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Merged
Rick-Methot-NOAA merged 17 commits into from
Sep 9, 2022
Merged

reduce output to console for ADMB 13 #312

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2a9a756
Refactor: File reading messages
k-doering-NOAA May 12, 2022
d94a856
Style: beginning of model setup console changes
k-doering-NOAA May 12, 2022
1a59415
Style: move population dynamics output to echoinput
k-doering-NOAA May 12, 2022
7771475
Style: remove duplicate info from console output
k-doering-NOAA May 12, 2022
420f7c2
Style: additional console changes
k-doering-NOAA May 12, 2022
cafcc37
feat: additional changes to console output
k-doering-NOAA May 24, 2022
27b0388
fix warnings re-if statements
k-doering-NOAA May 24, 2022
bec93ec
update readcontrol and readstarter
nschindler-noaa Jun 10, 2022
a1b53d4
Merge branch 'main' into console_cleanup
nschindler-noaa Jun 10, 2022
4971ff3
Merge branch 'main' into console_cleanup
nschindler-noaa Aug 31, 2022
2438662
fix '...': Treats ... as a word
kellijohnson-NOAA Sep 9, 2022
7580439
fix: Reduces spacing to 1
kellijohnson-NOAA Sep 9, 2022
b7c826f
fix: Changes Finished to Calculated
kellijohnson-NOAA Sep 9, 2022
ec82bd7
doc: Moves comment to cout
kellijohnson-NOAA Sep 9, 2022
50ae4e3
doc: Adds n iterations to echoinput
kellijohnson-NOAA Sep 9, 2022
6fee82c
fix: Increase consistency echoinput vs cout
kellijohnson-NOAA Sep 9, 2022
73abccd
fix: Changes MG setup to code
kellijohnson-NOAA Sep 9, 2022
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -33,7 +33,7 @@ body:
attributes:
label: Expected behavior
description: A clear and concise description of what you expected to happen.
placeholder: I expected...
placeholder: I expected ...
validations:
required: true
- type: textarea
Expand Down
14 changes: 9 additions & 5 deletions SS_benchfore.tpl
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Expand Up @@ -798,7 +798,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)
YPR_spr_profit = YPR_spr_revenue - Cost;
SPR_Fmult = Fmult;
if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
cout << " got Fspr " << SPR_Fmult << " " << SPR_actual / 100. << endl;
{
echoinput << "Calculated Fspr " << SPR_Fmult << " " << SPR_actual / 100. << endl;
}
Vbio_spr = totbio;
Vbio1_spr = smrybio;
Mgmt_quant(10) = equ_F_std;
Expand Down Expand Up @@ -896,7 +898,7 @@ FUNCTION void Get_Benchmarks(const int show_MSY)

Btgt_Fmult = F1(1);
if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
cout << " got_F0.1: " << Btgt_Fmult << endl;
echoinput << "Calculated F0.1: " << Btgt_Fmult << endl;
Comment thread
Rick-Methot-NOAA marked this conversation as resolved.
SPR_temp = SSB_equil;
Equ_SpawnRecr_Result = Equil_Spawn_Recr_Fxn(SR_parm_work(2), SR_parm_work(3), SSB_unf, Recr_unf, SPR_temp); // returns 2 element vector containing equilibrium biomass and recruitment at this SPR
Btgt = Equ_SpawnRecr_Result(1);
Expand Down Expand Up @@ -1060,7 +1062,9 @@ FUNCTION void Get_Benchmarks(const int show_MSY)

Btgt_Fmult = Fmult;
if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
cout << " got_Btgt " << Btgt_Fmult << " " << Btgt / SSB_unf << endl;
{
echoinput << "Calculated Btgt: " << Btgt_Fmult << " " << Btgt / SSB_unf << endl;
}
YPR_Btgt_enc = YPR_enc; // total encountered yield per recruit
YPR_Btgt_dead = YPR_dead; // total dead yield per recruit
YPR_Btgt_N_dead = YPR_N_dead; // total dead yield per recruit
Expand Down Expand Up @@ -1664,14 +1668,14 @@ FUNCTION void Get_Benchmarks(const int show_MSY)

Btgt_Fmult2 = Fmult;
if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
cout << " got_F_Blimit " << Btgt_Fmult2 << " " << Btgt2 / Blim_report << endl;
echoinput << "Calculated F_Blimit " << Btgt_Fmult2 << " " << Btgt2 / Blim_report << endl;
Comment thread
Rick-Methot-NOAA marked this conversation as resolved.
Mgmt_quant(18) = Btgt2;
Mgmt_quant(19) = equ_F_std;
Mgmt_quant(20) = sum(equ_catch_fleet(2)) * Equ_SpawnRecr_Result(2);
} // end finding F for Blimit

if (rundetail > 0 && mceval_counter == 0 && show_MSY == 1)
cout << " got Fmsy " << MSY_Fmult << " " << MSY << endl;
echoinput << "Calculated Fmsy " << MSY_Fmult << " " << MSY << endl;
Comment thread
Rick-Methot-NOAA marked this conversation as resolved.

