PR_for_spawn_recr_with_timevary_biology_also_SRR_AB #331
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# Check that MCMC using the NUTS algorithim in ADMB is reproducible with SS3 using the simple model. | |
# Developed with Cole Monnahan. | |
# Only runs on a pull request and a push to main if the tpl files have changed. | |
name: run-ss3-mcmc | |
on: | |
workflow_dispatch: | |
push: | |
paths: | |
- '**.tpl' | |
branches: | |
- main | |
pull_request: | |
types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review'] | |
paths: | |
- '**.tpl' | |
branches: | |
- main | |
# Check MCMC works | |
jobs: | |
run-ss3-no-est: | |
if: github.event.pull_request.draft == false | |
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: 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 stock synthesis | |
# 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, scripts to needed locations | |
run: | | |
mv test-models-repo/models/Simple/starter.ss starter.ss | |
mv test-models-repo/models/Simple/forecast.ss forecast.ss | |
mv test-models-repo/models/Simple/control.ss control.ss | |
mv test-models-repo/models/Simple/data.ss data.ss | |
mv SS330/ss3 ss3 | |
ls | |
- name: Change permissions on ss3 exe | |
run: sudo chmod a+x ss3 | |
- name: Run models without estimation | |
run: | | |
# Run NUTS algorithim in ADMB to make sure still works with stock synthesis | |
# run the simple model with -hbf option to get the necessary files | |
system("./ss3 -hbf") | |
# run the simple model 30 times using the NUTS algorithim | |
niters <- 100 | |
for (i in 1:niters) { | |
message("Running iteration ", i) | |
# run simple model | |
system("./ss3 -maxfn 0 -phase 40 -nohess -mcmc 10 -nuts -mcseed 1 -max_treedepth 3") | |
# read in adaption.csv | |
adapt_df <- read.csv("adaptation.csv") | |
if(i == 1) { | |
compare_val <- adapt_df[nrow(adapt_df), "stepsize__"] | |
message("Getting ref value from iteration ", i, ". Ref value is " , | |
compare_val) | |
} else { | |
message("Checking iteration ", i) | |
val_to_check <- adapt_df[nrow(adapt_df), "stepsize__"] | |
if(!identical(val_to_check, compare_val)) { | |
stop("First step size for iteration ", i ," (step size =", | |
val_to_check, | |
")", " was not equal to values in the first iteration (", | |
compare_val, ").") | |
} | |
} | |
} | |
message("No differences in step size among stock synthesis runs.") | |
shell: Rscript {0} |