Oxford ARC compilation

The build uses NEMO 3.7/4.0 + XIOS 2.0 as the example. For installing other versions, extrapolate from the other notes.

Annoyingly (!) everything basically works out of the box because all the dependency modules have been built already! This has not been the usual experience I have with XIOS and NEMO…

Building NEMO and XIOS

Log on first using:

ssh [-X] phys????@arcus-b.arc.ox.ac.uk

On first login doing module list should show no modules; if there are then might want to do module purge just for safety. Doing module avail shows the list of modules available. I’m going to use the gcc one, and by doing

module load /netcdf-parallel/4.4__mvapich2__gcc

this loads NetCDF4 as well as its dependencies (which should be HDF5, gcc4.9.2 and the relevant mvapich); I added that line to ~/.bashrc so it loads from now on when logging in. Then I did

echo $LD_LIBRARY_PATH
> /system/software/arcus-b/lib/netcdf/4.4/mvapich2-2.1.0__gcc-4.9.2/lib:/system/software/arcus-b/lib/hdf5/1.8.12/mvapich2-2.1.0__gcc-4.9.2/lib ...

which tells me where the NetCDF and HDF5 libraries live. So for XIOS I do

cd $DATA # <--- this is the "work" directory (which is generically not ~/)
mkdir XIOS
cd XIOS
svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk@1322 xios-2.0
cd xios2.0/arch
cp arch-GCC_LINUX.env arch-GCC_ARC.env
cp arch-GCC_LINUX.fcm arch-GCC_ARC.fcm
cp arch-GCC_LINUX.path arch-GCC_ARC.path

with

# arch-GCC_ARC.env

export HDF5_INC_DIR=/system/software/arcus-b/lib/hdf5/1.8.12/mvapich2-2.1.0__gcc-4.9.2/include
export HDF5_LIB_DIR=/system/software/arcus-b/lib/hdf5/1.8.12/mvapich2-2.1.0__gcc-4.9.2/lib

export NETCDF_INC_DIR=/system/software/arcus-b/lib/netcdf/4.4/mvapich2-2.1.0__gcc-4.9.2/include
export NETCDF_LIB_DIR=/system/software/arcus-b/lib/netcdf/4.4/mvapich2-2.1.0__gcc-4.9.2/lib

and the other two as default. Running

cd ../
./make_xios --full --prod --arch HKUST_HPC2 -j4 |& tee compile_log.txt

seems to do the job. I think I did go into bld.cfg and changed src_netcdf to src_netcdf4 for safety; don’t remember needing this in ARCHER (did need it when doing a local compilation). If that doesn’t work consider adding CPPFLAGS and LDFLAGS before the ./make_xios command to force the program to look in the specified place.

NEMO is then built as follows:

cd $DATA
mkdir NEMO
cd NEMO
svn co http://forge.ipsl.jussieu.fr/nemo/svn/NEMO/trunk@8666 nemo3.7-8666
cd nemo3.7-8666/NEMOGCM/ARCH
cp OLD/arch-gfortran_linux.fcm ./arch-GCC_ARC.fcm

using

# arch-GCC_ARC.fcm
# generic gfortran compiler options for linux
# 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>

%XIOS_HOME           $DATA/XIOS/xios-2.0

%CPP                 cpp
%CPPFLAGS            -P -traditional

%XIOS_INC            -I%XIOS_HOME/inc
%XIOS_LIB            -L%XIOS_HOME/lib -lxios

