Radiation analysis fix

.gitignore

@@ -1 +1,5 @@
 *~
+*.o
+*.mod
+*.DO_NOT_MODIFY.f90
+*.x

README.md

@@ -1,35 +1,122 @@
-# AM4 Instructions
-
-To checkout the source code for the AM4 model, use the following git command <br>
-
-```
-git clone -r https://github.com/NOAA-GFDL/AM4.git
-```
-
-# Source Code
+# GFDL AM4 Model
 
 [![DOI](https://zenodo.org/badge/102487636.svg)](https://zenodo.org/badge/latestdoi/102487636)
 
-The source code is located in the src directory. This repository contains the code for the following
-folders:
+This repository includes the public release of the GFDL AM4 model
+code.  The AM4 model is described in the
+[two](https://doi.org/10.1002/2017MS001208)
+[articles](https://doi.org/10.1002/2017MS001209) published in the
+[Journal of Advances in Modeling Earth Systems
+(JAMES)](https://agupubs.onlinelibrary.wiley.com/journal/19422466).
+More information on the model and access to the output is available on
+the [AM4 data and code
+site](http://data1.gfdl.noaa.gov/nomads/forms/am4.0/) at the
+[Geophysical Fluid Dynamics Laboratory
+(GFDL)](https://www.gfdl.noaa.gov).
+
+The layout of this package includes the following directories:
+
+* src - The source code for the AM4 model
+* exec - The build directory with Makefiles for building the model executable
+* run - Sample run script
+* analysis - Sample analysis scripts 
+
+## Cloning Instructions
+
+This repository uses [git
+submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to
+point to other repositories.  Thus, care should be taken when cloning,
+and updating the source to ensure all source.  To obtain all source,
+use the following git command
 
-* atmos_cubed_sphere
-* atmos_drivers
-* atmos_param
-* atmos_shared
-* ice_param
-* ice_sis
-* land_lad2
+```
+git clone --recursive https://github.com/NOAA-GFDL/AM4.git
+```
 
-The following folders are available on github and are linked as git submodules
+The `--recursive` option to `git clone` instructs git to recursively
+clone all submodules.  In the event the repository was not cloned
+using the `--recursive` option, the following step must be taken to
+obtain all sources:
 
-* MOM6
-* coupler
-* shared
+```
+# From within the AM4 parent directory
+git submodule update --init --recursive
+```
 
-# Analysis Scripts 
-Some of the climate analysis scripts run at NOAA GFDL and used in the AM4 documentation papers are located in the analysis directory.
-Within each analysis suite, there is a jupyter notebook, both readable and runnable from your local jupyter environment, provided all dependencies are installed.
+## Source Code
+
+All model source is contained in the [src](src) directory.  GFDL
+tracks code using the git version control system.  This package
+includes a single version of the following GFDL model components.  The
+git hash listed corresponds to the commit hash in the internal GFDL
+git repository.
+
+Component | Commit Hash
+--------- | -----------
+atmos_cubed_sphere | b8b05bf650c0d3293b538bdaceb894ba0fd6910b
+atmos_drivers | 5ee95d6abf0879594551dd7e6635dff4004c4010
+atmos_param | 2e94acfd8621e85216bf822c395a8c3f15a511a5
+atmos_shared | a557d4d7bab033ef1ad1d400a62fe07a97ccb477
+ice_param | 1553c8bc4f9a66791c89367b6f327147523155ed
+ice_sis | ccc7328dcd79706dd5c17c8bab660222886fc80b
+land_lad2 | a220288ecb289bf9d793d051fc5076072874ce07
+
+The following components are available in the
+[NOAA-GFDL](https://github.com/NOAA-GFDL) github organization:
+
+* [MOM6](https://github.com/NOAA-GFDL/MOM6)
+* [coupler](https://github.com/NOAA-GFDL/coupler)
+* [FMS](https://github.com/NOAA-GFDL/FMS) (as [shared](src/shared))
+
+## Building AM4
+
+The [exec](exec) directory contains Makefiles that can be used to
+build the AM4 executable.  These Makefiles were generated using the
+[Make Makefile (mkmf)](https://github.com/NOAA-GFDL/mkmf) program.
+Included in the exec direcgtory is a sample make template file for the
+Intel compilers ([intel.mk](exec/templates/intel.mk)).  This make
+template can be used on any system with a relatively recent version of
+the Intel compilers, the netCDF 4 library and the MPICH2 MPI library.
+Included in the [intel.mk](exec/templates/intel.mk) file are
+additional settings that can be modified during the build.
+
+## Obtaining the input data
+
+The input data required for running the AM4 model can be found on
+[GFDL's data
+portal](http://data1.gfdl.noaa.gov/nomads/forms/am4.0/) .
+
+The file `AM4.tar.gz` contains a configured run directory to run a
+sample experiment of the AM4 model.  Included in the tar file is a
+README.AM4_run with more instructions on how to configure the AM4 run
+directory.
+
+## Running AM4
+
+Included in the run directory is a sample run script for reference.
+To run the AM4 sample experiment, first download the data file
+mentioned in [Obtaining the Input data](#obtaining-the-input-data)
+section.  Modify the variables in the configuration section in the
+sample run script, and then run the script.
+
+The sample data and run script are configured to run on 216
+processors.  To run on a different number of processors, or modify the
+experiment, refer to the `README.AM4_run` file included in the AM4
+data tarball.
+
+Note: The `input.nml` file (found in the AM4 data tarball) contains
+Fortran namelists and namelist variables that modify, at run time, the
+model.  To learn more about the settings in the `input.nml` file,
+please refer to source code where the namelist/variable are defined.
+
+## Analysis Scripts 
+
+Some of the climate analysis scripts run at NOAA GFDL and used in the
+AM4 documentation papers are located in the analysis directory.
+Within each analysis suite, is a [jupyter
+notebook](https://jupyter-notebook.readthedocs.io/en/stable/), both
+readable and runnable from your local jupyter environment, provided
+all dependencies are installed.
 
