Push MARBL infrastructure from svn to git

Source code coming in a later commit, hoping to maintain SVN revision history.

.gitignore

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+.svn
+**/.svn

ChangeLog

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+===============================================================================
+Tag Creator: mlevy
+Developers:  mlevy
+Tag Date:    17 Mar 2016
+Tag Name:    MARBL/trunk_tags/MARBL0.0.0
+Tag Summary: Initial commit of MARBL code that compiles on its own
+===============================================================================

bld-test/Makefile

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+SRC_DIR=../src
+OBJ_DIR=../obj
+LIB_DIR=../lib
+INC_DIR=../include
+
+COMP_ARGS=OBJ_DIR=$(OBJ_DIR) LIB_DIR=$(LIB_DIR) INC_DIR=$(INC_DIR) CPPDEFS="-DECOSYS_NT=27 -DZOOPLANKTON_CNT=1 -DAUTOTROPH_CNT=3 -DGRAZER_PREY_CNT=3"
+
+all: intel
+
+intel:
+	cd $(SRC_DIR) ; make FC=ifort FCFLAGS="-O2 -free -module $(OBJ_DIR) -cpp -nogen-interface -fp-model source" $(COMP_ARGS) LIB_NAME=$(LIB_DIR)/libmarbl-intel.a
+
+pgi:
+	cd $(SRC_DIR) ; make FC=pgf90 FCFLAGS="-O2 -Mfree -module $(OBJ_DIR)" $(COMP_ARGS) LIB_NAME=$(LIB_DIR)/libmarbl-pgi.a
+
+gnu:
+	cd $(SRC_DIR) ; make FC=gfortran FCFLAGS="-O2 -ffree-form -J $(OBJ_DIR) -cpp" $(COMP_ARGS) LIB_NAME=$(LIB_DIR)/libmarbl-gnu.a
+
+clean:
+	rm -f $(OBJ_DIR)/* $(LIB_DIR)/* $(INC_DIR)/*

bld-test/hobart.sh

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+#!/bin/bash
+
+build() {
+  compiler=$1
+  rm -f ../obj/* ../include/*
+  module purge
+  module load compiler/$compiler
+  make $compiler
+}
+
+build intel
+build nag
+build gnu

bld-test/yellowstone.sh

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+#!/bin/bash
+
+build() {
+  compiler=$1
+  rm -f ../obj/* ../include/*
+  module purge
+  module load $compiler
+  make $compiler
+}
+
+build intel
+build gnu

include/.gitignore

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+*.mod

lib/.gitignore

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+*.a

obj/.gitignore

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+*.o
+*.mod
+*.d

src/Makefile

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+.SUFFIXES: .F90 .o
+extension = .F90
+
+SRC_DIR = .
+OBJ_DIR = .
+LIB_DIR = .
+INC_DIR = .
+FC = NONE
+
+LIB_NAME = $(LIB_DIR)/libmarbl.a
+
+# Dependency Generation
+MAKE_DEP = $(SRC_DIR)/makedep.py
+DEP_FILE = $(OBJ_DIR)/shared_deps.d
+
+ifeq ($(FC),NONE)
+  NOFC = TRUE
+endif
+
+MODULES = $(shell ls *.F90)
+
+# Some compilers produce ALL_UPPER_CASE.mod files
+ifeq ($(UCASE),TRUE)
+  MODS_TMP = $(shell echo $(MODULES) | tr '[a-z]' '[A-Z]')
+else
+  MODS_TMP = $(MODULES)
+endif
+ifneq ($(OBJ_DIR),$(INC_DIR))
+  INCS = $(addprefix $(INC_DIR)/,${MODS_TMP:.F90=.mod})
+endif
+MODS = $(addprefix $(OBJ_DIR)/,${MODS_TMP:.F90=.mod}) \
+       $(INCS)
+OBJS = $(addprefix $(OBJ_DIR)/,${MODULES:.F90=.o})
+
+ifeq ($(USE_DEPS),TRUE)
+  include $(DEP_FILE)
+endif
+
+### TARGETS ###
+
+all: lib
+
+# Create all object and module files
+# Note that .mod files need to be copied to INC_DIR if OBJ_DIR != INC_DIR
+
+$(OBJ_DIR)/%.o: $(SRC_DIR)/%.F90
+	$(FC) $(FCFLAGS) $(CPPDEFS) -c $< -o $@
+
+$(INC_DIR)/%.mod: $(OBJ_DIR)/%.mod
+ifneq ($(INC_DIR),$(OBJ_DIR))
+	cp $< $@
+endif
+
+### Combine into library
+$(LIB_NAME): $(OBJS)
+	ar -ru $(LIB_NAME) $(OBJS)
+
+$(DEP_FILE): $(MAKE_DEP) $(SRC_DIR)/*.F90
+	$(MAKE_DEP) $(DEP_FILE) $(OBJ_DIR) $(SRC_DIR)
+	@echo "Generated dependencies!"
+
+.PHONY: depends recurse check clean
+
+# Shorthand for making dependency file
+depends: $(DEP_FILE)
+
+# Shorthand for making the library (and all .mod files)
+lib: check depends
+	$(MAKE) -e -f $(SRC_DIR)/Makefile $(LIB_NAME) $(INCS) USE_DEPS=TRUE
+
+# Make sure a Fortran compiler was specified (the Makefile for the stand-alone
+# driver passes FC along with FCFLAGS, SRC_DIR, OBJ_DIR, LIB_DIR, and INC_DIR)
+check:
+	@$(if $(NOFC), echo "ERROR: you must specify FC (and it is recommended that \
+     you specify FCFLAGS as"; echo "well)."; echo "NOTE: if you have checked  \
+     out the stand-alone CVMix driver set then you should"; echo "run \"make  \
+     lib\" from the src/ directory to use CVMix compile options."; exit 1)
+
+# Remove library, object files, module files, and dependency file
+clean:
+	/bin/rm -f $(LIB_NAME) $(OBJS) $(MODS) $(DEP_FILE)
+

