clusterpost-execution/engine_lsf.js

Download data from the data provider to the local disk. Submit tasks to the job manager. Check if the task has finished and upload the results back to the data provider

module.exports = function (conf) {

	var fs = require('fs');
	var Promise = require('bluebird');
	var _ = require("underscore");
	var spawn = require('child_process').spawn;
	var path = require('path');
	var Joi = require('@hapi/joi');

	var executionmethods = require('./executionserver.methods')(conf);
	var clustermodel = require('clusterpost-model');

	var handler = {};

	handler.submitJob = function(doc, cwd){

		Joi.assert(doc, clustermodel.job);

		return new Promise(function(resolve, reject){
			var command = 'bsub';
			var parameters = doc.parameters;

			var params = [];

			if(doc.jobparameters){
				for(var i = 0; i < doc.jobparameters.length; i++){
                    var param = doc.jobparameters[i];
                    if(_.isObject(param)){
                    	if(param.flag){
                            params.push(param.flag);
	                    }
	                    if(param.name){
                            params.push(param.name);
	                    }	
                    }else{
                    	params.push(param);
                    }
                }
			}

			params.push("-cwd");
			params.push(cwd);
			params.push("-e");
			params.push(path.join(cwd, "stderr.err"));
			params.push("-o");
			params.push(path.join(cwd, "stdout.out"));
			params.push("-u");
			params.push(doc.userEmail);
			params.push("-J");
			params.push(doc.userEmail);

			
			params.push(doc.executable);
			if(parameters){
				for(var i = 0; i < parameters.length; i++){
					var param = parameters[i];
					if(_.isObject(param)){
                    	if(param.flag){
                            params.push(param.flag);
	                    }
	                    if(param.name){
                            params.push(param.name);
	                    }	
                    }else{
                    	params.push(param);
                    }
				}
			}

			try{
				const runcommand = spawn(command, params);

				var allerror = "";
				runcommand.stderr.on('data', function(data){
					allerror += data;
				});

				var alldata = "";
				runcommand.stdout.on('data', function(data){
					alldata += data;
				});

				//"sample: Job <898104> is submitted to default queue <day>"
				runcommand.on('close', function(code){
					if(code){
						resolve({
							status: 'FAIL',
							error: allerror + alldata
						});
					}else{
						var ind = alldata.indexOf('<') + 1;
	                    var jobid = alldata.substr(ind, alldata.indexOf('>') - ind);

						resolve({
							jobid : Number.parseInt(jobid),
							status: 'RUN'
						});
					}
				});
				
			}catch(e){
				reject({
					status: "FAIL",
					error: e
				});
			}

		});
		
	}

	handler.getJobStatus = function(doc){

		Joi.assert(doc.jobstatus, clustermodel.jobstatus);

		return new Promise(function(resolve, reject){

			try{

				var jobid = doc.jobstatus.jobid;
				if(!jobid && doc.jobstatus.stat){
					try{
						jobid = doc.jobstatus.stat.split("\n")[1].split(" ")[0];
					}catch(e){
						console.error(e);
					}
				}
				var params = ["-J", doc.userEmail, jobid];

				const ps = spawn('bjobs', params);

				var allerror = "";
				ps.stderr.on('data', function(data){
					allerror += data;
				});

				var alldata = "";
				ps.stdout.on('data', function(data){
					alldata += data;
				});

				//"sample success: 898104  jprieto DONE  day        killdevil-l donor_pool2 *gmail.com Feb 14 11:16"
				//"sample fail: Job <8981> is not found"

				ps.on('close', function(code){

					if(alldata && alldata.indexOf('DONE') !== -1 || allerror && allerror.indexOf('is not found') !== -1){
						resolve({
							status: 'DONE',
							stat: alldata
						});
					}else if(alldata && alldata.indexOf('EXIT') !== -1){
						resolve({
							status: 'EXIT',
							stat: alldata
						});
					}else if(code || allerror){
						resolve({
							status: 'FAIL',
							error: allerror
						});						
					}else{
						resolve({
							jobid: jobid,
							status: 'RUN',
							stat: alldata
						});	
					}
					
				});

			}catch(e){
				reject(e);
			}
			
		});
	}

	handler.killJob = function(doc){

		Joi.assert(doc.jobstatus, clustermodel.jobstatus);

		return new Promise(function(resolve, reject){

			try{

				var jobid = doc.jobstatus.jobid;
				var params = ["-J", doc.userEmail, jobid];

				const kill = spawn('bkill', params);

				var allerror = "";
				kill.stderr.on('data', function(data){
					allerror += data;
				});

				var alldata = "";
				kill.stdout.on('data', function(data){
					alldata += data;
				});

				kill.on('close', function(code){
					resolve({
						status: 'EXIT',
						stat: allerror + alldata
					});
				});


			}catch(e){
				reject(e);
			}
			
		});

	}

	return handler;
}