source: trunk/cleanup.php@ 5

Last change on this file since 5 was 5, checked in by us3, 11 years ago

Include STDOUT in EOJ email
File size: 23.7 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 "/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, $requestID, $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
37 $db = $us3_db;
38 write_log( "$me: debug db=$db; requestID=$requestID" );
39
40 $us3_link = mysql_connect( $dbhost, $user, $passwd );
41
42 if ( ! $us3_link )
43 {
44 write_log( "$me: could not connect: $dbhost, $user, $passwd" );
45 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
46 return( -1 );
47 }
48
49 $result = mysql_select_db( $db, $us3_link );
50
51 if ( ! $result )
52 {
53 write_log( "$me: could not select DB $db" );
54 mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
55 return( -1 );
56 }
57
58 // First get basic info for email messages
59 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
60 "WHERE HPCAnalysisRequestID=$requestID";
61 $result = mysql_query( $query, $us3_link );
62
63 if ( ! $result )
64 {
65 write_log( "$me: Bad query: $query" );
66 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
67 return( -1 );
68 }
69
70 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
71
72 $query = "SELECT personID FROM people " .
73 "WHERE personGUID='$investigatorGUID'";
74 $result = mysql_query( $query, $us3_link );
75
76 list( $personID ) = mysql_fetch_array( $result );
77
78 /*
79 $query = "SELECT clusterName, submitTime, queueStatus, method " .
80 "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
81 "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
82 "WHERE h.HPCAnalysisRequestID=$requestID";
83 */
84 $query = "SELECT clusterName, submitTime, queueStatus, method " .
85 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
86 "WHERE h.HPCAnalysisRequestID=$requestID " .
87 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
88
89 $result = mysql_query( $query, $us3_link );
90
91 if ( ! $result )
92 {
93 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
94 return( -1 );
95 }
96
97 if ( mysql_num_rows( $result ) == 0 )
98 {
99 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
100 return( -1 );
101 }
102
103 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
104
105 // Get the GFAC ID
106 $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
107 "WHERE HPCAnalysisRequestID=$requestID";
108
109 $result = mysql_query( $query, $us3_link );
110
111 if ( ! $result )
112 {
113 write_log( "$me: Bad query: $query" );
114 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
115 return( -1 );
116 }
117
118 list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
119
120 ////////
121 // Get data from global GFAC DB and insert it into US3 DB
122 // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
123
124 $result = mysql_select_db( $gDB, $gfac_link );
125
126 if ( ! $result )
127 {
128 write_log( "$me: Could not connect to DB $gDB" );
129 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
130 return( -1 );
131 }
132
133 $query = "SELECT status, cluster, id FROM analysis " .
134 "WHERE gfacID='$gfacID'";
135
136 $result = mysql_query( $query, $gfac_link );
137 if ( ! $result )
138 {
139 write_log( "$me: Could not select GFAC status for $gfacID" );
140 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
141 return( -1 );
142 }
143
144 list( $status, $cluster, $id ) = mysql_fetch_array( $result );
145
146 if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
147 {
148 $clushost = $cluster;
149 $clushost = preg_replace( "/\-local/", "", $clushost );
150 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
151 }
152
153 $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
154 "WHERE gfacID='$gfacID'";
155
156 $result = mysql_query( $query, $gfac_link );
157
158 if ( ! $result )
159 {
160 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
161 mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
162 return( -1 );
163 }
164
165 list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
166
167 // Save queue messages for post-mortem analysis
168 $query = "SELECT message, time FROM queue_messages " .
169 "WHERE analysisID = $analysisID " .
170 "ORDER BY time ";
171 $result = mysql_query( $query, $gfac_link );
172
173 if ( ! $result )
174 {
175 // Just log it and continue
176 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
177 }
178
179 $now = date( 'Y-m-d H:i:s' );
180 $message_log = "US3 DB: $db\n" .
181 "RequestID: $requestID\n" .
