propagation error

[v.bu...@gmail.com]

Hi,

I am trying to complete the Na+/Cl- association tutorial for NAMD, and everything works fine, until i try to do ./run.sh on the westpa folder after ./init.sh and i'm getting a propagation error that I can't seem to shake off:

-- ERROR    [west.propagators.executable] -- could not read coord from '/var/folders/8x/pnr_1mkx0lb3chvn0fgwzljw0000gn/T/tmpkZQ5yT': ValueError('cannot reshape array of size 303 into shape (51,2,3)',)

-- ERROR    [west.propagators.executable] -- could not read coord from '/var/folders/8x/pnr_1mkx0lb3chvn0fgwzljw0000gn/T/tmpYHkQNt': ValueError('cannot reshape array of size 303 into shape (51,2,3)',)

-- ERROR    [west.propagators.executable] -- could not read coord from '/var/folders/8x/pnr_1mkx0lb3chvn0fgwzljw0000gn/T/tmpWjygal': ValueError('cannot reshape array of size 303 into shape (51,2,3)',)

-- ERROR    [west.propagators.executable] -- could not read coord from '/var/folders/8x/pnr_1mkx0lb3chvn0fgwzljw0000gn/T/tmpZEVc24': ValueError('cannot reshape array of size 303 into shape (51,2,3)',)

-- ERROR    [west.propagators.executable] -- could not read coord from '/var/folders/8x/pnr_1mkx0lb3chvn0fgwzljw0000gn/T/tmpCbqoRE': ValueError('cannot reshape array of size 303 into shape (51,2,3)',)

-- ERROR    [west.sim_manager] -- propagation failed for 5 segment(s):

0

1

2

3

4

exception caught; shutting down

-- ERROR    [w_run] -- Traceback (most recent call last):

  File "/Users/ViolettaBurns/anaconda2/westpa/lib/cmds/w_run.py", line 65, in <module>

    sim_manager.run()

  File "/Users/ViolettaBurns/anaconda2/westpa/src/west/sim_manager.py", line 645, in run

    self.check_propagation()

  File "/Users/ViolettaBurns/anaconda2/westpa/src/west/sim_manager.py", line 544, in check_propagation

    raise PropagationError('propagation failed for {:d} segments'.format(len(failed_segments)))

PropagationError: propagation failed for 5 segments

I have tried everything I can think of. Any suggestions? I will be attending the workshop tomorrow and friday but I wanted to get this done before then.

Thanks.

Violetta Burns

Mertz Group, WVU.

[AJ Pratt]

Hi Violetta,

The "coord" dataset is distinct from the "pcoord" dataset, and the example given has a custom loader for the 'coord' dataset.  It looks like it's flattening it (that is, WESTPA is expecting a 51x2x3 matrix, but is instead getting a column of 303 values.  Same number of entries, formatted differently).

While it's possible to debug this, it's not really an essential part of the simulation and these sorts of functions can be finicky, anyway.  I'd recommend disabling it in your west.cfg.

Find the section that says "coord" (not pcoord!) in west.cfg under the "propagator" heading, and set it to disabled.

I think this is the west.cfg you're using.  Change this line to "enabled: false" and run the simulation again

https://github.com/westpa/westpa/blob/master/lib/examples/nacl_namd/west.cfg#L47

Best,

Audrey

---
A. Pratt
Graduate Student in Chemistry
Chong Lab, Room 338, Eberly Hall
University of Pittsburgh
Pittsburgh, PA 15260

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[v.bu...@gmail.com]

That worked.

Thank you so much Audrey!

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[ncf...@mix.wvu.edu]

Hey Audrey,

I'm Nick from the WESTPA workshop. The coord is necessary for the final step of the analysis right? I'm getting an error involving the coord when I call TrajWriter and I'm assuming that's because we turned it off so that data set doesn't exit.

Is the error that its the wrong shape for reading or that its too short for the resizing? 51x2x3 is 306. So are 3 values missing?

I'm trying to finish up the tutorials so we can make the proper modifications to run production on our system.

Thanks a bunch! :)

Nick  

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