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BioEM
Commit cd4d4d5d authored by David Rohr's avatar David Rohr
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initialize only on mpi rank 0

parent 08528178
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Showing with 127 additions and 119 deletions
bioem.cpp
View file @ cd4d4d5d
......@@ -87,136 +87,144 @@ int bioem::configure(int ac, char* av[])
// ****** And Precalculating necessary grids, map crosscorrelations and kernels ********
// *************************************************************************************
// *** Inizialzing default variables ***
std::string infile, modelfile, mapfile;
Model.readPDB = false;
param.writeAngles = false;
param.dumpMap = false;
param.loadMap = false;
RefMap.readMRC = false;
RefMap.readMultMRC = false;
// *************************************************************************************
cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
// *************************************************************************************
if (mpi_rank == 0)
{
// *** Inizialzing default variables ***
std::string infile, modelfile, mapfile;
Model.readPDB = false;
param.writeAngles = false;
param.dumpMap = false;
param.loadMap = false;
RefMap.readMRC = false;
RefMap.readMultMRC = false;
// *************************************************************************************
cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
// *************************************************************************************
// ********************* Command line reading input with BOOST ************************
try {
po::options_description desc("Command line inputs");
desc.add_options()
("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format")
("ReadMRC", "(Optional) If reading particle file in MRC format")
("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
("DumpMaps", "(Optional) Dump maps after they were red from maps file")
("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
("help", "(Optional) Produce help message")
;
po::positional_options_description p;
p.add("Inputfile", -1);
p.add("Modelfile", -1);
p.add("Particlesfile", -1);
p.add("ReadPDB", -1);
p.add("ReadMRC", -1);
p.add("ReadMultipleMRC", -1);
p.add("DumpMaps", -1);
p.add("LoadMapDump", -1);
po::variables_map vm;
po::store(po::command_line_parser(ac, av).
options(desc).positional(p).run(), vm);
po::notify(vm);
if((ac < 6)) {
std::cout << desc << std::endl;
return 1;
}
if (vm.count("help")) {
cout << "Usage: options_description [options]\n";
cout << desc;
return 1;
}
// ********************* Command line reading input with BOOST ************************
try {
po::options_description desc("Command line inputs");
desc.add_options()
("Inputfile", po::value<std::string>(), "(Mandatory) Name of input parameter file")
("Modelfile", po::value< std::string>() , "(Mandatory) Name of model file")
("Particlesfile", po::value< std::string>(), "(Mandatory) Name of paricles file")
("ReadPDB", "(Optional) If reading model file in PDB format")
("ReadMRC", "(Optional) If reading particle file in MRC format")
("ReadMultipleMRC", "(Optional) If reading Multiple MRCs")
("DumpMaps", "(Optional) Dump maps after they were red from maps file")
("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
("help", "(Optional) Produce help message")
;
po::positional_options_description p;
p.add("Inputfile", -1);
p.add("Modelfile", -1);
p.add("Particlesfile", -1);
p.add("ReadPDB", -1);
p.add("ReadMRC", -1);
p.add("ReadMultipleMRC", -1);
p.add("DumpMaps", -1);
p.add("LoadMapDump", -1);
po::variables_map vm;
po::store(po::command_line_parser(ac, av).
