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Quentin Lux committed Apr 6, 2016
1 parent 6fd55d9 commit e03a77e
Showing 1 changed file with 75 additions and 59 deletions.
134 changes: 75 additions & 59 deletions pbsjs.js
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Original file line number Diff line number Diff line change
@@ -1,3 +1,20 @@
/*
* Copyright (C) 2015-2016 Quantum HPC Inc.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

var cproc = require('child_process');
var spawn = cproc.spawnSync;
var fs = require("fs");
Expand All @@ -18,7 +35,7 @@ function spawnProcess(spawnCmd, spawnType, spawnDirection, pbs_config){
switch (pbs_config.method){
case "ssh":
spawnExec = pbs_config.ssh_exec;
spawnCmd = [pbs_config.username + "@" + pbs_config.serverName,"-i",pbs_config.secretAccessKey].concat(spawnCmd.split(" "));
spawnCmd = [pbs_config.username + "@" + pbs_config.serverName,"-o","StrictHostKeyChecking=no","-i",pbs_config.secretAccessKey].concat(spawnCmd.split(" "));
break;
case "local":
spawnExec = pbs_config.local_shell;
Expand All @@ -36,17 +53,19 @@ function spawnProcess(spawnCmd, spawnType, spawnDirection, pbs_config){
// Build the scp command
case "ssh":
spawnExec = pbs_config.scp_exec;
var file;
var destDir;
switch (spawnDirection){
case "send":
var file = spawnCmd[0];
var destDir = pbs_config.username + "@" + pbs_config.serverName + ":" + spawnCmd[1];
file = spawnCmd[0];
destDir = pbs_config.username + "@" + pbs_config.serverName + ":" + spawnCmd[1];
break;
case "retrieve":
var file = pbs_config.username + "@" + pbs_config.serverName + ":" + spawnCmd[0];
var destDir = spawnCmd[1];
file = pbs_config.username + "@" + pbs_config.serverName + ":" + spawnCmd[0];
destDir = spawnCmd[1];
break;
}
spawnCmd = ["-i",pbs_config.secretAccessKey,file,destDir]
spawnCmd = ["-o","StrictHostKeyChecking=no","-i",pbs_config.secretAccessKey,file,destDir];
break;
case "local":
spawnExec = pbs_config.local_copy;
Expand All @@ -71,7 +90,7 @@ function createJobWorkDir(pbs_config){
var jobWorkingDir = path.join(pbs_config.working_dir,createUID());

//Create workdir
var mkdirOutput = spawnProcess("[ -d "+jobWorkingDir+" ] || mkdir "+jobWorkingDir,"shell", null, pbs_config);
spawnProcess("[ -d "+jobWorkingDir+" ] || mkdir "+jobWorkingDir,"shell", null, pbs_config);

//TODO:handles error
return jobWorkingDir;
Expand All @@ -82,9 +101,9 @@ function createJobWorkDir(pbs_config){
function jsonifyQmgr(output){
var results=[];
// JSON output will be indexed by queues and server
results['queue']=[];
results['queues']=[];
results['server']={};
results.queue=[];
results.queues=[];
results.server={};
//Loop on properties
for (var i = 0; i < output.length; i++) {
if (output[i].indexOf('=') !== -1){
Expand All @@ -96,32 +115,32 @@ function jsonifyQmgr(output){
//TODO: do this more effentiely
switch (keys[1].trim()){
case 'server':
results['server'][keys[2].trim()] = value;
results.server[keys[2].trim()] = value;
break;
case 'queue':
// Order array under the queue name to easily store properties
results['queue'][keys[2].trim()] = results['queue'][keys[2].trim()] || {}; // initializes array if it is undefined
results['queue'][keys[2].trim()][keys[3].trim()] = value;
results.queue[keys[2].trim()] = results.queue[keys[2].trim()] || {}; // initializes array if it is undefined
results.queue[keys[2].trim()][keys[3].trim()] = value;
break;
}
}
}
// Loop on the sub-array 'queue' to reorganise it more JSON-like
for (var x in results['queue']){
for (var x in results.queue){
// Add the name of the queue
results['queue'][x]['name'] = x;
results['queues'].push(results['queue'][x]);
results.queue[x].name = x;
results.queues.push(results.queue[x]);
}
// Clear the sub-array
delete results['queue'];
delete results.queue;

