Cobaya - Polychord

[vivianmiranda]

Hi Jesus

My polychord keep crashing with this error

Traceback (most recent call last):
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/bin/cobaya-run", line 11, in
load_entry_point('cobaya', 'console_scripts', 'cobaya-run')()
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/cosmolike_core/cobaya/cobaya/cobaya/run.py", line 126, in run_script
run(info)
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/cosmolike_core/cobaya/cobaya/cobaya/run.py", line 67, in run
sampler.run()
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/cosmolike_core/cobaya/cobaya/cobaya/sampler.py", line 184, in exit
self.close(exception_type, exception_value, traceback)
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/cosmolike_core/cobaya/cobaya/cobaya/run.py", line 67, in run
sampler.run()
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/cosmolike_core/cobaya/cobaya/cobaya/samplers/polychord/polychord.py", line 226, in run
self.pc_prior, self.dumper)
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/lib/python2.7/site-packages/pypolychord-1.16-py2.7-linux-x86_64.egg/pypolychord/init.py", line 227, in run_polychord
return PolyChordOutput(settings.base_dir, settings.file_root)
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/lib/python2.7/site-packages/pypolychord-1.16-py2.7-linux-x86_64.egg/pypolychord/output.py", line 100, in init
self._create_pandas_table()
File "/scratch/midway2/viniciusvmb/krause/cosmo_cobaya6/lib/python2.7/site-packages/pypolychord-1.16-py2.7-linux-x86_64.egg/pypolychord/output.py", line 190, in _create_pandas_table
self._samples_table['loglike'] *= -0.5
File "/home/viniciusvmb/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 897, in f
result = method(self, other)
File "/home/viniciusvmb/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1069, in wrapper
result = safe_na_op(lvalues, rvalues)
File "/home/viniciusvmb/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1037, in safe_na_op
lambda x: op(x, rvalues))
File "pandas/_libs/algos_common_helper.pxi", line 1212, in pandas._libs.algos.arrmap_object
File "/home/viniciusvmb/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1037, in
lambda x: op(x, rvalues))
TypeError: can't multiply sequence by non-int of type 'float'

any clues? Here is my yaml file.

POLY_DES_PLANCK_MCMC_0.txt

[JesusTorrado]

Hi Vivian,

At first sight it looks like a bad PolyChord-Pandas interaction when loading the "equal_weights" file. I have just made quite a few tests on a virtual environment using your Python and PolyChord versions (and combining it with a range of Pandas versions) and I have been unable to reproduce it. The only way I have been able to reproduce that error is by manually setting an element of a pandas DataFrame to a sequence, and them multiplying by a number:

>>> import pandas
>>> a = pandas.DataFrame(columns=["a", "b"])
>>> a.iat[0, 0] = [1,2]
>>> a["a"] *= 0.5  # --> produces the same error

You should be able (I think) to reproduce the error yourself by running cobaya on the original chain in "resume" mode (it should skip PolyChord's run and try to load the output, which is what appears to be failing). If you can reproduce it this way, would you send me the "equal weights" file? (provately, if you prefer)

Worst case scenario, downgrade to PolyChord 1.15 (you are using a non-released 1.16 version) and it should produce the correct output running in resume mode on the last chain (but make a backup just in case).

Cheers
Jesús

[vivianmiranda]

Here is my equal_weight files it has Infinite -> does that help explain it? On Mar 28, 2019, at 2:23 PM, Jesús Torrado <notifications@github.com<mailto:notifications@github.com>> wrote: Hi Vivian, At first sight it looks like a bad PolyChord-Pandas interaction when loading the "equal_weights" file. I have just made quite a few tests on a virtual environment using your Python and PolyChord versions (and combining it with a range of Pandas versions) and I have been unable to reproduce it. The only way I have been able to reproduce that error is by manually setting an element of a pandas DataFrame to a sequence, and them multiplying by a number:

>> import pandas >> a = pandas.DataFrame(columns=["a", "b"]) >> a.iat[0, 0] = [1,2] >> a["a"] *= 0.5 # --> produces the same error

You should be able (I think) to reproduce the error yourself by running cobaya on the original chain in "resume" mode (it should skip PolyChord's run and try to load the output, which is what appears to be failing). If you can reproduce it this way, would you send me the "equal weights" file? (provately, if you prefer) Worst case scenario, downgrade to PolyChord 1.15 (you are using a non-released 1.16 version) and it should produce the correct output running in resume mode on the last chain (but make a backup just in case). Cheers Jesús — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#23 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ADD96HnDqo_rK0y30aZ_196Bs9JlJXELks5vbMI8gaJpZM4cP9hz>. 0.100000000000000E+001 Infinity 0.260378474942752E+001 0.706036240301655E+001 0.104962582088481E+001 0.815989518725719E-002 0.810263398586531E-001 0.268696481118102E-001 0.750043497089222E+000 0.345017216691584E-001 -0.162254674335593E-001 -0.254374447474508E-001 -0.229229063564868E-002 -0.396201644410850E-001 0.959966011491656E+000 0.103359621833476E+001 0.283069739381328E+001 0.185558266738775E+001 0.913992207065960E+000 -0.573177081000142E-001 -0.580111989725616E-001 0.148118616708988E-001 -0.875277738802189E-001 -0.658672330724403E-001 0.394274661343201E-001 0.118350122820921E+000 -0.141251471011857E-001 0.232792068627538E+001 -0.325693871985559E+001 0.990638609628791E+000 0.741764799929282E+002 0.875537744545024E+000 0.839018330064830E+001 0.226474855811912E+003 0.210774991406925E+003 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[JesusTorrado]

Indeed! As can be seen here, pandas-dev/pandas#10065, only "inf"/"-inf" is interpreted as infinity (it's a really old bug, and still open!).

