Update regression scripts and the manual

doc/browser/petsc.md

@@ -241,6 +241,6 @@ multiprocessor jobs, the display may have to be set on the command
 line, for instance as `-display :0` or similar; this must be given as
 the final option. For example,
 
-    mpiexec -n 2 pisms -view thk -display :0
+    mpiexec -n 2 pismr -eisII A -view thk -display :0
 
 allows a two processor run to view the ice thickness.

doc/sphinx/Makefile

@@ -9,7 +9,7 @@ INTERMEDIATE=diag.json diag-2.json dummy.nc pism_config.nc surface_input.nc
 dummy.nc:
 	# use a thermal bedrock layer model and run for 1 year to complete the
 	# bootstrapping
-	pisms -y 1 -Mbz 5 -Lbz 1000 -Mz 5 -Mx 5 -My 5 -o $@ -verbose 1
+	pismr -eisII A -y 1 -Mbz 5 -Lbz 1000 -Mz 5 -Mx 5 -My 5 -o $@ -verbose 1
 
 	# rename climatic_mass_balance: we need precipitation for an atmosphere model
 	ncrename -v climatic_mass_balance,precipitation -O $@ $@

doc/sphinx/climate_forcing/testing.rst

@@ -34,18 +34,18 @@ correctly:
 
 .. code-block:: none
 
-   mpiexec -n 2 pisms -eisII A -y 1000 -o state.nc
+   mpiexec -n 2 pismr -eisII A -y 1000 -o state.nc
    pismr -i state.nc -surface given -extra_times 0.0:0.1:2.5 \
          -extra_file movie.nc -extra_vars climatic_mass_balance,ice_surface_temp \
          -ys 0 -ye 2.5
 
-Using ``pisms`` merely generates demonstration climate data, using EISMINT II choices
-:cite:`EISMINT00`. The next run extracts the surface mass balance :var:`climatic_mass_balance`
-and surface temperature :var:`ice_surface_temp` from ``state.nc``. It then does nothing
-interesting, exactly because a constant climate is used. Viewing ``movie.nc`` we see these
-same values as from ``state.nc``, in variables :var:`climatic_mass_balance`,
-:var:`ice_surface_temp`, reported back to us as the time- and space-dependent climate at
-times ``ys:dt:ye``. It is a boring "movie."
+Using ``pismr -eisII A`` merely generates demonstration climate data, using EISMINT II
+choices :cite:`EISMINT00`. The next run extracts the surface mass balance
+:var:`climatic_mass_balance` and surface temperature :var:`ice_surface_temp` from
+``state.nc``. It then does nothing interesting, exactly because a constant climate is
+used. Viewing ``movie.nc`` we see these same values as from ``state.nc``, in variables
+:var:`climatic_mass_balance`, :var:`ice_surface_temp`, reported back to us as the time-
+and space-dependent climate at times ``ys:dt:ye``. It is a boring "movie."
 
 A more interesting example uses a :ref:`positive degree-day scheme <sec-surface-pdd>`.
 This scheme uses a variable called :var:`precipitation`, and a calculation of melting, to

doc/sphinx/installation/arch.rst

@@ -26,7 +26,7 @@ You can then install PISM and its dependencies with the following command:
    
    yay -Sy pism
 
-Once installed, the PISM binaries (e.g. ``pismr``, ``pisms``, various Python
+Once installed, the PISM binaries (e.g. ``pismr``, ``pismv``, various Python
 tools) are available in the PATH and do not require further intervention to
 work. It is recommended that the installation is manually verified with the
 instructions in section :ref:`sec-install-quick-tests`.

doc/sphinx/installation/quick-tests.rst

@@ -28,14 +28,14 @@ correctly.
 
