source: trunk/cleanup.php@ 6

Last change on this file since 6 was 6, checked in by gegorbet, 9 years ago

changes since 2013, mostly for airvata/thrift
File size: 23.8 KB
Line 
1<?php
2/*
3 * cleanup.php
4 *
5 * functions relating to copying results and cleaning up the gfac DB
6 *
7 */
8
9include_once "/export/home/us3/bin/listen-config.php";
10$me = 'cleanup.php';
11$email_address = '';
12$queuestatus = '';
13$jobtype = '';
14$db = '';
15$editXMLFilename = '';
16$status = '';
17
18function gfac_cleanup( $us3_db, $reqID, $gfac_link )
19{
20 global $dbhost;
21 global $user;
22 global $passwd;
23 global $db;
24 global $guser;
25 global $gpasswd;
26 global $gDB;
27 global $me;
28 global $work;
29 global $email_address;
30 global $queuestatus;
31 global $jobtype;
32 global $editXMLFilename;
33 global $submittime;
34 global $status;
35 global $stdout;
36 global $requestID;
37
38 $requestID = $reqID;
39 $db = $us3_db;
40 write_log( "$me: debug db=$db; requestID=$requestID" );
41
42 $us3_link = mysql_connect( $dbhost, $user, $passwd );
43
44 if ( ! $us3_link )
45 {
46 write_log( "$me: could not connect: $dbhost, $user, $passwd" );
47 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
48 return( -1 );
49 }
50
51 $result = mysql_select_db( $db, $us3_link );
52
53 if ( ! $result )
54 {
55 write_log( "$me: could not select DB $db" );
56 mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
57 return( -1 );
58 }
59
60 // First get basic info for email messages
61 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
62 "WHERE HPCAnalysisRequestID=$requestID";
63 $result = mysql_query( $query, $us3_link );
64
65 if ( ! $result )
66 {
67 write_log( "$me: Bad query: $query" );
68 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
69 return( -1 );
70 }
71
72 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
73
74 $query = "SELECT personID FROM people " .
75 "WHERE personGUID='$investigatorGUID'";
76 $result = mysql_query( $query, $us3_link );
77
78 list( $personID ) = mysql_fetch_array( $result );
79
80 /*
81 $query = "SELECT clusterName, submitTime, queueStatus, method " .
82 "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
83 "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
84 "WHERE h.HPCAnalysisRequestID=$requestID";
85 */
86 $query = "SELECT clusterName, submitTime, queueStatus, method " .
87 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
88 "WHERE h.HPCAnalysisRequestID=$requestID " .
89 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
90
91 $result = mysql_query( $query, $us3_link );
92
93 if ( ! $result )
94 {
95 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
96 return( -1 );
97 }
98
99 if ( mysql_num_rows( $result ) == 0 )
100 {
101 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
102 return( -1 );
103 }
104
105 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
106
107 // Get the GFAC ID
108 $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
109 "WHERE HPCAnalysisRequestID=$requestID";
110
111 $result = mysql_query( $query, $us3_link );
112
113 if ( ! $result )
114 {
115 write_log( "$me: Bad query: $query" );
116 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
117 return( -1 );
118 }
119
120 list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
121
122 ////////
123 // Get data from global GFAC DB and insert it into US3 DB
124 // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
125
126 $result = mysql_select_db( $gDB, $gfac_link );
127
128 if ( ! $result )
129 {
130 write_log( "$me: Could not connect to DB $gDB" );
131 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
132 return( -1 );
133 }
134
135 $query = "SELECT status, cluster, id FROM analysis " .
136 "WHERE gfacID='$gfacID'";
137
138 $result = mysql_query( $query, $gfac_link );
139 if ( ! $result )
140 {
141 write_log( "$me: Could not select GFAC status for $gfacID" );
142 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
143 return( -1 );
144 }
145
146 list( $status, $cluster, $id ) = mysql_fetch_array( $result );
147
148 if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
149 {
150 $clushost = $cluster;
151 $clushost = preg_replace( "/\-local/", "", $clushost );
152 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
153 }
154
155 $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
156 "WHERE gfacID='$gfacID'";
157
158 $result = mysql_query( $query, $gfac_link );
159
160 if ( ! $result )
161 {
162 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
163 mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
164 return( -1 );
165 }
166
167 list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
168
169 // Save queue messages for post-mortem analysis
170 $query = "SELECT message, time FROM queue_messages " .
