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MRC-CSO-SPHSU / simpaths_parallel

Code for running SimPaths in parallel
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[DOC]: manual #3

Open vkhodygo opened 1 year ago

vkhodygo commented 1 year ago

I'd like you to check the readme and correct/expand it.

andrewbaxter439 commented 1 year ago

Hi Vlad, was just reading it. Looks good! One thing that might need specified is that simpaths.jar is a full Simpaths archive compiled with dependencies in this instance.

I'm vaguely aware that you can compile a jar using maven with references to external dependencies, but never quite got that to work (the java call needed either a class path listing all library dependencies or full-dependency-compiled simpaths). I'm not sure if further simpaths documentation on this is available since I started out and fumbled my way through it as a novice.

Other brief query is whether the trailing commas has been fixed in updated versions of simpaths, which now incorporate the changes needed to do parallel runs?

vkhodygo commented 1 year ago

Looks good! One thing that might need specified is that simpaths.jar is a full Simpaths archive compiled with dependencies in this instance.

Feel free to add a PR with any changes you find reasonable.

Other brief query is whether the trailing commas has been fixed in updated versions of simpaths, which now incorporate the changes needed to do parallel runs?

I have no idea tbf. If true our lives have become a little bit easier, and we should remove this part.

andrewbaxter439 commented 1 year ago

As a note - I'm working on the most simple way to compile simpaths to an executable .jar. Ideally this would be running:

mvn clean package

in the simpaths root folder, then copying/linking the compiled jar to directory alongside do_full_run.sh. But at the moment that's not working (https://github.com/matteorichiardi/labsim/pull/32). If this can be fixed quickly the instructions can be added to README.md, otherwise the instructions on how to compile with IntelliJ might just have to stand in for now.

vkhodygo commented 1 year ago

Any progress so far?

andrewbaxter439 commented 1 year ago

As noted in other pull request had run out of time the other week to debug these bits. will follow-up at some point!