    .. code-block:: none
 
-      pisms -y 5000 -view thk,temppabase,velsurf_mag
+      pismr -eisII A -y 5000 -view thk,temppabase,velsurf_mag
 
    When using such viewers and ``mpiexec`` the additional final option ``-display :0`` is
    sometimes required to enable MPI to use X, like this:
 
    .. code-block:: none
 
-       mpiexec -n 2 pisms -y 5000 -view thk,temppabase,velsurf_mag -display :0
+       mpiexec -n 2 pismr -eisII A -y 5000 -view thk,temppabase,velsurf_mag -display :0
 
    Also ``-drawpause 0.1`` or similar may be needed if the figures are refreshing too fast.
 

doc/sphinx/manual/initialization/index.rst

@@ -11,9 +11,9 @@ There are three ways to start PISM:
   or
 - option :opt:`-i` :opt:`-bootstrap` reads an "incomplete" NetCDF file and uses heuristics
   to fill in needed fields, or
-- one of the executables ``pisms`` or ``pismv`` is used to initialize simplified-geometry
-  experiments or verification tests from formulas in the source code, and thus no input
-  file is required.
+- ``pismr -eisII ...`` and the ``pismv`` executable are used to initialize
+  simplified-geometry experiments and verification tests from formulas in the source code,
+  and thus no input file is required.
 
 One of the first two choices is required when using the executable ``pismr``. Modeling
 usually starts with the ``-i input.nc -bootstrap`` because real ice sheet observations are

doc/sphinx/manual/initialization/restarting.rst

@@ -10,15 +10,15 @@ run can be loaded with ":opt:`-i`":
 
 .. code-block:: none
 
-   pisms -eisII A -y 100 -o foo.nc
-   pisms -eisII A -i foo.nc -y 100 -o bar.nc
+   pismr -eisII A -y 100 -o foo.nc
+   pismr -eisII A -i foo.nc -y 100 -o bar.nc
 
 As noted, verification tests (section :ref:`sec-verif`) and simplified-geometry experiments
 (section :ref:`sec-simp`) do not need input files at all because they initialize from
 formulas in the source code. They can, however, be continued from saved model states using
 :opt:`-i`. Specifying the simplified geometry experiment or verification test *is*,
 however, necessary if the run is to continue with the climate inputs for that experiment
-or test. For example, based on the above ``pisms`` runs, it is valid to do
+or test. For example, based on the above ``pismr -eisII A`` runs, it is valid to do
 
 .. code-block:: none
 
@@ -38,7 +38,7 @@ resulting file, like this:
 
 .. code-block:: none
 
-   pisms -eisII A -y 10 -o foo.nc
+   pismr -eisII A -y 10 -o foo.nc
    ncdump -h foo.nc | less
 
 Note that variables in the output file have a ``pism_intent`` attribute. When

doc/sphinx/manual/modeling-choices/computational/grid.rst

@@ -112,7 +112,7 @@ For example:
 
 .. code-block:: bash
 
-   > pisms -grid.registration center \
+   > pismr -eisII A -grid.registration center \
            -Lx 10 -Mx 4 \
            -y 0 -verbose 1 \
            -o grid-test.nc
@@ -148,7 +148,7 @@ Compare this to
 
 .. code-block:: bash
 
-   > pisms -grid.registration corner \
+   > pismr -eisII A -grid.registration corner \
            -Lx 10 -Mx 5 \
            -y 0 -verbose 1 \
            -o grid-test.nc
@@ -268,7 +268,7 @@ For example,
 
 .. code-block:: none
 
-   mpiexec -n 3 pisms -Mx 101 -My 101 \
+   mpiexec -n 3 pismr -eisII A -Mx 101 -My 101 \
                       -Nx 1 -procs_x 101 \
                       -Ny 3 -procs_y 20,61,20
 

doc/sphinx/manual/modeling-choices/computational/time.rst

@@ -198,7 +198,7 @@ As an example, consider these two runs:
 
 .. code-block:: none
 
-   pisms -y 6000 -o foo.nc
+   pismr -eisII A -y 6000 -o foo.nc
    pismr -i foo.nc -y 0.001 -o bar.nc -o_size big
 
 The result of the second (short) run is a NetCDF file ``bar.nc`` which contains the full

doc/sphinx/manual/modeling-choices/dynamics/sia.rst

@@ -99,7 +99,7 @@ There are two associated parameters:
 - :config:`stress_balance.sia.bed_smoother.theta_min` is the minimum value of `\theta` in
   the parameterization.
 