options(desc).positional(p).run(), vm);
po::notify(vm);
if((ac < 6)) {
std::cout << desc << std::endl;
return 1;
}
if (vm.count("help")) {
cout << "Usage: options_description [options]\n";
cout << desc;
return 1;
}
if (vm.count("Inputfile"))
{
cout << "Input file is: ";
cout << vm["Inputfile"].as< std::string >() << "\n";
infile = vm["Inputfile"].as< std::string >();
}
if (vm.count("Modelfile"))
{
cout << "Model file is: "
<< vm["Modelfile"].as< std::string >() << "\n";
modelfile = vm["Modelfile"].as< std::string >();
}
if (vm.count("Inputfile"))
{
cout << "Input file is: ";
cout << vm["Inputfile"].as< std::string >() << "\n";
infile = vm["Inputfile"].as< std::string >();
}
if (vm.count("Modelfile"))
{
cout << "Model file is: "
<< vm["Modelfile"].as< std::string >() << "\n";
modelfile = vm["Modelfile"].as< std::string >();
}
if (vm.count("ReadPDB"))
{
cout << "Reading model file in PDB format.\n";
Model.readPDB = true;
}
if (vm.count("ReadPDB"))
{
cout << "Reading model file in PDB format.\n";
Model.readPDB = true;
}
if (vm.count("ReadMRC"))
{
cout << "Reading particle file in MRC format.\n";
RefMap.readMRC=true;
}
if (vm.count("ReadMRC"))
{
cout << "Reading particle file in MRC format.\n";
RefMap.readMRC=true;
}
if (vm.count("ReadMultipleMRC"))
{
cout << "Reading Multiple MRCs.\n";
RefMap.readMultMRC=true;
}
if (vm.count("ReadMultipleMRC"))
{
cout << "Reading Multiple MRCs.\n";
RefMap.readMultMRC=true;
}
if (vm.count("DumpMaps"))
{
cout << "Dumping Maps after reading from file.\n";
param.dumpMap = true;
}
if (vm.count("DumpMaps"))
{
cout << "Dumping Maps after reading from file.\n";
param.dumpMap = true;
}
if (vm.count("LoadMapDump"))
{
cout << "Loading Map dump.\n";
param.loadMap = true;
}
if (vm.count("LoadMapDump"))
{
cout << "Loading Map dump.\n";
param.loadMap = true;
if (vm.count("Particlesfile"))
{
cout << "Paricle file is: "
<< vm["Particlesfile"].as< std::string >() << "\n";
mapfile = vm["Particlesfile"].as< std::string >();
}
}
if (vm.count("Particlesfile"))
catch(std::exception& e)
{
cout << "Paricle file is: "
<< vm["Particlesfile"].as< std::string >() << "\n";
mapfile = vm["Particlesfile"].as< std::string >();
cout << e.what() << "\n";
return 1;
}
//check for consitency in multiple MRCs
if( RefMap.readMultMRC && not(RefMap.readMRC) ){
cout << "For Multiple MRCs command --ReadMRC is necesary too";
exit(1);
}
// ********************* Reading Parameter Input ***************************
// copying inputfile to param class
param.fileinput = infile.c_str();
param.readParameters();
// ********************* Reading Model Input ******************************
// copying modelfile to model class
Model.filemodel = modelfile.c_str();
Model.readModel();
// ********************* Reading Particle Maps Input **********************
// ********* HERE: PROBLEM if maps dont fit on the memory!! ***************
// copying mapfile to ref map class
param.filemap = mapfile.c_str();
RefMap.readRefMaps(param);
}
catch(std::exception& e)
{
cout << e.what() << "\n";
return 1;
}
//check for consitency in multiple MRCs
if( RefMap.readMultMRC && not(RefMap.readMRC) ){
cout << "For Multiple MRCs command --ReadMRC is necesary too";
exit(1);
}
// ********************* Reading Parameter Input ***************************
// copying inputfile to param class
param.fileinput = infile.c_str();
param.readParameters();
// ********************* Reading Model Input ******************************
// copying modelfile to model class
Model.filemodel = modelfile.c_str();
Model.readModel();
// ********************* Reading Particle Maps Input **********************
// ********* HERE: PROBLEM if maps dont fit on the memory!! ***************
// copying mapfile to ref map class
param.filemap = mapfile.c_str();
RefMap.readRefMaps(param);
#ifdef WITH_MPI
#endif
if (mpi_rank != 0) return(1);
// ****************** Precalculating Necessary Stuff *********************
precalculate();
......
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