001 /*
002 * CSHApplication.java
003 *
004 * Created on July 10, 2003, 11:22 AM
005 *
006 * This file is part of the STAR Scheduler.
007 * Copyright (c) 2002-2003 STAR Collaboration - Brookhaven National Laboratory
008 *
009 * STAR Scheduler is free software; you can redistribute it and/or modify
010 * it under the terms of the GNU General Public License as published by
011 * the Free Software Foundation; either version 2 of the License, or
012 * (at your option) any later version.
013 *
014 * STAR Scheduler is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * along with STAR Scheduler; if not, write to the Free Software
021 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
022 */
023 package gov.bnl.star.offline.scheduler.lsf;
024
025 import gov.bnl.star.offline.scheduler.*;
026 import gov.bnl.star.offline.scheduler.catalog.PhysicalFile;
027 import gov.bnl.star.offline.scheduler.util.FileListToolkit;
028 import gov.bnl.star.offline.scheduler.util.FilesystemToolkit;
029 import gov.bnl.star.offline.scheduler.util.VariablesToolkit;
030
031 import java.io.File;
032 import java.io.FileOutputStream;
033 import java.io.PrintStream;
034
035 import java.util.*;
036 import java.util.logging.Level;
037 import java.util.logging.Logger;
038
039
040 /** Application module for csh.
041 * <p>
042 * This module defines the interface of a csh task, and prepare the task
043 * information in the following environment variables:
044 * <p>
045 * $JOBID - the unique job id given by the scheduler<br>
046 * $FILESLIST - the file name of a text file containing the file list assigned to
047 * the job<br>
048 * $INPUTFILECOUNT - the number of files assigned to the job<br>
049 * $INPUTFILExx - the input files associated to the job<br>
050 * <p>
051 * @author Gabriele Carcassi, Jerome Lauret
052 * @version 1.0 2002/12/26
053 */
054 public class CSHApplication {
055 static private Logger log = Logger.getLogger(CSHApplication.class.getName());
056 private Request request;
057 private Job job;
058 private String scratchDir;
059 private String submissionCommand;
060 private Map variables;
061
062 /** Holds value of property recurseCopy. */
063 private boolean recurseCopy = false;
064
065 /** Holds the value for the property of EnvVariableLimit */
066 private int EnvVariableLimit;
067
068 /** Holds value of property copyScript. */
069 private String copyScript;
070
071 /** Holds value of property storageScript. */
072 private String storageScript;
073
074 /** Holds value of property registerScript. */
075 private String registerScript;
076
077 /** Creates a new instance of CSHApplication */
078 public CSHApplication() {
079 }
080
081 /** Returns the CSH application module. In the future, the application should
082 * be taken directly from the component library. This method is provided
083 * for compatibility with the old framework.
084 * @return the CSH application module
085 */
086 public static CSHApplication getInstance() {
087 return (CSHApplication) ComponentLibrary.getInstance().getComponent("CSHApplication");
088 }
089
090 /** Prepares the task, by creating the script. */
091 public void prepareJob() {
092 try {
093 PrintStream inputFileList = new PrintStream(new FileOutputStream(
094 new File(getInputFileListName())));
095 createInputFileList(inputFileList);
096 } catch (Exception e) {
097 log.log(Level.SEVERE, "Couldn't create the file list", e);
098 throw new RuntimeException("Couldn't create the file list " +
099 getInputFileListName() + ": " + e.getMessage());
100 }
101
102 try {
103 PrintStream cshScript = new PrintStream(new FileOutputStream(
104 new File(getCSHScriptName())));
105 createCSHScript(cshScript);
106 makeScriptFileExecutable(getCSHScriptName());
107 } catch (Exception e) {
108 log.log(Level.SEVERE, "Couldn't create the script", e);
109 throw new RuntimeException("Couldn't create the script " +
110 getCSHScriptName() + ": " + e.getMessage());
111 }
112 }
113
114 /** Returns the command line to execute the task set by <CODE>setJob</CODE>.
115 * @return Command line to execute the task
116 */
117 public String getCommandLine() {
118 return getCSHScriptName();
119 }
120
121 /* Calls chmod to make the script executable. */
122 private void makeScriptFileExecutable(String fileName) {
123 // Hack to make the Unit tests work on windows.
124 // chmod doesn't exist on Windows (if you don't have cygwin)
125 if (System.getProperty("os.name").startsWith("Win")) return;
126
127 try {
128 String chmod = "chmod +x " + fileName;
129 log.info("Executing \"" + chmod + "\"");
130
131 java.lang.Process shell = Runtime.getRuntime().exec(chmod);
132 shell.waitFor();
133 } catch (Exception e) {
134 log.log(Level.SEVERE, "Couldn't make the script executable", e);
135 throw new RuntimeException("Couldn't make the script " + fileName +
136 " executable", e);
137 }
138 }
139
140 /** Sets the task the application will have to prepare.
