Spin-up Runs¶

This section documents the workflows and results of a series of runs that were done to spin up the model to produce restart files that are representative of state of the Salish Sea over a 12 month period. The spin-up runs span the period from 12-Sep-2002 to 31-Dec-2003, with the last 12 months of that period providing the spun-up restart files. Those restart files can be used as initial conditions for research runs in other years.

The spin-up run results are stored in /ocean/dlatorne/MEOPAR/SalishSea/results/spin-up/. Directory names there indicate the date range of the run results that they contain; e.g. 1jan30jan/ contains the results of the 30 day 1-Jan-2003 to 30-Jan-2003 run. The restart files contained in the run directories have the name pattern SalishSea_dddddddd_restart.nc, where dddddddd is the number of time steps after 00:00 on 16-Sep-2002 (left padded with zeros). The model time step used for spin-up was 50 seconds. So, SalishSea_00069120_restart.nc would contain a snapshot of the model state at 00:00 on 26-Oct-2002 (69120 time-steps / (86400 s/day / 50 s/time-step) = 40 days).

Spin-up Sections¶

16-Sep-2002 to 21-Sep-2002¶

The first 6 days of spin-up were run on salish 1 day at a time. The lateral turbulent viscosity (NEMO namdyn_ldf namelist variable rn_ahm_0_lap) was intially set to 80 $$m^2/s$$ and reduced by 5 $$m^2/s$$ each day to 55 $$m^2/s$$ on day 6. That was done to stabilize the model as the initial boundary condition values (especially deep salinity) propogated through the moderate, uniform initial stratification that was set for the entire domain.

Note

These runs have nn_date0 set to the day for which the calculations are being done, not the day on which nn_it000 is 1 (see Value and Use of nn_date0). So, the tidal forcing is inconsistent. This does not invalidate these runs as part of spin-up because they are early in the spin-up, and the objective of spin-up is temperature, salinity, and velocity fields, not tides.

22-Sep-2002¶

After the nn_date0 issue was discovered 22-Sep was rerun with the following changes:

1. Viscosity was set to 55 $$m^2/s$$

2. nn_date0 was set to 20020916 so that tides were consistent with time in the spin-up. That means that there is a jump in the tidal forcing at the beginning of this run.

23-Sep-2002 to 25-Oct-2002¶

The next days of spin-up were run with the lateral turbulent viscosity (NEMO namdyn_ldf namelist variable rn_ahm_0_lap) set to as low as possible but high enough that the code did not blow up. The maximum value used was 55 $$m^2/s$$. This was done to to try to avoid too much Juan de Fuca deep water from reaching the bottom of the Strait of Georgia as happened in a 10d spin-up run started on 23-Sep. The fresh water in San Juan needs to be flushed to allow enough pre-mixing there. Harmonics for the M2 and K1 tides were calculated over the entire duration of this run with a resolution of 9 time steps (450 seconds). The results during this period also include sea surface height at selected locations for analysis of storm surges, and sea surface height and profiles of temperature, salinity, and u and v velocity components at 6 points along the thalweg and at a location in the Fraser River plume.

26-Oct-2002 –¶

Lack of stability in the previous runs and the continuous need to increase viscosity lead to an investigation of stability. It was determined that the viscosity was too high (currents in the SoG were smaller than observed), and the time step was too large for a vertical CFL condition. Reducing the time step (and reducing the viscosity) led o stable run of 26-Oct and onwards.

31-Oct-2002 –¶

Northern boundary was opened using tides (all 8 constituents) and seasonal T&S (based on Thomson and Huggett paper).

20-Dec-2002 –¶

Error in phase of northern boundary constituents was found and corrected (all 8 constituents).

10-Feb-2003 –¶

Error in the barotropic velocities at the western boundary was found and corrected. The length of the arrays needs to be carefully matched or ssh contaminates the velocities.

28-Sep-2003 –¶

Our northern cross-section is bigger than the cross-section where Thomson & Huggett measured their currents. Thus our flux in is too large. We corrected the K1 tides by the estimated amount 25% and the M2 tides by twice this to better agree with observations.