-This mechanism is turned off by default in executables ``pisms`` and ``pismv``.
+This mechanism is turned off by default in ``pismv``.
 
 Under the default :config:`output.size` (``medium``), PISM writes fields :var:`topgsmooth`
 and :var:`schoofs_theta` from this mechanism. The thickness relative to the smoothed

doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst

@@ -57,9 +57,9 @@ Here are minimal example runs to compare these models:
 
 .. code-block:: none
 
-   mpiexec -n 4 pisms -eisII A -y 8000 -o eisIIA_nobd.nc
-   mpiexec -n 4 pisms -eisII A -bed_def iso -y 8000 -o eisIIA_bdiso.nc
-   mpiexec -n 4 pisms -eisII A -bed_def lc -y 8000 -o eisIIA_bdlc.nc
+   mpiexec -n 4 pismr -eisII A -y 8000 -o eisIIA_nobd.nc
+   mpiexec -n 4 pismr -eisII A -bed_def iso -y 8000 -o eisIIA_bdiso.nc
+   mpiexec -n 4 pismr -eisII A -bed_def lc -y 8000 -o eisIIA_bdlc.nc
 
 Compare the :var:`topg`, :var:`usurf`, and :var:`dbdt` variables in the resulting output
 files. See also the comparison done in :cite:`BLKfastearth`.

doc/sphinx/manual/practical-usage/input-output.rst

@@ -61,7 +61,7 @@ Note the ``-help`` and ``-usage`` options for getting help at the command line.
      - Brief descriptions of the many PISM and PETSc options. The run occurs as usual
        according to the other options. (The option documentation does not get listed if
        the run didn't get started properly.) Use with a pipe into ``grep`` to get
-       usefully-filtered information on options, for example ``pisms -help | grep cold``.
+       usefully-filtered information on options, for example ``pismr -help | grep cold``.
 
    * - :opt:`-info`
      - Gives information about PETSc operations during the run.

doc/sphinx/manual/practical-usage/regridding.rst

@@ -26,7 +26,7 @@ as in this example: }
 
 .. code-block:: none
 
-    pisms -eisII A -Mx 101 -My 101 -Mz 201 -y 1000 \
+    pismr -eisII A -Mx 101 -My 101 -Mz 201 -y 1000 \
           -regrid_file foo.nc -regrid_vars thk,temp -o bar.nc
 
 By specifying regridded variables "``thk,temp``", the ice thickness and temperature values

doc/sphinx/manual/simplified-geometry/eismint-2.rst

@@ -45,7 +45,7 @@ Experiments E -- L are only documented in :cite:`EISIIdescribe`.
    :header-rows: 1
    :widths: 5,2
 
-   * - Command: "``pisms +``"
+   * - Command: "``pismr +``"
      - Relation to experiment A
 
    * - ``-eisII A -Mx 61 -My 61 -Mz 61 -Lz 5000 -y 2e5 -o eisIIA.nc``

examples/eismintII/runexp.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (C) 2013--2016 The PISM Authors
+# Copyright (C) 2013--2016, 2021 The PISM Authors
 
 # This is just a helper script to make running EISMINT II experiments easier.
 # It adds suggested diagnostics which help compare to the published experiments.
@@ -57,7 +57,7 @@ fi
 SKIP=5         # adjust upward for high res
 ROOT=eisII$EXP$MHOR
 echo "$SCRIPTNAME  run into steady state with constant climate forcing for $RUNTIME a"
-cmd="$PISM_MPIDO $NN pisms -eisII $EXP $GRIDORINPUT -ys 0 -y $DUR \
+cmd="$PISM_MPIDO $NN pismr -eisII $EXP $GRIDORINPUT -ys 0 -y $DUR \
  -skip -skip_max $SKIP -o $ROOT.nc -extra_file ex_$ROOT.nc \
  -extra_vars thk,temppabase,velsurf_mag,velbar_mag,flux_mag,diffusivity,bmelt,taud_mag \
  -extra_times 1000:1000:$DUR -ts_file ts_$ROOT.nc \