171 "WHERE analysisID = $analysisID " .
172 "ORDER BY time ";
173 $result = mysql_query( $query, $gfac_link );
174
175 if ( ! $result )
176 {
177 // Just log it and continue
178 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
179 }
180
181 $now = date( 'Y-m-d H:i:s' );
182 $message_log = "US3 DB: $db\n" .
183 "RequestID: $requestID\n" .
184 "GFAC ID: $gfacID\n" .
185 "Processed: $now\n\n" .
186 "Queue Messages\n\n" ;
187 if ( mysql_num_rows( $result ) > 0 )
188 {
189 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
190 $message_log .= "$time $message\n";
191 }
192
193 $query = "DELETE FROM queue_messages " .
194 "WHERE analysisID = $analysisID ";
195
196 $result = mysql_query( $query, $gfac_link );
197
198 if ( ! $result )
199 {
200 // Just log it and continue
201 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
202 }
203
204 // Save stdout, stderr, etc. for message log
205 $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
206 "WHERE gfacID='$gfacID' ";
207 $result = mysql_query( $query, $gfac_link );
208 try
209 {
210 // What if this is too large?
211 list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
212 }
213 catch ( Exception $e )
214 {
215 write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
216 // Just go ahead and clean up
217 }
218
219 // But let's allow for investigation of other large stdout and/or stderr
220 if ( strlen( $stdout ) > 20480000 ||
221 strlen( $stderr ) > 20480000 )
222 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
223
224 $message_log .= "\n\n\nStdout Contents\n\n" .
225 $stdout .
226 "\n\n\nStderr Contents\n\n" .
227 $stderr .
228 "\n\n\nGFAC Status: $status\n" .
229 "GFAC message field: $queue_msg\n";
230
231 // Delete data from GFAC DB
232 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
233
234 $result = mysql_query( $query, $gfac_link );
235
236 if ( ! $result )
237 {
238 // Just log it and continue
239 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
240 }
241
242 // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
243 global $submit_dir;
244
245 // Get the request guid (LIMS submit dir name)
246 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
247 "WHERE HPCAnalysisRequestID = $requestID ";
248 $result = mysql_query( $query, $us3_link );
249
250 if ( ! $result )
251 {
252 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
253 }
254
255 list( $requestGUID ) = mysql_fetch_array( $result );
256 $output_dir = "$submit_dir/$requestGUID";
257
258 // Try to create it if necessary, and write the file
259 // Let's use FILE_APPEND, in case this is the second time around and the
260 // GFAC job status was INSERTed, rather than UPDATEd
261 if ( ! is_dir( $output_dir ) )
262 mkdir( $output_dir, 0775, true );
263 $message_filename = "$output_dir/$db-$requestID-messages.txt";
264 file_put_contents( $message_filename, $message_log, FILE_APPEND );
265 // mysql_close( $gfac_link );
266
267 /////////
268 // Insert data into HPCAnalysis
269
270 $query = "UPDATE HPCAnalysisResult SET " .
271 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
272 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " .
273 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
274
275 $result = mysql_query( $query, $us3_link );
276
277 if ( ! $result )
278 {
279 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
280 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
281 return( -1 );
282 }
283
284 // Save the tarfile and expand it
285
286 if ( strlen( $tarfile ) == 0 )
287 {
288 write_log( "$me: No tarfile" );
289 mail_to_user( "fail", "No results" );
290 return( -1 );
291 }
292
293 // Shouldn't happen
294 if ( ! is_dir( "$work" ) )
295 {
296 write_log( "$me: $work directory does not exist" );
297 mail_to_user( "fail", "$work directory does not exist" );
298 return( -1 );
299 }
300
301 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
302 chdir( "$work/$gfacID" );
303
304 $f = fopen( "analysis.tar", "w" );
305 fwrite( $f, $tarfile );
306 fclose( $f );
307
308 $tar_out = array();
309 exec( "tar -xf analysis.tar 2>&1", $tar_out, $err );
310
311 if ( $err != 0 )
312 {
313 chdir( $work );
314 exec( "rm -r $gfacID" );
315 $output = implode( "\n", $tar_out );
316
317 write_log( "$me: Bad output tarfile: $output" );
318 mail_to_user( "fail", "Bad output file" );
319 return( -1 );
320 }
321
322 // Insert the model files and noise files
323 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
324 $noiseIDs = array();
325 $modelGUIDs = array();
326
327 foreach ( $files as $file )
328 {
329 $split = explode( ";", $file );
330
331 if ( count( $split ) > 1 )
332 {
333 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
334
335 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
336 list( $other, $variance ) = explode( "=", $variance );
337 list( $other, $meniscus ) = explode( "=", $meniscus );
338 }
339 else
340 $fn = $file;
341
342 if ( filesize( $fn ) < 100 )
343 {
344 write_log( "$me:fn is invalid $fn" );
345 mail_to_user( "fail", "Internal error\n$fn is invalid" );
346 return( -1 );
347 }
348
349 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
350 {
351 $xml = file_get_contents( $fn );
352 $statistics = parse_xml( $xml, 'statistics' );
353 $otherdata = parse_xml( $xml, 'id' );
354
355 $query = "UPDATE HPCAnalysisResult SET " .
356 "wallTime = {$statistics['walltime']}, " .
357 "CPUTime = {$statistics['cputime']}, " .
358 "CPUCount = {$statistics['cpucount']}, " .
359 "max_rss = {$statistics['maxmemory']}, " .
360 "startTime = '{$otherdata['starttime']}', " .
361 "endTime = '{$otherdata['endtime']}', " .
362 "mgroupcount = {$otherdata['groupcount']} " .
363 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
364 $result = mysql_query( $query, $us3_link );
365
366 if ( ! $result )
367 {
368 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
369 }
370
371 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
372
373 }
374
375 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
376 {
377 $xml = file_get_contents( $fn );
378 $noise_data = parse_xml( $xml, "noise" );
379 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
380 $desc = $noise_data[ 'description' ];
381 $modelGUID = $noise_data[ 'modelGUID' ];
382 $noiseGUID = $noise_data[ 'noiseGUID' ];
383
384 $query = "INSERT INTO noise SET " .
385 "noiseGUID='$noiseGUID'," .
386 "modelGUID='$modelGUID'," .
387 "editedDataID=1, " .
388 "modelID=1, " .
389 "noiseType='$type'," .
390 "description='$desc'," .
391 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
392
393 // Add later after all files are processed: editDataID, modelID
394
395 $result = mysql_query( $query, $us3_link );
396
397 if ( ! $result )
398 {
399 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
400 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
401 return( -1 );
402 }
403
404 $id = mysql_insert_id( $us3_link );
405 $file_type = "noise";
406 $noiseIDs[] = $id;
407
408 // Keep track of modelGUIDs for later, when we replace them
409 $modelGUIDs[ $id ] = $modelGUID;
410
411 }
412 else // It's a model file
413 {
414 $xml = file_get_contents( $fn );
415 $model_data = parse_xml( $xml, "model" );
416 $description = $model_data[ 'description' ];
417 $modelGUID = $model_data[ 'modelGUID' ];
418 $editGUID = $model_data[ 'editGUID' ];
419
420 $query = "INSERT INTO model SET " .
421 "modelGUID='$modelGUID'," .
422 "editedDataID=" .
423 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
424 "description='$description'," .
425 "MCIteration='$mc_iteration'," .
426 "meniscus='$meniscus'," .
427 "variance='$variance'," .
428 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
429
430 $result = mysql_query( $query, $us3_link );
431
432 if ( ! $result )
433 {
434 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
435 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
436 return( -1 );
437 }
438
439 $modelID = mysql_insert_id( $us3_link );
440 $id = $modelID;
441 $file_type = "model";
442
443 $query = "INSERT INTO modelPerson SET " .
