Merge pull request #263 from snek5000/remaining-clock-time

Using remaining clock time code from fluidsim_core

CHANGELOG.md

@@ -33,7 +33,8 @@ Security in case of vulnerabilities.
 ### Added
 
 - {func}`snek5000.output.base.Output.post_init_create_additional_source_files`,
-  {func}`snek5000.resources.get_base_templates` and {func}`snek5000.resources.get_base_template`.
+  {func}`snek5000.resources.get_base_templates` and
+  {func}`snek5000.resources.get_base_template`.
 
 ## [0.9.0rc0]
 

docs/examples/snek5000-tgv/src/snek5000_tgv/tgv.usr.f

@@ -110,7 +110,7 @@ subroutine userchk()
       ! for remaining_clock_time
       character*28 rct_file_name
       real rct_seconds_between_save
-      real remaining_clock_time
+      real remaining_clock_time, remaining_eq_time, delta_clock_time
 
       period_save = real(UPARAM(11))
 
@@ -132,7 +132,9 @@ subroutine userchk()
          if (.not. exist) then
             if (nid.eq.0) then
                open(11, File=rct_file_name)
-               write(11,'(a)') 'it,time,dt,remaining_clock_time'
+               write(11,'(a,a)')
+     &           'it,equation_times,dt,delta_clock_times,',
+     &           'remaining_equation_times,remaining_clock_times'
                close(11)
             endif
          endif
@@ -149,13 +151,22 @@ subroutine userchk()
 c      iostep_full = iostep
 c      call full_restart_save(iostep_full)
 
-      if ((nid .eq. 0) .and. (istep > 0)) then
+      if (nid .eq. 0) then
          call compute_remaining_clock_time(
-     &       rct_seconds_between_save, remaining_clock_time)
-         if (remaining_clock_time >= 0.0) then
+     &       rct_seconds_between_save, remaining_clock_time,
+     &       remaining_eq_time, delta_clock_time)
+         if (istep == 0) then
             open(10, File=rct_file_name, position='append')
-            write(10,'(I12,A,g14.8,A,g14.8,A,g14.8)')
-     &          istep,',',time,',',dt,',',remaining_clock_time
+            write(10,'(I12,A,g14.8,A,g14.8,A,g14.8,A)')
+     &          istep,',',time,',',dt,',',delta_clock_time,
+     &          ',nan,nan'
+            close(10)
+         elseif (remaining_clock_time >= 0.0) then
+            open(10, File=rct_file_name, position='append')
+            write(10,'(I12,A,g14.8,A,g14.8,A,g14.8,A,g14.8,A,g14.8)')
+     &          istep,',',time,',',dt,',',delta_clock_time,
+     &          ',',remaining_eq_time,
+     &          ',',remaining_clock_time
             close(10)
          endif
       endif
@@ -241,15 +252,15 @@ subroutine compute_energy_enstrophy(e1,e2,u,v,w)
       end
 c-----------------------------------------------------------------------
       subroutine compute_remaining_clock_time(
-     &    seconds_between_save, remaining_clock_time)
+     &    seconds_between_save, remaining_clock_time, remaining_eq_time,
+     &    delta_clock_time)
       implicit none
 
       include 'SIZE'
       include 'TOTAL'
 
       real seconds_between_save
-      real remaining_clock_time
-      real remaining_eq_time
+      real remaining_clock_time, remaining_eq_time
 
       real clock_time, delta_clock_time, delta_eq_time
 
@@ -260,11 +271,10 @@ subroutine compute_remaining_clock_time(
       save istep_next
 
