MPINodeStatus = {MPI_NODE_COUNT-1,1}["-1"];		/* reset semaphore */


path = HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "Utility" + DIRECTORY_SEPARATOR + "ReadDelimitedFiles.bf";
ExecuteAFile (path);


/* load analysis settings */

/*
this gets read first 	-> /Library/WebServer/Documents/upload/g7097skphqi84tm71imk60agb7/paths.txt
this becomes 0 			-> Automatic
this becomes 1			-> N/A
this becomes 2			-> HIV 25%
this becomes 3			-> All
*/


fscanf ("/home/art/wip/swenson/dutch_v3/prelim/_remote.txt", "Lines", paths);

_settings = {};
_settings["0"] = "Custom";
_settings["1"] = "CTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGT";
_settings["2"] = "HIV 25%";
_settings["3"] = "All";



jobsInProgress = Columns(paths);

for (_job = 0; _job < Columns(paths); _job = _job+1)
{
	//fprintf (stdout, paths[_job], "\n");
	received = SendAJob (_job);
	if (received)
	{
		jobsInProgress = jobsInProgress - 1;
	}
}


fprintf (stdout, "Master node is waiting for ", jobsInProgress, " more jobs to finish.\n");
for (_wait = 0; _wait < jobsInProgress; _wait = _wait+1)
{
	MPIReceive (-1, fromNode, theJob);
	fprintf (stdout, "Received job from node ", fromNode, "\n");
}

fprintf (stdout, "Analysis complete.\n");


function SendAJob (job)
{
	/*
	items = splitOnRegExp (paths[job], "/");
	filename = items[Abs(items)-1];
	stem = (paths[job])[0][Abs(paths[job]) - Abs(filename) - 1];
	
	items = splitOnRegExp (filename, "\\.");
	prefix = items[0]+"."+items[1];
	*/
	
	cmdString = "";
	cmdString * 256;
	
	cmdString * "stdinRedirect = {};\n";
	
	cmdString * "stdinRedirect[\"00\"] = \"Universal\";\n";
	
	target = paths[job]^{{" "}{""}};
	cmd = "stdinRedirect[\"01\"] = \""+target+"\";\n";
	cmdString * cmd;
	
	// alignment mode (automatic or select from list)
	cmd = "stdinRedirect[\"02\"] = \""+_settings[0]+"\";\n";
	cmdString * cmd;
	
	
	if (_settings[0] == "Automatic")
	{
		cmd = "stdinRedirect[\"03\"] = \""+_settings[2]+"\";\n";
		cmdString * cmd;
		cmd = "stdinRedirect[\"04\"] = \""+_settings[3]+"\";\n";
		cmdString * cmd;
		
		cmdString * "stdinRedirect[\"05\"] = \"CSV\";\n";
		
		cmd = "stdinRedirect[\"06\"] = \"" + target + ".csv";
		cmdString * cmd;
		cmdString * "\";\n";
	}
	else
	{
		// reference sequence
		cmd = "stdinRedirect[\"03\"] = \""+_settings[1]+"\";\n";
		cmdString * cmd;
		// substitution matrix
		cmd = "stdinRedirect[\"04\"] = \""+_settings[2]+"\";\n";
		cmdString * cmd;
		// filtering option
		cmd = "stdinRedirect[\"05\"] = \""+_settings[3]+"\";\n";
		cmdString * cmd;
		cmdString * "stdinRedirect[\"06\"] = \"CSV\";\n";
		
		cmd = "stdinRedirect[\"07\"] = \"" + target + ".csv";
		cmdString * cmd;
		cmdString * "\";\n";
	}
	
	cmdString * "ExecuteAFile (\"/home/art/wip/swenson/dutch_v3/scripts/emelineV2.5.bf\", stdinRedirect);";
	cmdString * 0;
	
	
	for (nodeID = 0; nodeID < MPI_NODE_COUNT -1; nodeID = nodeID + 1)
	{
		if (MPINodeStatus[nodeID] < 0)	/* semaphore indicates available node */
		{
			fprintf (stdout, "Sending job ", job, " to idle node ", nodeID+1, "\n");
			MPISend(nodeID+1, cmdString);
			MPINodeStatus[nodeID] = job;
			break;
		}
	}
	
	
	if (nodeID == MPI_NODE_COUNT-1)	/* looped through semaphore with no idle nodes */
	{
		MPIReceive (-1, fromNode, theJob);	/* wait until one of the node completes its job */
		oldJob = MPINodeStatus[fromNode-1];
		
		fprintf (stdout, "Sending job ", job, " to node ", fromNode, " that just finished job\n");
		MPISend (fromNode, cmdString);
		MPINodeStatus[fromNode-1] = job;
		
		return 1;	/* indicate that job is received */
	}
	
	return 0;
}