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Add ability to read matrix in "XYZ" format; new 'flatten' command #877

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Merged
merged 22 commits into from
Feb 1, 2021
Merged

Add ability to read matrix in "XYZ" format; new 'flatten' command #877

merged 22 commits into from
Feb 1, 2021

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drroe
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@drroe drroe commented Jan 31, 2021

Non-square matrices can now be read in via the read2d keyword, i.e. matrix data in the format:

<column> <row> <data>

The nosquare2d keyword needs to be specified. I should probably try to do a better job autodetecting this in the future.

Also adds the flatten command, used to convert a matrix to 1D array by dividing matrix elements up among the array somehow.

> help flatten
  [help flatten]
	name <output set name> [mode {sum|avg}] <input set args>

Useful for e.g. distributing elements of a pairwise matrix across its elements. For example, given a matrix with values like this:

X Y Value
1 3 5.0
1 4 4.0
2 3 2.0

The “flattened” 1D array with mode SUM would be determined as follows:

Element 1 = (5.0/2) + (4.0/2) = 4.5
Element 2 = (2.0/2) = 1.0
Element 3 = (5.0/2) + (2.0/2) = 3.5
Element 4 = (4.0/2) = 2.0

And the final 1D array would look like so:

Index Value
1     4.5
2     1.0
3     3.5
4     2.0

@drroe drroe added enhancement New Command New command for cpptraj labels Jan 31, 2021
@drroe drroe self-assigned this Jan 31, 2021
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lgtm-com bot commented Jan 31, 2021

This pull request introduces 2 alerts when merging 12e0236 into 702b1e5 - view on LGTM.com

new alerts:

  • 2 for Wrong type of arguments to formatting function

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drroe commented Jan 31, 2021

I'm getting messages like Failed to extract source.tar.gz in post-test steps. Maybe I'll try again tomorow.

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swails commented Jan 31, 2021

Failed to extract source.tar.gz

That's a transient Jenkins error. It was stashed in the first step and should be available in every future step. Re-running should fix it.

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drroe commented Feb 1, 2021

I'm not sure why, but Jenkins seems unstable lately. One run (number 5) took ~14 hours to fail; problem was a node unexpectedly closing down:

Cannot contact Supergirl: hudson.remoting.ChannelClosedException: Channel "hudson.remoting.Channel@34364954:Supergirl": Remote call on Supergirl failed. The channel is closing down or has closed down

The following restarted run failed on the Intel step because it couldn't extract the source:

Failed to extract source.tar.gz

I guess I will try restarting, but I eventually may need to remove the required status from Jenkins just so I can get this merged.

@AmberJenkins
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The PGI build in Jenkins failed.

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swails commented Feb 1, 2021 •
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I guess I will try restarting, but I eventually may need to remove the required status from Jenkins just so I can get this merged.

I think I found the issue with premature shutdowns and I've fixed it. I think switching the required builds to several of the GHA builds is a good move - I'd recommend switching regardless (I don't think Jenkins does any CMake builds, for instance).

Requiring the CMake builds that take 11 and 15 minutes will test a wider variety of options (OpenMP, MPI, sander API, etc.) should increase coverage.

@drroe drroe merged commit 34b6b50 into Amber-MD:master Feb 1, 2021
@drroe drroe deleted the read2dmatrix branch February 1, 2021 15:22
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@drroe @swails @AmberJenkins