Cross-platform compatibliity

.gitattributes

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+.gitattributes text eol=lf
+.gitignore text eol=lf
+Makefile text eol=lf
+*.yml text eol=lf
+LICENSE text eol=lf
+*.ipynb text eol=lf
+*.txt text eol=lf
+*.py text eol=lf
+*.sh text eol=lf
+*.c text eol=lf
+*.cpp text eol=lf
+*.f text eol=lf
+*.f90 text eol=lf
+*.for text eol=lf
+*.md text eol=lf
+*.rst text eol=lf
+*.csv text eol=lf
+*.m text eol=lf
+*.grc text eol=lf
+*.pas text eol=lf

.gitignore

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+*.out
+fort.12
+driver
+*.a
+*.o
+*.exe
+*.mod
+*.so
+CMakeFiles/
+CMakeCache.txt
+cmake_install.cmake
+Makefile
+build/
+*.egg-info/
+basic
+__pycache__/
+

.travis.yml

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+language: generic
+
+os:
+  - linux
+  - osx
+
+dist: trusty
+group: edge
+
+env: TRAVIS_PYTHON_VERSION=3.6  FC=gfortran
+
+notifications:
+  email: false
+
+git:
+  depth: 3
+
+addons:
+  apt:
+    packages:
+      - gfortran
+
+before_install:
+    - if [[ $TRAVIS_OS_NAME == osx ]]; then
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+        brew update;
+        brew install gcc;
+      else 
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      fi
+
+    - bash miniconda.sh -b -p $HOME/miniconda
+    - export PATH=$HOME/miniconda/bin:$PATH
+    - hash -r
+
+    - conda config --set always_yes yes --set changeps1 no
+    - conda update -q conda
+    - conda create -n test python=$TRAVIS_PYTHON_VERSION
+    - source activate test
+    - pip -q install coveralls
+
+install:
+  - python setup.py develop
+
+script: 
+    # test fortran-only "basic" program
+    - cd build
+    - cmake ..
+    - make
+    - cd ..
+    # separately (previous 4 lines not needed) test python access to Glow
+    - coverage run tests/test.py -v
+
+after_success: coveralls
+

CMakeLists.txt

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+cmake_minimum_required (VERSION 2.8.12)
+project(glow Fortran)
+
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ..)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ..)
+
+add_compile_options(-O3 -g)
+
+if(${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
+    add_compile_options(-debug full -traceback -fpe-all=0 -check all)
+else()
+    add_compile_options(-mtune=native -Warray-bounds -fexceptions -fbacktrace)
+endif()
+# --------- GLOW library -------------------
+add_library(glow cglow.f90 glow.f90 bands.f90 conduct.f90 egrid.f90 ephoto.f90 etrans.f90 exsect.f fieldm.f gchem.f90 geomag.f90 maxt.f90 mzgrid.f90 qback.f90 rcolum.f90 rout.f90 snoem.f90 snoemint.f90 solzen.f90 ssflux.f90 iri90.f nrlmsise00.f)
+#------------- basic example ------------
+add_executable(basic glowbasic.f90)
+target_link_libraries(basic glow)
+#include_directories(../build) # for .mod
+#---------- NetCDF (optional) ------------
+find_package(netCDF)
+if(netCDF_DIR)
+    include_directories(${netCDF_INCLUDE_DIR})
+
+    add_library(ionetcdf readtgcm.f90 output.f90 )
+    target_link_libraries(ionetcdf netcdff glow) # yes double "ff"
+else()
+    message(WARNING "NetCDF failed to be included " ${netCDF_INCLUDE_DIR})
+endif()
+#---------- MPI (optional) -------------
+find_package(MPI)
+if(MPI_Fortran_COMPILER)
+    # wrapper compiler mpif90
+    #set(CMAKE_Fortran_COMPILER ${MPI_Fortran_COMPILER}) 
+
+    add_definitions(${MPI_Fortran_COMPILE_FLAGS})
+    include_directories(${MPI_Fortran_INCLUDE_PATH})
+    add_compile_options(-pthread)
+
+    add_executable(driver glowdriver.f90 tzgrid.f90)
+    target_link_libraries(driver glow ionetcdf ${MPI_Fortran_LIBRARIES})
+else()
+    message(WARNING "MPI failed to be included " ${MPI_Fortran_LIBRARIES})
+endif()
+

Makefile.glowbasic

@@ -1,5 +1,5 @@
 #
-FC = ifort
+#FC = ifort
 
  FFLAGS = -O3
 #FFLAGS = -g $(DBGFLAGS)

Makefile.glowdriver

@@ -1,7 +1,7 @@
 #
 FC = mpif90
 
- FFLAGS = -fc=ifort -O3 -I $(INC_NETCDF)
+ FFLAGS = -O3 -I $(INC_NETCDF)
 #FFLAGS = -fc=ifort -g $(DBGFLAGS) -I $(INC_NETCDF)
 