%NCDF_INC            -I/system/software/arcus-b/lib/netcdf/4.4/mvapich2-2.1.0__gcc-4.9.2/include
%NCDF_LIB            -L/system/software/arcus-b/lib/netcdf/4.4/mvapich2-2.1.0__gcc-4.9.2/lib -lnetcdf -lnetcdff -lstdc++
%FC                  mpif90
%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -cpp -ffree-line-length-none
%FFLAGS              %FCFLAGS
%LD                  %FC
%LDFLAGS
%FPPFLAGS            -P -C -traditional
%AR                  ar
%ARFLAGS             -rs
%MK                  make
%USER_INC            %XIOS_INC %NCDF_INC
%USER_LIB            %XIOS_LIB %NCDF_LIB

followed by

cd ../CONFIG
./makenemo -r GYRE_PISCES -n GYRE_testing -m GCC_ARC -j0
nano GYRE_testing/cpp_GYRE_testing.fcm # (have key_top -> key_nosignedzero)
./makenemo -n GYRE_tesitng -m GCC_ARC -j4

and it should work. One more thing we will do is to make TOOLS/REBUILD_NEMO:

cd ../TOOLS
./maketools -n REBUILD_NEMO -m GCC_ARC

Running NEMO on the ARC

The system uses SLURM and the key commands are

  • sbatch [submit_nemo]: submits the job detailed in submit_nemo (see below)

  • scancel [job ID]: cancel the job

  • sinfo: check status of queues available

  • squeue -u $USER: check job info for $USER

sbatch could be used with arguments but I am going to have everything within submit_nemo itself. Check balance and budget account names with the mybalance command. Running sinfo shows the queue available is called compute. One thing to note is that ARC has 16 cores per node and this is reflected in the core/node request numbers.

Oxford ARC does have parallel NetCDF so I can use XIOS in detached mode. To do this I link xios_server.exe to the folder:

cd GYRE_testing/EXP00
ln -s $DATA/XIOS/xios2.0/bin/xios_server.exe .

Modify iodef.xml so that the user server boolean is true. Additionally I go into file_def_nemo.xml and swap out multiple_file at the top header to one_file, which then spits out a single NetCDF file. This however only works for the diagnostic files but not the restart files, so recombining the restart files we are going to call TOOLS/REBUILD_NEMO in the post-processing script.

The generic submission script I use (based on the one given on the NOCL page) is as follows (I have some ASCII art in there because I got bored at some point):

#!/bin/bash

# NOTE: Lines starting with "#SBATCH" are valid SLURM commands or statements,
#       while those starting with "#" and "##SBATCH" are comments.  Uncomment
#       "##SBATCH" line means to remove one # and start with #SBATCH to be a
#       SLURM command or statement.

#===============================================================
# DEFINE SOME JUNK FOR THE SUBMISSION (??? make this more flexible with e.g. queues?)
#===============================================================

#SBATCH -J gyre04       # job name
#SBATCH -o stdouterr    # output and error file name
#SBATCH -n 32           # total number of mpi tasks requested
#SBATCH -N 2            # total number of nodes requested
#SBATCH -p compute      # queue (partition) -- standard, development, etc.
#SBATCH -t 12:00:00     # maximum runtime

# Enable email notificaitons when job begins and ends, uncomment if you need it
##SBATCH --mail-user=user_name@ust.hk #Update your email address
##SBATCH --mail-type=begin
##SBATCH --mail-type=end

# Setup runtime environment if necessary
module purge
module load netcdf-parallel/4.4__mvapich2__gcc

#===============================================================
# LAUNCH JOB
#===============================================================

echo " _ __   ___ _ __ ___   ___         "
echo "| '_ \ / _ \ '_ ' _ \ / _ \        "
echo "| | | |  __/ | | | | | (_) |       "
echo "|_| |_|\___|_| |_| |_|\___/  v3.7  "

# Go to the job submission directory and run your application
cd /data/phys-geometric/phys1342/NEMO/nemo3.7-8666/NEMOGCM/CONFIG/GYRE_testing/EXP00
mpirun -n 2 ./xios_server.exe : -n 30 ./opa

#===============================================================
# POSTPROCESSING
#===============================================================

# kills the daisy chain if there are errors

if grep -q 'E R R O R' ocean.output ; then

  echo "E R R O R found, exiting..."
  echo "  ___ _ __ _ __ ___  _ __  "
  echo " / _ \ '__| '__/ _ \| '__| "
  echo "|  __/ |  | | | (_) | |    "
  echo " \___|_|  |_|  \___/|_|    "
  echo "check out ocean.output or stdouterr to see what the deal is "

  exit
else
  echo "going into postprocessing stage..."
  # cleans up files, makes restarts, moves files, resubmits this pbs

  bash ./postprocess.sh >& cleanup.log
  exit
fi

The ratio of XIOScore to NEMOcore I never found to lead to major differences for the size of runs I do (not larger than 300 cores); vaguely remember reading somewhere that XIOScore hovering between 5 to 10 per cent of NEMOcore is ok.

