//__________________________________________________________________________________
int main (int argc, char* argv[])
{
mainArgCount = argc - 1;
#ifdef __HYPHYMPI__
int rank,
size;
MPI_Init (&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
setParameter (mpiNodeID, (_Parameter)rank);
setParameter (mpiNodeCount, (_Parameter)size);
_hy_mpi_node_rank = rank;
if (rank == 0)
{
mpiNodesThatCantSwitch.Populate (size,1,0);
/* {
char hostname[256];
gethostname(hostname, sizeof(hostname));
printf("PID %d on %s ready for attach\n", getpid(), hostname);
fflush(stdout);
//getchar ();
} */
#endif
//for (long k=0; k<NSIG; k++)
//{
// signal(k, &hyphyBreak);
//}
#ifdef __HYPHYMPI__
}
#endif
char curWd[4096],
dirSlash = GetPlatformDirectoryChar ();
getcwd (curWd,4096);
_String baseDir (curWd),
argFile;
baseDir=baseDir & dirSlash;
pathNames&& &baseDir;
baseDirectory = baseDir;
baseArgDir = baseDirectory;
_ExecutionList ex;
#ifdef _OPENMP
systemCPUCount = omp_get_max_threads();
#endif
#ifdef _MINGW32_MEGA_
{
char pid[16];
snprintf (pid,16,"%u", GetCurrentProcessId());
_String pipeName = _String("\\\\.\\pipe\\MEGAPipe") & pid;
printf ("Pipe name = %s\n", pipeName.sData);
if ((_HY_MEGA_Pipe = CreateFile(pipeName.sData, GENERIC_WRITE, 0, NULL, OPEN_EXISTING, 0, NULL)) == INVALID_HANDLE_VALUE)
{
char* lpMsgBuf;
FormatMessage(
FORMAT_MESSAGE_ALLOCATE_BUFFER |
FORMAT_MESSAGE_FROM_SYSTEM |
FORMAT_MESSAGE_IGNORE_INSERTS,
NULL,
GetLastError(),
MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT),
(LPTSTR) &lpMsgBuf,
0, NULL );
FlagError (_String("Failed to create a pipe named '") & pipeName & "' to send data from HyPhy to MEGA. Error: "&lpMsgBuf);
}
}
#endif
for (long i=1; i<argc;i++)
{
_String thisArg (argv[i]);
if (thisArg.sData[0]=='-')
{
ProcessConfigStr (thisArg);
}
else
if (thisArg.beginswith ("BASEPATH="))
{
baseArgDir = thisArg.Cut(9,-1);
if (baseArgDir.sLength)
{
if (baseArgDir.sData[baseArgDir.sLength-1]!=dirSlash)
baseArgDir = baseArgDir&dirSlash;
baseDirectory = baseArgDir;
}
}
else
if (thisArg.beginswith ("USEPATH="))
{
baseDir = thisArg.Cut(8,-1);
errorFileName = baseDir & errorFileName;
messageFileName = baseDir & messageFileName;
pathNames.Delete (0);
pathNames&& &baseDir;
}
else
#ifdef __MP__
if (thisArg.beginswith ("CPU="))
{
_String cpus = thisArg.Cut(4,-1);
systemCPUCount = cpus.toNum();
if (systemCPUCount<1)
systemCPUCount = 1;
pthread_setconcurrency (systemCPUCount+1);
}
else
#endif
argFile = thisArg;
}
GlobalStartup();
if (calculatorMode)
{
printf ("\nHYPHY is running in calculator mode. Type 'exit' when you are finished.\n");
while (ExpressionCalculator()) ;
return 0;
}
if (pipeMode)
{
_String bfIn (stdin);
_ExecutionList exIn (bfIn);
exIn.Execute();
GlobalShutdown();
return 0;
}
// try to read the preferences
_String prefFile (curWd);
prefFile = prefFile & '/' & prefFileName;
FILE * testPrefFile = fopen (prefFile.sData,"r");
if (!testPrefFile)
{
prefFile = baseArgDir & prefFileName;
testPrefFile = fopen (prefFile.sData,"r");
}
if (testPrefFile)
{
fclose(testPrefFile);
ReadBatchFile (prefFile,ex);
ex.Execute();
ex.Clear();
}
//printf ("Node %d before mpiParallelOptimizer\n", rank);
#ifdef __HYPHYMPI__
if (rank>0)
{
//if (mpiParallelOptimizer || mpiPartitionOptimizer)
// mpiOptimizerLoop (rank, size);
//else
mpiNormalLoop (rank, size, baseDir);
/*argFile = "SHUTDOWN_CONFIRM";
