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Struggling to get gtest to work
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it refuses to work on windows.
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@CodeByDrescher
CodeByDrescher committed Jan 26, 2024
1 parent 8f0446f commit cdcab4c
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Showing 2 changed files with 88 additions and 125 deletions.
106 changes: 53 additions & 53 deletions Stochastic/Tests/statstest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
#include <iostream>
#include <cstdio>

#include "VCELL/SimulationMessaging.h"

const char* input_file_contents = R"INPUT_FILE(
<control>
STARTING_TIME 0.0
Expand Down Expand Up @@ -98,70 +100,68 @@ const std::map<int, double> expected_S0 = {

TEST(statstest,test1) {
std::cout << "Checkpoint 0" << std::endl;
char *temp_input_file_name = new char[1000] {0};
char *temp_output_file_name = new char[1000] {0};
std::string in_prefix = testing::TempDir() + "input_XXXXXX";
std::string out_prefix = testing::TempDir() + "output_XXXXXX";
strncpy(temp_input_file_name, in_prefix.c_str(), in_prefix.length());
strncpy(temp_output_file_name, out_prefix.c_str(), out_prefix.length());
//std::string inputFileName = std::tmpnam(nullptr);
std::string inputFileName {R"(C:\CustomTemp\testme_vcell.txt)"};
std::string outputFileName = std::tmpnam(nullptr);
std::map<int,double> results;
std::fstream inputFileStream{inputFileName};
ASSERT_TRUE(inputFileStream.fail());
std::cout << std::system_category().message(::GetLastError()) << std::endl;
std::cout << "Supposed file: " << inputFileName << std::endl;
return;
std::fstream outputFileStream{outputFileName};
ASSERT_FALSE(outputFileStream.fail());

// Setup the Gibson Solver input file
std::cout << "Checkpoint 1" << std::endl;
assert(mkstemp(temp_input_file_name) != -1);
assert(mkstemp(temp_output_file_name) != -1);
std::ofstream input_file (temp_input_file_name);
bool bWroteFile = false;
if (input_file.is_open()){
input_file << input_file_contents;
input_file.close();
bWroteFile = true;
}
ASSERT_TRUE(bWroteFile);
std::cout << " >> " << "Input: <" << inputFileName << ">;"<< std::endl;
std::cout << " >> " << "Output: <" << outputFileName << ">;"<< std::endl;
if (outputFileStream.is_open()) outputFileStream.close();
inputFileStream << input_file_contents;
inputFileStream.close();
return;

// Create the Gibson Solver
std::cout << "Checkpoint 2" << std::endl;
Gibson *gb= new Gibson(temp_input_file_name, temp_output_file_name);
auto *gb = new Gibson(inputFileName.c_str(), outputFileName.c_str());

// Launch the test
std::cout << "Checkpoint 3" << std::endl;
gb->march();

// Verify file contents
std::cout << "Checkpoint 4" << std::endl;
// verify file contents
std::ifstream outfile(temp_output_file_name);
string line;
getline(outfile, line); // remove header line
// std::cout << line << std::endl;
// std::cout.flush();

outputFileStream.open(outputFileName);
std::string line;
std::getline(outputFileStream, line); // remove header line
for (int i = 0; !outputFileStream.eof(); i++) {
std::getline(outputFileStream, line);
// if index found in expected_S0 map, store in results map
if (expected_S0.find(i) != expected_S0.end()){
float t, s0, s1, s2;
// extract space separated values for t, s0, s1 and s2 from line
std::stringstream line_stream(line);
line_stream >> t >> s0 >> s1 >> s2;
results[i] = s0;
}
}
outputFileStream.close();