The following post-processing script requires a few prepping (I make no apologies for the bad code and the script being fickle; feel free to modify as you see fit):

  • copying the nn_date0 line into namelist_cfg from say namelist_ref if it doesn’t exist already, because the time-stamps are modified by modifying nn_date0

  • do a search in namelist_cfg and make sure there is only ever one mention of nn_date0 (otherwise it grabs the wrong lines)

  • nn_date0 should not begin with zeros (e.g. 10101 rather than 010101 in yymmdd)

  • in the experiment folder, do mkdir RESTARTS OUTPUTS (otherwise there is no folder to copy into)

The postprocess.sh I cooked up is here:

#!/bin/bash
#! postprocess.sh
#! Script to clean up the NEMO outputs

export BASE_DIR=$DATA/NEMO/nemo3.7-8666/NEMOGCM/
export MODEL=GYRE
export NUM_CPU=30

# time-stamp increment, yymmdd
export DATE_INC=100000

# when to stop the daisy chaining, yymmdd
export THRESH=10

# error catching (only when restart files etc cannot be copied or made)
export ERR_CATCH=0

########################################################
# 0) recombine files to one netcdf (restarts and/or outputs)
# restarts: extract the restart file time-step stamp
#              based on the *0000.nc restart which should (!) always exist
#           rebuild the restart file in the submission directory
# outputs:  put them in manually and just do a grab
#           this assumes only files at the current time-stamp is there,
#              otherwise it will bug out as it grabs wrong files
########################################################

# restart files
export RES_TIMESTAMP=$(echo $(ls -d ${MODEL}_*_restart_0000.nc) | awk -F _ '{print $2 }')

$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${RES_TIMESTAMP}_restart $NUM_CPU
if (($? > 0)); then
  ERR_CATCH=$((ERR_CATCH + 1))
  echo "  ERR: making the restart file in the folder"
fi
##$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${RES_TIMESTAMP}_restart_ice $NUM_CPU

# output files (assumes a grid_T always exists)
#export OUT_FREQ=$(echo $(ls -d ${MODEL}_*_grid_T_0000.nc) | awk -F _ '{print $2 }')
#export OUT_START=$(echo $(ls -d ${MODEL}_*_grid_T_0000.nc) | awk -F _ '{print $3 }')
#export OUT_END=$(echo $(ls -d ${MODEL}_*_grid_T_0000.nc) | awk -F _ '{print $4 }')

#$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${OUT_FREQ}_${OUT_START}_${OUT_END}_grid_T $NUM_CPU
#$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${OUT_FREQ}_${OUT_START}_${OUT_END}_grid_U $NUM_CPU
#$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${OUT_FREQ}_${OUT_START}_${OUT_END}_grid_V $NUM_CPU
#$BASE_DIR/TOOLS/REBUILD_NEMO/rebuild_nemo ${MODEL}_${OUT_FREQ}_${OUT_START}_${OUT_END}_grid_W $NUM_CPU

# add more things in here if output freqs are different etc

########################################################
# 1) pull out some variables to modify namelist file
########################################################

# pull the number out
# add the increment to it for new date
# subtract appropriately to get the date stamp
#   (e.g. 110101 - 8871 = 101230) and bulk out zeros

export OLD_DATE_STR=$(grep -ri "nn_date0" namelist_cfg)
export OLD_DATE_NUM=$(echo ${OLD_DATE_STR} | sed -e 's/[^0-9 ]//g' | awk '{print $NF}')
export NEW_DATE_NUM=$((OLD_DATE_NUM + DATE_INC))

