porting to habanero

.gitignore

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+compile/build/
+compile/source/tools/cyrus-imapd-makedepend/Makefile
+compile/source/tools/cyrus-imapd-makedepend/Makefile.bak
+compile/source/tools/cyrus-imapd-makedepend/config.cache
+compile/source/tools/cyrus-imapd-makedepend/config.log
+compile/source/tools/cyrus-imapd-makedepend/config.status
+compile/source/tools/cyrus-imapd-makedepend/cppsetup.o
+compile/source/tools/cyrus-imapd-makedepend/ifparser.o
+compile/source/tools/cyrus-imapd-makedepend/include.o
+compile/source/tools/cyrus-imapd-makedepend/main.o
+compile/source/tools/cyrus-imapd-makedepend/makedepend
+compile/source/tools/cyrus-imapd-makedepend/parse.o
+compile/source/tools/cyrus-imapd-makedepend/pr.o

compile/build_MITgcm.bash

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+#!/usr/bin/env bash
+# --------------------------------------------------------------------------
+# this script build MITgcm for 1D BATS model
+# this only works on habanero for now
+# --------------------------------------------------------------------------
+set -o errexit
+set -o nounset
+# set -o xtrace
+
+###-------------------- habanero (Columbia Univ) --------------------------------------
+module load intel-parallel-studio/2017
+module load netcdf-fortran/4.4.4
+module load netcdf/gcc/64/4.4.0
+
+# set paths relative to $(pwd)/build
+MODS='../modify/1d_ballast_model'
+OPTFILE='../tools/build_options/linux_ia64_ifort_habanero'
+ROOTDIR='../source'
+GENMAKE='../tools/genmake2'
+
+if [ ! -d build ] ; then mkdir build ; fi
+cd build
+
+# GENERATE MAKE FILE
+${GENMAKE} -mods=${MODS} -optfile=${OPTFILE} -rootdir=${ROOTDIR}
+
+make depend
+make -j 4

compile/tools/build_options/linux_ia64_ifort_habanero

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+#!/bin/bash
+#
+# Tested on uv100.awi.de (SGI UV 100, details:
+#                         http://www.sgi.com/products/servers/uv/specs.html)
+# a) For more speed, provided your data size does not exceed 2GB you can
+#    remove -fPIC which carries a performance penalty of 2-6%.
+# b) You can replace -fPIC with '-mcmodel=medium -shared-intel' which may
+#    perform faster than -fPIC and still support data sizes over 2GB per
+#    process but all the libraries you link to must be compiled with
+#    -fPIC or -mcmodel=medium
+# c) flags adjusted for ifort 12.1.0
+
+if test "x$MPI" = xtrue ; then
+  CC=mpiicc
+  FC=mpiifort
+  F90C=mpiifort
+else
+  CC=icc
+  FC=ifort
+  F90C=ifort
+fi
+
+CPP='/lib/cpp  -traditional -P'
+EXTENDED_SRC_FLAG='-132'
+
+DEFINES='-DWORDLENGTH=4'
+LIBS="$(nf-config --flibs)"
+INCLUDES="$(nf-config --fflags)"
+INCLUDEDIRS="$(nf-config --includedir)"
+
+if test "x$MPI" = xtrue ; then
+   DEFINES+=' -DALLOW_USE_MPI -DALWAYS_USE_MPI'
+   LIBS+=" -L$I_MPI_ROOT/lib64 -lmpi"
+   INCLUDES+=" -I$I_MPI_ROOT/include64"
+   INCLUDEDIRS+=" $I_MPI_ROOT/include64"
+fi
+
+if test "x$IEEE" = x ; then
+    #  No need for IEEE-754
+    FFLAGS="$FFLAGS -WB -convert big_endian -assume byterecl -mcmodel=medium -shared-intel"
+    FOPTIM='-O3 -align -march=corei7 -axAVX'
+    NOOPTFLAGS='-O1'
+    NOOPTFILES='calc_oce_mxlayer.F fizhi_lsm.F fizhi_clockstuff.F'
+else
+    #  Try to follow IEEE-754
+    FFLAGS="$FFLAGS -W0 -WB -convert big_endian -assume byterecl -mcmodel=medium -shared-intel"
+    FOPTIM='-O0 -noalign'
+fi

running/scripts/run_1d_MITgcm_habanero.sh

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+#!/bin/sh
+#
+#SBATCH --account=ocp            # The account name for the job.
+#SBATCH --job-name=1d            # The job name.
+##SBATCH -N 1                     # The number of nodes to use.
+##SBATCH --exclusive
+#SBATCH -c 1                     # The number of cpu cores to use.
+#SBATCH --time=4:59:00           # The time the job will take to run 
+#SBATCH --mem-per-cpu=1gb        # The memory the job will use per cpu core.
+
+module load intel-parallel-studio/2017
+module load netcdf-fortran/4.4.4
+module load netcdf/gcc/64/4.4.0
+
+date
+./mitgcmuv 
+date
+