 DBGFLAGS = -debug full -traceback
@@ -17,17 +17,17 @@ DBGFLAGS += -fpe-all=0 # this traps all floating point exceptions
 #
 # Sources (in order of dependency):
 #
-SOURCES = cglow.f90 readtgcm.f90 output.f90 glowdriver.f90 glow.f90 bands.f90 conduct.f90 egrid.f90 ephoto.f90 etrans.f90 exsect.f fieldm.f gchem.f90 geomag.f90 maxt.f90 mzgrid.f90, qback.f90 rcolum.f90 rout.f90 snoem.f90 snoemint.f90 solzen.f90 ssflux.f90 tzgrid.f90, iri90.f nrlmsise00.f
+SOURCES = cglow.f90 mpicdf/readtgcm.f90 mpicdf/output.f90 mpicdf/glowdriver.f90 glow.f90 bands.f90 conduct.f90 egrid.f90 ephoto.f90 etrans.f90 exsect.f fieldm.f gchem.f90 geomag.f90 maxt.f90 mzgrid.f90, qback.f90 rcolum.f90 rout.f90 snoem.f90 snoemint.f90 solzen.f90 ssflux.f90 mpicdf/tzgrid.f90, iri90.f nrlmsise00.f
 
 OBJS := $(addsuffix .o, $(basename $(SOURCES)))
 EXEC = glow.exe
 
 $(EXEC): $(OBJS)
-	$(FC) -o -fc=ifort $@ $(OBJS) $(LIBS) $(LDFLAGS)
+	$(FC) -o $@ $(OBJS) $(LIBS) $(LDFLAGS)
 
 LIB_NETCDF = /home/tgcm/intel/netcdf-4.1.1/lib
 INC_NETCDF = /home/tgcm/intel/netcdf-4.1.1/include
-LIBS       = -L /usr/lib64 -lcurl -L$(LIB_NETCDF) -lnetcdf
+LIBS       = -L /usr/lib64 -lcurl -L$(LIB_NETCDF) -lnetcdff
 
 clean:
 	rm -f *.o *.mod $(EXEC)

README.md

@@ -1,10 +1,90 @@
+[![Build Status](https://travis-ci.org/scivision/GLOW.svg?branch=master)](https://travis-ci.org/scivision/GLOW)
+
 # GLOW
 The GLobal airglOW Model
 
 This directory contains:
-   Fortran-90 source code files,
-   Makefiles,
-   Example input and output files,
-   Example job script,
-   Subdirectory data/ contains input data files,
-   Subdirectory data/iri90 contains IRI input data files
+
+   * Modern Fortran source code files,
+   * Makefile
+   * CMakeLists.txt
+   * Example input and output files
+   * Example job script
+   * `data/` contains input data files,
+   * `data/iri90/` contains IRI input data files
+   * [Release Notes](ReleaseNotes.rst)
+
+
+## Python install
+This command automatically compiles the Fortran code to access from Python on any platform.
+
+    python setup.py develop
+
+You can then run the self-tests with
+
+    python tests/test.py -v
+
+## Fortran-only mode
+While many users use the Python interface to Glow, users on HPCC may want to use MPI directly in Fortran using the Makefiles or CMake. Here's how to compile the ``basic`` example with CMake.
+
+    cd build
+    cmake ..
+    make
+    cd ..
+
+This creates:
+
+
+executable  |  description
+------------|--------------
+basic        |   basic GLOW 
+driver  | MPI/NetCDF GLOW 
+
+### Fortran examples
+With regard to precision, at first try I occasionally see the least digit of precision in the text output files differ. 
+This can be related to Stan using Intel Fortran compiler and I'm using Gfortran.
+E.g. I get 4.34e-9 and Stan got 4.33e-9.
+
+I also get the message::
+
+    Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
+
+Which is a warning sign that different compilers and platforms may yield different results of unpredictable variance.
+
+
+
+#### Aurora example (night)
+Compare your results vs. Stan's results with `meld`:
+
+    ./basic < in.basic.aur > aur.basic.out
+
+    meld out.basic.aur aur.basic.out
+
+
+#### Aurora Example (night)
+
+    ./basic < in.basic.day > day.basic.out
+
+    meld out.basic.day day.basic.out
+
+### MPI Prereq
+Allows parallel execution of GLOW Fortran code for HPCC.
+
+    sudo apt install libopenmpi-dev
+
+### NetCDF prereq
+allows reading/writing data in NetCDF (optional). 
+You need both of these.
+
+    sudo apt install libnetcdf-dev libnetcdff-dev
+
+### Select Fortran compiler
+Simply use the variable `FC`. Example
+
+    cd build/
+    rm -r *
+
+    FC=ifort cmake ..
+    make
+
+NOTE: Using the Intel compiler requires that you have [built NetCDF using Intel Fortran](https://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers/)--this is an issue ANYTIME you use the Intel Compiler and NetCDF.