MPISendString (argFile, senderID);*/
}
else
{
#endif
if (!argFile.sLength)
{
long selection = -2;
if (!updateMode)
selection = DisplayListOfChoices();
if (selection == -1)
{
dialogPrompt = "Batch file to run:";
_String fStr (ReturnDialogInput (true));
if (logInputMode)
{
_String tts = loggedFileEntry&fStr;
loggedUserInputs && & tts;
}
PushFilePath (fStr);
ReadBatchFile (fStr,ex);
}
else
{
_String templ;
if (selection >= 0)
templ = baseArgDir &"TemplateBatchFiles" & dirSlash;
else
templ = baseArgDir & "TemplateBatchFiles" & dirSlash & "WebUpdate.bf";
if (selection >= 0)
templ= templ&*(_String*)(*(_List*)availableTemplateFiles(selection))(2);
PushFilePath (templ);
ReadBatchFile (templ,ex);
}
}
else
{
#ifndef __MINGW32__
if (argFile.sData[0] != '/')
argFile = baseDirectory & argFile;
#else
if (argFile.sData[1] != ':') // not an absolute path
argFile = baseDirectory & argFile;
#endif
PushFilePath (argFile);
ReadBatchFile (argFile,ex);
}
ex.Execute();
if (usePostProcessors && (!updateMode))
{
ReadInPostFiles();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.getChar(0) !='n' && c_str.getChar(0)!='N' )
{
long choice = DisplayListOfPostChoices();
while (choice != -1)
{
_ExecutionList postEx;
argFile = *(_String*)(*(_List*)availablePostProcessors(choice-1))(1);
PushFilePath (argFile);
ReadBatchFile (argFile, postEx);
postEx.Execute();
PopFilePath ();
printf ("\n\n**********Continue with result processing (y/n)?");
c_str = StringFromConsole();
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.getChar(0)=='n' || c_str.getChar(0)=='N' )
break;
choice = DisplayListOfPostChoices();
}
}
}
#ifdef __HYPHYMPI__
}
ReportWarning (_String ("Node ") & (long)rank & " is shutting down\n");
#endif
#ifdef _MINGW32_MEGA_
if (_HY_MEGA_Pipe != INVALID_HANDLE_VALUE)
CloseHandle (_HY_MEGA_Pipe);
#endif
PurgeAll (true);
GlobalShutdown ();
#ifdef __HYPHYMPI__
if (rank == 0)
printf ("\n\n");
#endif
}
bool _HYConsoleWindow::_ProcessMenuSelection (long msel)
{
switch (msel) {
case HY_WINDOW_MENU_ID_FILE+1:
SaveConsole ();
return true;
case 14:
_DoPrint ();
return true;
case 16:
((_HYTextBox*)GetObject(0))->_DoUndo(true);
return true;
case 17:
((_HYTextBox*)GetObject(0))->_DoCut(true);
return true;
case 18:
((_HYTextBox*)GetObject(0))->_DoCopy(true);
return true;
case HY_WINDOW_MENU_ID_EDIT+5:
((_HYTextBox*)GetObject(0))->_DoSelectAll(true);
return true;
case 21:
SetStatusLine ("Canceling");
terminateExecution = true;
return true;
case 22: {
GtkWidget * suspendItem = gtk_item_factory_get_widget_by_action(menu_items,22);
if (!isSuspended) {
isSuspended = true;
SetStatusLine (empty,empty,empty,-1,HY_SL_SUSPEND);
gtk_label_set_text (GTK_LABEL (gtk_bin_get_child(GTK_BIN(suspendItem))), "Resume");
updateTimer = false;
while (isSuspended) {
gtk_main_iteration_do(true);
}
} else {
isSuspended = false;
SetStatusLine (empty,empty,empty,-1,HY_SL_RESUME);
gtk_label_set_text (GTK_LABEL (gtk_bin_get_child(GTK_BIN(suspendItem))), "Suspend execution");
timerStart += clock()-lastTimer;
updateTimer = true;
}
return true;
}
case 23:
ShowMessagesLog();
return true;
case 24:
RunStandardAnalyses();
return true;
case 25:
displayAbout(false);
return true;
case HY_WINDOW_MENU_ID_EDIT+4:
((_HYTextBox*)GetObject(0))->_DoClear (true,true);
return true;
case 27:
HandlePreferences (globalPreferencesList,"HYPHY Preferences");
return true;
case 29:
