run-ss3-no-est #539
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Build SS3 and run test models without estimation (from .par) and no hessian | |
| # Runs on every push and PR (even draft PRs) ONLY if tpl files have changed. | |
| name: run-ss3-no-est | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - '**.tpl' | |
| # branches: | |
| # - main | |
| pull_request: | |
| paths: | |
| - '**.tpl' | |
| branches: | |
| - main | |
| # Run models without estimation, then try to run again with .ss_new | |
| jobs: | |
| run-ss3-no-est: | |
| runs-on: ubuntu-latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" | |
| steps: | |
| - name: Checkout ss3 repo | |
| uses: actions/checkout@v4 | |
| # - name: Get last compiled version of SS; alternative to compiling in same wkflow | |
| # uses: dawidd6/action-download-artifact@v2 | |
| # with: | |
| # workflow: build-centos.yml | |
| # workflow_conclusion: success | |
| # name: ss_linux | |
| # path: ss_linux | |
| - name: Checkout models repo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: 'nmfs-ost/ss3-test-models' | |
| path: test-models-repo | |
| - name: Update Ubuntu packages | |
| run: | | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| sudo apt-get install --only-upgrade libstdc++6 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| # - name: Get admb and put in path, linux | |
| # run: | | |
| # wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip | |
| # sudo unzip admb-13.1-linux.zip -d /usr/local/bin | |
| # sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb | |
| # echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH | |
| # - name: Build ss3 | |
| # run: | | |
| # rm -rf SS330 | |
| # mkdir SS330 | |
| # /bin/bash ./Make_SS_330_new.sh -b SS330 | |
| - name: Build stock synthesis with admb docker image | |
| run: | | |
| rm -rf SS330 | |
| rm -rf ss3_osx.tar | |
| mkdir SS330 | |
| chmod 777 SS330 | |
| /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 | |
| - name: Move exes and R scripts to needed locations | |
| run: | | |
| mv test-models-repo/models test-models-repo/model_runs | |
| mv SS330/ss3 test-models-repo/model_runs/ss3 | |
| mv test-models-repo/.github/r_scripts/run_from_par.R test-models-repo/run_from_par.R | |
| mv test-models-repo/.github/r_scripts/run_compare_noest.R test-models-repo/run_compare_noest.R | |
| - name: Change permissions on ss3 exes | |
| run: sudo chmod a+x test-models-repo/model_runs/ss3 | |
| - name: Run test models without estimation | |
| run: | | |
| cd test-models-repo && Rscript run_from_par.R | |
| - name: Download R packages to run models in parallel | |
| run: Rscript -e 'install.packages(c("parallely", "furrr", "future"))' | |
| - name: Run comparison using run_compare_noest.R file in test models repo | |
| run: | | |
| mkdir test-models-repo/run_R | |
| cd test-models-repo && Rscript run_compare_noest.R | |
| - name: Determine results of test using check_failed.R file in test models repo | |
| run: cd test-models-repo && Rscript .github/r_scripts/check_failed.R | |
| - name: Run models using the .ss_new files | |
| run: | | |
| # Get model names and file paths | |
| mod_names <- list.dirs("test-models-repo/model_runs", | |
| full.names = FALSE, recursive = FALSE) | |
| mod_paths <- list.dirs("test-models-repo/model_runs", | |
| full.names = TRUE, recursive = FALSE) | |
| print(mod_names) | |
| # Testing to see where issue is: | |
| # lapply(mod_paths, function(dir) {list.files(path = dir, full.names = TRUE)}) | |
| test_mod_path <- mod_paths[1] | |
| file.exists(file.path(test_mod_path, "starter.ss")) | |
| file.exists(file.path(test_mod_path, "starter.ss_new")) | |
| file.exists(file.path(test_mod_path, "forecast.ss")) | |
| file.exists(file.path(test_mod_path, "forecast.ss_new")) | |
| file.exists(file.path(test_mod_path, "data_echo.ss_new")) | |
| file.exists(file.path(test_mod_path, "control.ss_new")) | |
| file.remove(file.path(test_mod_path, "starter.ss")) | |
| file.remove(file.path(test_mod_path, "forecast.ss")) | |
| file.rename(file.path(test_mod_path, "starter.ss_new"), file.path(test_mod_path,"starter.ss")) | |
| file.rename(file.path(test_mod_path, "forecast.ss_new"), file.path(test_mod_path,"forecast.ss")) | |
| start <- readLines(file.path(test_mod_path, "starter.ss")) | |