// compare the expected and actual values
std::cout << "Checkpoint 5" << std::endl;
std::map<int,double> results;
int i = 0;
while (getline(outfile, line)){
// if index found in expected_S0 map, store in results map
if (expected_S0.find(i) != expected_S0.end()){
float t, s0, s1, s2;
// extract space separated values for t, s0, s1 and s2 from line
std::stringstream line_stream(line);
line_stream >> t >> s0 >> s1 >> s2;
results[i] = s0;
// std::cout << line << std::endl;
// std::cout.flush();
}
i++;
}
std::cout << "Checkpoint 6" << std::endl;
// compare the expected and actual values
double accum_error = 0.0;
double max_error = 0.0;
double accumulatedError = 0.0, maxIndividualError = 0.0;
for (auto const& expected : expected_S0){
double s0_given = expected.second;
double s0_computed = results[expected.first];
double abserr = std::abs(s0_given - s0_computed);
// std::cout << "t=" << expected.first << " expected=" << s0_given << " computed=" << s0_computed << " abserr=" << abserr << std::endl;
accum_error += abserr;
max_error = std::max(max_error, abserr);
double absoluteError = std::abs(expected.second - results[expected.first]);
// std::cout << "t=" << expected.first << " expected=" << expected.second << " computed=" << results[expected.first] << " abserr=" << abserr << std::endl;
accumulatedError += absoluteError;
maxIndividualError = std::max(maxIndividualError, absoluteError);
}
assert(accum_error < 0.015);
assert(max_error < 0.005);
assert(accumulatedError < 0.015);
assert(maxIndividualError < 0.005);
std::cout << "Checkpoint 7" << std::endl;

delete gb;
delete[] temp_input_file_name;
delete[] temp_output_file_name;
if (inputFileStream.is_open()) inputFileStream.close();
if (outputFileStream.is_open()) outputFileStream.close();
std::cout << "Checkpoint 8" << std::endl;
}
107 changes: 35 additions & 72 deletions Stochastic/VCellStoch/src/Gibson.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,13 @@
#include <string>
#include <iomanip>
#include <vector>
#include <stdint.h>
#include <math.h>
#include <stdlib.h>
#include <cstdint>
#include <cmath>
#include <cstdlib>
#include <random>
using namespace std;

#include <time.h>
#include <ctime>
#include "../include/IndexedTree.h"

#ifdef USE_MESSAGING
Expand All @@ -26,14 +26,12 @@ using namespace std;
const double double_infinity = numeric_limits<double>::infinity();
const double EPSILON = 1E-12;
const string Gibson::MY_T_STR = "t";

/*
*Empty constructor of Gibson. It will use the defalt settings in StochModel.
*/
Gibson::Gibson()
:StochModel(),
savedSampleCount(1),
lastTime (std::numeric_limits<long>::min( ))
{
: savedSampleCount(1), lastTime (std::numeric_limits<long>::min()) {
Tree=NULL;
currvals=NULL;
generator = new std::mt19937_64();
Expand All @@ -47,16 +45,13 @@ Gibson::Gibson()
* string, the output file(name), where the results are saved.
*/
Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
:StochModel(),
savedSampleCount(1),
lastTime (std::numeric_limits<long>::min( ))
{
Tree=NULL;
currvals=NULL;
generator = new std::mt19937_64();
distribution = new std::uniform_real_distribution<double>(0.0,1.0);

outfilename=arg_outfilename;
: savedSampleCount(1), lastTime (std::numeric_limits<long>::min( )) {
// TODO: Call basic constructor rather than duplicate lines
this->Tree = NULL;
this->currvals = NULL;
this->generator = new std::mt19937_64();
this->distribution = new std::uniform_real_distribution<>(0.0,1.0);
this->outfilename = arg_outfilename;

