With matplotlib 3.5.2, numpy 1.22.3 and Python 3.10.4 (defaults on Jureca with Stages/2023), the analysis.py script fails when using the scaling type 'threads' while it doesn't with scaling type 'nodes'. See the stacktrace below:
/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/ticker.py:795: VisibleDeprecationWarning:
Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated.
If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
locs = (np.asarray(_locs) - self.offset) / 10. ** self.orderOfMagnitude
AttributeError: 'numpy.ndarray' object has no attribute 'rint'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/p/scratch/cjinb33/ci-bennch/production/jureca/userdata/vogelsang1/1681206505/bennch/results/../analysis/analysis.py", line 50, in <module>
plot(
File "/p/scratch/cjinb33/ci-bennch/production/jureca/userdata/vogelsang1/1681206505/bennch/analysis/plot_helper.py", line 144, in plot
plt.savefig(f'{save_path}/{timer_hash}.png', dpi=600)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/pyplot.py", line 979, in savefig
res = fig.savefig(*args, **kwargs)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/figure.py", line 3046, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2295, in print_figure
self.figure.draw(renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/artist.py", line 73, in draw_wrapper
result = draw(artist, renderer, *args, **kwargs)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/artist.py", line 50, in draw_wrapper
return draw(artist, renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/figure.py", line 2828, in draw
self.execute_constrained_layout(renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/figure.py", line 3186, in execute_constrained_layout
return do_constrained_layout(fig, renderer, h_pad, w_pad,
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/_constrained_layout.py", line 110, in do_constrained_layout
make_layout_margins(layoutgrids, fig, renderer, h_pad=h_pad,
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/_constrained_layout.py", line 315, in make_layout_margins
pos, bbox = get_pos_and_bbox(ax, renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/_constrained_layout.py", line 548, in get_pos_and_bbox
tightbbox = ax.get_tightbbox(renderer=renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 4632, in get_tightbbox
bb_xaxis = self.xaxis.get_tightbbox(renderer)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/axis.py", line 1103, in get_tightbbox
ticks_to_draw = self._update_ticks()
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/axis.py", line 1046, in _update_ticks
major_labels = self.major.formatter.format_ticks(major_locs)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/ticker.py", line 223, in format_ticks
self.set_locs(values)
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/ticker.py", line 713, in set_locs
self._set_format()
File "/p/software/jurecadc/stages/2023/software/matplotlib/3.5.2-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/matplotlib/ticker.py", line 812, in _set_format
if np.abs(locs - np.round(locs, decimals=sigfigs)).max() < thresh:
File "<__array_function__ internals>", line 180, in round_
File "/p/software/jurecadc/stages/2023/software/SciPy-bundle/2022.05-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 3773, in round_
return around(a, decimals=decimals, out=out)
File "<__array_function__ internals>", line 180, in around
File "/p/software/jurecadc/stages/2023/software/SciPy-bundle/2022.05-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 3348, in around
return _wrapfunc(a, 'round', decimals=decimals, out=out)
File "/p/software/jurecadc/stages/2023/software/SciPy-bundle/2022.05-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 66, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/p/software/jurecadc/stages/2023/software/SciPy-bundle/2022.05-gcccoremkl-11.3.0-2022.1.0/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
TypeError: loop of ufunc does not support argument 0 of type numpy.ndarray which has no callable rint method
I got the suspicion, that the deprecation warning in the very first line could be the cause of the error here.
JanVogelsang
commented
1 year ago
With matplotlib 3.5.2, numpy 1.22.3 and Python 3.10.4 (defaults on Jureca with Stages/2023), the
analysis.pyscript fails when using the scaling type 'threads' while it doesn't with scaling type 'nodes'. See the stacktrace below:I got the suspicion, that the deprecation warning in the very first line could be the cause of the error here.