Add R21 PEV profiles #333

lmhaile · 2024-09-09T11:16:18Z

Hi everyone,

Just pushing the R21 vaccine profiles to the dev branch, which @NoSchID has checked over. If there are any downstream changes needed also happy to make them.

Thanks!

Dev

The recent dqrng 0.4.0 release has a few small incompatible changes that makes the build fail. The changes necessary have been applied to the dev branch already as part of larger pull requests #280 and #305. This commit cherry-picks just the fixes for the master branch.

Cherry-pick fixes for latest dqrng release.

The workflow runs on-demand by commenting `/benchmark` on any pull request. It runs a few iterations of both the base branch and the PR and posts the results back to the pull request as a comment. Additionally, detailed plots are available as images in the workflow artifacts. Unfortunately GitHub doesn't have a way for actions to upload images in comments. At the moment the workflow runs two benchmarks, one at a 10k population size and 10k time steps, and second one at 1M population size and 1k time steps. The workflow currently takes on the order of 1 hour to run. We can easily tweak the set of benchmarks in the future if we want to run more scenarios, or conversly if we want to reduce the total time. There is no long-term tracking of benchmark results yet. Doing so is tricky as the performance of the underlying CI is unlikely to be stable long-term.

It was merged into touchstone upstream.

I'm getting issues with 24.04 where pak installs some system packages with apt-get, some system services are upgraded and restarted and the CI runner is canceled. Not sure what the reason is, but 22.04 doesn't have this problem.

Add GitHub workflow for continuous benchmarking.

giovannic

Thanks for this! If you could run devtools::document() and then add and commit the updated documentation, then it'll be ready.

lmhaile · 2024-09-10T13:58:55Z

Hi Giovanni, when I try to document it errors out-- maybe not worth investigating if anyone else can document and push that version successfully?

Here's my traceback:

> devtools::document()
ℹ Updating malariasimulation documentation
Setting `RoxygenNote` to "7.3.2"
ℹ Loading malariasimulation
Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/Random.h:

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/adult_mosquito_eqs.cpp:
   Rcpp::XPtr<AdultMosquitoModel> create_adult_mosquito_model(Rcpp::XPtr<AquaticMosquitoModel> growth_model, double mu, double tau, double susceptible, double foim)
   void adult_mosquito_model_update(Rcpp::XPtr<AdultMosquitoModel> model, double mu, double foim, double susceptible, double f)
   std::vector<double> adult_mosquito_model_save_state(Rcpp::XPtr<AdultMosquitoModel> model)
   void adult_mosquito_model_restore_state(Rcpp::XPtr<AdultMosquitoModel> model, std::vector<double> state)
   Rcpp::XPtr<Solver> create_adult_solver(Rcpp::XPtr<AdultMosquitoModel> model, std::vector<double> init, double r_tol, double a_tol, size_t max_steps)

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/aquatic_mosquito_eqs.cpp:
   Rcpp::XPtr<AquaticMosquitoModel> create_aquatic_mosquito_model(double beta, double de, double mue, Rcpp::XPtr<Timeseries> k_timeseries, double gamma, double dl, double mul, double dp, double mup, size_t total_M, bool model_seasonality, double g0, std::vector<double> g, std::vector<double> h, double R_bar, double mum, double f, double rainfall_floor)
   void aquatic_mosquito_model_update(Rcpp::XPtr<AquaticMosquitoModel> model, size_t total_M, double f, double mum)
   Rcpp::XPtr<Solver> create_aquatic_solver(Rcpp::XPtr<AquaticMosquitoModel> model, std::vector<double> init, double r_tol, double a_tol, size_t max_steps)

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/mosquito_biology.cpp:
   double carrying_capacity(const size_t timestep, const bool model_seasonality, const double g0, const std::vector<double>& g, const std::vector<double>& h, const double K0, const double R_bar, const double rainfall_floor)
   double eggs_laid(double beta, double mu, double f)
   double rainfall(const size_t t, const double g0, const std::vector<double>& g, const std::vector<double>& h, const double floor)

\\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/processes.cpp:
   Rcpp::XPtr<process_t> exponential_process_cpp(Rcpp::XPtr<DoubleVariable> variable, const double rate)

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/solver.cpp:
   std::vector<double> solver_get_states(Rcpp::XPtr<Solver> solver)
   void solver_set_states(Rcpp::XPtr<Solver> solver, double t, std::vector<double> state)
   void solver_step(Rcpp::XPtr<Solver> solver)

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/solver.h:

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/timeseries.cpp:
   Rcpp::XPtr<Timeseries> create_timeseries(size_t size, double default_value)
   double timeseries_at(Rcpp::XPtr<Timeseries> timeseries, double timestep, bool linear)
   void timeseries_push(Rcpp::XPtr<Timeseries> timeseries, double value, double timestep)
   Rcpp::List timeseries_save_state(Rcpp::XPtr<Timeseries> timeseries)
   void timeseries_restore_state(Rcpp::XPtr<Timeseries> timeseries, Rcpp::List state)

Exports from \\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/utils.cpp:
   void random_seed(size_t seed)
   std::string random_save_state()
   void random_restore_state(std::string state)
   std::vector<size_t> bernoulli_multi_p_cpp(const std::vector<double> p)
   std::vector<size_t> bitset_index_cpp(Rcpp::XPtr<individual_index_t> a, Rcpp::XPtr<individual_index_t> b)
   Rcpp::IntegerVector fast_weighted_sample(size_t size, std::vector<double> probs)

\\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/src/RcppExports.cpp updated.
\\wpia-hn/Malaria/Lydia/quick_reclone/malariasimulation/R/RcppExports.R updated.
ℹ Re-compiling malariasimulation (debug build)
── R CMD INSTALL ───────────────────────────────────────────────────────────────
─  installing *source* package 'malariasimulation' ...
   ** using staged installation
   ** libs
   using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
   using C++14
   g++  -std=gnu++14 -I"C:/PROGRA~1/R/R-44~1.1/include" -DNDEBUG  -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/Rcpp/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/individual/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/BH/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/testthat/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/dqrng/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/sitmo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -I../inst/include/   -O2 -Wall -gdwarf-2 -mfpmath=sse -msse2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c Random.cpp -o Random.o
   Assembler messages:
   Fatal error: can't create Random.o: Invalid argument
   make: *** [C:/PROGRA~1/R/R-44~1.1/etc/x64/Makeconf:296: Random.o] Error 1
   ERROR: compilation failed for package 'malariasimulation'
─  removing 'C:/Users/lhaile/AppData/Local/Temp/Rtmp4gmpIa/devtools_install_5b0452d81bf5/malariasimulation'
Error:
! ! System command 'Rcmd.exe' failed
Hide Traceback
     ▆
  1. ├─devtools::document()
  2. │ └─roxygen2::roxygenise(pkg$path, roclets)
  3. │   └─roxygen2 (local) load_code(base_path)
  4. │     └─pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
  5. │       └─pkgbuild::compile_dll(path, quiet = quiet)
  6. │         ├─pkgbuild:::withr_with_makevars(...)
  7. │         │ ├─pkgbuild:::withr_with_envvar(...)
  8. │         │ │ └─base::force(code)
  9. │         │ └─base::force(code)
 10. │         ├─pkgbuild:::withr_with_envvar(c(DEBUG = "true"), build())
 11. │         │ └─base::force(code)
 12. │         └─pkgbuild::build()
 13. │           └─pkgbuild:::install_min(...)
 14. │             └─pkgbuild::rcmd_build_tools(...)
 15. │               ├─pkgbuild::with_build_tools(...)
 16. │               │ └─pkgbuild:::withr_with_path(rtools_path(), code)
 17. │               │   └─base::force(code)
 18. │               ├─base::withCallingHandlers(...)
 19. │               └─callr::rcmd_safe(...)
 20. │                 └─callr:::run_r(options)
 21. │                   ├─base::with(...)
 22. │                   └─base::with.default(...)
 23. │                     └─base::eval(substitute(expr), data, enclos = parent.frame())
 24. │                       └─base::eval(substitute(expr), data, enclos = parent.frame())
 25. │                         ├─callr:::with_envvar(...)
 26. │                         │ └─base::force(code)
 27. │                         ├─base::do.call(...)
 28. │                         └─processx (local) `<fn>`(...)
 29. │                           └─throw(...)
 30. │                             └─base::signalCondition(cond)
 31. └─pkgbuild (local) `<fn>`(`<systm___>`)
 32.   └─asNamespace("callr")$err$throw(e)

…lation into origin/r21_profiles

pwinskill · 2024-09-10T15:59:24Z

I've re-doc'd @lmhaile

giovannic · 2024-09-10T18:10:13Z

Hi Giovanni, when I try to document it errors out-- maybe not worth investigating if anyone else can document and push that version successfully?

