chem issue via Github, we recommend that you first view our tutorial videos on [youtube.geos-chem.org](http://youtube.geos-chem.org).  These videos will demonstrate how to use the Github issue trackers and how to receive notifications about issues that have been posted:
+
+  * [*Submitting GEOS-Chem issues on Github*](https://www.youtube.com/watch?v=dFBhdotYVf8&t=1103s)
+  * [*Subscribing to Github notifications*](https://www.youtube.com/watch?v=RuH6zeYuzuY)
+  * [*Searching for GEOS-Chem issues and pull requests*](https://www.youtube.com/watch?v=EiZC2vaXNnU&t=35s)
+
+### Use our other issue templates for non-discussion items
+
 This issue template is intended for extended discussions about open GEOS-Chem topics, both technical and scientific.  Please use one of the other issue templates for:
 
 * [Submitting a GEOS-Chem bug or technical issue](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=report-a-bug-or-technical-issue.md&title=%5BBUG%2FISSUE%5D);
 * [Asking a question about GEOS-Chem](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=ask-a-question-about-geos-chem.md&title=%5BQUESTION%5D); and/or
 * [Requesting a new GEOS-Chem feature](https://github.com/geoschem/geos-chem/issues/new?assignees=&labels=&template=request-a-new-feature.md&title=%5BFEATURE+REQUEST%5D.)
 
-Feel free to edit the section headers below accordingly
-
-Also feel free to remove all text above this section
+^^^^^^ YOU MAY DELETE ALL TEXT ABOVE THIS LINE WHEN CREATING YOUR ISSUE ^^^^^^
 
 ## Overview
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.5)
-project(GEOS_Chem VERSION 12.6.2 LANGUAGES Fortran)
+project(GEOS_Chem VERSION 12.6.3 LANGUAGES Fortran)
 
 # Set policies
 cmake_policy(SET CMP0054 NEW)
@@ -17,12 +17,12 @@ include(GC-Helpers)
 
 # Declare the BaseTarget. All GEOS-Chem targets depend on BaseTarget.
 # This is used to control the compiler options and definitions for GEOS-Chem
-# targets (via inheritance). 
+# targets (via inheritance).
 add_library(BaseTarget INTERFACE)
 
 # Put all of GEOS-Chem's mod files in a subdirectory of the build directory called mod
 set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
-target_include_directories(BaseTarget 
+target_include_directories(BaseTarget
 	INTERFACE ${CMAKE_CURRENT_BINARY_DIR}/mod
 )
 
@@ -31,9 +31,9 @@ list(APPEND CMAKE_PREFIX_PATH
 	# Possible NetCDF environment variables
 	$ENV{NetCDF_F_ROOT}         $ENV{NetCDF_C_ROOT}     $ENV{NetCDF_ROOT}
 	$ENV{NETCDF_F_ROOT}         $ENV{NETCDF_C_ROOT}     $ENV{NETCDF_ROOT}
-	$ENV{NetCDF_Fortran_ROOT} 
+	$ENV{NetCDF_Fortran_ROOT}
 	$ENV{NETCDF_FORTRAN_ROOT}
-    
+
 	# Possible GEOS-Chem's environmnet variables
 	$ENV{GC_F_BIN} 		$ENV{GC_BIN}
 	$ENV{GC_F_INCLUDE} 	$ENV{GC_INCLUDE}
@@ -58,19 +58,19 @@ get_repo_version(GC_REPO_VERSION ${CMAKE_CURRENT_SOURCE_DIR})
 message(STATUS "GEOS-Chem @ ${GC_REPO_VERSION}")
 
 if(NOT GC_EXTERNAL_CONFIG)
-	# This conditional block configures the GEOS-Chem build for GEOS-Chem 
+	# This conditional block configures the GEOS-Chem build for GEOS-Chem
 	# Classic. As mentioned above, it sets GCCLASSIC_EXE_TARGETS, RRTMG, GTMM
 	# TOMAS, MECH, and GCHP, and it configures the BaseTarget.
 
 	# Set CMAKE_BUILD_TYPE to Release by default
 	if(NOT CMAKE_BUILD_TYPE)
-		set(CMAKE_BUILD_TYPE "Release" 
+		set(CMAKE_BUILD_TYPE "Release"
 			CACHE STRING
 			"Set the build type"
 			FORCE
 		)
 	endif()
-	
+
 	# Display CMAKE_PREFIX_PATH and CMAKE_BUILD_TYPE
 	gc_pretty_print(SECTION "Useful CMake variables")
 	gc_pretty_print(VARIABLE CMAKE_PREFIX_PATH)
@@ -88,7 +88,7 @@ if(NOT GC_EXTERNAL_CONFIG)
 	if(EXISTS ${RUNDIR}/input.geos)
 		file(STRINGS ${RUNDIR}/input.geos GCHP REGEX ": *gchp_*")
 	elseif(EXISTS ${RUNDIR}/getRunInfo)
-		set(GCHP FALSE) # getRunInfo is only in GC-Classic run direcotries	
+		set(GCHP FALSE) # getRunInfo is only in GC-Classic run direcotries
 	elseif((NOT EXISTS RUNDIR) AND (DEFINED RUNDIR_SIM))
 		set(GCHP FALSE) # special case for building without a run directory
 		set(RUNDIR ${CMAKE_BINARY_DIR})
@@ -149,12 +149,12 @@ if(NOT GC_EXTERNAL_CONFIG AND NOT GC_TRY_RUN_PASSED)
 	endforeach()
 
 	# Try to compile and run try_compile.F90
-	try_run(RUN_FAILED COMPILED_OK 
+	try_run(RUN_FAILED COMPILED_OK
 		${CMAKE_CURRENT_BINARY_DIR}/try_compile 					# binary dir
 		${CMAKE_CURRENT_SOURCE_DIR}/CMakeScripts/try_compile.F90	# test source file
 		COMPILE_DEFINITIONS ${TRY_RUN_DEFINITIONS} ${BT_OPTIONS}	# compiler flags
 		LINK_LIBRARIES ${BT_LIBRARIES}								# link flags
-		CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${BT_INCLUDES}"			# include directories 
+		CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${BT_INCLUDES}"			# include directories
 		COMPILE_OUTPUT_VARIABLE COMPILE_OUTPUT
 		RUN_OUTPUT_VARIABLE RUN_OUTPUT
 	)

diff --git a/GeosCore/gc_classic_version.H b/GeosCore/gc_classic_version.H
@@ -13,4 +13,4 @@
       ! Z = updated for patches that do not break backwards compatibility
       !     with run directories from the last benchmarked version X.Y.0.
       !-----------------------------------------------------------------------
-      GC_CLASSIC_VERSION = '12.6.2'
+      GC_CLASSIC_VERSION = '12.6.3'