# 8871 for 30 days a month (so the RES_STAMP=yyyy1230)
# otherwise do 8870        (so the RES_STAMP=yyyy1231)
# do something else for other time units
export RES_STAMP=$(printf %08d $((NEW_DATE_NUM - 8871)))

########################################################
# 2) move files around and tidy up
########################################################

cp -pv ${MODEL}_${RES_TIMESTAMP}_restart.nc ./RESTARTS/${MODEL}_${RES_STAMP}_restart.nc
cp -pv ./output.namelist.dyn ./OUTPUTS/output.namelist.dyn.${RES_STAMP}
#cp -pv ${MODEL}_${RES_TIMESTAMP}_restart_ice.nc ./RESTARTS/${MODEL}_${RES_STAMP}_restart_ice.nc
#cp -pv ./output.namelist.ice ./OUTPUTS/output.namelist.ice.${RES_STAMP}
cp -pv ./ocean.output ./OUTPUTS/ocean.output.${RES_STAMP}
cp -pv ./solver.stat ./OUTPUTS/solver.stat.${RES_STAMP}
cp -pv ./stdouterr ./OUTPUTS/stdouterr.${RES_STAMP}
cp -pv ./namelist_cfg ./OUTPUTS/namelist_cfg.${RES_STAMP}

#cp -pv ./volume_transport ./OUTPUTS/volume_transport.${RES_STAMP}
#cp -pv ./salt_transport ./OUTPUTS/salt_transport.${RES_STAMP}
#cp -pv ./heat_transport ./OUTPUTS/heat_transport.${RES_STAMP}

rm -v ${MODEL}_${RES_TIMESTAMP}_restart*
rm -v restart.nc
#rm -v restart_ice.nc
rm -v ${MODEL}_*_????.nc
mv ${MODEL}*.nc ./OUTPUTS

cp -pv RESTARTS/${MODEL}_${RES_STAMP}_restart.nc ./restart.nc
if (($? > 0)); then
  ERR_CATCH=$((ERR_CATCH + 1))
  echo "  ERR: copying restart file into folder"
fi

#cp -pv RESTARTS/${MODEL}_${RES_STAMP}_restart_ice.nc ./restart_ice.nc
#if (($? > 0)); then
#  ERR_CATCH=$((ERR_CATCH + 1))
#  echo "  ERR: copying restart_ice file into folder"
#fi

########################################################
# 3) if all good, then modify namelist_cfg and resbumit
########################################################