// ***************** show management report SS_Label_740
if (show_MSY == 1)
Expand Down
61 changes: 27 additions & 34 deletions SS_global.tpl
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Expand Up @@ -890,7 +890,6 @@ GLOBALS_SECTION
BETWEEN_PHASES_SECTION
{
int j_phase = current_phase(); // this is the phase to come
cout << current_phase() - 1 << " " << niter << " -log(L): " << obj_fun << " between " << endl;

// SS_Label_Info_11.1 #Save last value of objective function
if (j_phase > 1)
Expand Down Expand Up @@ -922,16 +921,6 @@ BETWEEN_PHASES_SECTION
FINAL_SECTION
{
// SS_Label_Info_12.1 #Get run ending time
time(&finish);
elapsed_time = difftime(finish, start);
hour = long(elapsed_time) / 3600;
minute = long(elapsed_time) % 3600 / 60;
second = (long(elapsed_time) % 3600) % 60;
cout << endl
<< "In final section " << endl;
cout << "Finish time: " << ctime(&finish);
cout << "Elapsed time: ";
cout << hour << " hours, " << minute << " minutes, " << second << " seconds." << endl;

if (No_Report == 1)
{
Expand All @@ -940,9 +929,8 @@ FINAL_SECTION

else
{
cout << " Iterations: " << niter << " -log(L): " << obj_fun << endl;
cout << "Final gradient: " << objective_function_value::pobjfun->gmax << endl
<< endl;
cout << "Iterations: " << niter << endl;
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kellijohnson-NOAA marked this conversation as resolved.
echoinput << "Iterations: " << niter << endl;
if (objective_function_value::pobjfun->gmax > final_conv)
{
warnstream << "Final gradient: " << objective_function_value::pobjfun->gmax << " is larger than final_conv: " << final_conv;
Expand Down Expand Up @@ -997,7 +985,7 @@ FINAL_SECTION
}
}
if (mceval_phase() == 0)
cout << " finished COVAR.SSO" << endl;
echoinput << " finished COVAR.SSO" << endl;
}

// SS_Label_Info_12.3 #Go thru time series calculations again to get extra output quantities
Expand All @@ -1013,7 +1001,7 @@ FINAL_SECTION
if (Do_Forecast > 0)
{
show_MSY = 0;
Get_Forecast();
Get_Forecast(); // First call to forecast
}
k = Do_Dyn_Bzero;
for (j = styr - 2; j <= YrMax; j++)
Expand Down Expand Up @@ -1062,21 +1050,28 @@ FINAL_SECTION
{
Get_Benchmarks(show_MSY);
if (mceval_phase() == 0)
cout << " finished benchmark" << endl;
{
cout << "Finished calculating benchmarks" << endl;
echoinput << "Finished calculating benchmarks" << endl;
}
}
}
if (Do_Forecast >= 0)
{
report5 << "THIS FORECAST FOR PURPOSES OF GETTING DISPLAY QUANTITIES" << endl;
report5 << "THIS FORECAST IS FOR PURPOSES OF GETTING DISPLAY QUANTITIES" << endl;
if (did_MSY > 0)
show_MSY = 0; // so to not repeat forecast_report.sso
Get_Forecast();
if (mceval_phase() == 0)
cout << " finished forecast" << endl;
if (mceval_phase() == 0) {
cout << "Finished forecast" << endl;
echoinput << "Finished forecast" << endl;
}
}

if (write_bodywt > 0)
{
cout << "Writing wtatage.ss_new" << endl;
echoinput << "Writing wtatage.ss_new" << endl;
bodywtout << -9999 << " " << 1 << " " << 1 << " " << 1 << " " << 1 << " " << 0 << " " << Wt_Age_mid(1, 1) << " #terminator " << endl;
bodywtout.close();
}
Expand All @@ -1085,10 +1080,13 @@ FINAL_SECTION
// SS_Label_Info_12.3.4 #call fxn STDquant()
Process_STDquant();
if (mceval_phase() == 0)
cout << " finished StdDev quantities" << endl;
echoinput << "Finished StdDev quantities" << endl;
get_posteriors();
if (mceval_phase() == 0)
cout << " finished posteriors" << endl;
{
cout << "Finished posteriors" << endl;
echoinput << "Finished posteriors" << endl;
}