src/coupler/surface/EISMINTII.hh

@@ -1,4 +1,4 @@
-/* Copyright (C) 2014, 2015, 2016, 2017, 2018 PISM Authors
+/* Copyright (C) 2014, 2015, 2016, 2017, 2018, 2021 PISM Authors
  *
  * This file is part of PISM.
  *
@@ -27,8 +27,6 @@ namespace surface {
 
 /** EISMINT II climate inputs.
  *
- * This class should be removed together with the pisms executable
- * (once I get to that).
  */
 class EISMINTII : public PSFormulas {
 public:

src/icemodel/IceEISModel.cc

@@ -170,6 +170,7 @@ void IceEISModel::initialize_2d() {
 }
 
 void IceEISModel::bootstrap_2d(const File &input_file) {
+  (void) input_file;
   throw RuntimeError::formatted(PISM_ERROR_LOCATION,
                                 "EISMINT II mode does not support bootstrapping");
 }

test/regression/beddef_lc_restart.sh

@@ -14,7 +14,7 @@ rm -f $files
 set -e
 
 mpi="$MPIEXEC -n 3"
-pisms="$PISM_PATH/pisms"
+pisms="$PISM_PATH/pismr -eisII A"
 pismr="$PISM_PATH/pismr"
 
 # time step length

test/regression/temp_continuity.py

@@ -23,7 +23,7 @@ def run(cmd):
 dts = [100, 50]
 for dt in dts:
     try:
-        cmd = "{path}/pisms -eisII B -y 2400 -Mx 16 -My 16 -Mz 21 -Lbz 1000 -Mbz 11 -energy enthalpy -regrid_file in-temp-continuity.nc -regrid_vars thk -verbose 1 -max_dt {dt} -o out-temp-continuity.nc -output.sizes.medium temp -gradient mahaffy".format(path=pism_path, dt=dt)
+        cmd = "{path}/pismr -eisII B -y 2400 -Mx 16 -My 16 -Mz 21 -Lbz 1000 -Mbz 11 -energy enthalpy -regrid_file in-temp-continuity.nc -regrid_vars thk -verbose 1 -max_dt {dt} -o out-temp-continuity.nc -output.sizes.medium temp -gradient mahaffy".format(path=pism_path, dt=dt)
 
         run(cmd)
 

test/regression/test_01.sh

@@ -10,7 +10,7 @@ OPTS="-max_dt 1 -o_size small -energy enthalpy"
 set -e -x
 
 # generate an interesting file
-$PISM_PATH/pisms -energy enthalpy -Mx 6 -My 6 -Mz 5 -y 5000 -max_dt 500.0 -o baz-01.nc
+$PISM_PATH/pismr -eisII A -energy enthalpy -Mx 6 -My 6 -Mz 5 -y 5000 -max_dt 500.0 -o baz-01.nc
 
 # run for ten years, fixed time step
 $PISM_PATH/pismr -i baz-01.nc $OPTS -ys 0 -y 10 -o foo-01.nc

test/regression/test_03.sh

@@ -11,7 +11,7 @@ OPTS="-o_size small "
 set -e -x
 
 # Create a file to start from:
-$MPIEXEC -n 2 $PISM_PATH/pisms -energy enthalpy -y 1000 $OPTS -o foo-03.nc -Mx 31 -My 41
+$MPIEXEC -n 2 $PISM_PATH/pismr -eisII A -energy enthalpy -y 1000 $OPTS -o foo-03.nc -Mx 31 -My 41
 