182 "GFAC ID: $gfacID\n" .
183 "Processed: $now\n\n" .
184 "Queue Messages\n\n" ;
185 if ( mysql_num_rows( $result ) > 0 )
186 {
187 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
188 $message_log .= "$time $message\n";
189 }
190
191 $query = "DELETE FROM queue_messages " .
192 "WHERE analysisID = $analysisID ";
193
194 $result = mysql_query( $query, $gfac_link );
195
196 if ( ! $result )
197 {
198 // Just log it and continue
199 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
200 }
201
202 // Save stdout, stderr, etc. for message log
203 $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
204 "WHERE gfacID='$gfacID' ";
205 $result = mysql_query( $query, $gfac_link );
206 try
207 {
208 // What if this is too large?
209 list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
210 }
211 catch ( Exception $e )
212 {
213 write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
214 // Just go ahead and clean up
215 }
216
217 // But let's allow for investigation of other large stdout and/or stderr
218 if ( strlen( $stdout ) > 20480000 ||
219 strlen( $stderr ) > 20480000 )
220 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
221
222 $message_log .= "\n\n\nStdout Contents\n\n" .
223 $stdout .
224 "\n\n\nStderr Contents\n\n" .
225 $stderr .
226 "\n\n\nGFAC Status: $status\n" .
227 "GFAC message field: $queue_msg\n";
228
229 // Delete data from GFAC DB
230 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
231
232 $result = mysql_query( $query, $gfac_link );
233
234 if ( ! $result )
235 {
236 // Just log it and continue
237 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
238 }
239
240 // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
241 global $submit_dir;
242
243 // Get the request guid (LIMS submit dir name)
244 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
245 "WHERE HPCAnalysisRequestID = $requestID ";
246 $result = mysql_query( $query, $us3_link );
247
248 if ( ! $result )
249 {
250 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
251 }
252
253 list( $requestGUID ) = mysql_fetch_array( $result );
254 $output_dir = "$submit_dir/$requestGUID";
255
256 // Try to create it if necessary, and write the file
257 // Let's use FILE_APPEND, in case this is the second time around and the
258 // GFAC job status was INSERTed, rather than UPDATEd
259 if ( ! is_dir( $output_dir ) )
260 mkdir( $output_dir, 0775, true );
261 $message_filename = "$output_dir/$db-$requestID-messages.txt";
262 file_put_contents( $message_filename, $message_log, FILE_APPEND );
263 // mysql_close( $gfac_link );
264
265 /////////
266 // Insert data into HPCAnalysis
267
268 $query = "UPDATE HPCAnalysisResult SET " .
269 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
270 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " .
271 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
272
273 $result = mysql_query( $query, $us3_link );
274
275 if ( ! $result )
276 {
277 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
278 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
279 return( -1 );
280 }
281
282 // Save the tarfile and expand it
283
284 if ( strlen( $tarfile ) == 0 )
285 {
286 write_log( "$me: No tarfile" );
287 mail_to_user( "fail", "No results" );
288 return( -1 );
289 }
290
291 // Shouldn't happen
292 if ( ! is_dir( "$work" ) )
293 {
294 write_log( "$me: $work directory does not exist" );
295 mail_to_user( "fail", "$work directory does not exist" );
296 return( -1 );
297 }
298
299 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
300 chdir( "$work/$gfacID" );
301
302 $f = fopen( "analysis.tar", "w" );
303 fwrite( $f, $tarfile );
304 fclose( $f );
305
306 $tar_out = array();
307 exec( "tar -xf analysis.tar 2>&1", $tar_out, $err );
308
309 if ( $err != 0 )
310 {
311 chdir( $work );
312 exec( "rm -r $gfacID" );
313 $output = implode( "\n", $tar_out );
314
315 write_log( "$me: Bad output tarfile: $output" );
316 mail_to_user( "fail", "Bad output file" );
317 return( -1 );
318 }
319
320 // Insert the model files and noise files
321 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
322 $noiseIDs = array();
323 $modelGUIDs = array();
324
325 foreach ( $files as $file )
326 {
327 $split = explode( ";", $file );
328
329 if ( count( $split ) > 1 )
330 {
331 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
332
333 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
334 list( $other, $variance ) = explode( "=", $variance );
335 list( $other, $meniscus ) = explode( "=", $meniscus );
336 }
337 else
338 $fn = $file;
339
340 if ( filesize( $fn ) < 100 )
341 {
342 write_log( "$me:fn is invalid $fn" );
343 mail_to_user( "fail", "Internal error\n$fn is invalid" );
344 return( -1 );
345 }
346
347 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
348 {
349 $xml = file_get_contents( $fn );
350 $statistics = parse_xml( $xml, 'statistics' );
351 $otherdata = parse_xml( $xml, 'id' );
352
353 $query = "UPDATE HPCAnalysisResult SET " .