// SS_Label_Info_12.4.2 #Call fxn write_summaryoutput()
if (Do_CumReport > 0)
Expand All @@ -1114,17 +1112,17 @@ FINAL_SECTION
// SS_Label_Info_12.4 #Do Outputs
// SS_Label_Info_12.4.1 #Call fxn write_bigoutput()
write_bigoutput();
cout << " finished report.sso" << endl;
cout << "Finished final writing of report.sso" << endl;
echoinput << "Finished final writing of report.sso" << endl;
}
// SS_Label_Info_12.4.4 #Call fxn write_nudata() to create bootstrap data
if (N_nudata > 0)
{
cout << "Creating bootstrap files: " << N_nudata << " files";
cout << "Begin writing *.ss_new output files ... ";
write_nudata();
cout << " finished" << endl;

// SS_Label_Info_12.4.5 #Call fxn write_nucontrol() to produce control.ss_new
write_nucontrol();
cout << "Finished writing *.ss_new output files" << endl;
}
else
{
Expand All @@ -1134,28 +1132,22 @@ FINAL_SECTION
}
}

echoinput << "Begin final output calculations and warnings" << endl;
// SS_Label_Info_12.4.6 #Call fxn write_Bzero_output() appended to report.sso
if (pick_report_use(59) == "Y")
{
cout << "dynamic Bzero in FINAL_SECTION: ";
write_Bzero_output();
cout << " finished " << endl;
}

if (pick_report_use(54) == "Y" && Do_Benchmark > 0)
{
cout << "setup_benchmark: " << endl;
setup_Benchmark();
cout << "SPR_profile: ";
SPR_profile();
cout << " finished " << endl;
}

if (pick_report_use(55) == "Y" && Do_Benchmark > 0)
{
cout << "Global_MSY: ";
Global_MSY();
cout << " finished " << endl;
}

if (parm_adjust_method == 3)
Expand Down Expand Up @@ -1344,7 +1336,8 @@ REPORT_SECTION
get_time_series(); // in ADMB's report_section
evaluate_the_objective_function();
write_bigoutput();
cout << "Wrote bigoutput and bodywt for last_phase in REPORT_SECTION and before hessian, no benchmark or forecast " << endl;
echoinput << "Wrote first version of output files (before hessian, benchmark, and forecast)" << endl;
cout << "Wrote first version of output files (before hessian, benchmark, and forecast)" << endl;
save_for_report = 0;
write_bodywt = 0;
// SS2out.close();
Expand Down
35 changes: 20 additions & 15 deletions SS_objfunc.tpl
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Expand Up @@ -162,7 +162,7 @@ FUNCTION void evaluate_the_objective_function()
} // end having obs for this survey
}
if (do_once == 1)
cout << " did survey obj_fun " << surv_like << endl;
echoinput << "Finished survey obj_fun " << surv_like << endl;
}

// SS_Label_Info_25.2 #Fit to discard
Expand Down Expand Up @@ -234,7 +234,9 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " did discard obj_fun " << disc_like << endl;
{
echoinput << "Finished discard obj_fun " << disc_like << endl;
}
}

// SS_Label_Info_25.3 #Fit to mean body wt
Expand All @@ -246,7 +248,7 @@ FUNCTION void evaluate_the_objective_function()
mnwt_like(mnwtdata(3, i)) += 0.5 * (DF_bodywt + 1.) * log(1. + square(mnwtdata(6, i) - exp_mnwt(i)) / mnwtdata(9, i)) + mnwtdata(10, i);
}
if (do_once == 1)
cout << " did meanwt obj_fun " << mnwt_like << endl;
echoinput << " Finished meanwt obj_fun " << mnwt_like << endl;
}

// SS_Label_Info_25.4 #Fit to length comp
Expand Down Expand Up @@ -404,7 +406,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " did lencomp obj_fun " << length_like_tot << endl;
echoinput << "Finished lencomp obj_fun " << length_like_tot << endl;
}

