#42 For gaea C5 cce make template, set HAVE_GETTID macro

C5's environment contains its own gettid Linux system call
available in the GNU standard library.

More details: NOAA-GFDL/FMS#276

The error one sees is:
src/FMS/affinity/affinity.c:55:14: error: static declaration of 'gettid' follows non-static declaration
static pid_t gettid(void)
             ^
             /usr/include/bits/unistd_ext.h:34:16: note: previous declaration is here
             extern __pid_t gettid (void) __THROW;
                            ^
                            1 error generated.

templates/ncrc5-cce.mk

@@ -0,0 +1,258 @@
+# Template for the Cray CCE Compilers on a Cray System
+#
+# Typical use with mkmf
+# mkmf -t ncrc-cray.mk -c"-Duse_libMPI -Duse_netCDF" path_names /usr/local/include
+
+############
+# Commands Macros
+############
+FC = ftn
+CC = cc
+LD = ftn $(MAIN_PROGRAM)
+
+#######################
+# Build target macros
+#
+# Macros that modify compiler flags used in the build.  Target
+# macrose are usually set on the call to make:
+#
+#    make REPRO=on NETCDF=3
+#
+# Most target macros are activated when their value is non-blank.
+# Some have a single value that is checked.  Others will use the
+# value of the macro in the compile command.
+
+DEBUG =              # If non-blank, perform a debug build (Cannot be
+                     # mixed with REPRO or TEST)
+
+REPRO =              # If non-blank, erform a build that guarentees
+                     # reprodicuibilty from run to run.  Cannot be used
+                     # with DEBUG or TEST
+
+TEST  =              # If non-blank, use the compiler options defined in
+                     # the FFLAGS_TEST and CFLAGS_TEST macros.  Cannot be
+                     # use with REPRO or DEBUG
+
+VERBOSE =            # If non-blank, add additional verbosity compiler
+                     # options
+
+OPENMP =             # If non-blank, compile with openmp enabled
+
+NETCDF =             # If value is '3' and CPPDEFS contains
+                     # '-Duse_netCDF', then the additional cpp macro
+                     # '-Duse_LARGEFILE' is added to the CPPDEFS macro.
+
+                     # A list of -I Include directories to be added to the
+                     # the compile command.
+INCLUDES := $(shell pkg-config --cflags yaml-0.1)
+
+COVERAGE =           # Add the code coverage compile options.
+
+# Need to use at least GNU Make version 3.81
+need := 3.81
+ok := $(filter $(need),$(firstword $(sort $(MAKE_VERSION) $(need))))
+ifneq ($(need),$(ok))
+$(error Need at least make version $(need).  Load module gmake/3.81)
+endif
+
+# REPRO, DEBUG and TEST need to be mutually exclusive of each other.
+# Make sure the user hasn't supplied two at the same time
+ifdef REPRO
+ifneq ($(DEBUG),)
+$(error Options REPRO and DEBUG cannot be used together)
+else ifneq ($(TEST),)
+$(error Options REPRO and TEST cannot be used together)
+endif
+else ifdef DEBUG
+ifneq ($(TEST),)
+$(error Options DEBUG and TEST cannot be used together)
+endif
+endif
+
+# Required Preprocessor Macros:
+CPPDEFS += -Duse_netCDF
+
+# Additional Preprocessor Macros needed due to  Autotools and CMake
+CPPDEFS += -DHAVE_SCHED_GETAFFINITY -DHAVE_GETTID
+
+# Macro for Fortran preprocessor
+FPPFLAGS := $(INCLUDES)
+# Fortran Compiler flags for the NetCDF library
+FPPFLAGS += $(shell nf-config --fflags)
+
+# Base set of Fortran compiler flags
+FFLAGS = -s real64 -s integer32 -h byteswapio -e m -h keepfiles -e0 -ez -N1023
+
+# Flags based on perforance target (production (OPT), reproduction (REPRO), or debug (DEBUG)
+FFLAGS_OPT = -O3 -O fp2 -G2
+FFLAGS_REPRO = -O2 -O fp2 -G2
+FFLAGS_DEBUG = -g -R bc
+
+# Flags to add additional build options
+FFLAGS_NOOPENMP = -h noomp
+FFLAGS_VERBOSE = -e o -v
+FFLAGS_COVERAGE =
+
+# Macro for C preprocessor
+CPPFLAGS := $(INCLUDES)
+# C Compiler flags for the NetCDF library
+CPPFLAGS += $(shell nc-config --cflags)
+
+# Base set of C compiler flags
+CFLAGS =
+
+# Flags based on perforance target (production (OPT), reproduction (REPRO), or debug (DEBUG)
+CFLAGS_OPT = -O2
+CFLAGS_REPRO = -O2
+CFLAGS_DEBUG = -g
+
+# Flags to add additional build options
+CFLAGS_NOOPENMP = -h noomp
+CFLAGS_VERBOSE = -v -h display_opt
+CFLAGS_COVERAGE =
+
