Add ProgressBar to visualise progress in Simulate()

[TobiasDuswald]

Added a ProgressBar such that one clearly sees the progress of the simulation. Example output:

ET = Elapsed Time; TR = Time Remaining
[######                                          ] 135 / 1000 ( ET:  1649, TR:10566)[ms]

Examples:

1. No output (default)

[bdm-1.3.4] (base) 
~/tmp/soma_clustering/build on  master! ⌚ 12:34:13
$ ./soma_clustering
number of cells in subvolume: 2360
average neighbors in subvolume: 28
correctness coefficient: 0.0157542
Simulation completed successfully!

2. Show Simulation step every 100 steps

[bdm-1.3.4] (base) 
~/tmp/soma_clustering/build on  master! ⌚ 12:36:10
$ ./soma_clustering  --inline-config '{ "bdm::Param": { "show_simulation_step": 100 } }' 
Time step: 0
Time step: 100
Time step: 200
Time step: 300
Time step: 400
Time step: 500
Time step: 600
Time step: 700
Time step: 800
Time step: 900
number of cells in subvolume: 2384
average neighbors in subvolume: 26
correctness coefficient: 0.0468571
Simulation completed successfully!

3. Use the progress bar

~/tmp/soma_clustering/build on  master! ⌚ 12:34:29
$ ./soma_clustering  --inline-config '{ "bdm::Param": { "use_progress_bar": true } }'

ET = Elapsed Time; TR = Time Remaining
[##################################################] 1000 / 1000 ( ET: 11988, TR:    0)[ms]
number of cells in subvolume: 2456
average neighbors in subvolume: 26
correctness coefficient: 0.026382
Simulation completed successfully!

[FonsRademakers]

Hi Tobias, very nice to have this progress bar. Could we implement a bit friendlier command line argument parsing like: ./soma_clustering —show_simulation_step=100 Instead of ./soma_clustering --inline-config '{ "bdm::Param": { "show_simulation_step": 100 } }' Where unknown arguments are internally being transformed to an inline-config string. This makes command line arguments much more user friendly. Thanks, Fons.

…

On 17 Dec 2021, at 13:16, Tobias Duswald ***@***.***> wrote:  Added a ProgressBar such that one clearly sees the progress of the simulation. Example output: ET = Elapsed Time; TR = Time Remaining [###### ] 135 / 1000 ( ET: 1649, TR:10566)[ms] Examples: No output (default) [bdm-1.3.4] (base) ~/tmp/soma_clustering/build on  master! ⌚ 12:34:13 $ ./soma_clustering number of cells in subvolume: 2360 average neighbors in subvolume: 28 correctness coefficient: 0.0157542 Simulation completed successfully! Show Simulation step every 100 steps [bdm-1.3.4] (base) ~/tmp/soma_clustering/build on  master! ⌚ 12:36:10 $ ./soma_clustering --inline-config '{ "bdm::Param": { "show_simulation_step": 100 } }' Time step: 0 Time step: 100 Time step: 200 Time step: 300 Time step: 400 Time step: 500 Time step: 600 Time step: 700 Time step: 800 Time step: 900 number of cells in subvolume: 2384 average neighbors in subvolume: 26 correctness coefficient: 0.0468571 Simulation completed successfully! Use the progress bar ~/tmp/soma_clustering/build on  master! ⌚ 12:34:29 $ ./soma_clustering --inline-config '{ "bdm::Param": { "use_progress_bar": true } }' ET = Elapsed Time; TR = Time Remaining [##################################################] 1000 / 1000 ( ET: 11988, TR: 0)[ms] number of cells in subvolume: 2456 average neighbors in subvolume: 26 correctness coefficient: 0.026382 Simulation completed successfully! You can view, comment on, or merge this pull request online at: #237 Commit Summary 86fa27b Add ProgressBar class d6d73e3 Include the ProgressBar in the Scheduler 10f5f4e Add parameter for the ProgressBar 0548821 Add copyright File Changes (7 files) M src/core/param/param.cc (1) M src/core/param/param.h (12) M src/core/scheduler.cc (21) M src/core/scheduler.h (4) A src/core/util/progress_bar.cc (86) A src/core/util/progress_bar.h (51) M src/core/util/timing.h (1) Patch Links: https://github.com/BioDynaMo/biodynamo/pull/237.patch https://github.com/BioDynaMo/biodynamo/pull/237.diff — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[TobiasDuswald]

[...] Could we implement a bit friendlier command line argument parsing [...]

Hi Fons,
I think you're raising a very valid point. It goes a little beyond this PR so I created a card on Trello such that we can return to it as soon as there is some free time. Thanks for pointing it out!

[FonsRademakers]

Thanks for having created a Trello card. Cheers,Fons.

…

On 17 Dec 2021, at 13:58, Tobias Duswald ***@***.***> wrote: [...] Could we implement a bit friendlier command line argument parsing [...] Hi Fons, I think you're raising a very valid point. It goes a little beyond this PR so I created a card on Trello such that we can return to it as soon as there is some free time. Thanks for pointing it out! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.

-------------------------------------------------------------------------- Dr. Fons Rademakers CERN - European Organization for Nuclear Research Chief Research Officer 1211 Geneve 23, Switzerland CERN openlab Tel: +41227679248 Mobile: +41754113742 --------------------------------------------------------------------------