Index: /branches/2012/dev_MERGE_2012/NEMOGCM/ARCH/NOC/arch-ALTIX_NAUTILUS_MPT.fcm
===================================================================
--- /branches/2012/dev_MERGE_2012/NEMOGCM/ARCH/NOC/arch-ALTIX_NAUTILUS_MPT.fcm	(revision 3735)
+++ /branches/2012/dev_MERGE_2012/NEMOGCM/ARCH/NOC/arch-ALTIX_NAUTILUS_MPT.fcm	(revision 3736)
@@ -2,6 +2,8 @@
 # NCDF_HOME   root directory containing lib and include subdirectories for netcdf4
 # HDF5_HOME   root directory containing lib and include subdirectories for HDF5
+# XIOS_HOME   root directory containing lib for XIOS
 # NCDF_INC    netcdf include file
 # NCDF_LIB    netcdf library
+# XIOS_LIB    XIOS library
 # FC          Fortran compiler command
 # FCFLAGS     Fortran compiler flags
@@ -17,9 +19,12 @@
 
 
-%NCDF_HOME           /noc/users/jeff/packages/netcdf4/netcdf-4.1.3/xSSE2/intel11.1
-%HDF5_HOME           /noc/users/jeff/packages/hdf5/hdf5-1.8.7/xSSE2/intel11.1
+%NCDF_HOME           /fibre/omfman/NETCDF_PAR
+%HDF5_HOME           /fibre/omfman/NETCDF_PAR
+%XIOS_HOME           /fibre/omfman/XIOS
 %NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
-# Note use of -Bstatic because the library root directories are not accessible to the back-end compute nodes
-%NCDF_LIB            -L%HDF5_HOME/lib -L%NCDF_HOME/lib -Bstatic -lnetcdff -lnetcdf -lhdf5_fortran -lhdf5_hl -lhdf5 -Bdynamic -lz
+%XIOS_INC            -I%XIOS_HOME/inc 
+%XIOS_LIB            -L%XIOS_HOME/lib -lxios
+# Note use of -Bstatic because the library root directories may not be accessible to the back-end compute nodes
+%NCDF_LIB            -L%HDF5_HOME/lib -L%NCDF_HOME/lib -Bstatic -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -Bdynamic -lz
 %FC                  ifort
 %FCFLAGS             -r8 -O3 -fp-model precise -xT -ip -vec-report0
@@ -27,10 +32,10 @@
 %LD                  ifort
 %FPPFLAGS            -P -C -traditional
-%LDFLAGS             -lmpi
+%LDFLAGS             -lmpi -lstdc++
 %AR                  ar 
 %ARFLAGS             -r
 %MK                  gmake
-%USER_INC            %NCDF_INC
-%USER_LIB            %NCDF_LIB
+%USER_INC            %NCDF_INC %XIOS_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
 
 # - if debugging use these flags
Index: anches/2012/dev_MERGE_2012/NEMOGCM/ARCH/NOC/arch-ALTIX_NAUTILUS_SETTE.fcm
===================================================================
--- /branches/2012/dev_MERGE_2012/NEMOGCM/ARCH/NOC/arch-ALTIX_NAUTILUS_SETTE.fcm	(revision 3735)
+++ 	(revision )
@@ -1,34 +1,0 @@
-# ifort compiler options for NOCS ALTIX cluster nautilus using NetCDF4 libraries and minimal optimisation for the purposes of SETTE testing
-# NCDF_HOME   root directory containing lib and include subdirectories for netcdf4
-# HDF5_HOME   root directory containing lib and include subdirectories for HDF5
-# NCDF_INC    netcdf include file
-# NCDF_LIB    netcdf library
-# FC          Fortran compiler command
-# FCFLAGS     Fortran compiler flags
-# FFLAGS      Fortran 77 compiler flags
-# LD          linker
-# LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
-# FPPFLAGS    pre-processing flags
-# AR          assembler
-# ARFLAGS     assembler flags
-# MK          make
-# USER_INC    additional include files for the compiler,  e.g. -I<include dir>
-# USER_LIB    additional libraries to pass to the linker, e.g. -l<library>
-
-
-%NCDF_HOME           /noc/users/jeff/packages/netcdf4/netcdf-4.1.1/x86_64/intel10.1
-%HDF5_HOME           /noc/users/jeff/packages/hdf5/hdf5-1.8.4-patch1/x86_64/intel10.1
-%NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
-# Note use of -Bstatic because the library root directories are not accessible to the back-end compute nodes
-%NCDF_LIB            -L%HDF5_HOME/lib -L%NCDF_HOME/lib -Bstatic -lnetcdf -lhdf5_fortran -lhdf5_hl -lhdf5 -Bdynamic -lz
-%FC                  ifort
-%FCFLAGS             -r8 -O0
-%FFLAGS              -r8 -O0
-%LD                  ifort
-%FPPFLAGS            -P -C -traditional
-%LDFLAGS             -lmpi
-%AR                  ar 
-%ARFLAGS             -r
-%MK                  gmake
-%USER_INC            %NCDF_INC
-%USER_LIB            %NCDF_LIB
Index: /branches/2012/dev_MERGE_2012/NEMOGCM/SETTE/BATCH_TEMPLATE/batch-mpmd-ALTIX_NAUTILUS_MPT
===================================================================
--- /branches/2012/dev_MERGE_2012/NEMOGCM/SETTE/BATCH_TEMPLATE/batch-mpmd-ALTIX_NAUTILUS_MPT	(revision 3736)
+++ /branches/2012/dev_MERGE_2012/NEMOGCM/SETTE/BATCH_TEMPLATE/batch-mpmd-ALTIX_NAUTILUS_MPT	(revision 3736)
@@ -0,0 +1,105 @@
+#!/bin/bash 
+#!
