void RNAForestSZ::buildForest(unsigned int &pos, unsigned int &node) {
unsigned int node2;
switch (viennaStr_[pos]) {
case '.':
// set label
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
break;
case '(':
// left paring base
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
// build subforest right to (
node2=node;
node++;
pos++;
buildForest(pos,node);
// right bracket
assert(viennaStr_[pos]==')');
// right pairing base
if (baseStr_.length())
lb_[node]=alpha2RNA_Alpha(baseStr_[pos]);
else
lb_[node]=ALPHA_BASE;
lml_[node]=node;
node++;
lb_[node]=ALPHA_BASEPAIR;
lml_[node]=node2;
break;
case ')':
return;
break;
}
pos++;
node++;
if (pos<viennaStr_.length())
buildForest(pos,node);
}
RNAProfileAlignment::RNAProfileAlignment(const string &baseStr, const string &name, const string &constraint, double t)
: PPForestAli<RNA_Alphabet_Profile,RNA_Alphabet_Profile>(2*baseStr.length()),
m_name(name),
m_numStructures(1)
{
char *viennaStr=NULL;
// calculate partition function for the sequence
do_backtrack=1;
init_pf_fold(baseStr.length());
//if(constraint.length()>0)
//pf_fold((char*)baseStr.c_str(),(char*)constraint.c_str()); // expicit conversion to non-const value, but pf_fold does not alter baseStr
//else
pf_fold((char*)baseStr.c_str(),NULL); // expicit conversion to non-const value, but pf_fold does not alter baseStr
viennaStr=new char[baseStr.length()+1];
dangles=2;
fold((char*)baseStr.c_str(),viennaStr);
setSize(RNAFuncs::treeSize(viennaStr));
buildForest(baseStr,viennaStr,true);
free_pf_arrays();
delete[] viennaStr;
// hasSequence=true;
addStrName(name);
}
RNAForestSZ::RNAForestSZ(const std::string &baseStr, const std::string &viennaStr, const std::string &name)
: ForestSZ<RNA_Alphabet>(RNAFuncs::treeSize(viennaStr,false)),
baseStr_(baseStr), viennaStr_(viennaStr) {
unsigned int pos,node;
unsigned long basePairCount,maxDepth;
assert(RNAFuncs::isRNAString(baseStr));
RNAFuncs::isViennaString(viennaStr,basePairCount,maxDepth);
// check if base string and vienna string have the same length
// if(baseStr.length() > 0)
// if(baseStr.length() != viennaStr_.length())
// throw RNAForestExceptionInput(RNAForestExceptionInput::Error_BaseStringAndViennaStringIncompatible);
if (name.empty())
name_="unknown";
else
name_=name;
pos=0;
node=0;
buildForest(pos,node);
calcKeyroots();
// debug
/*
int i;
std::cout << "lb_:" << std::endl;
for(i=0;i<size_;i++)
std::cout << i << ": " << RNA_Alpha2alpha(lb_[i]) << std::endl;
std::cout << "lml_:" << std::endl;
for(i=0;i<size_;i++)
std::cout << i << ": " << lml_[i] << std::endl; */
}
RNAProfileAlignment::RNAProfileAlignment(const string &baseStr, const string &viennaStr, const string &name)
: PPForestAli<RNA_Alphabet_Profile,RNA_Alphabet_Profile>(RNAFuncs::treeSize(viennaStr)),
m_name(name),
m_numStructures(1)
{
buildForest(baseStr,viennaStr);
addStrName(name);
};
void compile(boost::program_options::variables_map vm,
string out_file_name,
string routine_name,
map<string,type*>& inputs,
map<string,type*>& inouts,
map<string,type*>& outputs,
vector<stmt*> const& prog)
{
// set up signal to end search after certain amount of time
int sMinutes = vm["limit"].as<int>();
if (sMinutes > 0) {
int sSeconds = sMinutes * 60;
signal(SIGALRM, sig_alarm_handler);
alarm(sSeconds);
}
// search strategy
enum search_strategy {exhaustive, orthogonal, random,
hybrid_orthogonal, ga, debug, thread};
search_strategy strat = ga;