354 "wallTime = {$statistics['walltime']}, " .
355 "CPUTime = {$statistics['cputime']}, " .
356 "CPUCount = {$statistics['cpucount']}, " .
357 "max_rss = {$statistics['maxmemory']}, " .
358 "startTime = '{$otherdata['starttime']}', " .
359 "endTime = '{$otherdata['endtime']}', " .
360 "mgroupcount = {$otherdata['groupcount']} " .
361 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
362 $result = mysql_query( $query, $us3_link );
363
364 if ( ! $result )
365 {
366 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
367 }
368
369 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
370
371 }
372
373 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
374 {
375 $xml = file_get_contents( $fn );
376 $noise_data = parse_xml( $xml, "noise" );
377 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
378 $desc = $noise_data[ 'description' ];
379 $modelGUID = $noise_data[ 'modelGUID' ];
380 $noiseGUID = $noise_data[ 'noiseGUID' ];
381
382 $query = "INSERT INTO noise SET " .
383 "noiseGUID='$noiseGUID'," .
384 "modelGUID='$modelGUID'," .
385 "editedDataID=1, " .
386 "modelID=1, " .
387 "noiseType='$type'," .
388 "description='$desc'," .
389 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
390
391 // Add later after all files are processed: editDataID, modelID
392
393 $result = mysql_query( $query, $us3_link );
394
395 if ( ! $result )
396 {
397 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
398 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
399 return( -1 );
400 }
401
402 $id = mysql_insert_id( $us3_link );
403 $file_type = "noise";
404 $noiseIDs[] = $id;
405
406 // Keep track of modelGUIDs for later, when we replace them
407 $modelGUIDs[ $id ] = $modelGUID;
408
409 }
410 else // It's a model file
411 {
412 $xml = file_get_contents( $fn );
413 $model_data = parse_xml( $xml, "model" );
414 $description = $model_data[ 'description' ];
415 $modelGUID = $model_data[ 'modelGUID' ];
416 $editGUID = $model_data[ 'editGUID' ];
417
418 $query = "INSERT INTO model SET " .
419 "modelGUID='$modelGUID'," .
420 "editedDataID=" .
421 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
422 "description='$description'," .
423 "MCIteration='$mc_iteration'," .
424 "meniscus='$meniscus'," .
425 "variance='$variance'," .
426 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
427
428 $result = mysql_query( $query, $us3_link );
429
430 if ( ! $result )
431 {
432 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
433 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
434 return( -1 );
435 }
436
437 $modelID = mysql_insert_id( $us3_link );
438 $id = $modelID;
439 $file_type = "model";
440
441 $query = "INSERT INTO modelPerson SET " .
442 "modelID=$modelID, personID=$personID";
443 $result = mysql_query( $query, $us3_link );
444 }
445
446 $query = "INSERT INTO HPCAnalysisResultData SET " .
447 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
448 "HPCAnalysisResultType='$file_type', " .
