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Merged
Rick-Methot-NOAA merged 4 commits into from
May 27, 2022
Merged

Added write_message and write_warning #327

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18d3f6a
Added write_message and write_warning
nschindler-noaa May 27, 2022
b43dd36
Reconfigured fatal message
nschindler-noaa May 27, 2022
a78d95f
Merge branch 'main' into 320-standardize-exit-message
nschindler-noaa May 27, 2022
6ec339d
Merge branch 'main' into 320-standardize-exit-message
Rick-Methot-NOAA May 27, 2022
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95 changes: 69 additions & 26 deletions SS_global.tpl
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ GLOBALS_SECTION
#include <fvar.hpp>
#include <vector>
#include <iostream>
#include <sstream>
#include <sys/types.h>
#include <sys/stat.h>
time_t start, finish;
Expand Down Expand Up @@ -121,9 +122,11 @@ GLOBALS_SECTION
ofstream SS_smry;
ofstream SIS_table;
// declare some entities that need global access
std::stringstream warnstream;
std::string usermsg;
int ParCount;
int timevary_parm_cnt;
int N_warn;
int N_warn = 0;
int styr;
int endyr;
int YrMax;
Expand Down Expand Up @@ -160,6 +163,38 @@ GLOBALS_SECTION
std::vector<int> Fparm_PH;
;
// function in GLOBALS to do the timing setup in the data section

// SS_Label_Function xxxa write_message(string,int,int); output a message with an option to exit (when fatal)
void write_message(std::string msg, int echo, int exitflag)
{
if (msg.length() > 0)
{
N_warn++;
warning << N_warn << ": " << msg << endl;

if (echo == 1)
{
if (exitflag == 1)
echoinput << "Exit: ";
echoinput << msg << endl;
}
if (exitflag == 1)
{
cout << " Fatal Error:" << endl;
cout << " -- " << msg << endl;
cout << " Exiting SS3. " << endl;
exit(1);
}
}
}
// SS_Label_Function_xxxb write_warning(int,int); output a warning with an option to exit (when fatal)
void write_warning(int echo, int exitflag)
{
std::string msg(warnstream.str());
write_message(msg, echo, exitflag);
warnstream.str("");
}

// SS_Label_Function_xxxx #get_data_timing() called by readdata
void get_data_timing(const dvector& to_process, const ivector& timing_constants, ivector i_result, dvector r_result, const dvector& seasdur, const dvector& subseasdur_delta, const dvector& azero_seas, const dvector& surveytime)
{
Expand Down Expand Up @@ -221,10 +256,12 @@ GLOBALS_SECTION
{
if (month >= 13.0)
{
N_warn++;
cout << "fatal read error, see warning" << endl;
warning << N_warn << " Fatal error. month must be <13.0, end of year is 12.99, value read is: " << month << endl;
exit(1);
warnstream << "Fatal error. month must be <13.0, end of year is 12.99, value read is: " << month;
write_warning(0, 1);
// N_warn++;
// cout << "fatal read error, see warning" << endl;
// warning << N_warn << " Fatal error. month must be <13.0, end of year is 12.99, value read is: " << month << endl;
// exit(1);
}
temp1 = max(0.00001, (month - 1.0) / 12.); // month as fraction of year
s = 1; // earlist possible seas;
Expand Down Expand Up @@ -376,12 +413,15 @@ GLOBALS_SECTION
tempvec.fill("{-10,10,0.,0.,5,6,4}");
if (baseparm_list(1) <= 0.0)
{
N_warn++;
warning << N_warn << " "
<< " cannot use multiplicative blocks for parameter with a negative lower bound; exit " << endl
warnstream << "cannot use multiplicative blocks for parameter with a negative lower bound; exit " << endl
<< baseparm_list(1) << " " << baseparm_list(2) << " " << baseparm_list(3) << endl;
cout << "exit, see warning" << endl;
exit(1);
write_warning(0,1);
// N_warn++;
// warning << N_warn << " "
// << " cannot use multiplicative blocks for parameter with a negative lower bound; exit " << endl
// << baseparm_list(1) << " " << baseparm_list(2) << " " << baseparm_list(3) << endl;
// cout << "exit, see warning" << endl;
// exit(1);
}
tempvec(1) = log(baseparm_list(1) / baseparm_list(3)); // max negative change
tempvec(2) = log(baseparm_list(2) / baseparm_list(3)); // max positive change
Expand Down Expand Up @@ -724,19 +764,23 @@ GLOBALS_SECTION
y = baseparm_list(10);
if (y < styr)
{
N_warn++;
warning << N_warn << " "
<< " reset parm_dev start year to styr for parm: " << j << " " << y << endl;
warnstream << "reset parm_dev start year to styr for parm: " << j << " " << y;
write_warning(0,0);
// N_warn++;
// warning << N_warn << " "
// << " reset parm_dev start year to styr for parm: " << j << " " << y << endl;
y = styr;
}
timevary_setup(10) = y;

