--- MITgcm/tools/build_options/linux_amd64_gfortran	2007/08/20 20:31:00	1.3
+++ MITgcm/tools/build_options/linux_amd64_gfortran	2014/10/01 23:12:14	1.26
@@ -1,45 +1,113 @@
 #!/bin/bash
-#
-#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/build_options/linux_amd64_gfortran,v 1.3 2007/08/20 20:31:00 ce107 Exp $
+
+#  $Header: /home/ubuntu/mnt/e9_copy/MITgcm/tools/build_options/linux_amd64_gfortran,v 1.26 2014/10/01 23:12:14 jmc Exp $
 #  $Name:  $
-#
 
-#  Tested with gcc-gfortran v4.0.x as shipped with Fedora Core 4.
-#  It fixes the ' \' versus ' &' terminator problem but some 
-#  namelist problems remain.  The biggest seems to be the inability
-#  of current gfortran versions to support namelist syntax such as:
+# Build options for gfortran compiler (GNU) on Linux AMD64 platform
 #
-#     fields(1,1) = 'UVELSLT ','VVELSLT ','WVELSLT ',
+#  Tested with gcc-gfortran v4.1.x as shipped with Fedora Core 6,7,8
+#         with gcc-gfortran v4.3.x as shipped with Fedora Core 9,10
 #
-#  which results in run-time errors.
-
+# OpenMP : Tested on dickens with gcc-gfortran v4.3.2 as shipped with FC 10
+#              on baudelaire with gcc-gfortran v4.4.5 as shipped with FC 13
+#              on danton     with gcc-gfortran v4.5.1 as shipped with FC 14
+#                            with gcc-gfortran v4.7.x as shipped with FC 17
+#                            with gcc-gfortran v4.8.1 as shipped with FC 19
+#              on acesgrid   with gcc-gfortran v4.6.0 as shipped with FC 15
+#
+# MPI : Tested on acesgrid (Fedora Core 15), using:
+#       module load gcc     (Version 4.6.0)
+#   and with mpich1:
+#       module load mvapich
+#   or  with mpich2:
+#       module load mvapich2
+#   or  with openmpi:
+#       module load openmpi
+# and on baudelaire.csail.mit.edu (FC13), using:
+#       export MPI_GCC_DIR=/srv/software/gcc/gcc-packages/gcc-4.4.5/mpich2/mpich2-1.3
+#       export MPI_INC_DIR=$MPI_GCC_DIR/include
+#       export PATH=$MPI_GCC_DIR/bin:$PATH
+#
+# and on IRIDIS at Southampton
+# http://www.southampton.ac.uk/isolutions/computing/hpc/iridis/
+#    with
+#       module load openmpi/1.4.3/gcc-4.3.3
+#    and
+#       export MPI_INC_DIR=$MPIROOT/include
+
+#-------
+# run with OpenMP: needs to set environment var. OMP_NUM_THREADS
+#    and generally, needs to increase the thread stack-size:
+#   -  sh,bash:
+#     > export OMP_NUM_THREADS=2
+#     > export GOMP_STACKSIZE=400m
+#   - csh,tcsh:
+#     > setenv OMP_NUM_THREADS 2
+#     > setenv GOMP_STACKSIZE 400m
+#-------
+
+if test "x$MPI" = xtrue ; then
+  CC=${CC:=mpicc}
+  FC=${FC:=mpif77}
+  F90C=${F90C:=mpif90}
+else
+  CC=gcc
+  FC=gfortran
+  F90C=gfortran
+fi
 
-FC=gfortran
-F90C=gfortran
-CC=gcc
 DEFINES='-DWORDLENGTH=4 -DNML_TERMINATOR'
-CPP='cpp  -traditional -P'
-NOOPTFLAGS='-O0'
+EXTENDED_SRC_FLAG='-ffixed-line-length-132'
+F90FIXEDFORMAT='-ffixed-form'
+GET_FC_VERSION="--version"
+OMPFLAG='-fopenmp'
 
