PopED + babelmixr2 for windows

[mattfidler]

Hi @andrewhooker

This allows windows based PopED models from babelmixr2 to be run in parallel without modifying any user code. This mean the same user code works on windows and linux/mac

[mattfidler]

In general it saves the babelmixr2 environment inside of the poped.db setup from babelmixr2. With the windows parallelization, this environment is sent to every R process node to load the DLLs. This will allow everything to be contained inside of babelmixr2 in case things like symbolic sensitivity gradient models are added to speed up PopED and rxode2. Right now there are 2 models/dlls generated for each poped database.

[mattfidler]

Had to add babelmixr2 development stack so these check correctly. After adding this to CRAN you can take out the babelmixr2 stack and can simply use the CRAN version.

[codecov]

Codecov Report

❌ Patch coverage is 60.97561% with 32 lines in your changes missing coverage. Please review.
✅ Project coverage is 44.68%. Comparing base (73bccdc) to head (d13e906).

Files with missing lines	Patch %	Lines
R/start_parallel.R	0.00%	5 Missing ⚠️
R/optimize_n.R	40.00%	3 Missing ⚠️
R/blockexp.R	0.00%	2 Missing ⚠️
R/ind_estimates.R	0.00%	2 Missing ⚠️
R/LEDoptim.R	0.00%	1 Missing ⚠️
R/LinMatrixLH.R	50.00%	1 Missing ⚠️
R/LinMatrixL_occ.R	0.00%	1 Missing ⚠️
R/blockopt.R	0.00%	1 Missing ⚠️
R/blockother.R	0.00%	1 Missing ⚠️
R/create_ofv.R	0.00%	1 Missing ⚠️
... and 14 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #79      +/-   ##
==========================================
+ Coverage   44.52%   44.68%   +0.15%     
==========================================
  Files         120      121       +1     
  Lines        8810     8892      +82     
==========================================
+ Hits         3923     3973      +50     
- Misses       4887     4919      +32     

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[mattfidler]

As babelmixr2 was released on CRAN development libraries are no longer neeeded.

[mattfidler]

The error in oldrel-1 is unrelated to this pull request.

[mattfidler]

Thanks Andy!

[andrewhooker]

Why do we need to add

start_parallel_env <- new.env(parent=emptyenv())
start_parallel_env$babelmixr2 <- NULL

outside of the function?

[mattfidler]

This is so it can be assigned in a global like environment.

The actual function is

parallel::clusterCall(cl, babelmixr2::.popedCluster, start_parallel_env$babelmixr2)

[andrewhooker]

Hi Matt,

Thanks for all your work on this. I am wondering if there is any way to achieve the same result without having to add the following code snippet in, essentially, every PopED function?

start_parallel_env$babelmixr2 <- poped.db$babelmixr2

Could you supply a minimal working example that I could test a bit with? My thought is that it should be a bit more efficient to just pass poped.db to start.parallel()

Andy

[mattfidler]

parallel::clusterCall(cl, babelmixr2::.popedCluster, start_parallel_env$babelmixr2)

Hi Matt,

Thanks for all your work on this. I am wondering if there is any way to achieve the same result without having to add the following code snippet in, essentially, every PopED function?

start_parallel_env$babelmixr2 <- poped.db$babelmixr2

Could you supply a minimal working example that I could test a bit with? My thought is that it should be a bit more efficient to just pass poped.db to start.parallel()

Andy

I originally tried this, but it dropped the $babelmixr2 in some functions. Perhaps you know how to keep it from dropping.

[mattfidler]

I simply used your examples and modified it.

You could try the warfarin one:

https://github.com/nlmixr2/babelmixr2/blob/175ca39b033df3b5020b7769157c175721abf29f/inst/poped/ex.2.c.warfarin.ODE.compiled.babelmixr2.R