Adjust tvg compatibility btarget

.github/workflows/build-ss3-warnings.yml

@@ -60,49 +60,48 @@ jobs:
           chmod 777 SS330
           /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -w &> warnings.txt
 
-      # Runs a set of commands using the runners shell
-      - name: Use R to parse warnings output
+      - name: Print warnings
+        run: cat warnings.txt
+
+      - name: Use R to parse warnings output and determine if amount of warnings has changed
         run: |
           txt <- readLines("warnings.txt", encoding = "UTF-8")
-          warn_line <- grep(pattern = "g++ -c -std=c++17 -O3 -Wall -Wextra -D_USE_MATH_DEFINES -DUSE_ADMB_CONTRIBS", x = txt, fixed = TRUE)
+          warn_line <- grep(pattern = "g++ -c -std=c++17 -O3 -Wall -Wextra -static-libstdc++ -static-libgcc -D_USE_MATH_DEFINES -DUSE_ADMB_CONTRIBS", x = txt, fixed = TRUE)
           end_warn_line <- grep(pattern = "*** Linking: ss3.obj ", x = txt, fixed = TRUE)
           if (length(warn_line) == 1 & length(end_warn_line) == 1) {
             txt <- txt[(warn_line+3):(end_warn_line-1)]
             rm_warn_start_lines <- grep(pattern = "/usr/local/admb/include/admodel.h: ", x = txt, fixed = TRUE, invert = TRUE)
             txt <- txt[rm_warn_start_lines]
             n_errors <- length(grep(pattern = "^ [0-9]", x = txt))
             message("There are ", n_errors, " warning messages related to SS3.")
-            write.table(n_errors, "n_warn.txt")
+            # write.table(n_errors, "n_warn.txt")
           } 
           writeLines(txt, "warnings_ss.txt")
-        # warn_line <- grep(pattern = "compiling a second time to get warnings", x = txt, fixed = TRUE)
-        # txt <- txt[(warn_line+1):length(txt)]
-        shell: Rscript {0}
-
-      - name: Print warnings
-        run: cat warnings_ss.txt
-
-      - name: Determine if fails/passes based on the number of warnings
-        run: |
           ref <- readLines(".github/workflows/reference_files/warnings_ss_ref.txt")
-          n_warn <- read.table("n_warn.txt")
-          n_warn <- as.integer(n_warn[1,1])
+          ref2 <- ref[!grepl("ss3.obj", ref) & nzchar(txt)]
+          n_warn <- n_errors
+          if(n_warn != 0){
+            n_warn <- as.integer(n_warn[1,1])
+          }
           if (n_warn > length(ref)) {
             stop("Increased number of warnings compared to reference warning file")
           } else {
               # n_warn doesn't take into account the "In file included from ss.cpp:7:"
               # so add 2 to add those lines back in
               if (n_warn+length(ref) < length(ref)){
-                stop("Number of warnings of decreased compared to reference warning file")
+                message("Number of warnings of decreased compared to reference warning file, if this is pushed to main, change the ref file")
               } else {
-                  message("Acceptable number of warnings")
+                  message(paste0("Acceptable number of warnings: ", n_warn))
               }
             }
         shell: Rscript {0}
 
+      - name: Print warnings
+        run: cat warnings_ss.txt
+
       - name: Archive warnings text file
         if: always()
         uses: actions/upload-artifact@main
         with:
           name: 'warnings_ss.txt'
-          path: warnings_ss.txt
+          path: warnings_ss.txt

.github/workflows/reference_files/warnings_ss_ref.txt

@@ -1,12 +1,3 @@
-/usr/local/admb/include/admodel.h:1915:38: warning: unused parameter 'gradients' [-Wunused-parameter]
- 1915 |   virtual void report(const dvector& gradients){;};
-      |                       ~~~~~~~~~~~~~~~^~~~~~~~~
-/usr/local/admb/include/admodel.h:2501:43: warning: unused parameter 'ofs' [-Wunused-parameter]
- 2501 |   virtual void save_value(const ofstream& ofs, int prec,const dvector&,
-      |                           ~~~~~~~~~~~~~~~~^~~
-/usr/local/admb/include/admodel.h:2501:52: warning: unused parameter 'prec' [-Wunused-parameter]
- 2501 |   virtual void save_value(const ofstream& ofs, int prec,const dvector&,
-      |                                                ~~~~^~~~
-/usr/local/admb/include/admodel.h:2502:10: warning: unused parameter 'offset' [-Wunused-parameter]
- 2502 |     int& offset){}
-      |     ~~~~~^~~~~~
+g++ -std=c++17 -O3 -oss3 ss3.obj "/usr/local/admb/lib/libadmb-contrib-x86_64-linux-g++13.a"
+*** Linking: ss3.obj 
+

