//__________________________________________________________________________________
void ReadInPostFiles(void)
{
if (!likeFuncList.lLength)
return;
_String fileIndex;
FILE* modelList = fopen (fileIndex.getStr(),"r");
fileIndex = baseArgDir &"TemplateBatchFiles/postprocessors.lst";
modelList = fopen (fileIndex.getStr(),"r");
fseek (modelList,0,SEEK_END);
unsigned long fLength = ftell(modelList);
fseek (modelList,0,SEEK_END);
fLength = ftell(modelList);
if (fLength)
{
rewind (modelList);
_String theData (fLength);
fread (theData.getStr(),sizeof (char), fLength, modelList);
_ElementaryCommand::ExtractConditions(theData,0,availablePostProcessors);
for (long i = 0; i<availablePostProcessors.countitems(); i++)
{
_String* thisString = (_String*)availablePostProcessors(i);
_List thisFile;
_ElementaryCommand::ExtractConditions(*thisString,thisString->FirstNonSpaceIndex(),thisFile,',');
if (thisFile.lLength!=3)
{
availablePostProcessors.Delete(i);
i--;
continue;
}
for (long j = 0; j<3; j++)
((_String*)thisFile(j))->StripQuotes();
if (*(_String*)thisFile(0)!=_String("SEPARATOR"))
{
fileIndex = *((_String*)pathNames(0)) &"TemplateBatchFiles/" & *(_String*)thisFile(1);
FILE* dummyFile = fopen (fileIndex,"r");
if (!dummyFile)
{
fileIndex =baseArgDir&"TemplateBatchFiles/"& *(_String*)thisFile(1);
dummyFile = fopen (fileIndex,"r");
}
if (dummyFile)
{
fclose (dummyFile);
_String* condition = (_String*)thisFile(2);
if (condition->sLength)
{
_Formula condCheck (*condition,nil);
_PMathObj condCheckRes = condCheck.Compute();
if ((!condCheckRes)||(condCheckRes->Value()<.5))
{
availablePostProcessors.Delete(i);
i--;
continue;
}
}
*(_String*)thisFile(1) = fileIndex;
availablePostProcessors.Replace(i,&thisFile,true);
continue;
}
}
availablePostProcessors.Delete(i);
i--;
}
}
}
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);
if (baseDir.getChar (baseDir.sLength-1) != dirSlash) {
baseDir=baseDir & dirSlash;
}
#if defined _HYPHY_LIBDIRECTORY_
_String libDir (_HYPHY_LIBDIRECTORY_);
if (libDir.getChar (libDir.sLength-1) != dirSlash) {
libDir=libDir & dirSlash;
}
pathNames&& &libDir;
#else
pathNames&& &baseDir;
_String libDir = baseDir;
#endif
_String argFile;
libDirectory = libDir;
libArgDir = libDirectory;
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 ("LIBPATH=")) {
libArgDir = thisArg.Cut(8,-1);
if (libArgDir.sLength) {
if (libArgDir.sData[libArgDir.sLength-1] != dirSlash) {
libArgDir = libArgDir & dirSlash;
}
libDirectory = libArgDir;
}
} 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
_String defaultBaseDirectory = *(_String*)pathNames(0);
mpiNormalLoop (rank, size, defaultBaseDirectory);
/*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
}