if (($ERR_CATCH > 0)) || ((${NEW_DATE_NUM} > $THRESH)); then
  if (($ERR_CATCH > 0)); then
    echo " "
    echo " "
    echo " "
    echo "ERR: caught a non-zero exit status, check cleanup.log for what the deal was"
    echo "ERR: caught a non-zero exit status, check cleanup.log for what the deal was"
  else
    echo "OK: grabbed time stamp ${NEW_DATE_NUM} larger than threshold ${THRESH}, breaking..."
    echo "OK: grabbed time stamp ${NEW_DATE_NUM} larger than threshold ${THRESH}, breaking..."
    # WARNING: this assumes that OLD_DATE_NUM is the only number within the file, which should
    #          really be true
    sed -i "s/${OLD_DATE_NUM}/${NEW_DATE_NUM}/g" namelist_cfg
  fi
  echo " "
  echo " "
  echo " "
  echo " "
  echo " ... a wild Totoro appeared and blocked your resubmission!"
  echo "         ,--'''',--.__,---[],-------._                               "
  echo "       ,'   __,'            \         \--''''''==;-                  "
  echo "     ,' _,-'  '/---.___     \       ___\   ,-'','                    "
  echo "    /,-'      / ;. ,.--'-.__\  _,-'' ,| ','   /                      "
  echo "   /''''''-._/,-|:\       []\,' '''-/:;-. '. /                       "
  echo "             '  ;:::      ||       /:,;  '-.\                        "
  echo "                =.,'__,---||-.____',.=                               "
  echo "                =(:\_     ||__    ):)=                               "
  echo "               ,'::::'----||::'--':::'._                             "
  echo "             ,':::::::::::||::::::::::::'.                           "
  echo "    .__     ;:::.-.:::::__||___:::::.-.:::\     __,                  "
  echo "       '''-;:::( O )::::>_|| _<::::( O )::::-'''                     "
  echo "   =======;:::::'-':::::::||':::::::'-':::::\=======                 "
  echo "    ,--'';:::_____________||______________::::''----.          , ,   "
  echo "         ; ::'._(    |    |||     |   )_,'::::\_,,,,,,,,,,____/,'_,  "
  echo "       ,;    :::'--._|____[]|_____|_.-'::::::::::::::::::::::::);_   "
  echo "      ;/ /      :::::::::,||,:::::::::::::::::::::::::::::::::::/    "
  echo "     /; ''''''----------/,'/,__,,,,,____:::::::::::::::::::::,'      "
  echo "     ;/                :);/|_;| ,--.. . '''-.:::::::::::::_,'        "
  echo "    /;                :::):__,'//''\\. ,--.. \:::,:::::_,'           "
  echo "   ;/              :::::/ . . . . . . //''\\. \::':__,'              "
  echo "   ;/          :::::::,' . . . . . . . . . . .:'::\                  "
  echo "   ';      :::::::__,'. ,--.. . .,--. . . . . .:'::'                 "
  echo "   ';   __,..--'''-. . //''\\. .//''\\ . ,--.. :':::'                "
  echo "   ;    /  \\ .//''\\ . . . . . . . . . //''\\. :'::'                "
  echo "   ;   /       . . . . . . . . . . . . . . . . .:'::'                "
  echo "   ;   (          . . . . . . . . . . . . . . . ;:::'                "
  echo "   ,:  ;,            . . . . . . . . . . . . . ;':::'                "
  echo "   ,:  ;,             . . . . . . . . . . . . .;':::'                "
  echo "   ,:   ;,             . . . . . . . . . . . . ;'::;'                "
  echo "     :   ;             . . . . . . . . . . . ,':::;                  "
  echo "      :   '.          . . . . . . . .. . . .,':::;'                  "
  echo "       :    '.       . . . . . . . . . . . ;::::;'                   "
  echo "        '.    '-.   . . . . . . . . . . ,-'::::;                     "
  echo "          ':_    ''--..___________..--'':::::;''                     "
  echo "             '._::,.:,.:,:_ctr_:,:,.::,.:_;''                        "
  echo "________________''\/'\/\/''''''\/'\/''\/'____________________________"

else
# WARNING: this assumes that OLD_DATE_NUM is the only number within the file, which should
  #          really be true
  sed -i "s/${OLD_DATE_NUM}/${NEW_DATE_NUM}/g" namelist_cfg

  echo "grabbed time stamp ${NEW_DATE_NUM} smaller than threshold ${THRESH}, resubmitting..."
  echo "grabbed time stamp ${NEW_DATE_NUM} smaller than threshold ${THRESH}, resubmitting..."
  echo "grabbed time stamp ${NEW_DATE_NUM} smaller than threshold ${THRESH}, resubmitting..."
  echo "grabbed time stamp ${NEW_DATE_NUM} smaller than threshold ${THRESH}, resubmitting..."
  echo " "
  echo "OK: ...and here is Christopher resbumitting the job for you......"
  echo "                  ,-.____,-.          "
  echo "                  /   ..   \          "
  echo "                 /_        _\         "
  echo "                |'o'      'o'|        "
  echo "               / ____________ \       "
  echo "             , ,'    '--'    '. .     "
  echo "            _| |              | |_    "
  echo "          /  ' '              ' '  \  "
  echo "         (    ',',__________.','    ) "
  echo "          \_    ' ._______, '     _/  "
  echo "             |                  |     "
  echo "             |    ,-.    ,-.    |     "
  echo "              \      ).,(      /      "
  echo "         gpyy   \___/    \___/        "
  sbatch submit_nemo

fi

exit

The output recombination steps have bene commented out because ARC does have parallel NetCDF4 and so the one_file option in field_def_nemo.xml already takes care of the outputs.