The Runs

Dates

dt s

Viscosity $$m^2/s$$

EVD $$m^2/s$$

Status

Platform

Note

Sep 23

50

50

100

blew up off Pender

Salish

Sep 23

50

55

100

complete

Salish

Sep 24

50

50

100

complete

Salish

Sep 25

50

45

100

complete

Salish

Sep 26

50

40

100

complete

Salish

Sep 27

50

35

100

complete

Salish

Sep 28

50

30

100

complete

Salish

Sep 29

50

25

100

complete

Salish

Sep 30

50

20

100

blew up off Stuart

Salish

Sep 30

50

25

100

blew up off Pender

Salish

Sep 30

50

30

100

complete

Salish

Oct 1-2

50

25

100

blew up BP Mouth

Salish

Oct 1

50

30

100

complete

Salish

Oct 2-3

50

30

100

complete

Salish

Oct 4-5

50

30

100

blew up off Stuart

Salish

Oct 4-5

50

35

100

complete

Salish

Oct 6-9

50

35

100

blew up BP Mouth

Jasper

Oct 6-7

50

40

100

complete

Jasper

first 2 days of 4

Oct 8-9

50

40

100

blew up NaN

Jasper

last 2 days of 4

Oct 8-9

50

45

100

complete

Jasper

first 2 days of 4

Oct 10-11

50

45

100

blew up off Pender

Jasper

last 2 days of 4

Oct 10-13

50

50

100

blew up off San J.

Jasper

Oct 10-13

50

50

150

complete

Jasper

Oct 14-17

50

50

150

complete

Jasper

first 4 days of 10

Oct 18-23

50

50

150

blew up off Pender

Jasper

last 6 days of 10

Oct 18-25

50

50

200

complete

Jasper

first 8 days of 10

Oct 26-27

50

50

200

blew up off Pender

Jasper

last 2 days of 10

Oct26-Nov4

50

55

200

blew up off Pender

Jasper

blew before prev.

Oct 26

10

20

20

complete

Salish

Oct 27-30

10

20

20

complete

Jasper

Oct 31

10

20

20

complete

Jasper

opened North

Nov 1-4

10

20

20

complete

Jasper

Nov 5-14

10

20

20

complete

Jasper

Nov 15-19

10

20

20

complete

Jasper

Nov 20-24

10

20

20

timed-out

Jasper

Nov 20-29

10

20

20

complete

Jasper

Nov30-Dec9

10

20

20

complete

Jasper

Dec 10-19

10

20

20

complete

Jasper

Dec 20-31

10

20

20

timed-out

Jasper

Dec 20-25

10

20

20

complete

Jasper

fixed North tides

Dec 26-31

10

20

20

complete

Jasper

Jan 1-5

10

20

20

complete

Jasper

Jan 6-10

10

20

20

complete

Jasper

Jan 11-20

10

20

20

complete

Jasper

5d restart files

Jan 21-30

10

20

20

complete

Jasper

5d restart files

Jan31-Feb9

10

20

20

complete

Jasper

Feb 10-19

10

20

20

complete

Jasper

fixed West bt vels

Feb20-Mar1

10

20

20

complete

Jasper

Mar 2-11

10

20

20

complete

Jasper

Mar 12-21

10

20

20

complete

Jasper

Mar 22-31

10

20

20

complete

Jasper

Apr 1-10

10

20

20

complete

Jasper

Apr 11-20

10

20

20

complete

Jasper

Apr 21-30

10

20

20

complete

Jasper

May 1-10

10

20

20

complete

Jasper

May 11-20

10

20

20

complete

Jasper

May 21-30

10

20

20

complete

Jasper

May31-Jun9

10

20

20

complete

Jasper

Jun 10-19

10

20

20

complete

Jasper

Jun 20-29

10

20

20

complete

Jasper

Jun30-Jul9

10

20

20

complete

Jasper

Jul 10-19

10

20

20

complete

Jasper

Jul 20-29

10

20

20

complete

Jasper

Jul30-Aug8

10

20

20

complete

Jasper

9-18 Aug

10

20

20

complete

Jasper

19-28 Aug

10

20

20

complete

Jasper

Aug29-Sep7

10

20

20

complete

Jasper

8-17 Sep

10

20

20

complete

Jasper

18-27 Sep

10

20

20

complete

Jasper

28Sep-7Oct

10

20

20

complete

Jasper

flux corr N tides

8-17 Oct

10

20

20

complete

Jasper

18-27 Oct

10

20

20

complete

Jasper

Oct28-Nov6

10

20

20

complete

Jasper

7-16 Nov

10

20

20

complete

Jasper

5d restart files

17-26 Nov

10

20

20

complete

Jasper

5d restart files

Nov27-Dec6

10

20

20

complete

Jasper

5d restart files

7-16 Dec

10

20

20

complete

Jasper

5d restart files

17-26 Dec

10

20

20

finished

Jasper

5d restart files

27-31 Dec

10

20

20

queued

Jasper

5d restart file

Spin-up Run Workflows¶

Run Preparation and Queuing¶

These are the steps to prepare and queue a spin-up run on jasper.westgrid.ca:

1. If the CGRF atmospheric forcing files for the period of the run are not already in place on jasper, prepare them. Files for the day before the run starts and the day after it finishes are required so that interpolation of forcing values in NEMO works, for example:

ssh jasper
cd MEOPAR/CGRF/
salishsea get_cgrf 2002-10-03 -d 10


You will be prompted for a userid and password for the goapp.ocean.dal.ca rsync server. Those credentials can also be supplied in the command via the --user and --password options.