SS_benchfore.tpl

@@ -1042,7 +1042,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     SSBpR_Calc(equ_Recr);
     F01_origin = YPR_opt / Fmult;
 
-    BTGT_target = 0.1; //  now relative to Bmark
+    BTGT_frac = 0.1; //  now relative to Bmark
     Btgttgt = F01_origin * 0.1;
     if (show_MSY == 1)
     {
@@ -1138,18 +1138,18 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
   {
     // ******************************************************
 
-    if (depletion_basis == 1) 
-      {Btgttgt = BTGT_target * SSB_virgin;}
+    if (depletion_basis == 1 && timevary_bio_4SRR != 0) 
+      {Btgttgt = BTGT_frac * SSB_virgin;}
     else
-      {Btgttgt = BTGT_target * SSB_unf;}  //  current SS3 approach uses benchmark biology
+      {Btgttgt = BTGT_frac * SSB_unf;}  //  current SS3 approach uses benchmark biology
 
       if (show_MSY == 1)
     {
      report5 << "#" << endl;
-     if (depletion_basis == 1)
-     {report5 << "Find_target_SSB as fraction: " << BTGT_target << " of Virgin SSB:" << SSB_virgin << endl;}
+     if (depletion_basis == 1 && timevary_bio_4SRR != 0)
+     {report5 << "Find_target_SSB as fraction: " << BTGT_frac << " of Virgin SSB:" << SSB_virgin << endl;}
      else
-     {report5 << "Find_target_SSB as fraction: " << BTGT_target << " of SSB_unf: "<< SSB_unf << endl;}
+     {report5 << "Find_target_SSB as fraction: " << BTGT_frac << " of SSB_unf: "<< SSB_unf << endl;}
      report5  << "Iter Fmult ann_F SPR Catch SSB Recruits SSB/Bzero Tot_catch";
 
     for (p = 1; p <= pop; p++)
@@ -1212,9 +1212,11 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
         }
         SSBpR_Calc(equ_Recr); //  where equ_Recr=1.0, so returned SSB_equil is in units of SSB/R,
         SSBpR_temp = SSB_equil;
+//        warning << equ_Recr << " " << SSB_equil << " " << SRparm_bench << " " << SSBpR_temp << endl;
         SPR_Btgt = SSBpR_temp / SSBpR_unf;  //  where SSBpR_unf = SSB_unf / Recr_unf so units of SSB/R; so result is SPR_Btgt = (fished SSB/R) / (unfished SSB/R)
         //  SPAWN-RECR:   calc equil spawn-recr for Btarget calcs;  need to make area-specific
         Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SRparm_bench, SSB0_4_SRR, R0_4_SRR, SSBpR_temp); //  returns 2 element vector containing equilibrium biomass and recruitment at this SPR
+//        warning << SSB0_4_SRR << " " << R0_4_SRR << Equ_SpawnRecr_Result << endl;
         yld1(ii) = Equ_SpawnRecr_Result(1);
       }
 
@@ -1247,7 +1249,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       if (show_MSY == 1)
       {
         report5 << j << " " << Fmult << " " << equ_F_std << " " << SPR_Btgt << " " << YPR_dead * Equ_SpawnRecr_Result(2) << " " << Btgt << " " << Equ_SpawnRecr_Result(2)
-                << " " << Btgt / SSB_unf << " " << sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
+                << " " << Btgt / (Btgttgt / BTGT_frac) << " " << sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
         for (p = 1; p <= pop; p++)
           for (gp = 1; gp <= N_GP; gp++)
           {
@@ -1774,7 +1776,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
       Nloops = 28;
     }
 