+# Optional Testing compile flags.  Mutually exclusive from DEBUG, REPRO, and OPT
+# *_TEST will match the production if no new option(s) is(are) to be tested.
+FFLAGS_TEST := $(FFLAGS_OPT)
+CFLAGS_TEST := $(CFLAGS_OPT)
+
+# Linking flags
+LDFLAGS := -h byteswapio
+LDFLAGS_NOOPENMP :=
+LDFLAGS_VERBOSE := -v
+LDFLAGS_COVERAGE :=
+
+# List of -L library directories to be added to the compile and linking commands
+LIBS := $(shell pkg-config --libs yaml-0.1)
+
+# Get compile flags based on target macros.
+ifdef REPRO
+CFLAGS += $(CFLAGS_REPRO)
+FFLAGS += $(FFLAGS_REPRO)
+else ifdef DEBUG
+CFLAGS += $(CFLAGS_DEBUG)
+FFLAGS += $(FFLAGS_DEBUG)
+else ifdef TEST
+CFLAGS += $(CFLAGS_TEST)
+FFLAGS += $(FFLAGS_TEST)
+else
+CFLAGS += $(CFLAGS_OPT)
+FFLAGS += $(FFLAGS_OPT)
+endif
+
+ifndef OPENMP
+CFLAGS += $(CFLAGS_NOOPENMP)
+FFLAGS += $(FFLAGS_NOOPENMP)
+LDFLAGS += $(LDFLAGS_NOOPENMP)
+endif
+
+ifdef VERBOSE
+CFLAGS += $(CFLAGS_VERBOSE)
+FFLAGS += $(FFLAGS_VERBOSE)
+LDFLAGS += $(LDFLAGS_VERBOSE)
+endif
+
+ifeq ($(NETCDF),3)
+  # add the use_LARGEFILE cppdef
+  CPPDEFS += -Duse_LARGEFILE
+endif
+
+ifdef COVERAGE
+ifdef BUILDROOT
+PROF_DIR=-prof-dir=$(BUILDROOT)
+endif
+CFLAGS += $(CFLAGS_COVERAGE) $(PROF_DIR)
+FFLAGS += $(FFLAGS_COVERAGE) $(PROF_DIR)
+LDFLAGS += $(LDFLAGS_COVERAGE) $(PROF_DIR)
+endif
+
+LDFLAGS += $(LIBS)
+
+#---------------------------------------------------------------------------
+# you should never need to change any lines below.
+
+# see the MIPSPro F90 manual for more details on some of the file extensions
+# discussed here.
+# this makefile template recognizes fortran sourcefiles with extensions
+# .f, .f90, .F, .F90. Given a sourcefile <file>.<ext>, where <ext> is one of
+# the above, this provides a number of default actions:
+
+# make <file>.opt	create an optimization report
+# make <file>.o		create an object file
+# make <file>.s		create an assembly listing
+# make <file>.x		create an executable file, assuming standalone
+#			source
+# make <file>.i		create a preprocessed file (for .F)
+# make <file>.i90	create a preprocessed file (for .F90)
+
+# The macro TMPFILES is provided to slate files like the above for removal.
+
+RM = rm -f
+TMPFILES = .*.m *.B *.L *.i *.i90 *.l *.s *.mod *.opt
+
+.SUFFIXES: .F .F90 .H .L .T .f .f90 .h .i .i90 .l .o .s .opt .x
+
+.f.L:
+	$(FC) $(FFLAGS) -c -listing $*.f
+.f.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f
+.f.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f
+.f.T:
+	$(FC) $(FFLAGS) -c -cif $*.f
+.f.o:
+	$(FC) $(FFLAGS) -c $*.f
+.f.s:
+	$(FC) $(FFLAGS) -S $*.f
+.f.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f *.o $(LDFLAGS)
+.f90.L:
+	$(FC) $(FFLAGS) -c -listing $*.f90
+.f90.opt:
+	$(FC) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.f90
+.f90.l:
+	$(FC) $(FFLAGS) -c $(LIST) $*.f90
+.f90.T:
+	$(FC) $(FFLAGS) -c -cif $*.f90
+.f90.o:
+	$(FC) $(FFLAGS) -c $*.f90
+.f90.s:
+	$(FC) $(FFLAGS) -c -S $*.f90
+.f90.x:
+	$(FC) $(FFLAGS) -o $*.x $*.f90 *.o $(LDFLAGS)
+.F.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F
+.F.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F
+.F.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F
+.F.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F
+.F.f:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F > $*.f
+.F.i:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F
+.F.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F
+.F.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F
+.F.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F *.o $(LDFLAGS)
+.F90.L:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -listing $*.F90
+.F90.opt:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -opt_report_level max -opt_report_phase all -opt_report_file $*.opt $*.F90
+.F90.l:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $(LIST) $*.F90
+.F90.T:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -cif $*.F90
+.F90.f90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -EP $*.F90 > $*.f90
+.F90.i90:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) -P $*.F90
+.F90.o:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c $*.F90
+.F90.s:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -c -S $*.F90
+.F90.x:
+	$(FC) $(CPPDEFS) $(FPPFLAGS) $(FFLAGS) -o $*.x $*.F90 *.o $(LDFLAGS)