449 "resultID=$id";
450
451 $result = mysql_query( $query, $us3_link );
452
453 if ( ! $result )
454 {
455 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
456 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
457 return( -1 );
458 }
459 }
460
461 // Now fix up noise entries
462 // For noise files, there is, at most two: ti_noise and ri_noise
463 // In this case there will only be one modelID
464
465 foreach ( $noiseIDs as $noiseID )
466 {
467 $modelGUID = $modelGUIDs[ $noiseID ];
468 $query = "UPDATE noise SET " .
469 "editedDataID=" .
470 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
471 "modelID=" .
472 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
473 "WHERE noiseID=$noiseID";
474
475 $result = mysql_query( $query, $us3_link );
476
477 if ( ! $result )
478 {
479 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
480 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
481 return( -1 );
482 }
483 }
484
485 // Copy results to LIMS submit directory (files there are deleted after 7 days)
486 global $submit_dir; // LIMS submit files dir
487
488 // Get the request guid (LIMS submit dir name)
489 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
490 "WHERE HPCAnalysisRequestID = $requestID ";
491 $result = mysql_query( $query, $us3_link );
492
493 if ( ! $result )
494 {
495 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
496 }
497
498 list( $requestGUID ) = mysql_fetch_array( $result );
499
500 chdir( "$submit_dir/$requestGUID" );
501 $f = fopen( "analysis.tar", "w" );
502 fwrite( $f, $tarfile );
503 fclose( $f );
504
505 // Clean up
506 chdir ( $work );
507 // exec( "rm -rf $gfacID" );
508
509 mysql_close( $us3_link );
510
511 /////////
512 // Send email
513
514 mail_to_user( "success", "" );
515}
516
517function mail_to_user( $type, $msg )
518{
519 // Note to me. Just changed subject line to include a modified $status instead
520 // of the $type variable passed. More informative than just "fail" or "success."
521 // See how it works for awhile and then consider removing $type parameter from
522 // function.
523 global $email_address;
524 global $submittime;
525 global $queuestatus;
526 global $status;
527 global $cluster;
528 global $jobtype;
529 global $org_name;
530 global $admin_email;
531 global $dbhost;
532 global $requestID;
533 global $gfacID;
534 global $editXMLFilename;
535 global $stdout;
536
537global $me;
538write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
539
540 // Get GFAC status and message
541 // function get_gfac_message() also sets global $status
542 $gfac_message = get_gfac_message( $gfacID );
543 if ( $gfac_message === false ) $gfac_message = "";
544
545 // Create a status to put in the subject line
546 switch ( $status )
547 {
548 case "COMPLETE":
549 $subj_status = 'completed';
550 break;
551
552 case "CANCELLED":
553 case "CANCELED":
554 $subj_status = 'canceled';
555 break;
556
557 case "FAILED":
558 $subj_status = 'failed';
559 break;
560
561 case "ERROR":
562 $subj_status = 'unknown error';
563 break;
564
565 default:
566 $subj_status = $status; // For now
567 break;
568
569 }
570
571 // Parse the editXMLFilename
572 list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
573 explode( ".", $editXMLFilename );
574
575 $headers = "From: $org_name Admin<$admin_email>" . "\n";
576 $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
577
578 // Set the reply address
579 $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
580 $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
581
582 // Try to avoid spam filters
583 $now = time();
584 $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
585 $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
586 $headers .= "MIME-Version: 1.0" . "\n";
587 $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
588
589 $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
590 $message = "
591 Your UltraScan job is complete:
592
593 Submission Time : $submittime
594 Analysis ID : $gfacID
595 RunID : $runID
596 EditID : $editID
597 Data Type : $dataType
598 Cell/Channel/Wl : $cell / $channel / $wl
599 Status : $queuestatus
600 Cluster : $cluster
601 Job Type : $jobtype
602 GFAC Status : $status
603 GFAC Message : $gfac_message
604 Stdout : $stdout
605 ";
606
607 if ( $type != "success" ) $message .= "Grid Ctrl Error : $msg\n";
608
609 // Handle the error case where an error occurs before fetching the
