timothydmorton/isochrones

Info: Interpolating incomplete tracks for feh = -1.5 during run nosetests isochrones

leizhenxin opened this issue · 5 comments

leizhenxin commented

It cost a longtime at interpolating tracks of feh =-1.5 when run nosetests isochrones for the first time on my macOS Bigsur system. So I closed the terminal and run nosetests isochrones in a new terminal. Then errors occurred like as follows:
......
chrones/tests/test_fits.py:6: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
from pandas.util.testing import assert_frame_equal
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
E...../Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/isochrones/priors.py:89: RuntimeWarning: divide by zero encountered in true_divide
sigma = 1.0 / np.sqrt(hn)
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00
E...
ERROR: isochrones.tests.test_basic.test_tracks
......

How can I generate all other missing tracks now? Need I to delete all the already existing tracks then run nosetests again? Actually, I cannot find the interpolated tracks in my Mac.

leizhenxin commented

I tried nosetests again after multinest was installed , but the problem is still exist:

...................
/Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/isochrones/tests/test_fits.py:6: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
from pandas.util.testing import assert_frame_equal
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 552.34i
E... MultiNest Warning: no resume file found, starting from scratch

MultiNest v3.10
Copyright Farhan Feroz & Mike Hobson
Release Jul 2015

no. of live points = 5
dimensionality = 5

ln(ev)= -10060.873166967840 +/- 0.56735137479931252
Total Likelihood Evaluations: 5
Sampling finished. Exiting MultiNest
. MultiNest Warning: no resume file found, starting from scratch

MultiNest v3.10
Copyright Farhan Feroz & Mike Hobson
Release Jul 2015

no. of live points = 20
dimensionality = 5

ln(ev)= -34.311953691583675 +/- NaN
Total Likelihood Evaluations: 327
Sampling finished. Exiting MultiNest
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3381.82
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3445.72
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3404.47
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3424.62
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3428.12
E...../Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/isochrones/priors.py:89: RuntimeWarning: divide by zero encountered in true_divide
sigma = 1.0 / np.sqrt(hn)
interpolating missing values in evolution tracks (feh=-1.5)': 80%|▊| 4/5 [00:00<00:00, 3358.80
E...
.................................

How can I solve this problem? Any suggestions are welcome

timothydmorton commented

These tables get created/stored by default in a ~/.isochrones directory, or in $ISOCHRONES if that environment variable is defined. Try to delete that directory and run the tests again; let me know if that works!

leizhenxin commented

Hi Tim,
Thank you for your useful information.
I deleted the tables in ~/.isochrones directory, then run nosetests again. It seems to work normally.
However, it stays at the stage of interpolating tracks of feh=-1.5 for the whole night (i.e., more than 8 hours), without any changes:
...........................
/Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/tables/attributeset.py:464: NaturalNameWarning: object name is not a valid Python identifier: 'axis1_name[Fe/H]'; it does not match the pattern ^[a-zA-Z_][a-zA-Z0-9_]*$; you will not be able to use natural naming to access this object; using getattr() will still work, though
check_attribute_name(name)
interpolating missing values in evolution tracks (feh=-4.0)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-3.5)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-3.0)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-2.5)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-2.0)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-1.75)': 100%|█| 196/196 [
.............................

Does it work normally ？ Should I stop the terminal and repeat the operation again? Or just waiting?

leizhenxin commented

It works! All tracks are interpolated now.
.................
from pandas.util.testing import assert_frame_equal
interpolating missing values in evolution tracks (feh=-1.5)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-1.25)': 100%|█| 196/196 [
interpolating missing values in evolution tracks (feh=-1.0)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-0.75)': 100%|█| 196/196 [
interpolating missing values in evolution tracks (feh=-0.5)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=-0.25)': 100%|█| 196/196 [
interpolating missing values in evolution tracks (feh=0.0)': 100%|█| 196/196 [00
interpolating missing values in evolution tracks (feh=0.25)': 100%|█| 196/196 [0
interpolating missing values in evolution tracks (feh=0.5)': 100%|█| 196/196 [00
...................

However, there is still a failure exist:

.........................................
Sampling finished. Exiting MultiNest
....../Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/numpy/core/shape_base.py:65: 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.
ary = asanyarray(ary)
........../Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/isochrones/priors.py:89: RuntimeWarning: divide by zero encountered in true_divide
sigma = 1.0 / np.sqrt(hn)
..F.......

FAIL: Testing with first entry from Gaia DR1 TGAS table

Traceback (most recent call last):
File "/Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/leizhenxin/opt/anaconda3/envs/isochrones/lib/python3.10/site-packages/isochrones/tests/test_query.py", line 38, in test_queries
assert tm.get_id() == b("03000819+0014074") # force byte literal b/c that's what gets returned
AssertionError

Ran 34 tests in 86.357s
............................................

How to solve these problem?

timothydmorton commented

That one failure is fine. I believe it has been marked as skipped in the latest version on the master branch here. I think you are good to go!