added instructions and scripts for manual compilation

MANUAL_COMPILATION.md

@@ -0,0 +1,52 @@
+# COMPILE NEMO MANUALLY
+
+NEMO and its dependencies are built and installed using spack where possible.
+
+The steps below are described in the order in which they need to be completed. Some need to be run once, and others will be used regularly, depending on your workflow.
+
+## Step 1- Setting compiler, versions etc
+
+The compiler to be used, and versions of the compiler and dependencies including PSyclone, HDF5, netCDF, BOOST are defined in `set_version.sh`. Directories to be used throughout the workflow are set in `set_directories.sh`. In general, all of steps 2 owards will need to repeated following a change to these files.
+
+The number of cores, sockets and other resources associated with a node are returned by `platform_info.sh`. Values are presently hard-coded for the ISAMBARD-AI nodes.
+
+## Step 2- Building and using the spack environment
+
+### ENSURE THAT SPACK HAS GCC AVAILABLE TO COMPILE NVHPC
+
+The script `build_spack.sh` installs the dependencies needed for building/running NEMO. In general this should only need to be run once per user for each compiler/version. This may take a long time to run if the compiler itself needs to be downloaded and installed.
+
+Some spack external package configurations are available in the spack-configs (for archer2 on spack v0.23 and isambard-ai on spack v1.1.1 latest)
+
+The script will ultimately create a spack environment named `nemo_$COMPILER_$VERSION`. This can be activated using `spack env activate nemo_$COMPILER_$VERSION`, noting this is done automatically by other scripts listed below.
+
+This script does not take any arguments or have any user-editable parts.
+
+## Step 3- Building XIOS
+
+Building XIOS via spack doesn not work at the time of writing, so it is built from source using `build.xios.sh`. In general this should only need to be run once per user for each compiler/version.
+
+NOTE- this script installs a specific revision of the XIOS trunk, defined in `set_version.sh` and `head` should be considered mutable.
+
+This script does not take any arguments or have any user-editable parts.
+
+## Step 4- Building PSyclone
+`build_psyclone.sh` clones (June 26 2025 version for now) psyclone repository and installs psyclone.
+
+## Step 5- Building NEMO
+
+`build_nemo.sh` clones a hard-coded repository and builds nemo itself.
+
+Use argument $1 as clean to create a fresh build instead. This script also contains tranformation and config selection option at the start
+
+NOTE: It is also possible to replace the MPI compiler with `psyclonefc` wrapper. Instructions on how to do this are in the [PSyclone repository] (https://github.com/stfc/PSyclone/tree/single_nemo_script/examples/nemo/scripts#set-up-environment-variables)
+
+## Step 6- Running NEMO
+
+The supplied `prep_nemo_input_example.sh` does not actually run nemo but rather prepares the input for a specific hard-coded example and generates a `sbatch` script.
+
+This script has number of MPI processes IPROC, JPROC.
+
+## Scripts in etc
+
+The `etc` directory contains scripts that users should not usually need to run directly. These set versions, directories, node resources etc, and apply various fixes as part of the build process.

README.md

@@ -3,16 +3,19 @@ This repository contains the spack package to build and install NEMO (Nucleus fo
 
 ![GitHub CI](https://github.com/ukri-bench/nemo/actions/workflows/ci-nemo.yml/badge.svg)
 
-## Recommended steps:
+## Manual compilation instructions
+Read [MANUAL_COMPILATION.md](MANUAL_COMPILATION.md)
+
+## Spack instructions:
 ### Copy spack configuration files
 Copy all files in spack-configs/yoursystem to .spack directory, check `environment.sh` for the location of `.spack`
 ### Install spack
-Spack v1 (latest) has changed how it handles compilers, the changes have been reflected in `spack-configs/archer2/packages.yaml`. Please install the latest spack version to use them.
+Spack v1 (latest) has changed how it handles compilers, the changes have been reflected in `spack-configs/isambard-ai/packages.yaml`. Please install the latest spack version to use them.
 ~~Install spack v0.23.1(recommended) or older. Spack v1 changed how it manages compilers inside `compilers.yaml` which breaks current config files.~~
 ### Modify the environment
 Modify `environment.sh` to set paths for your spack and temp directories. It is recommended that the temporary directory must be something fast and accessible since it will be used for spack build caches. Load this file with `source environment.sh` before proceeding.
 ### Add the repo
- Spack can add external repos with `spack repo add "path"`.
+ `spack repo add https://github.com/ukri-bench/spack-packages`.
 ### Install NEMO
 `spack install nemo%cce +mpi config=ORCA2_ICE_PISCES` or with a compiler of your choice.