//WinExec ("hh HYPHY HELP.chm",SW_SHOWNORMAL);
return true;
case 30:
if (OpenBatchFile (false)) {
ExecuteBatchFile();
PopFilePath();
}
return true;
case 31:
((_HYTextBox*)GetObject(0))->_DoRedo(true);
return true;
case 15:
postWindowCloseEvent (GetID());
gtk_main_quit ();
return true;
case 60: // expression calculator
if (calculatorMode) {
_HYTextBox *ib = (_HYTextBox*)hyphyConsoleWindow->GetObject(1);
ib->SetText ("exit");
hyphyConsoleWindow->ProcessEvent (generateTextEditChangeEvent(ib->GetID(),2));
calculatorMode = false;
//ib->SetText (empty);
} else {
calculatorMode = true;
while(calculatorMode&&ExpressionCalculator()) {}
calculatorMode = false;
}
return true;
case 61: { // execute selection
ExecuteSelection();
return true;
}
case 70: // New Tree
NewTreeWindow(-1);
return true;
case 71: // New Model
NewModel(nil);
return true;
case 72: // New Chart
NewChartWindow();
return true;
case 73: // New Genetic Code
NewGeneticCodeTable(0);
return true;
case 74: // New Database
NewDatabaseFile(0);
return true;
case 80: // Open Batch File
if (OpenBatchFile()) {
ExecuteBatchFile ();
}
return true;
case 81: // Open Data File
OpenDataFile();
return true;
case 82: // Open Tree
OpenTreeFile();
return true;
case 83: // Open Text
OpenTextFile();
return true;
case 84: // Open Table
OpenTable ();
return true;
case 85: // Open SQLite database
OpenDatabaseFile (nil);
return true;
case HY_WINDOW_MENU_ID_FILE-2:
ShowObjectInspector ();
return true;
default: {
msel -= 1000;
if (msel<availablePostProcessors.lLength) {
ExecuteAPostProcessor (*(_String*)(*(_List*)availablePostProcessors(msel))(1));
return 0;
}
msel-=1000;
if (msel<(long)recentPaths.lLength) {
if (msel == -1) {
for (long mi=0; mi<recentFiles.lLength; mi++) {
GtkWidget * recFile = gtk_item_factory_get_widget_by_action(hyphyConsoleWindow->menu_items,2000+mi);
if (recFile) {
gtk_item_factory_delete_item(hyphyConsoleWindow->menu_items,gtk_item_factory_path_from_widget(recFile));
}
}
recentPaths.Clear();
recentFiles.Clear();
} else {
if (argFileName) {
*argFileName = *(_String*)recentPaths(msel);
} else {
argFileName = new _String (*(_String*)recentPaths(msel));
}
if (OpenBatchFile(false)) {
ExecuteBatchFile ();
}
}
return true;
}
return true;
}
}
return _HYTWindow::_ProcessMenuSelection(msel);
}
//__________________________________________________________________________________
int main (int argc, char* argv[])
{
mainArgCount = argc - 1;
#ifdef __HYPHYMPI__
int rank,
size;
MPI_Init (&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
setParameter (mpiNodeID, (_Parameter)rank);
setParameter (mpiNodeCount, (_Parameter)size);
_hy_mpi_node_rank = rank;
if (rank == 0)
{
#endif
//for (long k=0; k<NSIG; k++)
//{
// signal(k, &hyphyBreak);
//}
#ifdef __HYPHYMPI__
}
#endif
char curWd[4096],
dirSlash = GetPlatformDirectoryChar ();
getcwd (curWd,4096);
_String baseDir (curWd),
argFile;
baseDir=baseDir & dirSlash;
pathNames&& &baseDir;
baseDirectory = baseDir;
baseArgDir = baseDirectory;
_ExecutionList ex;
#ifdef _OPENMP
systemCPUCount = omp_get_max_threads();
#endif
for (long i=1; i<argc;i++)
{
_String thisArg (argv[i]);
if (thisArg.sData[0]=='-')
{
ProcessConfigStr (thisArg);
}
else
if (thisArg.beginswith ("BASEPATH="))
{
baseArgDir = thisArg.Cut(9,-1);
if (baseArgDir.sLength)
{
if (baseArgDir.sData[baseArgDir.sLength-1]!=dirSlash)
baseArgDir = baseArgDir&dirSlash;
baseDirectory = baseArgDir;
