source: trunk/cleanup.php@ 1

Last change on this file since 1 was 1, checked in by zollarsd, 13 years ago

Initial import
File size: 23.7 KB
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[1]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
17function gfac_cleanup( $us3_db, $requestID, $gfac_link )
18{
19 global $dbhost;
20 global $user;
21 global $passwd;
22 global $db;
23 global $guser;
24 global $gpasswd;
25 global $gDB;
26 global $me;
27 global $work;
28 global $email_address;
29 global $queuestatus;
30 global $jobtype;
31 global $editXMLFilename;
32 global $submittime;
33
34 $db = $us3_db;
35 write_log( "$me: debug db=$db; requestID=$requestID" );
36
37 $us3_link = mysql_connect( $dbhost, $user, $passwd );
38
39 if ( ! $us3_link )
40 {
41 write_log( "$me: could not connect: $dbhost, $user, $passwd" );
42 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
43 return( -1 );
44 }
45
46 $result = mysql_select_db( $db, $us3_link );
47
48 if ( ! $result )
49 {
50 write_log( "$me: could not select DB $db" );
51 mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
52 return( -1 );
53 }
54
55 // First get basic info for email messages
56 $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
57 "WHERE HPCAnalysisRequestID=$requestID";
58 $result = mysql_query( $query, $us3_link );
59
60 if ( ! $result )
61 {
62 write_log( "$me: Bad query: $query" );
63 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
64 return( -1 );
65 }
66
67 list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result );
68
69 $query = "SELECT personID FROM people " .
70 "WHERE personGUID='$investigatorGUID'";
71 $result = mysql_query( $query, $us3_link );
72
73 list( $personID ) = mysql_fetch_array( $result );
74
75 /*
76 $query = "SELECT clusterName, submitTime, queueStatus, method " .
77 "FROM HPCAnalysisRequest h LEFT JOIN HPCAnalysisResult " .
78 "ON h.HPCAnalysisRequestID=HPCAnalysisResult.HPCAnalysisRequestID " .
79 "WHERE h.HPCAnalysisRequestID=$requestID";
80 */
81 $query = "SELECT clusterName, submitTime, queueStatus, method " .
82 "FROM HPCAnalysisRequest h, HPCAnalysisResult r " .
83 "WHERE h.HPCAnalysisRequestID=$requestID " .
84 "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
85
86 $result = mysql_query( $query, $us3_link );
87
88 if ( ! $result )
89 {
90 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
91 return( -1 );
92 }
93
94 if ( mysql_num_rows( $result ) == 0 )
95 {
96 write_log( "$me: US3 Table error - No records for requestID: $requestID" );
97 return( -1 );
98 }
99
100 list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
101
102 // Get the GFAC ID
103 $query = "SELECT HPCAnalysisResultID, gfacID FROM HPCAnalysisResult " .
104 "WHERE HPCAnalysisRequestID=$requestID";
105
106 $result = mysql_query( $query, $us3_link );
107
108 if ( ! $result )
109 {
110 write_log( "$me: Bad query: $query" );
111 mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
112 return( -1 );
113 }
114
115 list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result );
116
117 ////////
118 // Get data from global GFAC DB and insert it into US3 DB
119 // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
120
121 $result = mysql_select_db( $gDB, $gfac_link );
122
123 if ( ! $result )
124 {
125 write_log( "$me: Could not connect to DB $gDB" );
126 mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
127 return( -1 );
128 }
129
130 $query = "SELECT status, cluster, id FROM analysis " .
131 "WHERE gfacID='$gfacID'";
132
133 $result = mysql_query( $query, $gfac_link );
134 if ( ! $result )
135 {
136 write_log( "$me: Could not select GFAC status for $gfacID" );
137 mail_to_user( "fail", "Could not select GFAC status for $gfacID" );
138 return( -1 );
139 }
140
141 list( $status, $cluster, $id ) = mysql_fetch_array( $result );
142
143 if ( $cluster == 'bcf-local' || $cluster == 'alamo-local' )
144 {
145 $clushost = $cluster;
146 $clushost = preg_replace( "/\-local/", "", $clushost );
147 get_local_files( $gfac_link, $clushost, $requestID, $id, $gfacID );
148 }
149
150 $query = "SELECT id, stderr, stdout, tarfile FROM analysis " .