 ### Load NEMO and build your run directory
@@ -30,6 +33,7 @@ $ nemo-wrapper -h
   --extra-paths paths   Extra paths to link in the run directory (colon separated)
   +stats                Enable run.stat
   +timings              Enable NEMO timings in the timing.output file (requires: gnuplot)
+  +icebergs             Enable icebergs
   -h, --help            Show this help message and exit
 
 ```

build_nemo.sh

@@ -0,0 +1,255 @@
+#!/usr/bin/env bash
+
+# Copyright 2026 Aditya Sadawarte and Kaan Olgu
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+## Builds Nemo
+
+ORIGIN_DIR=$(pwd)
+
+# Get required versions and directories
+. ./etc/set_versions.sh
+. ./etc/set_directories.sh
+
+# Initialise spack
+. $SPACK_PATH/share/spack/setup-env.sh
+
+# Load the relevant environment previously created by build_spack,sh
+spack env activate ${ENVDIR}/nemo_${COMPILER}_${COMPVERP}
+
+CPREPROC=$(which cpp)
+if [[ ${COMPILER} == "oneapi" ]]; then
+	FCOMPILER=$(which mpiifx)
+	LINKER=$(which mpiifx)
+else
+	FCOMPILER=$(which mpif90)
+	LINKER=$(which mpif90)
+fi
+
+H5DIR=$(spack location -i hdf5%$COMPILER@${COMPVER})
+NCDIR=$(spack location -i netcdf-c%$COMPILER@${COMPVER})
+NFDIR=$(spack location -i netcdf-fortran%$COMPILER@${COMPVER})
+
+export PYTHONPATH=${PSYDIR}/examples/nemo/scripts:${PYTHONPATH}
+
+if [[ ! -d $NEMO_ROOT ]]; then
+	git clone https://forge.nemo-ocean.eu/nemo/nemo.git ${NEMO_ROOT}
+	cd ${NEMO_ROOT}
+	git switch --detach ${NMVER}
+fi
+
+# User settings
+#CONFIG_SRC='GOSI10p0.0_like_eORCA1'        # Name of the source configuration
+CONFIG_SRC='ORCA2_ICE_PISCES'        # Name of the source configuration
+CONFIG='BLDCFG'       # Name of the configuration to be built from ${CONFIG_SRC}
+#TRANS='omp_gpu_trans'     # Unset or comment for no tranform
+VERSION=5.0             # NEMO version
+
+INPUT_DIR=              # Path to NEMO input files for the configuration (leave blank if no files required)
+NEMO_USR_SRC_DIRS=()    # Directories containing extra NEMO source files (will be copied to source configuration MY_SRC directory)
+NEMO_USR_CFG_DIRS=()    # Directories containing extra NEMO configuration files (replacement namelist_cfg, etc)
+ARCH_EXTRA=             # Extra parameters to the arch file (required for cce)
+
+USE_MPI=yes             # Compile for use with MPI?
+USE_XIOS=no            # Compile for use with XIOS?
+BUILD=yes               # Perform the NEMO build? If "no", only link required runtime files
+USE_ICE=no
+
+# For psyclone transformations
+cp ${ORIGIN_DIR}/etc/sct_psyclone.sh ${NEMO_ROOT}/mk/ && chmod +x ${NEMO_ROOT}/mk/sct_psyclone.sh
+cp ${ORIGIN_DIR}/etc/makenemo ${NEMO_ROOT} && chmod +x ${NEMO_ROOT}/makenemo
+
+if [[ ${COMPILER} == 'nvhpc' ]]; then
+	FCFLAGS="-i4 -Mr8 -Mnovect -Mflushz -Minline -Mnofma -O2 -gopt -traceback -march=${CPU_ARCH}"
+	LDFLAGS="-i4 -Mr8 -Mnofma -march=${CPU_ARCH}"
+	if [[ ${TRANS} == 'omp_cpu_trans' ]]; then
+		FCFLAGS+=' -mp'
+		LDFLAGS+=' -mp'
+	elif [[ ${TRANS} == 'omp_gpu_trans' ]]; then
+		if [[ ${CUDA_ARCH_VALUE} -ge 90 ]]; then
+			FCFLAGS+=' -mp=gpu -gpu=mem:unified:nomanaged,math_uniform -Minfo=mp'
+			LDFLAGS+=' -mp=gpu -gpu=mem:unified:nomanaged,math_uniform -Minfo=mp'