}
}
else
if (thisArg.beginswith ("USEPATH="))
{
baseDir = thisArg.Cut(8,-1);
errorFileName = baseDir & errorFileName;
messageFileName = baseDir & messageFileName;
pathNames.Delete (0);
pathNames&& &baseDir;
}
else
#ifdef __MP__
if (thisArg.beginswith ("CPU="))
{
_String cpus = thisArg.Cut(4,-1);
systemCPUCount = cpus.toNum();
if (systemCPUCount<1)
systemCPUCount = 1;
#ifdef __MP2__
pthread_setconcurrency (systemCPUCount+1);
#endif
}
else
#endif
#ifdef __HYPHYMPI__
if (thisArg == _String("MPIOPTIMIZER"))
{
mpiParallelOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
else
if (thisArg == _String("MPIPARTITIONS"))
{
mpiPartitionOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
else
#endif
argFile = thisArg;
}
GlobalStartup();
if (calculatorMode)
{
printf ("\nHYPHY is running in calculator mode. Type 'exit' when you are finished.\n");
while (ExpressionCalculator()) ;
return 0;
}
if (pipeMode)
{
_String bfIn (stdin);
_ExecutionList exIn (bfIn);
exIn.Execute();
GlobalShutdown();
return 0;
}
// try to read the preferences
_String prefFile (curWd);
prefFile = prefFile & '/' & prefFileName;
FILE * testPrefFile = fopen (prefFile.sData,"r");
if (!testPrefFile)
{
prefFile = baseArgDir & prefFileName;
testPrefFile = fopen (prefFile.sData,"r");
}
if (testPrefFile)
{
fclose(testPrefFile);
ReadBatchFile (prefFile,ex);
ex.Execute();
ex.Clear();
}
//printf ("Node %d before mpiParallelOptimizer\n", rank);
#ifdef __HYPHYMPI__
if (rank>0)
{
if (mpiParallelOptimizer || mpiPartitionOptimizer)
mpiOptimizerLoop (rank, size);
else
mpiNormalLoop (rank, size, baseDir);
/*argFile = "SHUTDOWN_CONFIRM";
MPISendString (argFile, senderID);*/
}
else
{
#endif
if (!argFile.sLength)
{
long selection = -2;
if (!updateMode)
selection = DisplayListOfChoices();
if (selection == -1)
{
dialogPrompt = "Batch file to run:";
_String fStr (ReturnDialogInput (true));
if (logInputMode)
{
_String tts = loggedFileEntry&fStr;
loggedUserInputs && & tts;
}
PushFilePath (fStr);
ReadBatchFile (fStr,ex);
}
else
{
_String templ;
if (selection >= 0)
templ = baseArgDir &"TemplateBatchFiles" & dirSlash;
else
templ = baseArgDir & "TemplateBatchFiles" & dirSlash & "WebUpdate.bf";
if (selection >= 0)
templ= templ&*(_String*)(*(_List*)availableTemplateFiles(selection))(2);
PushFilePath (templ);
ReadBatchFile (templ,ex);
}
}
else
{
#ifndef __MINGW32__
if (argFile.sData[0] != '/')
argFile = baseDirectory & argFile;
#else
if (argFile.sData[1] != ':') // not an absolute path
argFile = baseDirectory & argFile;
#endif
PushFilePath (argFile);
ReadBatchFile (argFile,ex);
}
ex.Execute();
if (usePostProcessors && (!updateMode))
{
ReadInPostFiles();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.sData[0]!='n' && c_str.sData[0]!='N' )
{
long choice = DisplayListOfPostChoices();
while (choice != -1)
{
_ExecutionList postEx;
argFile = *(_String*)(*(_List*)availablePostProcessors(choice-1))(1);
PushFilePath (argFile);
ReadBatchFile (argFile, postEx);
postEx.Execute();
PopFilePath ();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.sData[0]=='n' || c_str.sData[0]=='N' ) break;
choice = DisplayListOfPostChoices();
}
}
}
#ifdef __HYPHYMPI__
}
argFile = _String ("Node ") & (long)rank & " is shutting down\n";
ReportWarning (argFile);
#endif
batchLanguageFunctions.Clear();
GlobalShutdown();
#ifdef __HYPHYMPI__
if (rank == 0)
printf ("\n\n");
#endif
}