-    //    Btgttgt=BTGT_target*SSB_virgin;   //  this is relative to virgin, not to the average biology from benchmark years
+    //    Btgttgt=BTGT_frac*SSB_virgin;   //  this is relative to virgin, not to the average biology from benchmark years
     double Blim_report;
     if (Blim_frac > 0.0)
     {
@@ -1971,7 +1973,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
     {
       report5 << "#" << endl
               << "Ratio_SSB/B0_as_target" << endl;
-      report5 << "Ratio_target  " << BTGT_target << endl;
+      report5 << "Ratio_target  " << BTGT_frac << endl;
       report5 << "Ratio_calc " << Btgt / SSB_unf << endl;
       report5 << "SPR@Btgt " << SPR_Btgt << endl;
       report5 << "Fmult " << Btgt_Fmult << endl;

SS_readcontrol_330.tpl

@@ -7026,7 +7026,7 @@
     }
     case 3: // compare to SPR_Btarget
     {
-      sprintf(onenum, "%d", int(100. * BTGT_target));
+      sprintf(onenum, "%d", int(100. * BTGT_frac));
       SPR_report_label += " (1-SPR)/(1-SPR_at_B" + onenum + "%)";
       break;
     }
@@ -7057,7 +7057,7 @@
     }
     case 3:
     {
-      sprintf(onenum, "%d", int(100. * BTGT_target));
+      sprintf(onenum, "%d", int(100. * BTGT_frac));
       F_report_label = "(F)/(F_at_B" + onenum + "%)";
       break;
     }

SS_readdata_330.tpl

@@ -3808,7 +3808,7 @@
   ivector Bmark_Yr(1,10);
   ivector Bmark_t(1,2); // for range of time values for averaging body size
   number SPR_target;
-  number BTGT_target;
+  number BTGT_frac;
   number Blim_frac;
   int MSY_units; // 1=dead catch, 2=retained catch, 3=retained catch profits
   vector CostPerF(1,Nfleet);
@@ -3937,8 +3937,8 @@
   echoinput << "next read SPR target and Biomass target as fractions" << endl;
   *(ad_comm::global_datafile) >> SPR_target;
   echoinput << SPR_target << " echoed SPR_target " << endl;
-  *(ad_comm::global_datafile) >> BTGT_target;
-  echoinput << BTGT_target << " echoed B_target " << endl;
+  *(ad_comm::global_datafile) >> BTGT_frac;
+  echoinput << BTGT_frac << " echoed BTGT_frac " << endl;
 
   if (Do_Benchmark == 3)
   {

SS_write_ssnew.tpl

@@ -1594,7 +1594,7 @@ FUNCTION void write_nucontrol()
   }
 
   NuFore << SPR_target << " # SPR target (e.g. 0.40)" << endl;
-  NuFore << BTGT_target << " # Biomass target (e.g. 0.40) as fraction of SSB_virgin if depletion basis = 1, else as fraction of SSB_unfished in benchmark" << endl;
+  NuFore << BTGT_frac << " # Biomass target (e.g. 0.40) as fraction of SSB_virgin if depletion basis = 1 or time_vary compatibility = 0, else as fraction of SSB_unfished in benchmark" << endl;
   if (Do_Benchmark != 3) NuFore << "#";
   NuFore << Blim_frac << " # COND: Do_Benchmark==3;  Blimit as fraction of Bmsy (neg value to use as frac of SSB_virgin or SSB_unfished) (e.g. 0.50)";
   NuFore << "#" << endl << "# Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm (enter actual year, or values of 0 or -integer to be rel. endyr)" << endl

warnings.txt

@@ -0,0 +1,13 @@
+!!version_info += "#V3.30.xx.yy;_safe;_compile_date:_";
+-- Building ss3 with docker in 'SS330' --
+*** Parse: ss3.tpl
+tpl2cpp ss3 || tpl2rem ss3
+
+*** Compile: ss3.cpp
+g++ -c -std=c++17 -O3 -Wall -Wextra -D_USE_MATH_DEFINES -DUSE_ADMB_CONTRIBS -I. -I"/usr/local/admb/include" -I"/usr/local/admb/include/contrib" -oss3.obj ss3.cpp
+
+*** Linking: ss3.obj 
+g++ -std=c++17 -O3 -oss3 ss3.obj "/usr/local/admb/lib/libadmb-contrib-x86_64-linux-g++13.a"
+
+Successfully built executable.
+