return results;
}

function jsonifyQnodes(output){
var results={};
// Store node name
results["name"] = output[0];
results.name = output[0];
// Look for properties
for (var i = 1; i < output.length; i++) {
if (output[i].indexOf('=')!== -1){
Expand All @@ -132,22 +151,22 @@ function jsonifyQnodes(output){
}
}
// Reorganise jobs into an array with jobId & jobProcs
if (results['jobs']){
if (results.jobs){
var runningJobs = [];
var jobData = results['jobs'].trim().split(/[,/]+/);
var jobData = results.jobs.trim().split(/[,/]+/);
// Parse jobs and forget trailing comma
for (var j = 0; j < jobData.length-1; j+=2) {
var newJob = {
jobId : jobData[j+1],
jobProcs : jobData[j],
}
};
runningJobs.push(newJob);
}
results['jobs'] = runningJobs;
results.jobs = runningJobs;
}
// Reorganise status
if (results['status']){
var statusData = results['status'].trim().split(/[,]+/);
if (results.status){
var statusData = results.status.trim().split(/[,]+/);
for (var k = 0; k < statusData.length; k+=2) {
// Skip jobs inside status for now : TODO: store those information
if (statusData[k] == 'jobs'){
Expand All @@ -157,7 +176,7 @@ function jsonifyQnodes(output){
}
results[statusData[k]] = statusData[k+1];
}
delete results['status'];
delete results.status;
}
return results;
}
Expand All @@ -179,7 +198,7 @@ function jsonifyQstat(output){
function jsonifyQstatF(output){
var results={};
// First line is Job Id
results['jobId'] = output[0].split(':')[1].trim();
results.jobId = output[0].split(':')[1].trim();

// Look for properties
for (var i = 1; i < output.length; i++) {
Expand All @@ -191,11 +210,11 @@ function jsonifyQstatF(output){
}

// Reorganise variable list into a sub-array
if (results['Variable_List']){
var variables = results['Variable_List'].trim().split(/[=,]+/);
results['Variable_List'] = {};
if (results.Variable_List){
var variables = results.Variable_List.trim().split(/[=,]+/);
results.Variable_List = {};
for (var k = 0; k < variables.length; k+=2) {
results['Variable_List'][variables[k]] = variables[k+1];
results.Variable_List[variables[k]] = variables[k+1];
}
}
return results;
Expand Down Expand Up @@ -224,14 +243,14 @@ function jsonifyQstatF(output){
// TODO: Consider piping the commands to qsub instead of writing script
function qscript_js(jobArgs, localPath, callback){
// General PBS command inside script
var PBScommand = "#PBS "
var PBScommand = "#PBS ";
var toWrite = "# Autogenerated script";

var jobName = jobArgs.jobName;

// The name has to be bash compatible: TODO expand to throw other erros
if (jobName.search(/[^a-zA-Z0-9]/g) !== -1){
return callback(new Error('Name cannot contain special characters'))
return callback(new Error('Name cannot contain special characters'));
}

// Generate the script path
Expand Down Expand Up @@ -266,10 +285,10 @@ function qscript_js(jobArgs, localPath, callback){
var mailArgs;
if(jobArgs.mailAbort){mailArgs = '-m a';}
if(jobArgs.mailBegins){
if (!mailArgs){mailArgs = '-m b'}else{mailArgs += 'b';}
if (!mailArgs){mailArgs = '-m b';}else{mailArgs += 'b';}
}
if(jobArgs.mailTerminates){
if (!mailArgs){mailArgs = '-m e'}else{mailArgs += 'e';}
if (!mailArgs){mailArgs = '-m e';}else{mailArgs += 'e';}
}

if (mailArgs){
Expand All @@ -282,7 +301,7 @@ function qscript_js(jobArgs, localPath, callback){

toWrite += "\n";
// Write to script
fs.writeFileSync(scriptFullPath,toWrite)
fs.writeFileSync(scriptFullPath,toWrite);

return callback(null, {
"message" : 'Script for job ' + jobName + ' successfully created',
Expand Down Expand Up @@ -316,7 +335,7 @@ function qnodes_js(pbs_config, nodeName, callback){

// Transmit the error if any
if (output.stderr){
return callback(new Error(output.stderr))
return callback(new Error(output.stderr));
}