 E.g.
 
@@ -38,14 +125,34 @@ E.g.
 * [Zonal_mean_zonal_wind_stress](analysis/bw/bw_atmos_zm_atl_pac_a1r/bw_atmos_atl_pac.1980-2014.ipynb)
 * [PCMDI Metrics Portrait Plot](analysis/pcmdimetrics/portraitPlot-AM4.AMIP.ipynb)
 
-Please refer https://www.gfdl.noaa.gov/am4.0-model for details about where to find model and OBS data used in the papers.
-
-For all analysis figures and pertaining data, please use the AM4 documentation papers as the original reference.
-Please direct your questions and feedback to [email protected]
-
-
-# Disclaimer
-
-The United States Department of Commerce (DOC) GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use.  DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information.  Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law.  Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce.  The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
-
-This project code is made available through GitHub but is managed by NOAA-GFDL at https://gitlab.gfdl.noaa.gov.
+## Model output and Other References
+
+Please refer to the [AM4 data and code
+site](http://data1.gfdl.noaa.gov/nomads/forms/am4.0/) for details
+about where to find model and OBS data used in the papers.
+
+For all analysis figures and pertaining data, please use the AM4
+documentation papers as the original reference.
+
+Please direct your questions and feedback to
+[email protected]
+
+## Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is
+provided on an 'as is' basis and the user assumes responsibility for
+its use.  DOC has relinquished control of the information and no
+longer has responsibility to protect the integrity, confidentiality,
+or availability of the information.  Any claims against the Department
+of Commerce stemming from the use of its GitHub project will be
+governed by all applicable Federal law.  Any reference to specific
+commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply
+their endorsement, recommendation or favoring by the Department of
+Commerce.  The Department of Commerce seal and logo, or the seal and
+logo of a DOC bureau, shall not be used in any manner to imply
+endorsement of any commercial product or activity by DOC or the United
+States Government.
+
+This project code is made available through GitHub but is managed by
+NOAA-GFDL at https://gitlab.gfdl.noaa.gov.

