w_assign error

[QVH]

Hello,

I tried to use the w_assign tool and received this error:

AttributeError: 'RectilinearBinMapper' object has no attribute 'nbins'

I also tried the command on one of the tutorial (WESTPA_Workshop_2018_Saglam) and got the same AttributeError:

AttributeError: 'VoronoiBinMapper' object has no attribute 'nbins'

If I run the w_ipa command, I would get an assign.h5 file but also get the same IndexError as one of the other users:

IndexError: index 2 is out of bounds for axis 0 with size 2

I installed the westpa-2020.03 from conda with python 3.7.8.

I really appreciate any help to get pass this error. Thank you

Kind regards,

- Q

[Anthony Bogetti]

Hello,

 

Thank you for your question.  What options are you using with w_assign?  Would you also be able to send along the west.cfg file and west.h5 file you are using in your analysis?  Maybe there is some connection between these errors from w_ipa, I will look into it and let you know.

 

Anthony

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[Quynh Vo]

Attachments available until Sep 23, 2020

Hi Anthony,

Thank you for the quick response.

I used the following commands for my own westpa run:

w_assign -W west.h5.copy -r west.cfg.copy

w_ipa -W west.h5.copy -r west.cfg.copy

for the tutorial:

w_assign -W west.tutorial.h5 -r west.tutorial.cfg --states-from-file states_8dims.yaml

Thank you!

- Q

Click to Download

west.cfg.copy

5 KB

Click to Download

west.h5.copy

28.1 MB

Click to Download

west.tutorial.cfg

2 KB

Click to Download

west.tutorial.h5

4.7 MB

Click to Download

states_8dims.yaml

214 bytes

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[Anthony Bogetti]

Hello,

 

It seems you are having the same issue as the other mailing list post, it’s numpy version 1.19 that seems to be throwing that error.  Sorry about that; I’ll look into fixing this on the conda channel.  For now, please downgrade numpy to 1.18 (conda install numpy=1.18) or see the yml file I attached to the previous error for my specific env to solve this problem for now.

 

Best,

Anthony

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/1B2CCD89-33FD-40FB-8D25-665BB8FC1616%40gmail.com.

 

[Quynh Vo]

Hi Anthony,

Thank you for the quick fix.

I downgraded numpy to 1.18 as suggested and w_ipa ran just fine.

However, w_assign still throws the same error. I’m interested in using the  --state-from-file flag. Is there a way to specify this flag with w_ipa?

Thank you!  

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/63127E91-636E-41E0-91EC-CC28881DA3B9%40hxcore.ol.

[Anthony Bogetti]

You should be able to copy the state definitions from your states_8dims.yaml file and paste them at the end of your west.cfg.  Running w_ipa with that west.cfg should then essentially do the same thing.  I was able to run w_ipa with this change and not have any errors.  Let me know if this is not giving you what you expect.

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/46287718-AE13-45FA-96E3-1ACE2E278B3E%40gmail.com.