y = baseparm_list(11);
if (y > YrMax)
{
N_warn++;
warning << N_warn << " "
<< " reset parm_dev end year to YrMax for parm: " << j << " " << y << endl;
warnstream << " reset parm_dev end year to YrMax for parm: " << j << " " << y;
write_warning(0,0);
// N_warn++;
// warning << N_warn << " "
// << " reset parm_dev end year to YrMax for parm: " << j << " " << y << endl;
y = YrMax;
}
timevary_setup(11) = y;
Expand Down Expand Up @@ -788,6 +832,7 @@ GLOBALS_SECTION
echoinput << "timevary_setup" << timevary_setup << endl;
return;
}

// } // end GLOBALS_SECTION

// SS_Label_Section_11. #BETWEEN_PHASES_SECTION
Expand Down Expand Up @@ -849,9 +894,8 @@ FINAL_SECTION
<< endl;
if (objective_function_value::pobjfun->gmax > final_conv)
{
N_warn++;
warning << N_warn << " "
<< "Final gradient: " << objective_function_value::pobjfun->gmax << " is larger than final_conv: " << final_conv << endl;
warnstream << "Final gradient: " << objective_function_value::pobjfun->gmax << " is larger than final_conv: " << final_conv;
write_warning(0, 0);
}

// SS_Label_Info_12.2 #Output the covariance matrix to covar.sso
Expand Down Expand Up @@ -1034,9 +1078,8 @@ FINAL_SECTION
else
{
{
N_warn++;
warning << N_warn << " "
<< "NOTE: No *.ss_new and fewer *.sso files written after mceval" << endl;
warnstream << "NOTE: No *.ss_new and fewer *.sso files written after mceval";
write_warning(0, 0);
}
}

Expand Down Expand Up @@ -1066,15 +1109,15 @@ FINAL_SECTION

if (parm_adjust_method == 3)
{
N_warn++;
warning << N_warn << " Time-vary parms not bound checked" << endl;
warnstream << "Time-vary parms not bound checked";
write_warning(0, 0);
}

// SS_Label_Info_12.4.7 #Finish up with final writes to warning.sso
if (N_changed_lambdas > 0)
{
N_warn++;
warning << N_warn << " Reminder: Number of lamdas !=0.0 and !=1.0: " << N_changed_lambdas << endl;
warnstream << "Reminder: Number of lamdas !=0.0 and !=1.0: " << N_changed_lambdas;
write_warning(0, 0);
}

if (Nparm_on_bound > 0)
Expand Down
50 changes: 26 additions & 24 deletions SS_readstarter.tpl
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,10 +59,11 @@
int niter // iteration count
int loop
int TG_t; // time counter (in seasons) for tag groups

int Fcast_catch_start
// int ParCount;
int retParCount;
int N_SC; // counter for starter comments
int N_SC; // counter for starter comments
int N_DC;
int N_CC;
int N_FC;
Expand All @@ -71,14 +72,14 @@