analysis/cjs1/radiation_atmos_av_mon/radiation_atmos_av_mon.ipynb

@@ -184,6 +184,46 @@
     "platform = 'desktop' "
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "####### load modules ###########\n",
+    "TMPDIR = os.environ[\"TMPDIR\"]\n",
+    "FRE_CODE_BASE = BASEDIR\n",
+    "PACKAGE_NAME = 'radiation_atmos_av_mon'\n",
+    "if not os.path.exists(TMPDIR):\n",
+    "     os.makedirs(TMPDIR)\n",
+    "if not os.path.exists(out_dir):\n",
+    "     os.makedirs(out_dir)            \n",
+    "if ( platform == 'hpcs-csc' ) or ( platform == 'desktop'):\n",
+    "    print(\"Running script on non-GFDL machine and public repo: skip module load\") \n",
+    "else:\n",
+    "    print \"ERROR: invalid platform: %s\" % platform\n",
+    "    exit(1)\n",
+    "\n",
+    "#---- Check if environment loaded correctly ---#\n",
+    "\n",
+    "###################\n",
+    "# run the script\n",
+    "##################\n",
+    "\n",
+    "\n",
+    "options = \"-i \"+in_data_dir+\" -d \"+descriptor+\" -y \"+yr1+\",\"+yr2+\" -o \"+out_dir\n",
+    "\n",
+    "command = FRE_CODE_BASE+\"/\"+PACKAGE_NAME+\"/radiation_atmos_av_mon.csh \"+options+\" \"+in_data_file\n",
+    "\n",
+    "print(command)\n",
+    "\n",
+    "cmd = subprocess.Popen('tcsh -c \"'+command+'\"',shell=True,stdout=PIPE,stdin=PIPE, stderr=PIPE)\n",
+    "output, errors = cmd.communicate()\n",
+    "#print output, errors "
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {

exec/Makefile

@@ -0,0 +1,56 @@
+# Makefile for Experiment 'cm4p12_warsaw'
+
+BUILDROOT = $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
+SRCROOT = $(abspath $(BUILDROOT)../src)/ # Final '/' added to denote directory
+
+MK_TEMPLATE = $(BUILDROOT)templates/intel.mk
+
+# Override default compile options. See templates/intel.mk for more compile options.
+# BLD_TYPE configures the type of build, PROD (production), REPRO (regression) or
+# DEBUG (debug options)
+BLD_TYPE = PROD
+OPENMP = t # Build with OpenMP enabled
+
+include $(MK_TEMPLATE)
+
+SUBMAKEFLAGS = BUILDROOT=$(BUILDROOT) SRCROOT=$(SRCROOT) MK_TEMPLATE=$(MK_TEMPLATE) BLD_TYPE=$(BLD_TYPE)
+
+fms_cm4p12_warsaw.x: coupler/libcoupler.a ice_sis/libice_sis.a atmos_dyn/libatmos_dyn.a land_lad2/libland_lad2.a atmos_phys/libatmos_phys.a mom6/libmom6.a fms/libfms.a
+	$(LD) $^ $(LDFLAGS) -o $@ $(STATIC_LIBS)
+
+fms/libfms.a:  FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)fms $(@F)
+
+atmos_phys/libatmos_phys.a: fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)atmos_phys $(@F)
+
+atmos_dyn/libatmos_dyn.a: atmos_phys/libatmos_phys.a fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)atmos_dyn $(@F)
+
+ice_sis/libice_sis.a: mom6/libmom6.a fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)ice_sis $(@F)
+
+land_lad2/libland_lad2.a: fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)land_lad2 $(@F)
+
+# MOM6 is currently unable to run with OpenMP enabled
+mom6/libmom6.a: fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) --directory=$(BUILDROOT)mom6 $(@F)
+
+coupler/libcoupler.a: atmos_dyn/libatmos_dyn.a ice_sis/libice_sis.a atmos_phys/libatmos_phys.a mom6/libmom6.a land_lad2/libland_lad2.a fms/libfms.a FORCE
+	$(MAKE) $(SUBMAKEFLAGS) OPENMP=$(OPENMP) --directory=$(BUILDROOT)coupler $(@F)
+
+FORCE:
+
+clean:
+	$(MAKE) --directory=$(BUILDROOT)fms clean
+	$(MAKE) --directory=$(BUILDROOT)atmos_phys clean
+	$(MAKE) --directory=$(BUILDROOT)atmos_dyn clean
+	$(MAKE) --directory=$(BUILDROOT)ice_sis clean
+	$(MAKE) --directory=$(BUILDROOT)land_lad2 clean
+	$(MAKE) --directory=$(BUILDROOT)mom6 clean
+	$(MAKE) --directory=$(BUILDROOT)coupler clean
+
+clean_all: clean
+	$(RM) *.x
+