Here's my traceback:
...
─ installing source package 'malariasimulation' ...
** using staged installation
** libs
using C++ compiler: 'G__1.EXE (GCC) 13.2.0'
using C++14
g++ -std=gnu++14 -I"C:/PROGRA1/R/R-441.1/include" -DNDEBUG -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/Rcpp/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/individual/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/BH/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/testthat/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/dqrng/include' -I'C:/Users/lhaile/AppData/Local/R/win-library/4.4/sitmo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include/ -O2 -Wall -gdwarf-2 -mfpmath=sse -msse2 -mstackrealign -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c Random.cpp -o Random.o
Assembler messages:
Fatal error: can't create Random.o: Invalid argument
make: *** [C:/PROGRA1/R/R-44~1.1/etc/x64/Makeconf:296: Random.o] Error 1
ERROR: compilation failed for package 'malariasimulation'
─ removing 'C:/Users/lhaile/AppData/Local/Temp/Rtmp4gmpIa/devtools_install_5b0452d81bf5/malariasimulation'
Error:
! ! System command 'Rcmd.exe' failed
Hide Traceback
▆

├─devtools::document()

│ └─roxygen2::roxygenise(pkg$path, roclets)

│ └─roxygen2 (local) load_code(base_path)

│ └─pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)

│ └─pkgbuild::compile_dll(path, quiet = quiet)

│ ├─pkgbuild:::withr_with_makevars(...)

│ │ ├─pkgbuild:::withr_with_envvar(...)

│ │ │ └─base::force(code)

│ │ └─base::force(code)

│ ├─pkgbuild:::withr_with_envvar(c(DEBUG = "true"), build())

│ │ └─base::force(code)

│ └─pkgbuild::build()

│ └─pkgbuild:::install_min(...)

│ └─pkgbuild::rcmd_build_tools(...)

│ ├─pkgbuild::with_build_tools(...)

│ │ └─pkgbuild:::withr_with_path(rtools_path(), code)

│ │ └─base::force(code)

│ ├─base::withCallingHandlers(...)

│ └─callr::rcmd_safe(...)

│ └─callr:::run_r(options)

│ ├─base::with(...)

│ └─base::with.default(...)

│ └─base::eval(substitute(expr), data, enclos = parent.frame())

│ └─base::eval(substitute(expr), data, enclos = parent.frame())

│ ├─callr:::with_envvar(...)

│ │ └─base::force(code)

│ ├─base::do.call(...)

│ └─processx (local) <fn>(...)

│ └─throw(...)

│ └─base::signalCondition(cond)

└─pkgbuild (local) <fn>(<systm___>)

└─asNamespace("callr")$err$throw(e)

Very bizarre error message!..

giovannic and others added 12 commits July 3, 2023 16:42

Merge pull request #255 from mrc-ide/dev

efa84f7

Dev

Update pkgdown.yml

8c799fc

Update _pkgdown.yml

397a7b7

Merge pull request #311 from mrc-ide/fix-dqrng

fdd7c68

Cherry-pick fixes for latest dqrng release.

Remove raw data upload.

142d857

It was merged into touchstone upstream.

Fix reporting of cancelled jobs

14f1cbc

Downgrade ubuntu back to 22.04.

45f8c3f

I'm getting issues with 24.04 where pak installs some system packages with apt-get, some system services are upgraded and restarted and the CI runner is canceled. Not sure what the reason is, but 22.04 doesn't have this problem.

Add R_GC_MEM_GROW

89b7199

Merge pull request #304 from mrc-ide/continuous-benchmarking

e598c66

Add GitHub workflow for continuous benchmarking.

pushed R21 profiles

6ecab00

lmhaile requested review from giovannic, pwinskill and NoSchID September 9, 2024 11:16

giovannic requested changes Sep 10, 2024

View reviewed changes

pwinskill added 2 commits September 10, 2024 16:42

Merge branch 'r21_profiles' of https://github.com/mrc-ide/malariasimu…

0932eb7

…lation into origin/r21_profiles

Redocument and tidy reference for vaccine profiles

c02b450

giovannic approved these changes Sep 10, 2024

View reviewed changes

pwinskill approved these changes Sep 11, 2024

View reviewed changes

Merge branch 'dev' into r21_profiles

2d84551

giovannic merged commit db57035 into dev Sep 12, 2024
4 checks passed

giovannic deleted the r21_profiles branch September 12, 2024 08:23

giovannic mentioned this pull request Sep 12, 2024

Dev #335

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Add R21 PEV profiles #333

Add R21 PEV profiles #333

lmhaile commented Sep 9, 2024

giovannic left a comment

lmhaile commented Sep 10, 2024

pwinskill commented Sep 10, 2024

giovannic commented Sep 10, 2024

Add R21 PEV profiles #333

Add R21 PEV profiles #333

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lmhaile commented Sep 10, 2024

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