if (vm["search"].as<std::string>().compare("ex") == 0) {
strat = exhaustive;
}
else if (vm["search"].as<std::string>().compare("debug") == 0) {
strat = debug;
}
else if (vm["search"].as<std::string>().compare("orthogonal") == 0) {
strat = orthogonal;
}
else if (vm["search"].as<std::string>().compare("random") == 0) {
strat = random;
}
else if (vm["search"].as<std::string>().compare("hybrid_orthogonal") == 0) {
strat = hybrid_orthogonal;
}
else if (vm["search"].as<std::string>().compare("ga") == 0) {
strat = ga;
}
else if (vm["search"].as<std::string>().compare("thread") == 0) {
strat = thread;
}
else {
std::cout << "Error: unknown search strategy (--search):" << vm["search"].as<std::string>() << "\n\n";
exit(0);
}
// which backend
bool noptr;
if (vm["backend"].as<std::string>().compare("noptr") == 0) {
noptr = true;
} else {
noptr = false;
}
std::cout << noptr << std::endl;
// partitiong FIXME can't turn off anymore?
/*
bool partitionSet = true;
if (vm.count("partition_off")) {
partitionSet = false;
}
*/
bool mpi = false;
if (vm.count("distributed")) {
mpi = true;
}
string pathToTop = getcwd(NULL,0);
pathToTop += "/";
// std::cout << pathToTop << std::endl;
// set up temporary workspace
string tmpPath, fileName, path;
if (setUpWorkSpace(out_file_name, fileName, path, tmpPath, pathToTop,
vm.count("delete_tmp"))) {
std::cout << "Failed to set up temporary directory for unique implementations\n";
return;
}
// set all work to be performed in temporary work directory
out_file_name = tmpPath + fileName;
// {{{ COST MODELS
std::list<versionData*> orderedVersions;
string testParam = vm["test_param"].as<std::string>();
string start, stop, step;
string::size_type pos = testParam.find_first_of(":");
if (pos != string::npos)
start = testParam.substr(0, pos);
string::size_type last = pos+1;
pos = testParam.find_first_of(":",last);
if (pos != string::npos)
stop = testParam.substr(last, pos-last);
step = testParam.substr(pos+1,string::npos);
if (boost::lexical_cast<int>(start) > boost::lexical_cast<int>(stop)) {
std::cout << "Test parameters are illegal (start > stop)\n";
std::cout << "\tstart: " << start << "\n";
std::cout << "\tstop: " << stop << "\n";
return;
}
modelMsg msg(boost::lexical_cast<int>(start),
boost::lexical_cast<int>(stop),
boost::lexical_cast<int>(step));
msg.pathToTop = pathToTop;
// build_machine 0 -> parallel, 1 -> serial
// msg.parallelArch = build_machine((char*)(pathToTop.c_str()),0);
if (msg.parallelArch == NULL) {
std:: cout << "Error attempting to get cost with parallel analytic model\n";
//return;
}
// msg.serialArch = build_machine((char*)(pathToTop.c_str()),1);
// if (msg.serialArch == NULL) {
// std:: cout << "Error attempting to get cost with parallel analytic model\n";
//return;
// }
// analyticSerial, tempCount, analyticParallel, symbolic, noModel
vector<model_typ> models;
models.clear();
// the model we want to rank with should go first in this list
//models.push_back(noModel);
models.push_back(analyticParallel);
//models.push_back(analyticSerial);
//models.push_back(tempCount);
// }}}
precision_type = vm["precision"].as<std::string>();
#ifdef MODEL_TIME
// time spent in memmodel routines
boost::timer memmodelTimer;
double memmodelTotal = 0.0;
#endif
/* Model deprecated
double threshold;
if (vm.count("use_model")) {
std::cout << "\nAnalytic model enabled\n";
threshold = vm["threshold"].as<double>();