// SS_Label_Info_25.5 #Fit to age composition
Expand Down Expand Up @@ -540,7 +542,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " did agecomp obj_fun " << age_like_tot << endl;
echoinput << "Finished agecomp obj_fun " << age_like_tot << endl;
}

// SS_Label_Info_25.6 #Fit to mean size@age
Expand Down Expand Up @@ -574,7 +576,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " did meanlength obj_fun " << sizeage_like << endl;
echoinput << "Finished meanlength obj_fun " << sizeage_like << endl;
}

// SS_Label_Info_25.7 #Fit to generalized Size composition
Expand Down Expand Up @@ -653,7 +655,7 @@ FUNCTION void evaluate_the_objective_function()
Morphcomp_like -= Morphcomp_obs(iobs, 5) * Morphcomp_obs(iobs)(6, k) * log(elem_div(Morphcomp_exp(iobs)(6, k), Morphcomp_obs(iobs)(6, k)));
}
if (do_once == 1)
cout << " did morphcomp obj_fun " << Morphcomp_like << endl;
cout << "Finished morphcomp obj_fun " << Morphcomp_like << endl;
}

// SS_Label_Info_25.9 #Fit to tag-recapture
Expand Down Expand Up @@ -692,7 +694,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " did tag obj_fun " << TG_like1 << endl
cout << "Finished tag obj_fun " << TG_like1 << endl
<< TG_like2 << endl;
}

Expand All @@ -706,7 +708,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " initequ_catch -log(L) " << equ_catch_like << endl;
echoinput << " initequ_catch -log(L) " << equ_catch_like << endl;

// SS_Label_Info_25.11 #Fit to catch by fleet/season
if (F_Method > 1)
Expand Down Expand Up @@ -736,7 +738,7 @@ FUNCTION void evaluate_the_objective_function()
}
}
if (do_once == 1)
cout << " catch -log(L) " << catch_like << endl;
echoinput << " catch -log(L) " << catch_like << endl;
}

// SS_Label_Info_25.12 #Likelihood for the recruitment deviations
Expand Down Expand Up @@ -809,7 +811,7 @@ FUNCTION void evaluate_the_objective_function()
if (do_recdev == 4)
regime_like += square(sum_recdev);
if (do_once == 1)
cout << " did recruitdev obj_fun " << recr_like << " " << sd_offset_rec << " " << two_sigmaRsq << endl;
echoinput << "Finished recruitdev obj_fun " << recr_like << " " << sd_offset_rec << " " << two_sigmaRsq << endl;
}
if (Do_Forecast > 0 && do_recdev > 0)
{
Expand Down Expand Up @@ -1106,7 +1108,7 @@ FUNCTION void evaluate_the_objective_function()

if (do_once == 1)
{
cout << " OK with obj_func " << obj_fun << endl;
echoinput << " OK with obj_func " << obj_fun << endl;
if (SSB_yr(endyr) < 0.01 * SSB_yr(styr))
{
warnstream << "1st iteration warning: ssb(endyr)/ssb(styr)= " << SSB_yr(endyr) / SSB_yr(styr) << "; suggest start with larger R0 to get near 0.4; or use depletion fleet option";
Expand Down Expand Up @@ -1612,10 +1614,13 @@ FUNCTION void get_posteriors()
//********************************************************************
/* SS_Label_FUNCTION 33 get_posteriors (MCMC eval) */
if (rundetail > 1)
cout << " mceval counter: " << mceval_counter << endl;
{
cout << "mceval counter: " << mceval_counter << endl;
}
if (rundetail == 0 && double(mceval_counter) / 200. == double(mceval_counter / 200.))
cout << " mceval counter: " << mceval_counter << endl;

{
cout << "mceval counter: " << mceval_counter << endl;
}
if (mceval_header == 0 && mceval_phase()) // first pass through the mceval phase
{
// delete any old mcmc output files
Expand Down
3 changes: 2 additions & 1 deletion SS_param.tpl
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Expand Up @@ -17,7 +17,8 @@ PARAMETER_SECTION
// clang-format on
// set the filename to all ADMB output files to "ss.[ext]"
ad_comm::adprogram_name = "ss";
echoinput << "now in PARAMETER_SECTION " << endl;
echoinput << "Begin setting up parameters" << endl;
cout << "Begin setting up parameters ... ";
if (readparfile >= 1)
{
cout << " read parm file" << endl;
Expand Down
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