2. Create a YAML run description file for the run in the SS-run-sets/SalishSea/spin-up/ directory. That can be done by copying and renaming a previous run file. The name pattern for run description files is SalishSea.ddmmmddmmm.yaml, where ddmmmddmmm is the day and month of the first and last days of the run; e.g. SalishSea.23sep2oct.yaml. The 2nd ddmmm is omitted for 1 day long runs.

The values that must be set correctly in every new spin-up run description file are:

• initial conditions in the forcing stanza, which must be set to the path and file name of the restart file to use as initial conditions for the run, typically the last restart file from the previous spin-up run

• the namelist.time file name in the namelists stanza (see below)

Other namelist file names may also be used to set special conditions for the run. In general, the namelists from SS-run-sets/SalishSea/ are used unless there are changes for a particular spin-up run. Special condition namelists are created and commited to version control in the spin-up/ directory.

A typical spin-up run description file looks like:

# salishsea command processor run description for Salish Sea case
#
# Spin-up run
#
# Salish Sea full domain with:
#   Smoothed JdF mouth bathymetry
#   S4-1 uniform initial T and S, depth corrected
#   Open, unstructured western boundary across Strait of Juan de Fuca
#     Tidal forcing
#     Masson model, depth corrected, T, S, U & V
#   Monthly climatology river run-off forcing, all rivers
#   Atmospheric forcing from CGRF dataset
#     Atmospheric pressure as inverse sea surface height effect enabled

config_name: SalishSea

paths:
NEMO-code: ../../../NEMO-code/
forcing: ../../../NEMO-forcing/
runs directory: ../../../SalishSea/

grid:
# If relative, paths are taken from forcing path above
coordinates: coordinates_seagrid_SalishSea.nc
bathymetry: bathy_meter_SalishSea2.nc

forcing:
# If relative, paths are taken from forcing path above
atmospheric: ../CGRF/NEMO-atmos/
initial conditions: ../../../SalishSea/results/spin-up/22sep/SalishSea_00012096_restart.nc
open boundaries: open_boundaries/
rivers: rivers/

namelists:
- namelist.time.23sep24sep
- ../namelist.domain
- ../namelist.surface
- ../namelist.lateral
- ../namelist.bottom
- ../namelist.tracers
- namelist.dynamics.nu55evd100  # 23sep24sep run only
- ../namelist.compute.6x14

3. Create a namelist.time file for the run in the SS-run-sets/SalishSea/spin-up/ directory. That can be done by copying and renaming a previous run file. The name pattern for run description files is namelist.time.ddmmmddmmm, where ddmmmddmmm is the day and month of the first and last days of the run; e.g. namelist.time.23sep2oct. The 2nd ddmmm is omitted for 1 day long runs.

The values that must be set correctly in every new spin-up run namelist.time file are:

• nn_it000: the first time step for the run, typically 1 greater than the final time step of the previous run that is included in the name of the restart in the run description file

• nn_itend: the final time step for the run, nn_it000 + days * 8640 - 1, where days is the run duration in days

• nn_date0: the date when nn_it000 was 1; i.e. 20021026 Note that this convention changes in NEMO 3.6

• nit000_han: the first time step for tidal harmonic analysis, typically the same value as nn_it000

• nitend_han: the final time step for tidal harmonic analysis, typically the same value as nn_itend

Also ensure that ln_rstart is set to .true.

