Basic NaCl AMBER tutorial

[Mac Kevin Braza]

Hi folks, 

I am starting the WESTPA Basic NaCl in AMBER from https://github.com/westpa/westpa_tutorials . I am new to WE and WESTPA suite of tools. After setting up my env.sh and source init.sh, this error occured

(westpa-2020.02) mbraza:basic_nacl_amber$ vi env.sh 

(westpa-2020.02) mbraza:basic_nacl_amber$ source init.sh

Traceback (most recent call last):

  File "/home/mbraza/miniconda3/envs/westpa-2020.02/westpa-2020.03/lib/cmds/w_init.py", line 4, in <module>

    import os, sys, logging, numpy, operator, argparse

  File "/home/mbraza/miniconda3/lib/python3.8/site-packages/numpy/__init__.py", line 131

    raise ImportError(msg) from e

                              ^

SyntaxError: invalid syntax

May I know on what specific error did this came from? 

I am using miniconda3 and westpa-2020.02 version. I did not change anything else, except for the amber.sh and westpa.sh. 

Thank you!

Sincerely,

Kevin

[Jeremy Leung]

Hi Kevin,

Thank you for your interest in WESTPA!

Looking at your traceback, it seems like it was an import issue with numpy.  Would you be able to send me your env.sh and init.sh so I can take a look at what the problem is?

I am also interested in how you installed WESTPA. Did you do it via a conda install or via the source code on GitHub?

Thanks,

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]

--
You received this message because you are subscribed to the Google Groups "westpa-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to westpa-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/3724bfb7-45e8-49b9-b4b9-9bac1595b941n%40googlegroups.com.

[Mac Kevin Braza]

Hi Jeremy,

Thank you for your reply!

Here is the env.sh and init.sh that I used.

I installed WESTPA via conda install and I followed your guide from https://github.com/westpa/westpa/wiki/WESTPA-Quick-Installation

I was able to run basic_nacl/ however I encountered PropagationError. Thank you for your help!

Sincerely,

Kevin

[Jeremy Leung]

Hi Kevin,

That's great you were able to solve the initial problem.

If you look at west.log, you see the propagation error is because WESTPA did not correctly receive the progress coordinate values. It was expecting 51 data points (the NaCl distance for the basis state and 50 frames that are saved) and got 0:

-- ERROR    [west.propagators.executable] -- could not read pcoord from '/tmp/tmptnuhcq40': ValueError('progress coordinate data has incorrect shape (0, 1) [expected (51, 1)]')

This is usually caused by a) pcoord calculation failure or b) incorrect code that failed to pass to $WEST_PCOORD_RETURN. (documented here). Since you're running the NaCl tutorial, I suspect a) is the problem.

I suggest looking at a few things:

1) Check seg_logs/000001-000000.log and get_pcoord.log to see if the cause of the error is documented.

2) Trying out the script in common_files/get_dist.py separately to see if it's running correctly.

3) Did w_init receive it in the first try? Check the west.h5 file to see if the pcoord exists in the first iteration.

a) launch ipython and run the following commands:

        import h5py

        f = h5py.File('west.h5','r')

        f['iterations']['iter_00000001']['pcoord'][0]

b) Are the outputs 0s? or are they meaningful numbers?

I also noticed that you commented out the WEST_PYTHON line and the conda activate lines in env.sh, which might interfere with WESTPA trying to call python for those calculations. I would run echo $WEST_PYTHON in the command line to see if it is pointing to the correct python path, and fix that in your env.sh if it's not correct.

Hope that helps! I'm happy to answer more questions when they arise.

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]

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/6a75cb46-c9c0-49bf-9fb8-d5e6225a8098n%40googlegroups.com.
<west.log><init.sh><run.sh><env.sh>

[Mac Kevin Braza]

Hi Jeremy,

Thank you for pointing that out! I just realized that mdtraj was not installed yet and I was able to run it smoothly after installing it. Can you verify if this is the output that we are expecting with the NaCl run? Thank you!

Sincerely,

Kevin

You received this message because you are subscribed to a topic in the Google Groups "westpa-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/westpa-users/EfgFLKSuFt8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to westpa-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/4D35BC05-A834-4F40-89A2-9E52D69CA8B5%40gmail.com.

[Jeremy Leung]

Hi Kevin,

Those are what you're supposed to get. Congratulations on completing your first WESTPA simulation!

Let us know if you have any more questions.

Cheers,

Jeremy L.

On 17 Aug 2021, at 4:05 PM, 'Mac Kevin Braza' via westpa-users <westpa...@googlegroups.com> wrote:

Hi Jeremy,

Thank you for pointing that out! I just realized that mdtraj was not installed yet and I was able to run it smoothly after installing it. Can you verify if this is the output that we are expecting with the NaCl run? Thank you!

Sincerely,

Kevin

<image.png>

<image.png>

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/CAP-6Gt1Z2UvDnWBPe5%3Db0Zwx4%2BpwAQ9BAsRmDuZSsq8z%2B1GvyA%40mail.gmail.com.

[Mac Kevin Braza]

Thank you Jeremy! This is awesome!

Sincerely,

Kevin

To view this discussion on the web visit https://groups.google.com/d/msgid/westpa-users/0BD3A49B-B7AA-44B3-AF5F-9D82F008A3A2%40gmail.com.