610 // user's email address
611 if ( $email_address == "" ) $email_address = $admin_email;
612
613 mail( $email_address, $subject, $message, $headers );
614}
615
616function parse_xml( $xml, $type )
617{
618 $parser = new XMLReader();
619 $parser->xml( $xml );
620
621 $results = array();
622
623 while ( $parser->read() )
624 {
625 if ( $parser->name == $type )
626 {
627 while ( $parser->moveToNextAttribute() )
628 {
629 $results[ $parser->name ] = $parser->value;
630 }
631
632 break;
633 }
634 }
635
636 $parser->close();
637 return $results;
638}
639
640// Function to get information about the current job GFAC
641function get_gfac_message( $gfacID )
642{
643 global $serviceURL;
644 global $me;
645
646 $hex = "[0-9a-fA-F]";
647 if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
648 ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
649 {
650 // Then it's not a GFAC job
651 return false;
652 }
653
654 $url = "$serviceURL/jobstatus/$gfacID";
655 try
656 {
657 $post = new HttpRequest( $url, HttpRequest::METH_GET );
658 $http = $post->send();
659 $xml = $post->getResponseBody();
660 }
661 catch ( HttpException $e )
662 {
663 write_log( "$me: Job status not available - $gfacID" );
664 return false;
665 }
666
667 // Parse the result
668 $gfac_message = parse_message( $xml );
669
670 return $gfac_message;
671}
672
673function parse_message( $xml )
674{
675 global $status;
676 $status = "";
677 $gfac_message = "";
678
679 $parser = new XMLReader();
680 $parser->xml( $xml );
681
682 $results = array();
683
684 while( $parser->read() )
685 {
686 $type = $parser->nodeType;
687
688 if ( $type == XMLReader::ELEMENT )
689 $name = $parser->name;
690
691 else if ( $type == XMLReader::TEXT )
692 {
693 if ( $name == "status" )
694 $status = $parser->value;
695 else
696 $gfac_message = $parser->value;
697 }
698 }
699
700 $parser->close();
701 return $gfac_message;
702}
703
704function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
705{
706 global $work;
707 global $work_remote;
708 global $me;
709 global $db;
710 global $status;
711
712 // Figure out local working directory
713 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
714 $pwd = chdir( "$work/$gfacID" );
715
716 // Figure out remote directory
717 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
718
719 // Get stdout, stderr, output/analysis-results.tar
720 $output = array();
721// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
722//
723// exec( $cmd, $output, $stat );
724// if ( $stat != 0 )
725// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
726//
727// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
728// exec( $cmd, $output, $stat );
729// if ( $stat != 0 )
730// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
731
732 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
733 exec( $cmd, $output, $stat );
734 if ( $stat != 0 )
735 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
736
737 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
738 exec( $cmd, $output, $stat );
739 if ( $stat != 0 )
740 {
741 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
742 sleep( 10 );
743 write_log( "$me: RETRY" );
744 exec( $cmd, $output, $stat );
745 if ( $stat != 0 )
746 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
747 }
748
749 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
750 exec( $cmd, $output, $stat );
751 if ( $stat != 0 )
752 {
753 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
754 sleep( 10 );
755 write_log( "$me: RETRY" );
756 exec( $cmd, $output, $stat );
757 if ( $stat != 0 )
758 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
759 }
760
761 // Write the files to gfacDB
762
763 if ( file_exists( "stderr" ) ) $stderr = file_get_contents( "stderr" );
764 if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
765 if ( file_exists( "analysis-results.tar" ) )
766 $tarfile = file_get_contents( "analysis-results.tar" );
767
768 $query = "UPDATE analysis SET " .
769 "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
770 "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
771 "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
772
773 $result = mysql_query( $query, $gfac_link );
774
775 if ( ! $result )
776 {
777 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
778 echo "Bad query\n";
779 return( -1 );
780 }
781}
782?>
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