444 "modelID=$modelID, personID=$personID";
445 $result = mysql_query( $query, $us3_link );
446 }
447
448 $query = "INSERT INTO HPCAnalysisResultData SET " .
449 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
450 "HPCAnalysisResultType='$file_type', " .
451 "resultID=$id";
452
453 $result = mysql_query( $query, $us3_link );
454
455 if ( ! $result )
456 {
457 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
458 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
459 return( -1 );
460 }
461 }
462
463 // Now fix up noise entries
464 // For noise files, there is, at most two: ti_noise and ri_noise
465 // In this case there will only be one modelID
466
467 foreach ( $noiseIDs as $noiseID )
468 {
469 $modelGUID = $modelGUIDs[ $noiseID ];
470 $query = "UPDATE noise SET " .
471 "editedDataID=" .
472 "(SELECT editedDataID FROM model WHERE modelGUID='$modelGUID')," .
473 "modelID=" .
474 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
475 "WHERE noiseID=$noiseID";
476
477 $result = mysql_query( $query, $us3_link );
478
479 if ( ! $result )
480 {
481 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
482 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
483 return( -1 );
484 }
485 }
486
487 // Copy results to LIMS submit directory (files there are deleted after 7 days)
488 global $submit_dir; // LIMS submit files dir
489
490 // Get the request guid (LIMS submit dir name)
491 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
492 "WHERE HPCAnalysisRequestID = $requestID ";
493 $result = mysql_query( $query, $us3_link );
494
495 if ( ! $result )
496 {
497 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
498 }
499
500 list( $requestGUID ) = mysql_fetch_array( $result );
501
502 chdir( "$submit_dir/$requestGUID" );
503 $f = fopen( "analysis.tar", "w" );
504 fwrite( $f, $tarfile );
505 fclose( $f );
506
507 // Clean up
508 chdir ( $work );
509 // exec( "rm -rf $gfacID" );
510
511 mysql_close( $us3_link );
512
513 /////////
514 // Send email
515
516 mail_to_user( "success", "" );
517}
518
519function mail_to_user( $type, $msg )
520{
521 // Note to me. Just changed subject line to include a modified $status instead
522 // of the $type variable passed. More informative than just "fail" or "success."
523 // See how it works for awhile and then consider removing $type parameter from
524 // function.
525 global $email_address;
526 global $submittime;
527 global $queuestatus;
528 global $status;
529 global $cluster;
530 global $jobtype;
531 global $org_name;
532 global $admin_email;
533 global $db;
534 global $dbhost;
535 global $requestID;
536 global $gfacID;
537 global $editXMLFilename;
538 global $stdout;
539
540global $me;
541write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
542
543 // Get GFAC status and message
544 // function get_gfac_message() also sets global $status
545 $gfac_message = get_gfac_message( $gfacID );
546 if ( $gfac_message === false ) $gfac_message = "";
547
548 // Create a status to put in the subject line
549 switch ( $status )
550 {
551 case "COMPLETE":
552 $subj_status = 'completed';
553 break;
554
555 case "CANCELLED":
556 case "CANCELED":
557 $subj_status = 'canceled';
558 break;
559
560 case "FAILED":
561 $subj_status = 'failed';
562 break;
563
564 case "ERROR":
565 $subj_status = 'unknown error';
566 break;
567
568 default:
569 $subj_status = $status; // For now
570 break;
571
572 }
573
574 // Parse the editXMLFilename
575 list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
576 explode( ".", $editXMLFilename );
577
578 $headers = "From: $org_name Admin<$admin_email>" . "\n";
579 $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
580
581 // Set the reply address
582 $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
583 $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
584
585 // Try to avoid spam filters
586 $now = time();
587 $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
588 $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
589 $headers .= "MIME-Version: 1.0" . "\n";
590 $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
591
592 $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
593 $message = "
594 Your UltraScan job is complete:
595
596 Submission Time : $submittime
597 Analysis ID : $gfacID
598 Request ID : $requestID ( $db )
599 RunID : $runID
600 EditID : $editID
601 Data Type : $dataType
602 Cell/Channel/Wl : $cell / $channel / $wl
603 Status : $queuestatus
604 Cluster : $cluster
605 Job Type : $jobtype
606 GFAC Status : $status
607 GFAC Message : $gfac_message