+		else
+			FCFLAGS+=' -mp=gpu -gpu=mem:managed,math_uniform -Minfo=mp'
+			LDFLAGS+=' -mp=gpu -gpu=mem:managed,math_uniform -Minfo=mp'
+		fi
+	fi
+elif [[ ${COMPILER} == 'gcc' ]]; then
+	FCFLAGS="-fdefault-real-8 -O2 -funroll-all-loops -fcray-pointer -ffree-line-length-none -mcpu=${CPU_ARCH}"
+	LDFLAGS="-fdefault-real-8 -mcpu=${CPU_ARCH}"
+	if [[ ${TRANS} == 'omp_cpu_trans' ]]; then
+		FCFLAGS+=' -fopenmp'
+		LDFLAGS+=' -fopenmp'
+	elif [[ ${TRANS} == 'omp_gpu_trans' ]]; then
+		FCFLAGS+=' -fopenmp -foffload=nvptx-none'
+		LDFLAGS+=' -fopenmp -foffload=nvptx-none'
+	fi
+elif [[ ${COMPILER} == 'oneapi' ]]; then
+	FCFLAGS="-i4 -r8 -O2 -fp-model strict -xHost -fno-alias -march=${CPU_ARCH}"
+	LDFLAGS="-i4 -r8 -march=${CPU_ARCH}"
+	if [[ ${TRANS} == 'omp_cpu_trans' ]]; then
+		FCFLAGS+=' -fiopenmp'
+		LDFLAGS+=' -fiopenmp'
+	elif [[ ${TRANS} == 'omp_gpu_trans' ]]; then
+		FCFLAGS+=' -fiopenmp -fopenmp-targets=${GPU_ARCH}'
+		LDFLAGS+=' -fiopenmp -fopenmp-targets=${GPU_ARCH}'
+	fi
+elif [[ ${COMPILER} == 'cce' ]]; then
+	FCFLAGS="-em -s integer32 -s real64 -O2 -hvector_classic -hflex_mp=intolerant -N1023 -M878 -eF"
+	LDFLAGS="-eF"
+	ARCH_EXTRA="bld::tool::fc_modsearch -J"
+fi
+
+# Check source config exists
+if [[ -d ${NEMO_ROOT}/cfgs/${CONFIG_SRC} ]] ; then
+    CONFIG_ROOT=${NEMO_ROOT}/cfgs
+    MAKENEMO_CFG=yes
+elif [[ -d ${NEMO_ROOT}/tests/${CONFIG_SRC} ]] ; then
+    CONFIG_ROOT=${NEMO_ROOT}/tests
+    MAKENEMO_TST=yes
+else
+    echo "No such source configuration \"${CONFIG_SRC}\""
+    exit 1
+fi
+
+if [[ $1 == 'clean' ]]; then
+	rm -rf ${CONFIG_ROOT}/${CONFIG}
+fi
+
+ARCH=fort
+export XIOS_PATH=${XIOSDIR}
+
+# Let's generate our arch file
+cat << EOF > ${NEMO_ROOT}/arch/arch-fort.fcm
+%NCDFF_HOME          ${NFDIR}
+%NCDFC_HOME          ${NCDIR}
+%HDF5_HOME           ${H5DIR}
+%XIOS_HOME           ${XIOSDIR}
+%PSYCLONE_HOME       ${PSYDIR}
+
+%NCDF_INC            -I%NCDFF_HOME/include
+%NCDF_LIB            -L%NCDFF_HOME/lib -lnetcdff -L%NCDFC_HOME/lib -lnetcdf -L%HDF5_HOME/lib -lhdf5_hl -lhdf5 -lhdf5
+%XIOS_INC            -I%XIOS_HOME/inc
+%XIOS_LIB            -L%XIOS_HOME/lib -lxios -lstdc++
+
+%CPP	             $CPREPROC -Dkey_nosignedzero
+%FC                  $FCOMPILER
+%PROD_FCFLAGS        $FCFLAGS
+%DEBUG_FCFLAGS       -O0 -g -Minfo=all -i4 -r8
+%FFLAGS              
+%LD                  $FCOMPILER
+%LDFLAGS             $LDFLAGS -Wl,-rpath=%HDF5_HOME/lib -Wl,-rpath=%NCDFF_HOME/lib -Wl,-rpath=%XIOS_HOME/lib
+%FPPFLAGS            -P -traditional
+%AR                  ar
+%ARFLAGS             -rs
+%MK                  gmake
+%USER_INC            %XIOS_INC %NCDF_INC
+%USER_LIB            %XIOS_LIB %NCDF_LIB
+%DEBUG_FCFLAGS       -O0 -i4 -r8 -traceback
+${ARCH_EXTRA}
+EOF
+
+NEMO_MY_SRC=${CONFIG_ROOT}/${CONFIG_SRC}/MY_SRC     # Path to the MY_SRC directory of the source configuration
+RUN_DIR=${CONFIG_ROOT}/${CONFIG}/EXP00              # Path to the runtime directory of the built configuration
+
+# XIOS settings
+case ${USE_XIOS} in
+    'yes')
+        [ -z ${XIOS_PATH} ] && echo "XIOS_PATH must be defined if 'USE_XIOS=yes'" && exit 1
+        XIOS_EXE=${XIOS_PATH}/bin/xios_server.exe