151 "WHERE gfacID='$gfacID'";
152
153 $result = mysql_query( $query, $gfac_link );
154
155 if ( ! $result )
156 {
157 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
158 mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
159 return( -1 );
160 }
161
162 list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
163
164 // Save queue messages for post-mortem analysis
165 $query = "SELECT message, time FROM queue_messages " .
166 "WHERE analysisID = $analysisID " .
167 "ORDER BY time ";
168 $result = mysql_query( $query, $gfac_link );
169
170 if ( ! $result )
171 {
172 // Just log it and continue
173 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
174 }
175
176 $now = date( 'Y-m-d H:i:s' );
177 $message_log = "US3 DB: $db\n" .
178 "RequestID: $requestID\n" .
179 "GFAC ID: $gfacID\n" .
180 "Processed: $now\n\n" .
181 "Queue Messages\n\n" ;
182 if ( mysql_num_rows( $result ) > 0 )
183 {
184 while ( list( $message, $time ) = mysql_fetch_array( $result ) )
185 $message_log .= "$time $message\n";
186 }
187
188 $query = "DELETE FROM queue_messages " .
189 "WHERE analysisID = $analysisID ";
190
191 $result = mysql_query( $query, $gfac_link );
192
193 if ( ! $result )
194 {
195 // Just log it and continue
196 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
197 }
198
199 // Save stdout, stderr, etc. for message log
200 $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
201 "WHERE gfacID='$gfacID' ";
202 $result = mysql_query( $query, $gfac_link );
203 try
204 {
205 // What if this is too large?
206 list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
207 }
208 catch ( Exception $e )
209 {
210 write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
211 // Just go ahead and clean up
212 }
213
214 // But let's allow for investigation of other large stdout and/or stderr
215 if ( strlen( $stdout ) > 20480000 ||
216 strlen( $stderr ) > 20480000 )
217 write_log( "$me: stdout + stderr larger than 20M - $gfacID\n" );
218
219 $message_log .= "\n\n\nStdout Contents\n\n" .
220 $stdout .
221 "\n\n\nStderr Contents\n\n" .
222 $stderr .
223 "\n\n\nGFAC Status: $status\n" .
224 "GFAC message field: $queue_msg\n";
225
226 // Delete data from GFAC DB
227 $query = "DELETE from analysis WHERE gfacID='$gfacID'";
228
229 $result = mysql_query( $query, $gfac_link );
230
231 if ( ! $result )
232 {
233 // Just log it and continue
234 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
235 }
236
237 // Copy queue messages to LIMS submit directory (files there are deleted after 7 days)
238 global $submit_dir;
239
240 // Get the request guid (LIMS submit dir name)
241 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
242 "WHERE HPCAnalysisRequestID = $requestID ";
243 $result = mysql_query( $query, $us3_link );
244
245 if ( ! $result )
246 {
247 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
248 }
249
250 list( $requestGUID ) = mysql_fetch_array( $result );
251 $output_dir = "$submit_dir/$requestGUID";
252
253 // Try to create it if necessary, and write the file
254 // Let's use FILE_APPEND, in case this is the second time around and the
255 // GFAC job status was INSERTed, rather than UPDATEd
256 if ( ! is_dir( $output_dir ) )
257 mkdir( $output_dir, 0775, true );
258 $message_filename = "$output_dir/$db-$requestID-messages.txt";
259 file_put_contents( $message_filename, $message_log, FILE_APPEND );
260 // mysql_close( $gfac_link );
261
262 /////////
263 // Insert data into HPCAnalysis
264
265 $query = "UPDATE HPCAnalysisResult SET " .
266 "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
267 "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " .
268 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
269
270 $result = mysql_query( $query, $us3_link );
271
272 if ( ! $result )
273 {
274 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
275 mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
276 return( -1 );
277 }
278
279 // Save the tarfile and expand it
280
281 if ( strlen( $tarfile ) == 0 )
282 {
283 write_log( "$me: No tarfile" );
284 mail_to_user( "fail", "No results" );
285 return( -1 );
286 }
287
288 // Shouldn't happen
289 if ( ! is_dir( "$work" ) )
290 {
291 write_log( "$me: $work directory does not exist" );
292 mail_to_user( "fail", "$work directory does not exist" );
293 return( -1 );
294 }
295
296 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
297 chdir( "$work/$gfacID" );
298
299 $f = fopen( "analysis.tar", "w" );
300 fwrite( $f, $tarfile );
301 fclose( $f );
302
303 $tar_out = array();
304 exec( "tar -xf analysis.tar 2>&1", $tar_out, $err );
305
306 if ( $err != 0 )
307 {
308 chdir( $work );
309 exec( "rm -r $gfacID" );
310 $output = implode( "\n", $tar_out );
311
312 write_log( "$me: Bad output tarfile: $output" );
313 mail_to_user( "fail", "Bad output file" );
314 return( -1 );
315 }
316
317 // Insert the model files and noise files
318 $files = file( "analysis_files.txt", FILE_IGNORE_NEW_LINES );
319 $noiseIDs = array();
320 $modelGUIDs = array();
321
322 foreach ( $files as $file )
323 {
324 $split = explode( ";", $file );
325
326 if ( count( $split ) > 1 )
327 {
328 list( $fn, $meniscus, $mc_iteration, $variance ) = explode( ";", $file );
329
330 list( $other, $mc_iteration ) = explode( "=", $mc_iteration );
331 list( $other, $variance ) = explode( "=", $variance );
332 list( $other, $meniscus ) = explode( "=", $meniscus );
333 }
334 else
335 $fn = $file;
336
337 if ( filesize( $fn ) < 100 )
338 {
339 write_log( "$me:fn is invalid $fn" );
340 mail_to_user( "fail", "Internal error\n$fn is invalid" );
341 return( -1 );
342 }
343
344 if ( preg_match( "/^job_statistics\.xml$/", $fn ) ) // Job statistics file
345 {
346 $xml = file_get_contents( $fn );
347 $statistics = parse_xml( $xml, 'statistics' );
348 $otherdata = parse_xml( $xml, 'id' );
349
350 $query = "UPDATE HPCAnalysisResult SET " .
351 "wallTime = {$statistics['walltime']}, " .
352 "CPUTime = {$statistics['cputime']}, " .
353 "CPUCount = {$statistics['cpucount']}, " .
354 "max_rss = {$statistics['maxmemory']}, " .
355 "startTime = '{$otherdata['starttime']}', " .
356 "endTime = '{$otherdata['endtime']}', " .
357 "mgroupcount = {$otherdata['groupcount']} " .
358 "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
359 $result = mysql_query( $query, $us3_link );
360
361 if ( ! $result )
362 {
363 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
364 }
365
366 file_put_contents( "$output_dir/$fn", $xml ); // Copy to submit dir
367
368 }
369
370 else if ( preg_match( "/\.noise/", $fn ) > 0 ) // It's a noise file
371 {
372 $xml = file_get_contents( $fn );
373 $noise_data = parse_xml( $xml, "noise" );
374 $type = ( $noise_data[ 'type' ] == "ri" ) ? "ri_noise" : "ti_noise";
375 $desc = $noise_data[ 'description' ];
376 $modelGUID = $noise_data[ 'modelGUID' ];
377 $noiseGUID = $noise_data[ 'noiseGUID' ];
378
379 $query = "INSERT INTO noise SET " .
380 "noiseGUID='$noiseGUID'," .
381 "modelGUID='$modelGUID'," .
382 "editedDataID=1, " .
383 "modelID=1, " .
384 "noiseType='$type'," .
385 "description='$desc'," .
386 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
387
388 // Add later after all files are processed: editDataID, modelID
389
390 $result = mysql_query( $query, $us3_link );
391
392 if ( ! $result )
393 {
394 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
395 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
396 return( -1 );
397 }
398
399 $id = mysql_insert_id( $us3_link );
400 $file_type = "noise";
401 $noiseIDs[] = $id;
402
403 // Keep track of modelGUIDs for later, when we replace them
404 $modelGUIDs[ $id ] = $modelGUID;
405
406 }
407 else // It's a model file
408 {
409 $xml = file_get_contents( $fn );
410 $model_data = parse_xml( $xml, "model" );
411 $description = $model_data[ 'description' ];
412 $modelGUID = $model_data[ 'modelGUID' ];
413 $editGUID = $model_data[ 'editGUID' ];
414
415 $query = "INSERT INTO model SET " .