src/makedep.py

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+#!/usr/bin/env python
+
+# usage: makedep.py $(DEP_FILE) $(OBJ_DIR) $(SRC_DIR) [$(SRC_DIR2)]
+
+# Generate $DEP_FILE in $OBJ_DIR (arguments 1 and 2, respectively)
+# Read in every file in $SRC_DIR and $SRC_DIR2 (arguments 3 and 4)
+# Only depend on modules located in $SRC_DIR or $SRC_DIR2
+
+import os, sys, re
+
+try:
+  dep_file = sys.argv[1]
+except:
+  dep_file = "depends.d"
+
+try:
+  obj_dir = sys.argv[2]
+except:
+  obj_dir = '.'
+
+try:
+  src_dir = sys.argv[3]
+except:
+  src_dir = '.'
+
+try:
+  src_dir2 = sys.argv[4]
+except:
+  src_dir2 = src_dir
+
+try:
+  inc_dir = sys.argv[5]
+  files_in_inc_dir = os.listdir(inc_dir)
+except:
+  inc_dir = 'NONE'
+
+fout = open(dep_file, 'w')
+files_in_src_dir =  os.listdir(src_dir)
+if src_dir != src_dir2:
+  files_in_src_dir.extend(os.listdir(src_dir2))
+
+for src_file in files_in_src_dir:
+  file_name, file_ext = os.path.splitext(src_file)
+  if file_ext == '.F90':
+    try:
+      fin = open(src_dir+'/'+src_file,"r")
+    except:
+      fin = open(src_dir2+'/'+src_file,"r")
+    for line in fin:
+      if re.match('^ *[Uu][Ss][Ee]',line):
+        line_array = line.split()
+        # statements are usually "use module, only : subroutine"
+        # so we need to strip away the , to get the module name
+        file_used = line_array[1].split(',')[0]
+        if file_used+'.F90' in files_in_src_dir:
+          print file_name+'.o depends on '+file_used+'.o'
+          fout.write(obj_dir+'/'+file_name+'.o: '+obj_dir+'/'+file_used+'.o\n')
+        else:
+          if inc_dir != 'NONE':
+            if file_used+'.mod' in files_in_inc_dir:
+              print file_name+'.o depends on '+file_used+'.mod'
+              fout.write(obj_dir+'/'+file_name+'.o: '+inc_dir+'/'+file_used+'.mod\n')
+            else:
+              # Check for upper case
+              file_used = file_used.upper()
+              if file_used+'.mod' in files_in_inc_dir:
+                print file_name+'.o depends on '+file_used+'.mod'
+                fout.write(obj_dir+'/'+file_name+'.o: '+inc_dir+'/'+file_used+'.mod\n')
+    fin.close