 # Run for 0 years:
 $MPIEXEC -n 2 $PISM_PATH/pismr -i foo-03.nc -y 0 $OPTS -o bar-03.nc

test/regression/test_05.sh

@@ -11,7 +11,7 @@ OPTS="-i foo-05.nc -bootstrap -Mx 41 -My 61 -Mz 21 -Lz 5000 -y 0 -o_size small"
 set -e -x
 
 # Create a file to bootstrap from (with a non-trivial bed topography):
-$PISM_PATH/pisms -eisII I -Mx 121 -My 61 -Mz 21 -y 0 -o foo-05.nc 
+$PISM_PATH/pismr -eisII I -Mx 121 -My 61 -Mz 21 -y 0 -o foo-05.nc
 
 # Bootstrap from this file and run for 0 years:
 $MPIEXEC -n 2 $PISM_PATH/pismr $OPTS -o bar-05.nc 

test/regression/test_08.sh

@@ -8,15 +8,15 @@ echo "Test # 8: regridding: coarse -> fine -> coarse (vertical direction)."
 # The list of files to delete when done.
 files="coarse1-08.nc coarse2-08.nc fine1-08.nc fine2-08.nc"
 
-# -grid.registration corner is needed to match default settings of pisms
+# -grid.registration corner is needed to match default settings of pismr -eisII A
 OPTS="-y 0 -grid.registration corner"
 
 set -e -x
 
 # Create a file to regrid from:
-$PISM_PATH/pisms -energy enthalpy -Mx 10 -My 10 -Mz 11 -y 6000 -max_dt 300.0 -o coarse1-08.nc
+$PISM_PATH/pismr -eisII A -energy enthalpy -Mx 10 -My 10 -Mz 11 -y 6000 -max_dt 300.0 -o coarse1-08.nc
 # Create another file with a finer grid:
-$PISM_PATH/pisms -energy enthalpy -Mx 10 -My 10 -Mz 21 -y 6000 -max_dt 300.0 -o fine1-08.nc
+$PISM_PATH/pismr -eisII A -energy enthalpy -Mx 10 -My 10 -Mz 21 -y 6000 -max_dt 300.0 -o fine1-08.nc
 
 # Coarse -> fine:
 $PISM_PATH/pismr -i fine1-08.nc -regrid_file coarse1-08.nc -regrid_vars enthalpy $OPTS -o fine2-08.nc

test/regression/test_09.sh

@@ -13,7 +13,7 @@ rm -f $files
 set -e -x
 
 # Create a file to bootstrap from (with a non-trivial bed topography):
-$MPIEXEC -n 1 $PISM_PATH/pisms -eisII I -Mx 51 -My 60 -Mz 21 -Mbz 21 -Lbz 1000 -y 0 -o foo-09.nc
+$MPIEXEC -n 1 $PISM_PATH/pismr -eisII A -Mx 51 -My 60 -Mz 21 -Mbz 21 -Lbz 1000 -y 0 -o foo-09.nc
 
 # Bootstrap from this file and run for 0 years:
 $MPIEXEC -n 2 $PISM_PATH/pismr -i foo-09.nc -bootstrap $OPTS -o bar-09.nc

test/regression/test_10.sh

@@ -14,7 +14,7 @@ set -e -x
 NRANGE="1 2 3 4 5"
 
 # Create a file to bootstrap from:
-$MPIEXEC -n 1 $PISM_PATH/pisms -eisII I -Mx 51 -My 101 -y 0 -o foo0-10.nc
+$MPIEXEC -n 1 $PISM_PATH/pismr -eisII A -eisII I -Mx 51 -My 101 -y 0 -o foo0-10.nc
 