608 Stdout : $stdout
609 ";
610
611 if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
612
613 // Handle the error case where an error occurs before fetching the
614 // user's email address
615 if ( $email_address == "" ) $email_address = $admin_email;
616
617 mail( $email_address, $subject, $message, $headers );
618}
619
620function parse_xml( $xml, $type )
621{
622 $parser = new XMLReader();
623 $parser->xml( $xml );
624
625 $results = array();
626
627 while ( $parser->read() )
628 {
629 if ( $parser->name == $type )
630 {
631 while ( $parser->moveToNextAttribute() )
632 {
633 $results[ $parser->name ] = $parser->value;
634 }
635
636 break;
637 }
638 }
639
640 $parser->close();
641 return $results;
642}
643
644// Function to get information about the current job GFAC
645function get_gfac_message( $gfacID )
646{
647 global $serviceURL;
648 global $me;
649
650 $hex = "[0-9a-fA-F]";
651 if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
652 ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
653 {
654 // Then it's not a GFAC job
655 return false;
656 }
657
658 $url = "$serviceURL/jobstatus/$gfacID";
659 try
660 {
661 $post = new HttpRequest( $url, HttpRequest::METH_GET );
662 $http = $post->send();
663 $xml = $post->getResponseBody();
664 }
665 catch ( HttpException $e )
666 {
667 write_log( "$me: Job status not available - $gfacID" );
668 return false;
669 }
670
671 // Parse the result
672 $gfac_message = parse_message( $xml );
673
674 return $gfac_message;
675}
676
677function parse_message( $xml )
678{
679 global $status;
680 $status = "";
681 $gfac_message = "";
682
683 $parser = new XMLReader();
684 $parser->xml( $xml );
685
686 $results = array();
687
688 while( $parser->read() )
689 {
690 $type = $parser->nodeType;
691
692 if ( $type == XMLReader::ELEMENT )
693 $name = $parser->name;
694
695 else if ( $type == XMLReader::TEXT )
696 {
697 if ( $name == "status" )
698 $status = $parser->value;
699 else
700 $gfac_message = $parser->value;
701 }
702 }
703
704 $parser->close();
705 return $gfac_message;
706}
707
708function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
709{
710 global $work;
711 global $work_remote;
712 global $me;
713 global $db;
714 global $status;
715
716 // Figure out local working directory
717 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
718 $pwd = chdir( "$work/$gfacID" );
719
720 // Figure out remote directory
721 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
722
723 // Get stdout, stderr, output/analysis-results.tar
724 $output = array();
725// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
726//
727// exec( $cmd, $output, $stat );
728// if ( $stat != 0 )
729// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
730//
731// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
732// exec( $cmd, $output, $stat );
733// if ( $stat != 0 )
734// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
735
736 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
737 exec( $cmd, $output, $stat );
738 if ( $stat != 0 )
739 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
740
741 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
742 exec( $cmd, $output, $stat );
743 if ( $stat != 0 )
744 {
745 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
746 sleep( 10 );
747 write_log( "$me: RETRY" );
748 exec( $cmd, $output, $stat );
749 if ( $stat != 0 )
750 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
751 }
752
753 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
754 exec( $cmd, $output, $stat );
755 if ( $stat != 0 )
756 {
757 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
758 sleep( 10 );
759 write_log( "$me: RETRY" );
760 exec( $cmd, $output, $stat );
761 if ( $stat != 0 )
762 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
763 }
764
765 // Write the files to gfacDB
766
767 if ( file_exists( "stderr" ) ) $stderr = file_get_contents( "stderr" );
768 if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
769 if ( file_exists( "analysis-results.tar" ) )
770 $tarfile = file_get_contents( "analysis-results.tar" );
771
772 $query = "UPDATE analysis SET " .
773 "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
774 "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
775 "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
776
777 $result = mysql_query( $query, $gfac_link );
778
779 if ( ! $result )
780 {
781 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
782 echo "Bad query\n";
783 return( -1 );
784 }
785}
786?>
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