TerenceSperringerJr
commented
7 years ago https://github.com/PublicHealthDynamicsLab/FRED/wiki/Parameter-Sweeps#baseline-parameter-file
Baseline Parameter File First create a file called, for example, params.base that contains parameters that are fixed for all jobs in the parameter sweep. The contents will depend on the purpose if the study. Here is an example:
% cat params.base days = 100 fips = 42065
If I use a parameter instead of fips for this example (such as counties = 53033), fred_jobs will run to completion. Given the error above I'd say that the fips parameter isn't processing correctly.
Update: Actually it looks like counties = 53033 is ignored and has no effect on the used parameters according to the log.
Update: The problem seems to arise within /FRED/src/Place_List.cc lines 307 - 341
// get population_id from fips
char line_string[FRED_STRING_SIZE];
char* line;
char* city;
char* state;
char* county;
char* fips;
int found = 0;
int fipsLength = strlen(Global::FIPS_code);
if(fipsLength == 5) {
FILE* fp = Utils::fred_open_file(Place_List::Counties_file);
if(fp == NULL) {
Utils::fred_abort("counties file |%s| NOT FOUND\n", Place_List::Counties_file);
}
while(fgets(line_string, FRED_STRING_SIZE - 1, fp) != NULL) {
line = line_string;
city = strsep(&line, "\t");
state = strsep(&line, "\t");
county = strsep(&line, "\t");
fips = strsep(&line, "\n");
// printf("city = |%s| state = |%s| county = |%s| fips = |%s|\n",
// city,state,county,fips);
if(strcmp(Global::FIPS_code, fips) == 0) {
found = 1;
break;
}
}
fclose(fp);
if(found) {
Utils::fred_log("FOUND a county = |%s County %s| for fips = |%s|\n", county, state, fips);
sprintf(Global::Synthetic_population_id, "%s_%s", Global::Synthetic_population_version, fips);
} else {
Utils::fred_abort("Sorry, could not find a county for fips = |%s|\n", Global::FIPS_code);
}
} else if(fipsLength == 2) {
gallowdd
After configuring Cygwin with a custom startup batch and an edit or two (see: #43), I was able to get as far as the fred_plot instructions at the bottom of this page: https://github.com/PublicHealthDynamicsLab/FRED/wiki/Parameter-Sweeps
After running
tasks &(generated byfred_make_parametersandfred_make_tasks), I receive the following errors:task.R0=1.0.outdoesn't tell me a whole lot:but
task.R0=1.0itself is a script that contains:It seems that
fred_job -k R0=1.0 -p PARAMDIR/params.R0=1.0 -n 10 -m 1is where my troubles lie as running it produces the aborted errors above.Update: So I tried
fred_job -k R0=1.0 -p PARAMDIR/params.R0=1.0 -n 1and still got the same error.However, I discovered that
RESULTS/JOB/12/DATA/OUToutputs an error file,err1.txt:FRED ERROR: Sorry, could not find a county for fips = |42065|Checking the bottom of DATA/OUT/LOG1 I find the last two lines are:
But opening
/FRED/input_files/countries/usa/US_counties.txtand performing a search for '42065' produces 121 matches.