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separating main from simulate + multi config input
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@aghaeifar
aghaeifar committed Mar 3, 2023
1 parent a0bd5a9 commit d8bc1a6
Showing 1 changed file with 75 additions and 62 deletions.
137 changes: 75 additions & 62 deletions microvascular_gpu.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@
* Descrip : simulating BOLD in microvascular network
* -------------------------------------------------------------------------- */

// compile : nvcc microvascular_gpu.cu -Xptxas -v -O3 -arch=compute_86 -code=sm_86 -Xcompiler -fopenmp
// compile(lin) : nvcc microvascular_gpu.cu -Xptxas -v -O3 -arch=compute_86 -code=sm_86 -Xcompiler -fopenmp -o sim_microvascular
// compile(win) : nvcc microvascular_gpu.cu -Xptxas -v -O3 -arch=compute_86 -code=sm_86 -Xcompiler /openmp -std=c++17 -o sim_microvascular

#include <random>
#include <filesystem>
Expand All @@ -20,63 +21,10 @@

using namespace std;

int main(int argc, char * argv[])
bool simulate(simulation_parameters param, std::map<std::string, std::vector<std::string> > filenames, std::vector<float> sample_length_scales)
{
std::string config_files;
if(argc > 2)
{
std::cout << "Usage: " << argv[0] << " <config_file>" << std::endl;
return 1;
}
if(argc == 2)
config_files = argv[1];

map<string, vector<string> > filenames = {{"fieldmap", vector<string>()},
{"xyz0", vector<string>()},
{"xyz1", vector<string>()},
{"m0", vector<string>()},
{"m1", vector<string>()} };

std::vector<float> sample_length_scales, fieldmap;
std::vector<float> fieldmap;
std::vector<char> mask;
simulation_parameters param;

// ========== read config file ==========
param.fieldmap_size[0] = param.fieldmap_size[1] = param.fieldmap_size[2] = 0;
param.sample_length[0] = param.sample_length[1] = param.sample_length[2] = 0.f;
if(reader::read_config(config_files, param, sample_length_scales, filenames) == false)
{
std::cout << ERR_MSG << "reading config file failed. Aborting...!" << std::endl;
return 1;
}

if (param.seed == 0)
param.seed = std::random_device{}();

param.n_timepoints = param.TR / param.dt; // includes start point

// ========== simulating steady-state signal ==========
if(param.enSteadyStateSimulation)
{
simulate_steady_state(param);
std::cout<< std::string(30, '-') << std::endl;
}

// ========== Dump Settings ==========
if(param.enDebug)
{
std::cout << "Dumping settings:" << std::endl;
for (std::map<std::string, std::vector<std::string>>::iterator it=filenames.begin(); it!=filenames.end(); ++it, std::cout << std::endl)
for (int i = 0; i< it->second.size(); i++)
std::cout << it->first << "[" << i << "] = " << it->second.at(i) << std::endl;

for (int32_t i = 0; i < param.n_sample_length_scales; i++)
std::cout << "Sample length scale " << i << " = " << sample_length_scales[i] << std::endl;

param.dump();
std::cout<< std::string(30, '-') << std::endl;
}

// ========== checking GPU(s) ==========
int32_t device_count;
checkCudaErrors(cudaGetDeviceCount(&device_count));
Expand All @@ -97,12 +45,12 @@ int main(int argc, char * argv[])
bool hasXYZ0 = false;
// ========== load files (field-maps, xyz0, m0) ==========
if(reader::read_fieldmap(filenames.at("fieldmap")[fieldmap_no], fieldmap, mask, param) == false)
return 1;
return false;

if(filenames.at("xyz0")[fieldmap_no].empty() == false)
{
if(reader::read_file(filenames.at("xyz0")[fieldmap_no], XYZ0) == false)
return 1;
return false;