}
*/
std::vector<std::pair<int, double> >::iterator itr;
graph g;
std::vector<algo> algos;
//std::cerr << "finished parsing" << std::endl;
program2graph(prog, inputs, inouts, outputs, g);
//std::cerr << "graph created" << std::endl;
//std::ofstream out44("lower0.dot");
//print_graph(out44, g);
//out44.close();
//use yices to compute types externally
//#define TYPES
#ifdef TYPES
std::ofstream out("lower0.dot");
print_graph(out, g);
out.close();
generate_constraints(g);
#endif
compute_types(g);
#ifdef TYPES
std::ofstream out("lower1.dot");
print_graph(out, g);
out.close();
exit(0);
#endif
update_sizes(g);
update_dim_info(g);
init_algos(algos);
assign_algorithms(algos, g);
//std::cerr << "algorithms assigned" << std::endl;
assign_work(algos, g);
//std::cerr << "work assigned" << std::endl;
rewrite_fun rewriters[] =
{ flip_transpose, //0
flip_transpose_stride, //1
merge_tmp_output, //2
merge_tmp_cast_output, //3
remove_intermediate_temporary, //4
merge_gets, //5
merge_sumto_store, //6
move_temporary, //7
remove_cast_to_output, //8
remove_input_to_cast, //9
remove_cast_to_cast, //10
merge_same_cast, //11
straighten_top_level_scalar_ops,//12
reduce_reductions //13
};
optim_fun optimizers[] =
{ fuse_loops, //0
fuse_loops_nested, //1
merge_scalars, //2
pipeline, //3
fuse_loops_n //4
};
optim_fun_chk checkers[] =
{ check_fuse_loops,
check_fuse_loops_nested,
check_merge_scalars,
check_pipeline,
check_fuse_loops_n
};
partition_fun partition[] = {
part_mult_left_result, //0
part_mult_right_result, //1
part_mult_left_right, //2
part_mult_scl_row, //3
part_mult_scl_col, //4
partition_add_col, //5
partition_add_row, //6
part_mult_scl, //7
partition_add //8
};
rewrite_fun part_checkers[] = {
check_part_mult_left_result,
check_part_mult_right_result,
check_part_mult_left_right,
check_part_mult_scl_row,
check_part_mult_scl_col,
check_partition_add_col,
check_partition_add_row,
check_part_mult_scl,
check_partition_add
};
vector<rewrite_fun> rewrites(rewriters, rewriters +
sizeof(rewriters) / sizeof(rewrite_fun));
vector<optim_fun> optimizations(optimizers, optimizers +
sizeof(optimizers) / sizeof(optim_fun));
vector<optim_fun_chk> checks(checkers, checkers +
sizeof(checkers) / sizeof(optim_fun_chk));
vector<rewrite_fun> part_checks(part_checkers, part_checkers +
sizeof(part_checkers)/sizeof(rewrite_fun));
vector<partition_fun> partitioners(partition, partition +
sizeof(partition) / sizeof(partition_fun));
//std::cerr << "about to start lowering and optimizine" << std::endl;
std::stack<work_item> s;
string history = "";
#ifdef DUMP_DOT_FILES
std::ofstream out("lower1.dot");
print_graph(out, g);
out.close();
#endif
#ifdef DUMP_GRAPHS
graphToQuery(g,out_file_name,0,0);
#endif
if (vm.count("correctness")) {
createCorrectnessTest(g, routine_name, out_file_name, inputs,
outputs,msg,noptr);
}
// keep copy of base graph around
graph *baseGraph = new graph(g);
// {{{ Partition Space
code_generation codetype = threadtile;
string spec = vm["level1"].as<std::string>();
if (!spec.empty()) {
string::size_type pos = spec.find_first_of(" ");
if (pos == string::npos) {
std::cout << "Bad format for level1 arg:" << spec << endl;
exit(0);
} else {
string codetype_str = spec.substr(0, pos);
if (codetype_str == "thread") {
codetype = threadtile;
} else if (codetype_str == "cache") {
codetype = cachetile;
} else {
std::cout << "Bad format for level1 arg:" << spec << endl;