141 * @param request the request that originated the task
142 * @param job the job to be executed
143 */
144 public void setJob(Request request, Job job) {
145 this.request = request;
146 this.job = job;
147 scratchDir = null;
148 submissionCommand = null;
149 variables = null;
150 }
151
152 /** Sets the scratch directory for the temporary output files of the job.
153 * @param scratchDir the temporary output directory
154 */
155 public void setScratchDir(String scratchDir) {
156 this.scratchDir = scratchDir;
157 }
158
159 /** Sets the submittion command used to submit the job. This will be included in the
160 * script for resubmission.
161 * @param submissionCommand the command line to submit the job to the batch system
162 */
163 public void setSubmissionCommand(String submissionCommand) {
164 this.submissionCommand = submissionCommand;
165 }
166
167 /** Generates the csh script to be submitted through LSF.
168 * @param out the stream on which to print the script
169 */
170 private void createCSHScript(PrintStream out) {
171 // Sets the shell that will interpret the script
172
173 ////////////test area////////////////
174 Map config = (Map) ComponentLibrary.getInstance().getComponent("registerScript");
175
176 out.println("#!/bin/csh");
177
178 out.println("# ------------------- ");
179 out.println("# Script generated at " + new Date() +
180 " by the STAR scheduler and submitted with");
181 out.println("# " + submissionCommand);
182 out.println("# ------------------- ");
183
184 Map env = getEnvironmentVariables();
185
186 Iterator variables = env.keySet().iterator();
187 Iterator FilesNameVariable = env.keySet().iterator();
188
189 // Sets all the environment variable.
190 out.println();
191 out.println("# Preparing environment variables");
192
193 String varName, varValue;
194
195
196 int counter=0;
197 String padding="";
198 while (variables.hasNext()) { //First pass prints all the environment variables that do not start with “INPUTFILE”
199 varName = (String) variables.next();
200 varValue = (String) env.get(varName);
201 if((! varName.startsWith("INPUTFILE")) || (varName.matches("INPUTFILECOUNT"))){
202 out.println(padding + "setenv " + varName + " " + varValue);
203 }
204 }
205
206 while (FilesNameVariable.hasNext()) { //Second pass prints all the environment variables that start with “INPUTFILE”
207 varName = (String) FilesNameVariable.next();
208 varValue = (String) env.get(varName);
209 if(varName.startsWith("INPUTFILE") && (! varName.matches("INPUTFILECOUNT"))){
210 if (counter == EnvVariableLimit){
211 out.println("#");
212 out.println("# Note: The configuration requested a limitation of the");
213 out.println("# number of INPUTFILE(n) environemnt variables at "+EnvVariableLimit);
214 out.println("# The rest of the variables will be commented.");
215 out.println("#");
216 padding = "# ";
217 }
218 counter++;
219 out.println(padding + "setenv " + varName + " " + varValue);
220 }
221 }
222
223 // Creates the scratch directory
224 out.println();
225 out.println("# Creating the scratch directory, return failure status");
226 out.println("mkdir -p $SCRATCH");
227 out.println("set STS=$status");
228 out.println("if (! -d $SCRATCH) then");
229 out.println(" echo \"Scheduler:: Failed to create $SCRATCH on $HOST\"");
230 out.println(" exit $STS");
231 out.println("endif");
232
233 // Adds the command to be executed
234 out.println();
235 out.println("###################################################");
236 //out.println("/bin/csh -s ___EOD"+job.getJobID()+"__");
237 out.println("# User command BEGIN ----------------------------->");
238
239 out.println(request.getCommand());
240
241 out.println("# <------------------------------User command BEGIN");
242 //out.println("___EOD"+job.getJobID()+"__");
243 out.println("###################################################");
244
245 // Copy output files
246 out.println();
247 out.println("# Copy output files (if any where specified)");
248
249 out.print(generateScriptFragment(request.getOutputList()));
250
251 // Delete the scratch directory
252 out.println();
253 out.println("# Delete the scratch directory");
254 out.println("/bin/rm -fr $SCRATCH");
255 }
256
257 String generateScriptFragment(List outputList) {
258 StringBuffer buffer = new StringBuffer();
259 for (int nOutput = 0; nOutput < outputList.size(); nOutput++) {
260 OutputFile output = (OutputFile) outputList.get(nOutput);
261 if (output.getActionList().size() != 0) {
262 buffer.append("setenv OUTPUTFILE").append(nOutput).append(" file:/$SCRATCH/").