| start[1:10] | |
| first_val_line <- grep("read from .par file", start, fixed = TRUE) | |
| first_val_line | |
| datname <- gsub(" #_datfile", "", start[first_val_line-2]) | |
| ctlname <- gsub(" #_ctlfile", "", start[first_val_line-1]) | |
| print(datname) | |
| print(ctlname) | |
| # file.exists(file.path(test_mod_path, datname)) | |
| # file.exists(file.path(test_mod_path, ctlname)) | |
| # file.remove(file.path(test_mod_path, datname)) | |
| # file.remove(file.path(test_mod_path, ctlname)) | |
| # file.rename(file.path(test_mod_path, "data_echo.ss_new"), file.path(test_mod_path, datname)) | |
| # file.rename(file.path(test_mod_path, "control.ss_new"), file.path(test_mod_path, ctlname)) | |
| # file.remove(file.path(test_mod_path, "control.ss_new")) | |
| # file.remove(file.path(test_mod_path, "Report.sso")) | |
| # # see if model finishes without error | |
| # system(paste0("cd ", test_mod_path, " && ../ss3 -stopph 0 -nohess")) | |
| # model_ran <- file.exists(file.path(test_mod_path, "control.ss_new")) | |
| # return(model_ran) | |
| shell: Rscript {0} | |
| # - name: Run models using the .ss_new files | |
| # run: | | |
| # # Create function to run models using .ss_new files | |
| # run_ssnew <- function(dir) { | |
| # wd <- getwd() | |
| # print(wd) | |
| # on.exit(system(paste0("cd ", wd))) | |
| # # delete old starter files, rename forecast.ss_new and starter.ss_new files | |
| # file.remove(file.path(dir, "starter.ss")) | |
| # file.remove(file.path(dir, "forecast.ss")) | |
| # file.rename(file.path(dir, "starter.ss_new"), file.path(dir,"starter.ss")) | |
| # file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss")) | |
| # # rename control and data files to standardized names (from the starter files) | |
| # start <- readLines(file.path(dir, "starter.ss")) | |
| # first_val_line <- grep("0=use init values in control file", start, fixed = TRUE) | |
| # datname <- start[first_val_line-2] | |
| # ctlname <- start[first_val_line-1] | |
| # print(datname) | |
| # print(ctlname) | |
| # file.remove(file.path(dir, datname)) | |
| # file.remove(file.path(dir, ctlname)) | |
| # file.rename(file.path(dir,"data_echo.ss_new"), file.path(dir, datname)) | |
| # file.rename(file.path(dir, "control.ss_new"), file.path(dir, ctlname)) | |
| # # run the models without estimation | |
| # file.remove(file.path(dir, "Report.sso")) | |
| # # see if model finishes without error | |
| # system(paste0("cd ", dir, " && ../ss3 -stopph 0 -nohess")) | |
| # model_ran <- file.exists(file.path(dir, "control.ss_new")) | |
| # return(model_ran) | |
| # } | |
| # # Setup parallel | |
| # ncores <- parallelly::availableCores(omit = 1) | |
| # future::plan(future::multisession, workers = ncores) | |
| # # Run models in parallel using .ss_new files and print out error messages | |
| # mod_ran <- furrr::future_map(mod_paths, function(x) {tryCatch(run_ssnew(x), | |
| # error = function(e) print(e) | |
| # )} | |
| # ) | |
| # mod_errors <- mod_names[unlist(lapply(mod_ran, function(x) "simpleError" %in% class(x)))] | |
| # success <- TRUE | |
| # # Print list of models with errors if there are any | |
| # if(length(mod_errors) > 0) { | |
| # message("Model code with errors were: ", paste0(mod_errors, collapse = ", "), | |
| # ". See error list above for more details.") | |
| # success <- FALSE | |
| # } else { | |
| # message("All code ran without error, but model runs may still have failed.") | |
| # } | |
| # # Print list of models that didn't run if there are any | |
| # mod_no_run <- mod_names[unlist(lapply(mod_ran, function(x) isFALSE(x)))] # false means model didn't run | |
| # if(length(mod_no_run) > 0) { | |
| # message("Models that didn't run are ", paste0(mod_no_run, collapse = ", ")) | |
| # success <- FALSE | |
| # } else { | |
| # message("All models ran without error.") | |
| # } | |
| # # Determine if job fails or passes | |
| # if(success == FALSE) { | |
| # stop("Job failed due to code with errors or models that didn't run.") | |
| # } else { | |
| # message("Job passed! All models successfully ran.") | |
| # } | |
| # shell: Rscript {0} | |
| - name: Archive results | |
| uses: actions/upload-artifact@main | |
| if: always() | |
| with: | |
| name: 'result_textfiles' | |
| path: test-models-repo/run_R/ |