std::cout << "needs to be thread or cache" << endl;
exit(0);
}
}
int err = parse_range(&partition_bounds[0][0],
&partition_bounds[0][1],
&partition_bounds[0][2],
spec.substr(pos+1));
if (err) {
std::cout << "Couldn't parse range for level1: " << spec << endl;
exit(0);
}
if (partition_bounds[0][0] > partition_bounds[0][1]) {
std::cout << "Test parameters are illegal (start > stop)\n";
std::cout << "\tstart: " << partition_bounds[0][0] << "\n";
std::cout << "\tstop: " << partition_bounds[0][1] << "\n";
exit(0);
}
// Now level 2
string spec = vm["level2"].as<std::string>();
std::cout << "spec:" << spec << endl;
if (!spec.empty()) {
MAX_PARTS = 2;
string::size_type pos = spec.find_first_of(" ");
cout << "pos = " << pos << endl;
if (pos == string::npos) {
std::cout << "Bad format for level2 arg:" << spec << endl;
exit(0);
} else {
string codetype_str = spec.substr(0, pos);
cout << "codetype_str: '" << codetype_str << "'" << endl;
if (codetype_str == "thread" && codetype==cachetile) {
std::cout << "ERROR: threads inside tile loops not supported" << endl;
std::cout << "consider swapping level1 and level2 args" << endl;
exit(0);
} else if (codetype_str == "cache" && codetype==threadtile) {
codetype = bothtile;
} else {
std::cout << "Bad format for level2 arg:" << spec << endl;
std::cout << "needs to be thread or cache" << endl;
exit(0);
}
}
int err = parse_range(&partition_bounds[1][0],
&partition_bounds[1][1],
&partition_bounds[1][2],
spec.substr(pos+1));
if (err) {
std::cout << "Couldn't parse range for level2: " << spec.substr(pos) << endl;
exit(0);
}
if (partition_bounds[1][0] > partition_bounds[1][1]) {
std::cout << "Test parameters are illegal (start > stop)\n";
std::cout << "\tstart: " << partition_bounds[1][0] << "\n";
std::cout << "\tstop: " << partition_bounds[1][1] << "\n";
exit(0);
}
} else {
// Only 1 level specified
MAX_PARTS = 1;
}
} else {
// no idea what this will do!
// Maybe we should just throw an error here? Or at least a warning?
std::cout << "WARNING: No threading or cache tiling specified" << endl;
std::cout << "Performing Loop fusion only, search may get confused" << endl;
MAX_PARTS = 0;
}
// }}}
// initializing the partition type forest
// cout << "initializing partition forest..." << endl;
vector< partitionTree_t* > partitionForest;
buildForest(partitionForest, g, MAX_PARTS);
// cout << "success" << endl;
/*
for (int i = 0; i < partitionForest.size(); ++i) {
partitionTree_t *t = partitionForest[i];
if (t != NULL) {
stringstream o;
o << "tree" << i << ".dot";
ofstream treefile(o.str().c_str());
printTree(treefile, t);
}
}
*/
initial_lower(g, algos, rewrites);
//std::cout << "finished lowering and rewriting" << std::endl;
#ifdef DUMP_DOT_FILES
std::ofstream out2("lower2.dot");
print_graph(out2, g);
out2.close();
#endif
#if 0
for (int i = 0; i < g.num_vertices(); ++i)
if (g.info(i).op & OP_ANY_ARITHMATIC)
cout << i << "\t";
cout << "\n";
#endif
int reps = vm["empirical_reps"].as<int>();
if (vm.count("distributed")) {
createMPIEmpiricalTest(g, routine_name, out_file_name, inputs,
outputs, noptr, reps);
} else if (!vm.count("empirical_off")) {
createEmpiricalTest(g, routine_name, out_file_name, inputs,
outputs, noptr, reps);
}
compile_details_t cDetails(routine_name,tmpPath,fileName,
vm.count("correctness"),
vm.count("use_model"),
!vm.count("empirical_off"),
noptr, mpi, codetype,
