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bennch-plot's Issues

Problem running microcircuit example

Hi!

I am trying to run the microsircuit.py example, but I am not getting it to work.

There seems to be quite alot of arguments that are not allowed anymore,
https://github.com/INM-6/benchplot/blob/e2f93d4d9bc06ac3f9bf8e5174f50feeb6be99b6/examples/microcircuit/microcircuit.py#L38-L42

but, also after copying these out I get problems. This concerns the B.plot_main() lines, and as I am not familiar with benchplot I do not know how best to fix this.

I also had a problem with the multi-area-model example, but this just concerned line 50
https://github.com/INM-6/benchplot/blob/e2f93d4d9bc06ac3f9bf8e5174f50feeb6be99b6/examples/multi-area-model/multi-area-model.py#L50

Here I got

TypeError: unhashable type: 'numpy.ndarray'

Copying out the line made the example run through. Is this a known error?

I am using Python 3.7.10.

Handle case if benchmark results contain only one simulation

Raises currently an IndexError:

Traceback (most recent call last):
  File "../analysis/analysis.py", line 50, in <module>
    plot(
  File "/p/project/cjinb33/jinb3320/repositories/beNNch/analysis/plot_helper.py", line 59, in plot
    B.plot_fractions(axis=ax1,
  File "/p/project/cjinb33/jinb3320/repositories/beNNch/plot/benchplot/bench_plot.py", line 247, in plot_fractions
    axis.fill_between(np.squeeze(self.df[self.x_axis]),
  File "/p/software/jurecadc/stages/2020/software/SciPy-Stack/2021-gcccoremkl-10.3.0-2021.2.0-Python-3.8.5/lib/python3.8/site-packages/matplotlib-3.3.1-py3.8-linux-x86_64.egg/matplotlib/__init__.py", line 1438, in inner
    return func(ax, *map(sanitize_sequence, args), **kwargs)
  File "/p/software/jurecadc/stages/2020/software/SciPy-Stack/2021-gcccoremkl-10.3.0-2021.2.0-Python-3.8.5/lib/python3.8/site-packages/matplotlib-3.3.1-py3.8-linux-x86_64.egg/matplotlib/axes/_axes.py", line 5301, in fill_between
    return self._fill_between_x_or_y(
  File "/p/software/jurecadc/stages/2020/software/SciPy-Stack/2021-gcccoremkl-10.3.0-2021.2.0-Python-3.8.5/lib/python3.8/site-packages/matplotlib-3.3.1-py3.8-linux-x86_64.egg/matplotlib/axes/_axes.py", line 5229, in _fill_between_x_or_y
    for idx0, idx1 in cbook.contiguous_regions(where):
  File "/p/software/jurecadc/stages/2020/software/SciPy-Stack/2021-gcccoremkl-10.3.0-2021.2.0-Python-3.8.5/lib/python3.8/site-packages/matplotlib-3.3.1-py3.8-linux-x86_64.egg/matplotlib/cbook/__init__.py", line 1253, in contiguous_regions
    idx, = np.nonzero(mask[:-1] != mask[1:])
IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed

Decide if just one data point shall be plotted or if the plotting should fail with a message that the function is not applicable for the provided type of data.

vlines, hlines

Add functionality to pass list of numbers, colors to plot vertical or horizontal lines.

Developer documentation missing

plot_params.py and bench_plot.py are missing developer documentation. All functions should have a docstring with a (short) description of what the function does, parameters and return values.

There should also be a docstring at the top stating what the file does. See for instance hl_api_simulation.py from NEST.

Should there also be a copyright header like we have in NEST?

Definition of nvp

The number of virtual processes nvp is calculated like this:

nvp = threads_per_task * tasks_per_node

This is the number of processes per node, but shouldn't it rather be the number of processes across all nodes?

nvp = threads_per_task * tasks_per_node * num_nodes

Problems running examples

When I try running the included multi-area model example, I get the following error message:

python examples/multi-area-model/multi-area-model.py 
Traceback (most recent call last):
  File "examples/multi-area-model/multi-area-model.py", line 17, in <module>
    B = bp.BenchPlot(**args)
TypeError: __init__() got an unexpected keyword argument 'data_hash'

The same is true for ram.py, microcircuit.py and minimal_microcircuit.py. I guess this can be fixed by instead using data_file, but then I get this error message, and this I am not sure how to fix:

Traceback (most recent call last):
  File "examples/multi-area-model/multi-area-model.py", line 17, in <module>
    B = bp.BenchPlot(**args)
TypeError: __init__() got an unexpected keyword argument 'catalogue_path'

Update README

README should be updated and include some information. Most importantly:

  • some sentences about what benchplot does
  • how to install it
  • simplest way of running it

Maybe also link to examples folder and benchmarking framework?

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