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	tREADME.md - pism-exp-gsw - ice stream and sediment transport experiments
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	tREADME.md (6090B)
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	1 MISMIP in PISM
	2 ==============
	3
	4 This directory contains scripts that can be used to run MISMIP experimen…
	5
	6 Older PISM versions included C++ code managing MISMIP experiments. With …
	7
	8 Step by step instructions
	9 -------------------------
	10
	11 First of all, you will need to copy or symlink `util/PISMNC.py` into the
	12 current directory to make sure that Python will be able to import it.
	13
	14 The script `run.py` is used to generate a `bash` scripts performing MISM…
	15 experiments. Running `run.py --help` produces the following:
	16
	17 Usage: run.py [options]
	18
	19 Creates a script running MISMIP experiments.
	20
	21 Options:
	22 -h, --help show this help message and exit
	23 --initials=INITIALS Initials (3 letters)
	24 -e EXPERIMENT, --experiment=EXPERIMENT
	25 MISMIP experiments (one of '1a', '1b', '2a',…
	26 '3a', '3b')
	27 -s STEP, --step=STEP MISMIP step number
	28 -u, --uniform_thickness
	29 Use uniform 10 m ice thickness
	30 -a, --all Run all experiments
	31 -m MODE, --mode=MODE MISMIP grid mode
	32 --Mx=MX Custom grid size; use with --mode=3
	33 --model=MODEL Models: 1 - SSA only; 2 - SIA+SSA
	34 --executable=EXECUTABLE
	35 Executable to run, e.g. 'mpiexec -n 4 pismr'
	36
	37 For example, to set up MISMIP experiment `1a` using grid mode 1, a 12 km…
	38
	39 ./run.py -e 1a --mode=1 > experiment-1a-mode-1.sh
	40
	41 This will create `experiment-1a-mode-1.sh` as well as the bootstrapping …
	42 `MISMIP_boot_1a_M1_A1.nc` and configuration files corresponding to each …
	43 in the experiment.
	44
	45 Run in the backround with 2 cores and saving output to a text file this …
	46
	47 bash experiment-1a-mode-1.sh 2 >& out.1a-mode-1 &
	48
	49 You can also copy the script (along with
	50 `MISMIP_boot_1a_M1_A1.nc` and `MISMIP_conf_1a_A*.nc`) to a supercomputer…
	51 do the run later. For such application, the script helpfully uses envir…
	52 `PISM_BIN` and `PISM_MPIDO`. For example, on some Cray machines you migh…
	53
	54 PISM_MPIDO="aprun -n " bash experiment-1a-mode-1.sh 32
	55
	56 will use `aprun` on 32 cores. Alternatively, you can use
	57
	58 ./run.py -e 1a --mode=1 --executable="aprun -n 32 pismr"
	59
	60 or similar to skip the "preamble" handling environment variables and get…
	61 commands.
	62
	63
	64 Refined grid runs
	65 -----------------
	66
	67 The above "grid mode 1" runs use 150 grid spaces in the MISMIP modeling …
	68 which is 301 grid points in PISM's (doubled) domain. The domain is doub…
	69 PISM is easiest configure as a whole ice sheet model with ice free ocean…
	70 edge of the computation domain. (Compare the example in `examples/jako/…
	71
	72 To run a higher resolution 3 km grid, with somewhat-improved grounding l…
	73 performance, ask the `run.py` script to put option `-Mx 1201` into the b…
	74 script:
	75
	76 ./run.py -e 1a --mode=3 --Mx=1201 > experiment-1a-mode-3.sh
	77
	78 Then this is a 4 core run:
	79
	80 bash experiment-1a-mode-3.sh 4 >& out.1a-mode-3 &
	81
	82
	83 Technical details
	84 -----------------
	85
	86 The script `MISMIP.py` contains MISMIP parameters and the code needed to
	87 compute the semi-analytic grounding line location and the corresponding
	88 thickness profile for each experiment.
	89
	90 The script `prepare.py` contains functions using `MISMIP.py` to generate
	91 PISM-readable NetCDF files with semi-analytic ice thickness profiles, and
	92 the prescribed accumulation map. It can be imported as a module or run
	93 as a script to generate PISM bootstrapping files.
	94
	95 The script `run.py` generates `bash` scripts performing MISMIP runs using
	96 `MISMIP.py` and `prepare.py`.
	97
	98 Implementation details
	99 ----------------------
	100
	101 We can turn PISM's default sliding law into MISMIP's power law by settin…
	102 threshold speed to 1 meter per second, which will make it inactive.
	103
	104 The `-pseudo_plastic_uthreshold` command-line option takes an argument i…
	105
	106 The MISMIP parameter C corresponds to `tauc` in PISM. It can be set usin…
	107
	108 The MISMIP power law exponent `m` corresponds to `-pseudo_plastic_q` in …
	109
	110 We use the `-config_override` option to set other MISMIP-specific parame…
	111
	112 Note that PISM does not at this time implement the stopping criteria des…
	113
	114 Post-processing
	115 ---------------
	116
	117 Converting PISM output files to ASCII files following MISMIP
	118 specifications is left as an exercise.
	119
	120 However, we do provide the `plot.py` script for visualization.
	121
	122 It plots modeled ice flux as a function of the distance from the divide …
	123
	124 We see a discontinuity in the flux at the grounding
	125 line. This is an issue in PISM that needs to be addressed to improve its
	126 handling of the grounding line motion. For example, try
	127
	128 ./plot.py ABC1_1a_M1_A1.nc -f -o flux.png
	129
	130 Run `plot.py --help` for a list of command-line options. You can also pr…
	131
	132 ./plot.py ABC*.nc
	133
	134 will create geometry profile and ice flux plots for all matched files.
	135
	136 Also, note that the variable `ice_area_glacierized_grounded` in `ts_ABC1…
	137 allows one to see time-dependent changes in the grounding line location
	138 because grounded ice area is proportional to the distance from the divid…
	139 grounding line.