+#PBS -N NEMO
+#PBS -l select=NODES:ncpus=8:mpiprocs=4
+#PBS -l place=scatter:excl
+#PBS -l walltime=00:59:00
+#PBS -q nemo
+#PBS -W group_list=nemo
+#PBS -j oe
+#
+  OCEANCORES=NPROCS
+  XIOCORES=NXIOPROCS
+  export SETTE_DIR=DEF_SETTE_DIR
+#
+# load sette functions (only post_test_tidyup needed)
+#
+  . ${SETTE_DIR}/all_functions.sh
+###############################################################
+#
+# set up mpp computing environment
+#
+#
+# Local settings. These settings are for a particular machine (the ALTIX ICE system at NOCS)
+# at a particular stage of that machine's evolution. This template file is provided for
+# illustration purposes only and will not work on any other machine. There should, however,
+# be sufficient similarity with other MPP platforms and batch systems for this example to provide
+# a useful guide for experienced users
+#
+  module load mpt/2.03
+  export MPT_HOME=/opt/sgi/mpt/mpt-2.03
+  export NC4_HOME=/fibre/omfman/NETCDF_PAR
+  export HD5_HOME=/fibre/omfman/NETCDF_PAR
+  export XIO_HOME=/fibre/omfman/XIOS
+  export SVN_HOME=/nerc/packages/subversion/v1.7.2
+  export FTN_LIB=/sw/Intel/fce/11.1.072/lib/intel64
+  export ICC_LIB=/sw/Intel/cce/11.1.072/lib/intel64
+#
+  echo Running on host `hostname`
+  echo Time is `date`
+  echo PBS job ID is $PBS_JOBID
+  echo This jobs runs on the following machines:
+  echo `cat $PBS_NODEFILE | uniq`
+# 
+# Create a machine file for MPI
+  cat $PBS_NODEFILE | uniq > host.file.$PBS_JOBID
+#
+  echo export LD_LIBRARY_PATH=${MPT_HOME}/lib:${ICC_LIB}:${FTN_LIB}:${NC4_HOME}/lib:${HD5_HOME}/lib:${SVN_HOME}/lib:${LD_LIBRARY_PATH}
+  export LD_LIBRARY_PATH=${MPT_HOME}/lib:${ICC_LIB}:${FTN_LIB}:${NC4_HOME}/lib:${HD5_HOME}/lib:${SVN_HOME}/lib:${LD_LIBRARY_PATH}
+# 
+  echo export PATH=${MPT_HOME}/bin:${SVN_HOME}/bin:$PATH
+  export PATH=${MPT_HOME}/bin:${SVN_HOME}/bin:$PATH
+#
+  export PSM_SHAREDPORTS=1
+  echo export MPI_PPN=4
+  echo export MPI_PPN_CLIST="2-3-6-7-0-1-4-5"
+  echo export OMP_NUM_THREADS=1 
+#
+# Don't remove neither change the following line
+# BODY
+#
+# Test specific settings. Do not hand edit these lines; the fcm_job.sh script will set these
+# (via sed operating on this template job file). Note that the number of compute nodes required
+# (half-populated on the NOCS ALTIX system) is also set by the fcm_job.sh on the PBS select
+# header line above.
+#
+# These variables are needed by post_test_tidyup function in all_functions.sh
+#
+  export INPUT_DIR=DEF_INPUT_DIR
+  export CONFIG_DIR=DEF_CONFIG_DIR
+  export NEMO_VALIDATION_DIR=DEF_NEMO_VALIDATION
+  export NEW_CONF=DEF_NEW_CONF
+  export CMP_NAM=DEF_CMP_NAM
+  export TEST_NAME=DEF_TEST_NAME
+  export EXE_DIR=DEF_EXE_DIR
+#
+# end of set up
+###############################################################
+#
+# change to the working directory 
+#
+# cd $PBS_O_WORKDIR
+  cd $EXE_DIR
+  echo Directory is `pwd`
+  if [ ! -f ./xios_server.exe ] && [ -f ${XIO_HOME}/bin/xios_server.exe ] 
+   then
+     cp ${XIO_HOME}/bin/xios_server.exe .
+  fi
+  if [ ! -f ./xios_server.exe ]
+   then
+     echo "./xios_server.exe not found"
+     echo "run aborted"
+     exit
+  fi
+#
+#
+#  Run the parallel MPI executable 
+#
+  echo "Running time ${MPT_HOME}/bin/mpiexec_mpt -np " $XIOCORES " ./xios_server.exe : -np " $OCEANCORES " ./opa"
+#
+  time ${MPT_HOME}/bin/mpiexec_mpt -np $XIOCORES ./xios_server.exe :  -np $OCEANCORES ./opa
+#
+  post_test_tidyup
+# END_BODY
+# Don't remove neither change the previous line
+  exit