std::cout << "Checking XYZ0 is not in the mask..." << std::endl;
uint32_t t = is_masked(XYZ0, mask, &param);
Expand All @@ -117,7 +65,7 @@ int main(int argc, char * argv[])
if(filenames.at("m0")[fieldmap_no].empty() == false)
{
if(reader::read_file(filenames.at("m0")[fieldmap_no], M0) == false)
return 1;
return false;
}
else
{ // all spins are aligned with B0 (M0 = (0, 0, 1))
Expand All @@ -137,7 +85,7 @@ int main(int argc, char * argv[])
if (hasXYZ0 && param.n_sample_length_scales > 1)
{
std::cout << ERR_MSG << "loading XYZ0 from file while having more than 1 sample length scales is not supported!" << std::endl;
return 1;
return false;
}

// ========== distributing between devices ==========
Expand Down Expand Up @@ -242,14 +190,79 @@ int main(int argc, char * argv[])

// ========== save results ==========
output_header hdr(3, param.n_spins, device_count, param.n_sample_length_scales);
if(filenames.at("m1")[fieldmap_no].empty() == true) // create a filename if not specified
filenames.at("m1")[fieldmap_no] = std::filesystem::path(config_files).filename().string() + "_" + std::filesystem::path(filenames.at("fieldmap")[fieldmap_no]).filename().string();
save_output(M1, filenames.at("m1")[fieldmap_no], hdr, sample_length_scales);

if(filenames.at("xyz1")[fieldmap_no].empty() == false) // do not save if filename is empty
save_output(XYZ1, filenames.at("xyz1")[fieldmap_no], hdr, sample_length_scales);

std::cout << std::string(50, '=') << std::endl;
}
return true;
}


int main(int argc, char * argv[])
{
std::vector<std::string> config_files;
if(argc < 2)
{
std::cout << "Usage: " << argv[0] << " <config_file>" << std::endl;
return 1;
}
for(uint8_t i=1; i<argc; i++)
config_files.push_back(argv[i]);

std::cout << "Running " << config_files.size() << " simulation(s)..." << std::endl;
for(uint8_t cnf=0; cnf<config_files.size(); cnf++)
{
map<string, vector<string> > filenames = {{"fieldmap", vector<string>()},
{"xyz0", vector<string>()},
{"xyz1", vector<string>()},
{"m0", vector<string>()},
{"m1", vector<string>()} };

std::vector<float> sample_length_scales;
simulation_parameters param;

// ========== read config file ==========
param.fieldmap_size[0] = param.fieldmap_size[1] = param.fieldmap_size[2] = 0;
param.sample_length[0] = param.sample_length[1] = param.sample_length[2] = 0.f;
if(reader::read_config(config_files[cnf], param, sample_length_scales, filenames) == false)
{
std::cout << ERR_MSG << "reading config file failed. Aborting...!" << std::endl;
return 1;
}

if (param.seed == 0)
param.seed = std::random_device{}();

param.n_timepoints = param.TR / param.dt; // includes start point

// ========== simulating steady-state signal ==========
if(param.enSteadyStateSimulation)
{
simulate_steady_state(param);
std::cout<< std::string(30, '-') << std::endl;
}

// ========== Dump Settings ==========
if(param.enDebug)
{
std::cout << "Dumping settings:" << std::endl;
for (std::map<std::string, std::vector<std::string>>::iterator it=filenames.begin(); it!=filenames.end(); ++it, std::cout << std::endl)
for (int i = 0; i< it->second.size(); i++)
std::cout << it->first << "[" << i << "] = " << it->second.at(i) << std::endl;

for (int32_t i = 0; i < param.n_sample_length_scales; i++)
std::cout << "Sample length scale " << i << " = " << sample_length_scales[i] << std::endl;

param.dump();
std::cout<< std::string(30, '-') << std::endl;
}

if(simulate(param, filenames, sample_length_scales) == false)
return 1;
}
std::cout << "Simulation(s) finished successfully!" << std::endl;
return 0;
}

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