       remaining_clock_time = -1.0
-      if (istep .eq. 1) then
-        call cpu_time(clock_time_last)
+      delta_clock_time = 0.0
+      if (istep .eq. 0) then
         eq_time_last = time
-        istep_last = 1
-        istep_next = 2
+        istep_next = 1
       elseif ((istep .eq. istep_next) .or. (lastep .eq. 1)) then
         call cpu_time(clock_time)
         delta_clock_time = clock_time - clock_time_last
@@ -278,10 +288,14 @@ subroutine compute_remaining_clock_time(
         else
           remaining_eq_time = (nsteps - istep) * dt
         endif
-        istep_next = istep + int((istep - istep_last) *
+        if (istep .eq. 1) then
+          istep_next = 2
+        else
+          istep_next = istep + int((istep - istep_last) *
      &      seconds_between_save / delta_clock_time)
-        if (istep_next .eq. istep) then
-          istep_next = istep_next + 1
+          if (istep_next .eq. istep) then
+            istep_next = istep_next + 1
+          endif
         endif
         istep_last = istep
         remaining_clock_time = remaining_eq_time / delta_eq_time *

docs/tuto_tgv.myst.md

@@ -139,6 +139,24 @@ The command `snek-ipy-load` can be used to start a IPython session and load the
 simulation saved in the current directory.
 ```
 
++++
+
+## How long was the run?
+
+`snek5000-tgv` saves a file `remaining_clock_time.csv` during the simulation. It can be
+read manually,
+
+```{code-cell} ipython3
+!cat {path_run}/remaining_clock_time.csv
+```
+
+and there is also an object `sim.output.remaining_clock_time` to load and plot these
+data (which is especially useful during the simulation!):
+
+```{code-cell} ipython3
+sim.output.remaining_clock_time.plot()
+```
+
 ## Parse, load and plot information contained in the Nek5000 log
 
 The object `sim.output.print_stdout` (see
@@ -273,3 +291,9 @@ ax.figure
 
 Note that we use for this tutorial very small and coarse simulations, which explain the
 differences between our results and the reference!
+
+Let us see what gives the `remaining_clock_time` plot after the second simulation:
+
+```{code-cell} ipython3
+sim.output.remaining_clock_time.plot()
+```

requirements/dev.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --extra=dev --output-file=requirements/dev.txt --resolver=backtracking requirements/vcs_packages.in setup.cfg
@@ -127,8 +127,9 @@ fluiddyn==0.5.1
     #   fluidsim-core
     #   snek5000
     #   snek5000 (setup.cfg)
-fluidsim-core==0.7.1
+fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
     # via
+    #   -r requirements/vcs_packages.in
     #   snek5000
     #   snek5000 (setup.cfg)
 fonttools==4.38.0
@@ -161,12 +162,9 @@ imagesize==1.4.1
     # via sphinx
 importlib-metadata==5.1.0
     # via
-    #   fluidsim-core
     #   jupyter-cache
     #   keyring
     #   myst-nb
-    #   nbconvert
-    #   sphinx
     #   twine
 inflection==0.5.1
     # via

requirements/docs.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --extra=docs --output-file=requirements/docs.txt --resolver=backtracking requirements/vcs_packages.in setup.cfg
@@ -94,8 +94,9 @@ fluiddyn==0.5.1
     #   fluidsim-core
     #   snek5000
     #   snek5000 (setup.cfg)
-fluidsim-core==0.7.1
+fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
     # via
+    #   -r requirements/vcs_packages.in
     #   snek5000
     #   snek5000 (setup.cfg)
 fonttools==4.38.0
@@ -124,11 +125,8 @@ imagesize==1.4.1
     # via sphinx
 importlib-metadata==5.1.0
     # via
-    #   fluidsim-core
     #   jupyter-cache
     #   myst-nb
-    #   nbconvert
-    #   sphinx
 inflection==0.5.1
     # via
     #   snek5000

requirements/main.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --output-file=requirements/main.txt --resolver=backtracking setup.cfg
@@ -54,8 +54,6 @@ h5py==3.7.0
     #   h5netcdf