A typical namelist.time file looks like:

!! Run timing control
!!
!! *Note*: The time step is set in the &namdom namelist in the namelist.domain
!!         file.
!!
&namrun        !   Parameters of the run
!-----------------------------------------------------------------------
cn_exp      = "SalishSea"  ! experience name
nn_it000    =      302401  ! first time step
nn_itend    =      388800  ! last time step (std 1 day = 8640 re: rn_rdt in &namdom)
nn_date0    =    20021026  ! date at nit_0000 = 1 (format yyyymmdd)
! used to adjust tides to run date (regardless of restart control)
nn_leapy    =       1      ! Leap year calendar (1) or not (0)
ln_rstart   =  .true.      ! start from rest (F) or from a restart file (T)
nn_rstctl   =       2      ! restart control => activated only if ln_rstart = T
!   = 0 nn_date0 read in namelist
!   = 1 nn_date0 read in namelist
!       nn_it000 check consistency between namelist and restart
!   = 2 nn_date0 read in restart
!       nn_it000 check consistency between namelist and restart
nn_istate   =       0      ! output the initial state (1) or not (0)
nn_stock    =    43200      ! frequency of creation of a restart file (modulo referenced to 1)
ln_clobber  =  .true.      ! clobber (overwrite) an existing file
&end

&nam_diaharm   !   Harmonic analysis of tidal constituents ('key_diaharm')
!-----------------------------------------------------------------------
nit000_han = 302401  ! First time step used for harmonic analysis
nitend_han = 388800  ! Last time step used for harmonic analysis
nstep_han  =     90  ! Time step frequency for harmonic analysis
!! Names of tidal constituents
tname(1)   = 'K1'
tname(2)   = 'M2'
&end

4. Create any special condition namelist files and ensure that they are correctly included in the nameslists stanza of the run description file.

5. Choose or create an iodef.xml file for the run. The name pattern for iodef.xml files is iodef.nnt.xml, where nn is the frequency of output of the *_grid_[TUV].nc files, and t is the output interval; e.g. iodef.1d.xml.

6. Create or update a TORQUE batch job file for the run. The name pattern for batch job files is SalishSea.nnd.pbs, where nn is the duration of the run in days; e.g. SalishSea.10d.pbs.

The values that must be set correctly for every job are:

• The ddmmmddmmm part in the following lines:

• #PBS -N: the job name

• #PBS -o: the path and name for stdout from the job

• #PBS -e: the path and name for stderr from the job

• RESULTS_DIR=: the path and name of the results directory where the run results are to be gathered

• The walltime limit; e.g.

#PBS -l walltime=16:00:00


Runs typically required about 80 minutes of compute time per model-day if they allocated to the fast (X5675) nodes on jasper. However, if a run is allocated to the slow (L5420) nodes on jasper it can take nearly 180 minutes of compute time per model-day. It appears to be more advantageous to request that only fast nodes be used rather than requesting sufficient run walltime to allow runs to complete on the slow nodes. The directive to request only fast nodes is:

Wall time values that have been found to be adequate are 3h for a 2d run, 8h for a 5d run, and 16h for a 10d run.

A typical TORQUE batch job file looks like:

#!/bin/bash

#PBS -N SpinUp26oct4nov
#PBS -S /bin/bash
#PBS -l procs=84
# memory per processor
#PBS -l pmem=2gb
#PBS -l walltime=16:00:00
#PBS -l feature=X5675
# email when the job [b]egins and [e]nds, or is [a]borted
#PBS -m bea
#PBS -M sallen@eos.ubc.ca
#PBS -o ../SpinUp26oct4nov/stdout
#PBS -e ../SpinUp26oct4nov/stderr

RESULTS_DIR=../SpinUp26oct4nov

cd $PBS_O_WORKDIR echo working dir:$(pwd)

echo "Starting run at $(date)" mkdir -p$RESULTS_DIR
mpirun ./nemo.exe
echo "Ended run at $(date)" echo "Results gathering started at$(date)"
$PBS_O_HOME/.local/bin/salishsea gather --no-compress SalishSea*.yaml$RESULTS_DIR
chmod go+rx $RESULTS_DIR chmod go+r$RESULTS_DIR/*
echo "Results gathering ended at $(date)" echo "Scheduling cleanup of run directory" echo rmdir$PBS_O_WORKDIR > /tmp/SpinUp26oct4nov_cleanup
at now + 1 minutes -f /tmp/SpinUp26oct4nov_cleanup 2>&1

7. Commit and push the run set file changes for each run prior to queuing the run so that there is a clear record of runs in the SS-run-sets repo. Don’t forget to add any files created for a run to the repo.

8. Prepare the run, copy the TORQUE batch job file to the run directory, go to the run directory, and submit the job to the scheduler:

salishsea prepare SalishSea.23sep24sep.yaml iodef.1d.xml
cp SalishSea.2d.pbs ../../../SalishSea/bb1357d6-8c6e-11e3-bdd0-0025902b0cdc
pushd ../../../SalishSea/bb1357d6-8c6e-11e3-bdd0-0025902b0cdc
qsub SalishSea.2d.pbs