ifstream infile;
string instring;
Expand All @@ -69,67 +64,41 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
while(infile >> instring)
{
//load control info.
if (instring == "STARTING_TIME")
{
if (instring == "STARTING_TIME"){
infile >> STARTING_TIME;
}
else if (instring == "BMULTIBUTNOTHISTO")
{
} else if (instring == "BMULTIBUTNOTHISTO"){
infile >> bMultiButNotHisto;
}
else if (instring == "ENDING_TIME")
{
} else if (instring == "ENDING_TIME"){
infile >> ENDING_TIME;
}
else if (instring == "SAVE_PERIOD")
{
} else if (instring == "SAVE_PERIOD"){
infile >> SAVE_PERIOD;
flag_savePeriod=true;
}
else if (instring == "MAX_ITERATION")
{
} else if (instring == "MAX_ITERATION"){
infile >> MAX_ITERATION;
}
else if (instring == "TOLERANCE")
{
} else if (instring == "TOLERANCE"){
infile >> TOLERANCE;
}
else if (instring == "SAMPLE_INTERVAL")
{
} else if (instring == "SAMPLE_INTERVAL"){
infile >> SAMPLE_INTERVAL;
}
else if (instring == "MAX_SAVE_POINTS")
{
} else if (instring == "MAX_SAVE_POINTS"){
infile >> MAX_SAVE_POINTS;
}
else if (instring == "NUM_TRIAL")
{
} else if (instring == "NUM_TRIAL"){
infile >> NUM_TRIAL;
}
else if (instring == "SEED")
{
} else if (instring == "SEED"){
infile >> SEED;
}
//load listofvars
else if (instring == "TotalVars")
{
} else if (instring == "TotalVars"){ //load listofvars
int varCount;
infile >> varCount;
string name;
double amount;
for(int i=0;i<varCount;i++)
{
for(int i=0;i<varCount;i++){
infile >> name;
infile >> amount;
listOfVarNames.push_back(name);
listOfIniValues.push_back((uint64_t)amount);
StochVar *var=new StochVar((uint64_t)amount);
listOfVars.push_back(var);
}
}
//load listOfProcesses
else if (instring == "TotalProcesses")
{
} else if (instring == "TotalProcesses"){ //load listOfProcesses
int pCount;
infile >> pCount;
string name;
Expand All @@ -140,15 +109,11 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
Jump *jp=new Jump();
listOfProcesses.push_back(jp);
}
}
//load process description to set up processes
else if (instring == "TotalDescriptions")
{
} else if (instring == "TotalDescriptions") { //load process description to set up processes
int dCount,idx;
infile >> dCount;
string name,str;
for(int i=0;i<dCount;i++)//loop through each process description
{
for(int i=0;i<dCount;i++){ //loop through each process description
infile >> name >> name;// "process name"
//find the process in listOfProcesses using it's name
idx=getProcessIndex(name);
Expand Down Expand Up @@ -201,10 +166,9 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
}
}
//setup IndexedTree
Tree=new IndexedTree();
for(int i=0;i<listOfProcesses.size();i++)
{
Tree->addProcess(listOfProcesses[i]);
Tree = new IndexedTree();
for(auto & listOfProcesse : listOfProcesses){
Tree->addProcess(listOfProcesse);
}
infile.close();
if (NUM_TRIAL > MAX_ALLOWED_POINTS) {
Expand All @@ -214,7 +178,6 @@ Gibson::Gibson(const char* arg_infilename, const char* arg_outfilename)
VCELL_EXCEPTION(invalid_argument,"Stochastic initialization: Server save points " << MAX_SAVE_POINTS << " exceeds limit of " << MAX_ALLOWED_POINTS);
}


if(NUM_TRIAL > 1 && !bMultiButNotHisto){
//this must be a gibson 'histogram' sim,
//java gui not allow setting of MAX_SAVE_POINTS and default is too low
Expand Down Expand Up @@ -270,12 +233,12 @@ Gibson::~Gibson()
//delete indexedTree
delete Tree;
//delete variables
for(int i=0;i<listOfVars.size();i++)
delete listOfVars[i];
for(auto & listOfVar : listOfVars)
delete listOfVar;
listOfVars.clear();
//delete proccesses
for(int i=0;i<listOfProcesses.size();i++)
delete listOfProcesses[i];
for(auto & listOfProcesse : listOfProcesses)
delete listOfProcesse;
listOfProcesses.clear();
//delete vectors
listOfVarNames.clear();
Expand Down

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