-if test "x$DEVEL" != x ; then
-    FFLAGS='-g -Wall -W -ffpe-trap=invalid,zero,overflow -fbounds-check'
-else
-    FFLAGS=''
-fi
+NOOPTFLAGS='-O0'
+NOOPTFILES=''
 
-# Requires gfortran from 2006 onwards for -fconvert=big-endian
+CFLAGS='-O0'
+#- Requires gfortran from 2006 onwards for -fconvert=big-endian
 FFLAGS="$FFLAGS -fconvert=big-endian -fimplicit-none"
+#- for big setups, compile & link with "-fPIC" or set memory-model to "medium":
+#CFLAGS="$CFLAGS -fPIC"
+#FFLAGS="$FFLAGS -fPIC"
+#-  with FC 19, need to use this without -fPIC (which cancels -mcmodel option):
+ CFLAGS="$CFLAGS -mcmodel=medium"
+ FFLAGS="$FFLAGS -mcmodel=medium"
+#- might want to use '-fdefault-real-8' for fizhi pkg:
+#FFLAGS="$FFLAGS -fdefault-real-8 -fdefault-double-8"
 
-if test "x$IEEE" = x ; then
-    #  No need for IEEE-754
+if test "x$IEEE" = x ; then     #- with optimisation:
+   #- full optimisation
     FOPTIM='-O3 -funroll-loops'
+    NOOPTFILES="$NOOPTFILES ini_masks_etc.F"
+   #- can use -O2 (safe optimisation) to avoid Pb with some gcc version of -O3:
+   #FOPTIM='-O2 -funroll-loops'
 else
-    #  Try to follow IEEE-754
+   # these may also be useful, but require specific gfortran versions:
+   # -Wnonstd-intrinsics        for gfortran <= 4.3
+   # -Wintrinsics-std           for gfortran >= 4.4
+   # -Wno-tabs                  for gfortran >= 4.3
+   # -Wno-unused-dummy-argument for gfortran >= 4.6
+   #FFLAGS="$FFLAGS -Waliasing -Wampersand -Wsurprising -Wline-truncation"
+   #- or simply:
+    FFLAGS="$FFLAGS -Wall"
+   #- to get plenty of warnings: -Wall -Wextra (older form: -Wall -W) or:
+   #FFLAGS="$FFLAGS -Wconversion -Wimplicit-interface -Wunused-labels"
+  if test "x$DEVEL" = x ; then  #- no optimisation + IEEE :
     FOPTIM='-O0'
+  else                          #- development/check options:
+    FOPTIM='-O0 -g -fbounds-check'
+    FOPTIM="$FOPTIM -ffpe-trap=invalid,zero,overflow -finit-real=inf"
+  fi
 fi
+
 F90FLAGS=$FFLAGS
 F90OPTIM=$FOPTIM
-CFLAGS=$FOPTIM
+
+INCLUDEDIRS=''
+INCLUDES=''
+LIBS=''
 
 if [ "x$NETCDF_ROOT" != x ] ; then
     INCLUDEDIR="${NETCDF_ROOT}/include"
@@ -74,4 +142,18 @@
 elif test -d /usr/local/include/netcdf.inc ; then
     INCLUDES='-I/usr/local/include'
     LIBS='-L/usr/local/lib64'
+elif test -d /usr/include/netcdf.inc ; then
+    INCLUDES='-I/usr/include'
+    LIBS='-L/usr/lib64'
+fi
+
+if [ -n "$MPI_HOME" -a -z "$MPI_INC_DIR" ]; then
+    MPI_INC_DIR="$MPI_HOME/include"
+fi
+if [ -n "$MPI_INC_DIR" -a "x$MPI" = xtrue ] ; then
+    INCLUDES="$INCLUDES -I$MPI_INC_DIR"
+    INCLUDEDIRS="$INCLUDEDIRS $MPI_INC_DIR"
+    #- used for parallel (MPI) DIVA
+    MPIINCLUDEDIR="$MPI_INC_DIR"
+   #MPI_HEADER_FILES='mpif.h mpiof.h'
 fi