 # Bootstrap:
 for NN in $NRANGE;

test/regression/test_13.sh

@@ -4,13 +4,13 @@ PISM_PATH=$1
 MPIEXEC=$2
 
 # Test name:
-echo "Test #13: enthalpy symmetry near the base (pisms -energy enthalpy)."
+echo "Test #13: enthalpy symmetry near the base (pismr -eisII A -energy enthalpy)."
 # The list of files to delete when done.
 files="simp_exper-13.nc"
 
 rm -f $files
-# run pisms
-$MPIEXEC -n 2 $PISM_PATH/pisms -y 10e3 -Lz 5000 -Mx 12 -My 12 -o_size big -energy enthalpy -o simp_exper-13.nc
+# run pismr -eisII A
+$MPIEXEC -n 2 $PISM_PATH/pismr -eisII A -y 10e3 -Lz 5000 -Mx 12 -My 12 -o_size big -energy enthalpy -o simp_exper-13.nc
 
 ncpdq -a z,y,x -O simp_exper-13.nc simp_exper-13.nc
 

test/regression/test_23.sh

@@ -16,7 +16,7 @@ rm -f $files
 set -e -x
 
 # create foo-23.nc (at about 6500 years we get some basal melting...)
-$MPIEXEC -n 2 $PISM_PATH/pisms -energy enthalpy -y 6500 $opts -o foo-23.nc
+$MPIEXEC -n 2 $PISM_PATH/pismr -eisII A -energy enthalpy -y 6500 $opts -o foo-23.nc
 
 # bootstrap from it, re-gridding all the variables we can
 $PISM_PATH/pismr -i foo-23.nc -bootstrap -regrid_file foo-23.nc -y 0 $opts -o bar-23.nc

test/regression/test_27.sh

@@ -12,7 +12,7 @@ rm -f $files
 
 set -e -x
 
-$PISM_PATH/pisms -eisII A -y 1000 -view velsurf,thk -Mbz 11 -Lbz 1000 -o_size small -o simp_exper-27.nc
+$PISM_PATH/pismr -eisII A -eisII A -y 1000 -view velsurf,thk -Mbz 11 -Lbz 1000 -o_size small -o simp_exper-27.nc
 
 if [ $? != 0 ];
 then

test/regression/test_28.sh

@@ -15,7 +15,7 @@ set -e
 set -x
 
 # create a (complete) dataset to bootstrap from:
-$MPIEXEC -n 2 $PISM_PATH/pisms -y 100 -o foo-28.nc
+$MPIEXEC -n 2 $PISM_PATH/pismr -eisII A -y 100 -o foo-28.nc
 
 OPTS="-i foo-28.nc -bootstrap -Mx 61 -My 61 -Mz 11 -y 10 -Lz 1000"
 # bootstrap and run for 100 years:

test/regression/test_31.sh

@@ -16,7 +16,7 @@ set -e
 set -x
 
 # prepare input files with temp and liqfrac and with temp only
-$PISM_PATH/pisms -Mx 3 -My 3 -energy enthalpy -y 10 -o temp-liqfrac.nc -o_size big
+$PISM_PATH/pismr -eisII A -Mx 3 -My 3 -energy enthalpy -y 10 -o temp-liqfrac.nc -o_size big
 ncks -x -v enthalpy -O temp-liqfrac.nc temp-liqfrac.nc
 ncks -x -v liqfrac -O temp-liqfrac.nc temp.nc
 

test/regression/test_32.sh

@@ -12,7 +12,7 @@ OPTS="-ys 0 -y 0 -i foo-32.nc -bootstrap -regrid_file foo-32.nc -Lz 4000 -Mx 31
 set -e -x
 
 # Create the file to regrid and bootstrap from:
-$PISM_PATH/pisms -energy enthalpy -y 500 -o foo-32.nc -o_size big
+$PISM_PATH/pismr -eisII A -energy enthalpy -y 500 -o foo-32.nc -o_size big
 
 # Bootstrap from this file:
 $PISM_PATH/pismr $OPTS -o bar-32.nc

test/regression/test_33.sh

@@ -15,7 +15,7 @@ set -e
 set -x
 
 # prepare input files with temp and liqfrac and with temp only
-$PISM_PATH/pisms -y 100 -o in.nc
+$PISM_PATH/pismr -eisII A -y 100 -o in.nc
 
 $PISM_SOURCE_DIR/examples/python/sia_forward.py -i in.nc -o out.nc