263 append(output.getFromScratch()).append("\n");
264 for (int nOutputAction = 0; nOutputAction < output.getActionList().size(); nOutputAction++) {
265 if (output.getActionList().get(nOutputAction) instanceof OutputCopyAction) {
266 buffer.append(generateScriptFragment(nOutput, (OutputCopyAction) output.getActionList().get(nOutputAction)));
267 } else if (output.getActionList().get(nOutputAction) instanceof OutputRegisterAction) {
268 buffer.append(generateScriptFragment(nOutput, (OutputRegisterAction) output.getActionList().get(nOutputAction)));
269 } else {
270 log.severe("Unsupported OutputAction time found: " + output.getActionList().get(nOutputAction).getClass().getName());
271 throw new RuntimeException("Unsupported OutputAction time found");
272 }
273 }
274 } else {
275 if (recurseCopy) {
276 buffer.append("/bin/cp -r $SCRATCH/").append(output.getFromScratch()).append(" ").
277 append(output.getToURL().getPath()).append("\n");
278 } else {
279 buffer.append("/bin/cp $SCRATCH/").append(output.getFromScratch()).append(" ").
280 append(output.getToURL().getPath()).append("\n");
281 }
282 }
283 }
284 return buffer.toString();
285 }
286
287 String generateScriptFragment(int nOutput, OutputCopyAction action) {
288 StringBuffer fragment = new StringBuffer();
289 if (action.getFileRef() != null) {
290 if (action.getStorageService() != null) {
291 fragment.append("setenv OUTPUTFILE").append(nOutput).append('_').
292 append(action.getFileRef()).append(" `").append(getStorageScript()).
293 append(" \"").append(action.getStorageService()).append("\" `").
294 append(action.getURI().getPath()).append("\n");
295
296 } else {
297 fragment.append("setenv OUTPUTFILE").append(nOutput).append('_').
298 append(action.getFileRef()).append(" ").
299 append(action.getURI()).append("\n");
300 }
301 fragment.append(getCopyScript()).append(" $OUTPUTFILE").append(nOutput).
302 append(" $OUTPUTFILE").append(nOutput).append('_').append(action.getFileRef()).
303 append("\n");
304 } else {
305 fragment.append(getCopyScript()).append(" $OUTPUTFILE").append(nOutput);
306 if (action.getStorageService() != null) {
307 fragment.append(" `").append(getStorageScript()).
308 append(" \"").append(action.getStorageService()).append("\" `").
309 append(action.getURI().getPath()).append("\n");
310 } else {
311 fragment.append(" ").append(action.getURI()).append("\n");
312 }
313 }
314 return fragment.toString();
315 }
316
317 String generateScriptFragment(int nOutput, OutputRegisterAction action) {
318 StringBuffer fragment = new StringBuffer();
319 fragment.append(getRegisterScript()).append(" $OUTPUTFILE").append(nOutput);
320 if (action.getFileRef() != null) {
321 fragment.append('_'). append(action.getFileRef());
322 }
323 int queryStart = action.getURI().getSchemeSpecificPart().indexOf('?');
324 queryStart++;
325 fragment.append(" '").
326 append(action.getURI().getSchemeSpecificPart().substring(queryStart)).append("'\n");
327 return fragment.toString();
328 }
329
330 /** Generates the input file list. It consists of full path names, one line for each
331 * one.
332 * @param out the stream on which to print the file list
333 */
334 private void createInputFileList(PrintStream out) {
335 if ("paths".equals(request.getFileListType())) {
336 FileListToolkit.createPathsFileList(out, job.getInput());
337 } else if ("rootd".equals(request.getFileListType())) {
338 FileListToolkit.createRootdFileList(out, job.getInput());
339 }
340 }
341
342 /** Returns the name for the csh script.
343 * @return the csh script name
344 */
345 public String getCSHScriptName() {
346 return FilesystemToolkit.getCurrentDirectory() + "/sched" +
347 job.getJobID() + ".csh";
348 }
349
350 /** Returns the name for the input file list file.
