update to ADMB 13.0 (#54)

* change to lower warning count To use after fixing error msgs in ss3 * change workflow from admb 12.3 to 13.0 - requires now compiling admb from source for Mac OS * fix filename error * fix workflow for mac (checkout instead of unzip) * increase timeout limit (cancelled mac build) * increase timeout limit even further * switch to newer ubuntu -hoping to fix "'GLIBC_2.34' not found" * newer version of r-lib action * build linux from source - admb-project/admb#272 * switch run with est action to Windows - linux build is much slower right now * fix issues with switch from linux to windows * Revert "fix issues with switch from linux to windows" This reverts commit d6f0725415cbb3a7463b68c6ae9f02a981ae0137. * Revert "switch run with est action to Windows" This reverts commit 6a6a99676dc4f90541f6cd08e99f0748355e2ea5. * switch run action to build linux from source * update more workflows for admb 13.0 * fix ADMB 13.0 build for warnings workflow * fix admb location for warnings workflow * attempt fix for warnings build * another attempt to fix build with warnings * attempt another fix for warnings build * add diagnostics to debug failing build * yet another try * use revised linux distribution * fix extra line caused fail * another try for warnings build * add display of warnings to console * fix filter for warnings * restore simpler linux install Co-authored-by: Kathryn Doering <[email protected]>
nmfs-ost · Sep 9, 2022 · ab8dcd9 · ab8dcd9
1 parent 1cf155e
commit ab8dcd9
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Showing 6 changed files with 92 additions and 59 deletions.
diff --git a/build-ss3-warnings.yml b/build-ss3-warnings.yml
@@ -19,18 +19,27 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@master
 
-      - name: Get admb and put in path
+      - name: Get admb and put in path, linux
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
-      - name: Build stock synthesis with warnings
+      - name: Build stock synthesis with warnings displayed in console
         run: |
           rm -rf SS330
+          rm -rf ss_osx.tar
           mkdir SS330
-          /bin/bash ./Make_SS_330_new.sh -a /usr/local/bin/admb-12.3 -b SS330 -w &> warnings.txt
+          /bin/bash ./Make_SS_330_new.sh -a /usr/local/bin/admb-13.0 -b SS330 -w
+
+      - name: Build stock synthesis with warnings again to save to file
+        run: |
+          rm -rf SS330
+          rm -rf ss_osx.tar
+          mkdir SS330
+          /bin/bash ./Make_SS_330_new.sh -a /usr/local/bin/admb-13.0 -b SS330 -w &> warnings.txt
+
       # Runs a set of commands using the runners shell
       - name: Use R to parse warnings output
         run: |
@@ -39,7 +48,7 @@ jobs:
             x = txt,
             fixed = TRUE)
           txt <- txt[(warn_line+1):length(txt)]
-          rm_warn_start_lines <- grep(pattern = "/usr/local/bin/admb-12.3", x = txt,
+          rm_warn_start_lines <- grep(pattern = "/usr/local/bin/admb-13.0", x = txt,
             fixed = TRUE)
           all_warning_end_lines <- grep(pattern = "^", x = txt, fixed = TRUE)
           to_rm <- NULL
@@ -61,7 +70,7 @@ jobs:
         run: |
           n_warn <- read.table("n_warn.txt")
           n_warn <- as.integer(n_warn[1,1])
-          if (n_warn > 83) {
+          if (n_warn > 68) {
             stop("Increased number of warnings")
           } else {
             message("Acceptable number of warnings")

diff --git a/build-ss3.yml b/build-ss3.yml
@@ -17,41 +17,65 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-2019}
-          - {os: macOS-latest}
+          - {os: windows-latest}
+          - {os: macos-latest}
           - {os: ubuntu-latest}
-    # Limit run time to 15 min to avoid wasting action minutes.
-    timeout-minutes: 15
+    # Limit run time to 90 min to avoid wasting action minutes.
+    # was set to 15 and then 30 minutes previously, but compiling admb
+    # on mac took too long
+    timeout-minutes: 90
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
       - name: Get admb and put in path, windows
-        if: matrix.config.os == 'windows-2019'
+        if: matrix.config.os == 'windows-latest'
         run: |
-          Invoke-WebRequest -Uri https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-windows.zip -OutFile "D:\a\stock-synthesis\stock-synthesis\admb-12.3.zip"
-          Expand-Archive -LiteralPath "D:\a\stock-synthesis\stock-synthesis\admb-12.3.zip" -DestinationPath "D:\a\stock-synthesis\stock-synthesis\"
-          echo "D:\a\stock-synthesis\stock-synthesis\admb-12.3\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+          Invoke-WebRequest -Uri https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-windows.zip -OutFile "D:\a\stock-synthesis\stock-synthesis\admb-13.0.zip"
+          Expand-Archive -LiteralPath "D:\a\stock-synthesis\stock-synthesis\admb-13.0.zip" -DestinationPath "D:\a\stock-synthesis\stock-synthesis\"
+          echo "D:\a\stock-synthesis\stock-synthesis\admb-13.0\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
 