int frac_female_pointer;
int finished_minimize;
int icycle
int No_Report // flag to skip output reports after MCMC and MCeval
int mcmcFlag
int noest_flag
int icycle;
int No_Report; // flag to skip output reports after MCMC and MCeval
int mcmcFlag;
int noest_flag;
number temp;
number temp1;
int save_for_report;
int bigsaver; // (save_for_report>0) || ((sd_phase() || mceval_phase()) && (initial_params::mc_phase==0))
int bigsaver; // (save_for_report>0) || ((sd_phase() || mceval_phase()) && (initial_params::mc_phase==0))
int write_bodywt;
int write_bodywt_save;
int save_gparm;
Expand All @@ -93,9 +94,9 @@
!! special_flag=0;

int Nparm_on_bound;
int on;
int SDmode;
int maxI;
int on;
int SDmode;
int maxI;

LOCAL_CALCS
maxI=999;
Expand All @@ -111,10 +112,10 @@
TG_t=0; Fcast_catch_start=0; retParCount=0; N_SC=0; N_DC=0; N_CC=0; N_FC=0; catch_mult_pointer=0; frac_female_pointer=0; icycle=0; No_Report=0;
mcmcFlag=0; noest_flag=0; temp=0; temp1=0; save_gparm_print=0;
finished_minimize=0;
// SS_Label_Info_1.1.2 #arrays for parameter labels are created in GLOBAL
// adstring_array NumLbl;
// adstring_array GenderLbl; // gender label
// adstring_array CRLF; // blank to terminate lines
// SS_Label_Info_1.1.2 #arrays for parameter labels are created in GLOBAL
// adstring_array NumLbl;
// adstring_array GenderLbl; // gender label
// adstring_array CRLF; // blank to terminate lines

CRLF+="";
GenderLbl+="Fem";
Expand All @@ -126,17 +127,16 @@
GP_Lbl+="_GP_5";
GP_Lbl+="_GP_6";
onenum=" ";
for (i=1;i<=199;i++) /* SS_loop: fill string NumLbl with numbers (start at 1) */
for (i = 1; i <= 199; i++) /* SS_loop: fill string NumLbl with numbers (start at 1) */
{
sprintf(onenum, "%d", i);
NumLbl+=onenum+CRLF(1);
sprintf(onenum, "%d", i);
NumLbl += onenum + CRLF(1);
}
for (i=0;i<=198;i++) /* SS_loop: fill string NumLbl0 with numbers (start at 0) */
for (i = 0; i <= 198; i++) /* SS_loop: fill string NumLbl0 with numbers (start at 0) */
{
sprintf(onenum, "%d", i);
NumLbl0+=onenum+CRLF(1);
sprintf(onenum, "%d", i);
NumLbl0 += onenum + CRLF(1);
}

pick_report_name+="DEFINITIONS report:1";pick_report_use+="N";
pick_report_name+="LIKELIHOOD report:2";pick_report_use+="N";
pick_report_name+="Input_Variance_Adjustment report:3";pick_report_use+="N";
Expand Down Expand Up @@ -200,11 +200,13 @@

// check command line inputs

if ( (on=option_match(argc,argv,"-noest"))>-1)
if ((on = option_match(argc,argv,"-noest")) > -1)
{
cout<<"SS3 is not configured to work with -noest; use -maxI instead which overrides maxphase in starter.ss"<<endl;
N_warn++; warning<<N_warn<<" SS3 exited with -noest, use -maxI <maxphase> instead"<<endl;
exit(1);
warnstream << "SS3 is not configured to work with -noest; use -maxI <maxphase> instead which overrides maxphase in starter.ss";
write_warning(0,1);
// cout<<"SS3 is not configured to work with -noest; use -maxI instead which overrides maxphase in starter.ss"<<endl;
// N_warn++; warning<<N_warn<<" SS3 exited with -noest, use -maxI <maxphase> instead"<<endl;
// exit(1);
}

if ( (on=option_match(argc,argv,"-maxI"))>-1 || (on=option_match(argc,argv,"-stopph"))>-1)
Expand Down