351 * @return the input file list name
352 */
353 public String getInputFileListName() {
354 return "sched" + job.getJobID() + ".list";
355 }
356
357
358 private Map getEnvironmentVariables() {
359 if (variables != null) {
360 return variables;
361 }
362
363 variables = new Hashtable();
364
365 variables = new TreeMap(job.getEnv());
366 variables.put("JOBID", job.getJobID());
367 variables.put("REQUESTID", job.getRequestID());
368 variables.put("PROCESSID", job.getProcessID());
369
370 // FIXME: scratch dir should be passed in a nicer way
371 variables.put("SCRATCH", scratchDir);
372 variables.put("FILELIST", getInputFileListName());
373
374 List inputList = job.getInput();
375 variables.put("INPUTFILECOUNT", Integer.toString(inputList.size()));
376
377 for (int nFile = 0; nFile < inputList.size(); nFile++) {
378 PhysicalFile file = (PhysicalFile) inputList.get(nFile);
379 variables.put("INPUTFILE" + nFile,
380 file.getPath() + "/" + file.getFilename());
381 }
382
383
384 //If there is only one input file per csh make an Environment Variable called FILEBASENAME
385 if(inputList.size() == 1){
386 PhysicalFile file = (PhysicalFile) inputList.get(0);
387 if(! (file.getFilename().indexOf(".") == -1))
388 variables.put("FILEBASENAME",file.getFilename().substring(0,file.getFilename().indexOf(".")));
389 else
390 variables.put("FILEBASENAME",file.getFilename());
391 }
392 else{ //All other times FILEBASENAME will be set to this value
393 variables.put("FILEBASENAME","FILEBASENAME.NOT.INITIALIZED." + job.getJobID());
394 }
395
396 return variables;
397 }
398
399 /** Returns the file for standard input redirection.
400 * @return stdin file
401 */
402 public String getStdin() {
403 if (job.getStdin() != null) {
404 return VariablesToolkit.substituteVariables(job.getStdin().getPath(),
405 CSHApplication.getInstance().getEnvironmentVariables());
406 }
407
408 return null;
409 }
410
411 /** Returns the file for standard output redirection.
412 * @return stdout file
413 */
414 public String getStdout() {
415 if (job.getStdout() != null) {
416 if (job.getStdout() == Request.discard) {
417 return "/dev/null";
418 }
419
420 return VariablesToolkit.substituteVariables(job.getStdout().getPath(),
421 CSHApplication.getInstance().getEnvironmentVariables());
422 }
423
424 return null;
425 }
426
427 /** Returns the file for standard error redirection.
428 * @return stderr file
429 */
430 public String getStderr() {
431 if (job.getStderr() != null) {
432 if (job.getStderr() == Request.discard) {
433 return "/dev/null";
434 }
435
436 return VariablesToolkit.substituteVariables(job.getStderr().getPath(),
437 CSHApplication.getInstance().getEnvironmentVariables());
438 }
439
440 return null;
441 }
442
443 /** Returns the job name to be assigned to the batch system.
444 * @return the job name to be used by the batch system
445 */
446 public String getJobName() {
447 return request.getName();
448 }
449
450 /** Getter for property recurseCopy.
451 * @return Value of property recurseCopy.
452 *
453 */
454 public boolean isRecurseCopy() {
455 return this.recurseCopy;
456 }
457
458 /** Setter for property recurseCopy.
459 * @param recurseCopy New value of property recurseCopy.
460 *
461 */
462 public void setRecurseCopy(boolean recurseCopy) {
463 this.recurseCopy = recurseCopy;
464 }
465
466
467 /** Getter for property EnvVariableLimit.
468 * @return Value of property EnvVariableLimit.
469 *
470 */
471 public int getEnvVariableLimit() {
472 return this.EnvVariableLimit;
473 }
474
475 /** Setter for property EnvVariableLimit.
476 * @param EnvVariableLimit New value of property EnvVariableLimit.
477 *
478 */
479 public void setEnvVariableLimit(int EnvVariableLimit) {
480 this.EnvVariableLimit = EnvVariableLimit;
481 }
482
483
484 /** Getter for property copyScript.
485 * @return Value of property copyScript.
486 *
487 */
488 public String getCopyScript() {
489 return this.copyScript;
490 }
491
492 /** Setter for property copyScript.
493 * @param copyScript New value of property copyScript.
494 *
495 */
496 public void setCopyScript(String copyScript) {
497 this.copyScript = copyScript;
498 }
499
500 /** Getter for property storageScript.
501 * @return Value of property storageScript.
502 *
503 */
504 public String getStorageScript() {
505 return this.storageScript;
506 }
507
508 /** Setter for property storageScript.
509 * @param storageScript New value of property storageScript.
510 *
511 */
512 public void setStorageScript(String storageScript) {
513 this.storageScript = storageScript;
514 }
515
516 /** Getter for property registerScript.
517 * @return Value of property registerScript.
518 *
519 */
520 public String getRegisterScript() {
521 return this.registerScript;
522 }
523
524 /** Setter for property registerScript.
525 * @param registerScript New value of property registerScript.
526 *
527 */
528 public void setRegisterScript(String registerScript) {
529 this.registerScript = registerScript;
530 }
531
532 }