+        [ ! -f ${XIOS_EXE} ] && echo "No XIOS executable found at \"${XIOS_EXE}\"" && exit 1
+	[ "${XIOSVER}" -eq 3 ] && DEL_KEYS+=(key_xios)
+	[ "${XIOSVER}" -eq 3 ] && ADD_KEYS+=(key_xios3)
+        ;;
+    'no')
+        DEL_KEYS+=(key_xios key_iomput)
+        ;;
+esac
+
+# MPI settings
+if [[ ${USE_MPI} == 'no' ]] ; then
+    case ${VERSION} in
+        4.2*|5.0*)
+            ADD_KEYS+=(key_mpi_off)
+            ;;
+        4.0*)
+            DEL_KEYS+=(key_mpp_mpi)
+            ;;
+    esac
+fi
+
+if [[ ${ARCH} =~ 'nvfortran' ]] ; then
+            ADD_KEYS+=(key_nosignedzero)
+fi
+
+if [[ ${USE_ICE} == 'no' ]] ; then
+  DEL_KEYS+=(key_si3)
+fi
+
+if [[ ${CONFIG_SRC} == "ORCA2_ICE_PISCES" ]]; then
+  DEL_KEYS+=(key_top)
+fi
+
+# Build NEMO executable
+if [[ ${BUILD} == "yes" ]] ; then
+    # Copy user src files to MY_SRC
+    [[ ! -z ${NEMO_USR_SRC_DIRS} && ! -d ${NEMO_MY_SRC} ]] && mkdir -p ${NEMO_MY_SRC}
+    for d in ${NEMO_USR_SRC_DIRS[*]} ; do
+        if [ -d ${d} ] ; then
+            for i in $(find ${d} -maxdepth 1 -type f) ; do
+                cp -v ${i} ${NEMO_MY_SRC}
+            done
+        fi
+    done
+
+    # Run build
+    cd ${NEMO_ROOT}
+    echo -e "
+               ${MAKENEMO_CFG:+-r ${CONFIG_SRC}} ${MAKENEMO_TST:+-a ${CONFIG_SRC}} -n ${CONFIG}
+               "
+    ./makenemo -j $NCPUS \
+               -m ${ARCH} ${TRANS:+-p ${PSYDIR}/examples/nemo/scripts/$TRANS.py} \
+               ${MAKENEMO_CFG:+-r ${CONFIG_SRC}} ${MAKENEMO_TST:+-a ${CONFIG_SRC}} -n ${CONFIG} \
+               ${DEL_KEYS:+del_key "${DEL_KEYS[*]}"} ${ADD_KEYS:+add_key "${ADD_KEYS[*]}"}
+
+fi
+
+echo -e "STAGE 2 COMPLETED!"
+
+
+# Link runtime files
+if [ -d ${RUN_DIR} ] ; then
+    cd ${RUN_DIR}
+
+    # Input files
+    if [[ ! -z ${INPUT_DIR} ]] ; then
+        [ ! -d ${INPUT_DIR} ] && echo "No such input file directory \"${INPUT_DIR}\"" && exit 1
+        for i in ${INPUT_DIR}/* ; do
+            [ ! -f $(basename ${i}) ] && ln -sv ${i}
+        done
+    fi
+
+    # XIOS executable
+    if [[ ${USE_XIOS} == "yes" ]] ; then
+        [ ! -f $(basename ${XIOS_EXE}) ] && ln -sv ${XIOS_EXE}
+    fi
+
+    # User cfg files
+    for d in ${NEMO_USR_CFG_DIRS[*]} ; do
+        if [ -d ${d} ] ; then
+            for i in $(find ${d} -maxdepth 1 -type f) ; do
+                ln -sfv ${i}
+            done
+        fi
+    done
+else
+    echo "No such run directory ${RUN_DIR}"
+    exit 1
+fi
+echo -e "STAGE 3 COMPLETED!"
+
+echo Put extract the tarball to...
+pwd
+
+

build_psyclone.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+# Copyright 2026 Aditya Sadawarte and Kaan Olgu
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+## Builds XIOS
+
+
+# Get required versions and directories
+. ./etc/set_versions.sh
+. ./etc/set_directories.sh
+
+# Initialise spack
+. $SPACK_PATH/share/spack/setup-env.sh 
+
+# Load the relevant environment previously created by build_spack,sh
+spack env activate ${ENVDIR}/nemo_${COMPILER}_${COMPVERP}
+
+# Check out PSyclone
+rm -rf ${PSYDIR}
+git clone https://github.com/stfc/PSyclone.git ${PSYDIR}
+cd ${PSYDIR}
+
+#
+git checkout nemo_v5
+
+# install
+python -m pip install .
+