-      - name: Get admb and put in path, mac
-        if: matrix.config.os == 'macOS-latest'
+      - name: checkout admb, mac
+        if: matrix.config.os == 'macos-latest'
+        uses: actions/checkout@v2
+        with:
+          repository: admb-project/admb
+          path: admb
+          ref: admb-13.0
+      - name: clean, mac
+        if: matrix.config.os == 'macos-latest'
+        run: cd admb && make clean
+      - name: see where admb is, mac
+        if: matrix.config.os == 'macos-latest'
         run: |
-          curl https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-macos.zip -L -o admb-12.3.zip
-          unzip admb-12.3.zip -d /usr/local/bin
-          ls /usr/local/bin
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
-          
+          ls
+          cd admb && ls
+      - name: compile admb, mac
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          cd admb && make 
+      - name: see where admb is, mac
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          cd admb && ls -l
+      - name: put admb in path, mac
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          sudo mv admb /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb
+          echo "/usr/local/bin/admb" >> $GITHUB_PATH
+
       - name: Get admb and put in path, linux
         if: matrix.config.os == 'ubuntu-latest'
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
       - name: Set up R
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: 'release'
       - name: Fetch tags
@@ -61,7 +85,7 @@ jobs:
 
       - name: Get the last tag on windows
         id: get-latest-tag-win
-        if: matrix.config.os == 'windows-2019'
+        if: matrix.config.os == 'windows-latest'
         run: |
           git tag
           $latest_tag = (git describe --abbrev=0 --tags)
@@ -75,15 +99,15 @@ jobs:
 
       - name: pull the last tag value to use in the Rscript on windows
         id: get-version-win
-        if: matrix.config.os == 'windows-2019'
+        if: matrix.config.os == 'windows-latest'
         run: |
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag }} -FilePath .github/last_tag.txt
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag_commit }} -FilePath .github/last_tag_commit.txt
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.commit}} -FilePath .github/last_commit.txt
 
       - name: Get the last tag on unix
         id: get-latest-tag-unix
-        if: matrix.config.os == 'macOS-latest' || matrix.config.os == 'ubuntu-latest'
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'ubuntu-latest'
         run: |
           git tag
           latest_tag=$(git describe --abbrev=0 --tags)
@@ -97,7 +121,7 @@ jobs:
 
       - name: pull the last tag value to use in the Rscript on unix
         id: get-version-unix
-        if: matrix.config.os == 'macOS-latest' || matrix.config.os == 'ubuntu-latest'
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'ubuntu-latest'
         run: |
           echo "${{ steps.get-latest-tag-unix.outputs.tag }}" > .github/last_tag.txt
           echo "${{ steps.get-latest-tag-unix.outputs.tag_commit }}" > .github/last_tag_commit.txt
@@ -168,14 +192,14 @@ jobs:
         shell: Rscript {0}
 
       - name: Build stock synthesis for windows
-        if: matrix.config.os == 'windows-2019'
+        if: matrix.config.os == 'windows-latest'
         run: |
           cd Compile
           ./Make_SS_safe.bat
           ./Make_SS_fast.bat
 
       - name: Move exes to a new folder on windows
-        if: matrix.config.os == 'windows-2019'
+        if: matrix.config.os == 'windows-latest'
         run: |
           mkdir SS330
           mv Compile/ss.exe SS330/
@@ -184,7 +208,7 @@ jobs:
           mv SS330/ss_opt.exe SS330/ss_opt_win.exe
 
       - name: Build stock synthesis for mac
-        if: matrix.config.os == 'macOS-latest'
+        if: matrix.config.os == 'macos-latest'
         run: |
           rm -rf SS330
           rm -rf ss_osx.tar
@@ -202,13 +226,13 @@ jobs:
           /bin/bash ./Make_SS_330_new.sh -b SS330 -o -p
 
       - name: Verify binary on mac
-        if: matrix.config.os == 'macOS-latest'
+        if: matrix.config.os == 'macos-latest'
         run: |
           shasum -a 256 SS330/ss
           shasum -a 256 SS330/ss_opt
           
       - name: Delete unneeded files and change exe names on mac
-        if: matrix.config.os == 'macOS-latest'
+        if: matrix.config.os == 'macos-latest'
         run: |
           cd SS330
           rm *.obj *.htp *.cpp ss_opt.tpl

diff --git a/run-ss3-mcmc.yml b/run-ss3-mcmc.yml
@@ -1,4 +1,4 @@
-# Check mcmc wrosk
+# Check mcmc works
 name: run-ss3-mcmc
 
 on:
@@ -26,12 +26,12 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@master
 
-      - name: Get admb and put in path
+      - name: Get admb and put in path, linux
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
       - name: Build stock synthesis
         run: |

diff --git a/run-ss3-no-est.yml b/run-ss3-no-est.yml
@@ -33,12 +33,12 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@master
 
-      - name: Get admb and put in path
+      - name: Get admb and put in path, linux
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
       - name: Build stock synthesis
         run: |

diff --git a/run-ss3-with-est.yml b/run-ss3-with-est.yml
@@ -24,12 +24,12 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@master
 
-      - name: Get admb and put in path
+      - name: Get admb and put in path, linux
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
       - name: Build stock synthesis
         run: |

diff --git a/test-r4ss-with-ss3.yml b/test-r4ss-with-ss3.yml
@@ -32,12 +32,12 @@ jobs:
       - name: install r4ss
         run: Rscript -e 'remotes::install_github("r4ss/r4ss")'
 
-      - name: Get admb and put in path
+      - name: Get admb and put in path, linux
         run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-12.3/admb-12.3-linux.zip
-          sudo unzip admb-12.3-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-12.3/bin/admb
-          echo "/usr/local/bin/admb-12.3/bin" >> $GITHUB_PATH
+          wget https://github.com/admb-project/admb/releases/download/admb-13.0/admb-13.0-linux.zip
+          sudo unzip admb-13.0-linux.zip -d /usr/local/bin
+          sudo chmod 755 /usr/local/bin/admb-13.0/bin/admb
+          echo "/usr/local/bin/admb-13.0/bin" >> $GITHUB_PATH
 
       - name: Build stock synthesis
         run: |