 idna==3.4
     # via requests
-importlib-metadata==5.1.0
-    # via fluidsim-core
 inflection==0.5.1
     # via snek5000 (setup.cfg)
 jinja2==3.1.2
@@ -160,5 +158,3 @@ xarray==2022.12.0
     # via pymech
 yte==1.5.1
     # via snakemake
-zipp==3.11.0
-    # via importlib-metadata

requirements/tests-editable.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --extra=tests --output-file=requirements/tests.txt --resolver=backtracking requirements/vcs_packages.in setup.cfg
@@ -70,8 +70,9 @@ fluiddyn==0.5.1
     #   fluidsim-core
     #   snek5000
     #   snek5000 (setup.cfg)
-fluidsim-core==0.7.1
+fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
     # via
+    #   -r requirements/vcs_packages.in
     #   snek5000
     #   snek5000 (setup.cfg)
 fonttools==4.38.0
@@ -88,8 +89,6 @@ h5py==3.7.0
     #   h5netcdf
 idna==3.4
     # via requests
-importlib-metadata==5.1.0
-    # via fluidsim-core
 inflection==0.5.1
     # via
     #   snek5000
@@ -267,5 +266,3 @@ xarray==2022.12.0
     # via pymech
 yte==1.5.1
     # via snakemake
-zipp==3.11.0
-    # via importlib-metadata

requirements/tests.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --extra=tests --output-file=requirements/tests.txt --resolver=backtracking requirements/vcs_packages.in setup.cfg
@@ -70,8 +70,9 @@ fluiddyn==0.5.1
     #   fluidsim-core
     #   snek5000
     #   snek5000 (setup.cfg)
-fluidsim-core==0.7.1
+fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
     # via
+    #   -r requirements/vcs_packages.in
     #   snek5000
     #   snek5000 (setup.cfg)
 fonttools==4.38.0
@@ -88,8 +89,6 @@ h5py==3.7.0
     #   h5netcdf
 idna==3.4
     # via requests
-importlib-metadata==5.1.0
-    # via fluidsim-core
 inflection==0.5.1
     # via
     #   snek5000
@@ -267,5 +266,3 @@ xarray==2022.12.0
     # via pymech
 yte==1.5.1
     # via snakemake
-zipp==3.11.0
-    # via importlib-metadata

requirements/vcs_packages.in

@@ -4,5 +4,5 @@
 snek5000-phill @ git+https://github.com/snek5000/snek5000-phill.git
 snek5000-cbox @ git+https://github.com/snek5000/snek5000-cbox.git
 # TODO before releases: comment out these 2 lines
-# fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
+fluidsim-core @ hg+https://foss.heptapod.net/fluiddyn/fluidsim#subdirectory=lib
 # pymech @ git+https://github.com/eX-Mech/pymech.git

src/snek5000/output/remaining_clock_time.py

@@ -2,11 +2,38 @@
 
 """
 
+import numpy as np
+
+from fluidsim_core.output.remaining_clock_time import RemainingClockTime as Base
+
 from .simple_csv import OutputWithCsvFileAndParam
 
 
-class RemainingClockTime(OutputWithCsvFileAndParam):
+class RemainingClockTime(OutputWithCsvFileAndParam, Base):
     INDEX_USERPARAM = 12
     _tag = "remaining_clock_time"
     _param_name = "period_save_in_seconds"
     _param_default_value = 5.0
+
+    def _load_times(self):
+        df = self.load()
+        data = {key: df[key].values for key in df.keys()}
+        data["full_clock_time"] = np.nansum(data["delta_clock_times"])
+        data["equation_time_start"] = df.loc[0, "equation_times"]
+        return data
+
+    def load(self):
+        df = super().load()
+        df["delta_equation_times"] = df.equation_times.diff()
+        delta_time_inds = df.it.diff()
+        df["clock_times_per_timestep"] = df["delta_clock_times"] / delta_time_inds
+        keys = (
+            "delta_clock_times",
+            "delta_equation_times",
+            "clock_times_per_timestep",
+        )
+        df.loc[df["it"] == 0, keys] = np.nan
+        return df
+
+    def plot(self):
+        self.plot_clock_times()

tests/test_tgv.py

@@ -14,3 +14,5 @@ def test_tgv(sim_tgv_executed):
     df = sim.output.remaining_clock_time.load()
     assert isinstance(df, pd.DataFrame)
     assert len(df) >= 2
+
+    sim.output.remaining_clock_time.plot()