&inputs, &inouts, &outputs);
build_details_t bDetails(&part_checks, &partitioners,
&checks, &optimizations,
&algos, &rewrites,
&models, &msg);
// int maxT = max(0,msg.parallelArch->threads);
// std::cout << "Testing with " << maxT << " threads, step = " << min(4,maxT) << std::endl;
// int stride = 2;
// {{{ Strategy cases
switch (strat) {
case exhaustive:
{
std::cout << "entering exhaustive search" << endl;
//int numVersions = 5;
int bestVersion = smart_exhaustive(g, *baseGraph,
cDetails, bDetails);
// One way or another we have selected a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case orthogonal:
{
std::cout << "entering orthogonal search" << endl;
//int numVersions = 5;
int bestVersion = orthogonal_search(g, *baseGraph,
cDetails, bDetails);
// One way or another we have selected a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case random:
{
std::cout << "entering random search" << endl;
int seconds = vm["random_count"].as<int>();
int bestVersion = genetic_algorithm_search(g, *baseGraph,
partitionForest,
seconds, 1, false, cDetails, bDetails).best_version; // pop = 1
// One way or another we have selected a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case hybrid_orthogonal:
{
std::cout << "entering hybrid orthogonal search " << endl;
int bestVersion = smart_hybrid_search(g, *baseGraph,
cDetails, bDetails);
// One way or another we have selected a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case debug:
{
std::cout << "entering debug search " << endl;
int bestVersion = debug_search(g, *baseGraph, partitionForest,
cDetails, bDetails);
// One way or another we have selected a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case ga:
{
std::cout << "entering genetic algorithm search " << endl;
bool gamaxfuse = true;
if (vm.count("ga_nomaxfuse")) {
gamaxfuse = false;
}
int seconds = vm["ga_timelimit"].as<int>();
int popsize = vm["ga_popsize"].as<int>();
int bestVersion = -1;
if (vm.count("ga_noglobalthread")) {
bestVersion = genetic_algorithm_search(g, *baseGraph,
partitionForest, seconds, popsize, gamaxfuse,
cDetails, bDetails).best_version;
} else if (vm.count("ga_exthread")) {
bestVersion = ga_exthread(g, *baseGraph,
partitionForest, seconds, gamaxfuse, popsize, cDetails,
bDetails);
} else { // global thread
bestVersion = ga_thread(g, *baseGraph,
partitionForest, seconds, gamaxfuse, popsize, cDetails,
bDetails);
}
// One way or another we have selected
// a version we are calling the best
// or we failed
if (bestVersion < 0) {
std::cout << "All versions failed to generate or compile\n";
return;
}
else {
std::cout << "\n----------------------------------\n";
std::cout << "Best Version: " << fileName + "__" << bestVersion << ".c\n";
}
// copy best version to same directory as input .m file
// and report location
handleBestVersion(fileName,path,tmpPath,bestVersion);
break;
}
case thread:
{
int thread_search(graph &g, graph &baseGraph,
vector<partitionTree_t*> part_forest,
compile_details_t &cDet,
build_details_t &bDet);
std::cout << "entering thread search " << endl;
thread_search(g, *baseGraph, partitionForest,
cDetails, bDetails);
break;
}
}
// }}}
deleteForest(partitionForest);
}
/**
* コンストラクタ
* rootsには、２つの頂点を１ペアとして、頂点ペアが並んでいる。各ペアは、エッジに対応する。
* つまり、roots.size()は、偶数であるはず。
*/
BFSForest::BFSForest(RoadGraph* roads, QList<RoadVertexDesc> roots) {
this->roads = roads;
this->roots = roots;
buildForest();
}