//Detect empty values
Expand All @@ -325,10 +344,10 @@ function qnodes_js(pbs_config, nodeName, callback){
output = output.split('\n\n');
var nodes = [];
//Loop on each node, the last one is blank due to \n\n
for (var i = 0; i < output.length-1; i++) {
for (var j = 0; j < output.length-1; j++) {
//Split at lign breaks
output[i] = output[i].trim().split(/[\n;]+/);
nodes.push(jsonifyQnodes(output[i]));
output[j] = output[j].trim().split(/[\n;]+/);
nodes.push(jsonifyQnodes(output[j]));
}
return callback(null, nodes);
}
Expand Down Expand Up @@ -362,21 +381,21 @@ function qstat_js(pbs_config, jobId, callback){
var output = spawnProcess(remote_cmd,"shell",null,pbs_config);
// Transmit the error if any
if (output.stderr){
return callback(new Error(output.stderr))
return callback(new Error(output.stderr));
}

// If no error but zero length, the user is not authorized
if (output.stdout.length == 0){
return callback(new Error('You are not authorized to consult that job'));
// If no error but zero length, the user is has no job running or is not authorized
if (output.stdout.length === 0){
return callback(null,[]);
}

if (jobList){
output = output.stdout.split('\n');
// First 2 lines are not relevant
var jobs = [];
for (var i = 2; i < output.length-1; i++) {
output[i] = output[i].trim().split(/[\s]+/);
jobs.push(jsonifyQstat(output[i]));
for (var j = 2; j < output.length-1; j++) {
output[j] = output[j].trim().split(/[\s]+/);
jobs.push(jsonifyQstat(output[j]));
}
return callback(null, jobs);
}else{
Expand Down Expand Up @@ -404,7 +423,7 @@ function qdel_js(pbs_config,jobId,callback){
var remote_cmd = pbs_config.binaries_dir + "qdel";
if (args.length !== 1){
// Return an error
return callback(new Error('Please specify the jobId'))
return callback(new Error('Please specify the jobId'));
}else{
jobId = args.pop();
// Default print everything
Expand All @@ -414,7 +433,7 @@ function qdel_js(pbs_config,jobId,callback){

// Transmit the error if any
if (output.stderr){
return callback(new Error(output.stderr))
return callback(new Error(output.stderr));
}
// Job deleted returns
return callback(null, {"message" : 'Job ' + jobId + ' successfully deleted'});
Expand All @@ -436,7 +455,7 @@ function qmgr_js(pbs_config, qmgrCmd, callback){
callback = args.pop();

var remote_cmd = pbs_config.binaries_dir + "qmgr -c ";
if (args.length == 0){
if (args.length === 0){
// Default print everything
remote_cmd += "'p s'";
}else{
Expand All @@ -447,7 +466,7 @@ function qmgr_js(pbs_config, qmgrCmd, callback){

// Transmit the error if any
if (output.stderr){
return callback(new Error(output.stderr))
return callback(new Error(output.stderr));
}

output = output.stdout.split('\n');
Expand Down Expand Up @@ -515,11 +534,11 @@ function qfind_js(pbs_config, jobId, callback){
// Check if the user is the owner of the job
qstat_js(pbs_config,jobId, function(err,data){
if(err){
return callback(err,data)
return callback(err,data);
}

// Check if the user downloads the appropriate files
var jobWorkingDir = path.resolve(data["Variable_List"]["PBS_O_WORKDIR"]);
var jobWorkingDir = path.resolve(data.Variable_List.PBS_O_WORKDIR);

// Remote find command
// TOOD: put in config file
Expand Down Expand Up @@ -556,7 +575,7 @@ function qfind_js(pbs_config, jobId, callback){
}
return callback(null, fileList);

})
});

}

Expand All @@ -565,11 +584,11 @@ function qretrieve_js(pbs_config, jobId, fileList, localDir, callback){
// Check if the user is the owner of the job
qstat_js(pbs_config,jobId, function(err,data){
if(err){
return callback(err,data)
return callback(err,data);
}

// Check if the user downloads the appropriate files
var jobWorkingDir = path.resolve(data["Variable_List"]["PBS_O_WORKDIR"]);
var jobWorkingDir = path.resolve(data.Variable_List.PBS_O_WORKDIR);

for (var file in fileList){
var filePath = fileList[file];
Expand All @@ -589,13 +608,10 @@ function qretrieve_js(pbs_config, jobId, fileList, localDir, callback){
return callback(null,{
"message" : 'Files for the job ' + jobId + ' have all been retrieved in ' + localDir
});

})
});

}



module.exports = {
qnodes_js : qnodes_js,
qstat_js : qstat_js,
Expand Down

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