plothist error

[Mac Kevin Braza]

Hi folks,

I wanna ask for help on knowing what might be the error in our plothist analysis.

(westpa-2020.05) mbraza:TSCC-test$ w_pdist -W west.h5

(westpa-2020.05) mbraza:TSCC-test$ plothist average pdist.h5 "0::dihedral angle" "1::com distance"

Operation:      Constructing histograms

(python3:20300): GLib-CRITICAL **: 15:07:41.707: g_hash_table_contains: assertion 'hash_table != NULL' failed

Progress:       100% [=============================================================================================================================================================================================]

(python3:20300): GLib-CRITICAL **: 15:07:41.707: g_hash_table_insert_internal: assertion 'hash_table != NULL' failed

Segmentation fault (core dumped)

I am using Python3.8 and westpa-2020.05 release. Not sure where's the error coming from. I have west.h5 available and west.cfg files both in the same directory. Thank you for your help!

Sincerely,

Kevin

[Leung, Jeremy]

Hi Kevin,

I have a feeling it's related to your pdist.h5 having invalid numbers (e.g. NULL or NaN). Would you be able to email me that (or check it yourself to see if it's containing any invalid numbers?)?

It might also be worth looking at the west.h5 pcoord dataset to double check if there are any weird numbers. If it's in pdist.h5, it's likely carried over from the raw data.

FYI, plothist only requires the pdist.h5 to plot, so it's unnecessary for the west.h5 and west.cfg to be in the same folder after running w_pdist.

-- JL

P.S.  Thanks for keeping up to date with our releases! 

--
Jeremy M. G. Leung
PhD Candidate, Chemistry
Graduate Student Researcher, Chemistry 

University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

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[Mac Kevin Braza]

Hi Jeremy,

Thanks for your advice! Sure, I am attaching our pdist.h5 here. Weirdly enough, my lab mate, Shirley Ahn, have made it work with her workstation with the same dataset and was able to plot it accordingly. I can also share how the generated plot looks like if you need to. Though, I still cannot regenerate it on my end. Thank you Jeremy!

Sincerely,

Kevin

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[Leung, Jeremy]

Hi Kevin,

I was also unable to reproduce your error on a fresh installation of 2020.05. 

I have the following suggestions:

1) It might work itself out if you reinstall/update glib, since that's throwing the error?

2) Make sure you have the following list of dependencies in the python env you're using, as it seems like you installed 2020.05 from the source code, which doesn't take care of dependencies:

- cython

- numpy

- scipy

- h5py

- pyyaml

- pyzmq

- matplotlib-base

- blessings

- ipykernel

3) Another idea is to start a new conda environment and just install 2020.03 via conda and see if it works. We're still working on pushing 2020.05 onto conda, but 2020.03 should be fine for plothist and such.

Regards,

Jeremy L.

--
Jeremy M. G. Leung
PhD Candidate, Chemistry
Graduate Student Researcher, Chemistry 

University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

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<pdist.h5><west.h5><west.cfg><iter_20_pcoord_hist.pdf><iter_20_dihedral_hist.pdf>

[Matthew Zwier]

Kevin,

It is extremely rare for Python to crash as you are seeing here. The problem appears to be that some Python module depending on glib is loading, and glib itself is loading in a corrupted state. This could happen by having a different version of glib on your LD_LIBRARY_PATH that's getting pulled in before the proper version. Jeremy's idea of a clean Conda install would help here, as would emptying your LD_LIBRARY_PATH prior to setting conda environment variables. It's also possible that conda's environment variables are not being set properly, so the system glib is being pulled in when conda expects its own version. A conda reinstall would help with that, too.

Cheers,

Matt Z.

[Mac Kevin Braza]

Hi Matt and Jeremy,

Thank you for your suggestions! I reinstall my anaconda and decided to use westpa-2020.03. On top of that, I followed Jeremy's suggestion to check all dependencies and install them to double check that they are available. I know I am getting closer to the solution, can you take a look again with this new error? 

(westpa-2020.03) mbraza:TSCC-test$ w_pdist -W west.h5
Traceback (most recent call last):
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/w_pdist.py", line 4, in <module>
    from westtools import (WESTParallelTool, WESTDataReader, WESTDSSynthesizer, IterRangeSelection,
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westtools/__init__.py", line 2, in <module>
    from .core import WESTTool, WESTParallelTool, WESTToolComponent, WESTSubcommand, WESTMasterCommand
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westtools/core.py", line 7, in <module>
    import westpa
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westpa/__init__.py", line 1, in <module>
    from . import _rc
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westpa/_rc.py", line 11, in <module>
    from .yamlcfg import YAMLConfig
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westpa/yamlcfg.py", line 21, in <module>
    from westpa.binning import NopMapper
  File "/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westpa/binning/__init__.py", line 1, in <module>
    from . import _assign
ImportError: cannot import name '_assign' from partially initialized module 'westpa.binning' (most likely due to a circular import) (/home/mbraza/Documents/WESTPA/westpa-2020.03/lib/west_tools/westpa/binning/__init__.py)
(westpa-2020.03) mbraza:TSCC-test$ 

Can you suggest a solution so I can solve this on my end? Thank you Matt and Jeremy! I appreciate all the help.

Sincerely,

Kevin

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[Anthony Bogetti]

Hi Kevin,

Thank you for your continued patience as we troubleshoot and try to get this working for you!  The 2020.05 version of WESTPA is now available on conda so let's try this one more time.  I just did this myself in a fresh conda environment.  Go ahead and try the following in a new shell and let me know if any part is not working for you.

1. mkdir test && cd test

2. conda create -n westpa-2020.05-test -c conda-forge westpa

3. conda activate westpa-2020.05-test

4. source $HOME/anaconda3/envs/westpa-2020.05-test/westpa-2020.05/westpa.sh #You will need to change the bold part to the path of your specific anaconda installation

5. which w_pdist #This is just a test to make sure the paths were set up correctly, ideally you would see the path to the installation in the command above

This should take care of all the required dependencies too.  Then go ahead and copy in the h5 file you want to analyze and run w_pdist like you have been.

Best,

Anthony

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[Mac Kevin Braza]

Hi Anthony, Matt, and Jeremy,

Thank you so much for helping me here! I reinstalled WESTPA according to Anthony's suggestion. 

I was able to run w_pdist with westpa-2020.05 version. I was able to generate the plot we needed, and I'm so happy to see them. 

You are awesome Anthony, Matt, and Jeremy! Thank you for your patience, too!

Sincerely,

Kevin

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[Anthony Bogetti]

Hi Kevin,

Awesome! Let us know if you have any other questions.

Best,

Anthony

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