Since we can't do anything about this, have you tried downgrading to PolyChord 1.15 and resuming? Otherwise, try commenting out lines 98-103 of pypolychord/output.py in your PolyChord source (the original one, not the Cobaya interface).

In any case, it's really strange that you are getting infinities in the posterior value of the equal weights samples file. Did the sampling succeed? What's in the second column of the original PolyChord .txt file?

[vivianmiranda]

Hi Here is my txt file Planck 2018 has a limitation in maximum ClEE (simall like) so I had to include this line of code in Planck python -> that is producing a lot of infinity when running DES+Planck chains with DES priors [cid:967ea84b-f3b8-4e94-b818-8ff0c910bf07@namprd19.prod.outlook.com] On Mar 28, 2019, at 3:39 PM, Jesús Torrado <notifications@github.com<mailto:notifications@github.com>> wrote: Indeed! As can be seen here, pandas-dev/pandas#10065<pandas-dev/pandas#10065>, only "inf"/"-inf" is interpreted as infinity (it's a really old bug, and still open!). Since we can't do anything about this, have you tried downgrading to PolyChord 1.15 and resuming? Otherwise, try commenting out lines 98-103 of pypolychord/output.py in your PolyChord source (the original one, not the Cobaya interface). In any case, it's really strange that you are getting infinities in the posterior value of the equal weights samples file. Did the sampling succeed? What's in the second column of the original PolyChord .txt file? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#23 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ADD96DoY2ROqoOUJe--myh6CH6yQNgydks5vbNQngaJpZM4cP9hz>. 0.100000000000000E+001 Infinity 0.260378474942752E+001 0.706036240301655E+001 0.104962582088481E+001 0.815989518725719E-002 0.810263398586531E-001 0.268696481118102E-001 0.750043497089222E+000 0.345017216691584E-001 -0.162254674335593E-001 -0.254374447474508E-001 -0.229229063564868E-002 -0.396201644410850E-001 0.959966011491656E+000 0.103359621833476E+001 0.283069739381328E+001 0.185558266738775E+001 0.913992207065960E+000 -0.573177081000142E-001 -0.580111989725616E-001 0.148118616708988E-001 -0.875277738802189E-001 -0.658672330724403E-001 0.394274661343201E-001 0.118350122820921E+000 -0.141251471011857E-001 0.232792068627538E+001 -0.325693871985559E+001 0.990638609628791E+000 0.741764799929282E+002 0.875537744545024E+000 0.839018330064830E+001 0.226474855811912E+003 0.210774991406925E+003 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[JesusTorrado]

Sorry, I can't see the attached file (I mean your modification to the Planck likelihood: the txt output I can see).

In any case, I think I found the source of the problem: at some point in the last few months, PolyChord started accepting points with -inf posterior (it didn't before: they were rejected automatically), so if your initial sample does not find a finite logposterior, PolyChord assumes there is no point with finite posterior and finished prematurely. I still need to think how to deal with this (maybe increasing the nprior option of PolyChord, which is not very efficient) but for now what I would recommend you is to downgrade to the last fully-compatible PolyChord version, which is commit ef02bb (either clone and checkout that hash, or install with cobaya-install and it should grab it automatically).

Please, let me know if that works so that I can close this issue, and I will start taking a look at how to integrate the new PolyChord behaviour.

[vivianmiranda]

Thank you I am testing this right now here is my change to planck likelihood in cobaya #VM begins test = False # CLIK EE AMPLITUDE ERROR for j in range(1,32): if(cl["ee"][j]*j*(j+1)/2.0/3.14159265359>0.293): test = True # CAMB LENSING NORMALIZATION WARNING if('pp' in self.requested_cls) : if(cl['pp'][10] > 1e-7): test = True if(test == True) : loglike = -1e30 else : loglike = self.clik(self.vector)[0] # loglike = self.clik(self.vector)[0] #VM ends On Mar 28, 2019, at 4:27 PM, Jesús Torrado <notifications@github.com<mailto:notifications@github.com>> wrote: Sorry, I can't see the attached file (I mean your modification to the Planck likelihood: the txt output I can see). In any case, I think I found the source of the problem: at some point in the last few months, PolyChord started accepting points with -inf posterior (it didn't before: they were rejected automatically), so if your initial sample does not find a finite logposterior, PolyChord assumes there is no point with finite posterior and finished prematurely. I still need to think how to deal with this (maybe increasing the nprior option of PolyChord, which is not very efficient) but for now what I would recommend you is to downgrade to the last fully-compatible PolyChord version, which is commit ef02bb (either clone and checkout that hash, or install with cobaya-install and it should grab it automatically). Please, let me know if that works so that I can close this issue, and I will start taking a look at how to integrate the new PolyChord behaviour. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#23 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ADD96O7XJews-XTvaOmHb7txvF2bqkHXks5vbN9wgaJpZM4cP9hz>.

[JesusTorrado]

Closing for now. Please, reopen if the error re-appears (with the PolyChord version installed with cobaya-install).