416 "modelGUID='$modelGUID'," .
417 "editedDataID=" .
418 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
419 "description='$description'," .
420 "MCIteration='$mc_iteration'," .
421 "meniscus='$meniscus'," .
422 "variance='$variance'," .
423 "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
424
425 $result = mysql_query( $query, $us3_link );
426
427 if ( ! $result )
428 {
429 write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
430 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
431 return( -1 );
432 }
433
434 $modelID = mysql_insert_id( $us3_link );
435 $id = $modelID;
436 $file_type = "model";
437
438 $query = "INSERT INTO modelPerson SET " .
439 "modelID=$modelID, personID=$personID";
440 $result = mysql_query( $query, $us3_link );
441 }
442
443 $query = "INSERT INTO HPCAnalysisResultData SET " .
444 "HPCAnalysisResultID='$HPCAnalysisResultID', " .
445 "HPCAnalysisResultType='$file_type', " .
446 "resultID=$id";
447
448 $result = mysql_query( $query, $us3_link );
449
450 if ( ! $result )
451 {
452 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
453 mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
454 return( -1 );
455 }
456 }
457
458 // Now fix up noise entries
459 // For noise files, there is, at most two: ti_noise and ri_noise
460 // In this case there will only be one modelID
461
462 foreach ( $noiseIDs as $noiseID )
463 {
464 $modelGUID = $modelGUIDs[ $noiseID ];
465 $query = "UPDATE noise SET " .
466 "editedDataID=" .
467 "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
468 "modelID=" .
469 "(SELECT modelID FROM model WHERE modelGUID='$modelGUID')" .
470 "WHERE noiseID=$noiseID";
471
472 $result = mysql_query( $query, $us3_link );
473
474 if ( ! $result )
475 {
476 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
477 mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
478 return( -1 );
479 }
480 }
481
482 // Copy results to LIMS submit directory (files there are deleted after 7 days)
483 global $submit_dir; // LIMS submit files dir
484
485 // Get the request guid (LIMS submit dir name)
486 $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
487 "WHERE HPCAnalysisRequestID = $requestID ";
488 $result = mysql_query( $query, $us3_link );
489
490 if ( ! $result )
491 {
492 write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
493 }
494
495 list( $requestGUID ) = mysql_fetch_array( $result );
496
497 chdir( "$submit_dir/$requestGUID" );
498 $f = fopen( "analysis.tar", "w" );
499 fwrite( $f, $tarfile );
500 fclose( $f );
501
502 // Clean up
503 chdir ( $work );
504 // exec( "rm -rf $gfacID" );
505
506 mysql_close( $us3_link );
507
508 /////////
509 // Send email
510
511 mail_to_user( "success", "" );
512}
513
514function mail_to_user( $type, $msg )
515{
516 // Note to me. Just changed subject line to include a modified $status instead
517 // of the $type variable passed. More informative than just "fail" or "success."
518 // See how it works for awhile and then consider removing $type parameter from
519 // function.
520 global $email_address;
521 global $submittime;
522 global $queuestatus;
523 global $status;
524 global $cluster;
525 global $jobtype;
526 global $org_name;
527 global $admin_email;
528 global $dbhost;
529 global $requestID;
530 global $gfacID;
531 global $editXMLFilename;
532
533global $me;
534write_log( "$me mail_to_user(): sending email to $email_address for $gfacID" );
535
536 // Get GFAC status and message
537 // For right now, since we don't get clear and concise message
538 // $gfac_message = get_gfac_message( $gfacID );
539 // if ( $gfac_message === false ) $gfac_message = "";
540
541 // Create a status to put in the subject line
542 switch ( $status )
543 {
544 case "COMPLETE":
545 $subj_status = 'completed';
546 break;
547
548 case "CANCELLED":
549 case "CANCELED":
550 $subj_status = 'canceled';
551 break;
552
553 case "FAILED":
554 $subj_status = 'failed';
555 break;
556
557 case "ERROR":
558 $subj_status = 'unknown error';
559 break;
560
561 default:
562 $subj_status = $status; // For now
563 break;
564
565 }
566
567 // Parse the editXMLFilename
568 list( $runID, $editID, $dataType, $cell, $channel, $wl, $ext ) =
569 explode( ".", $editXMLFilename );
570
571 $headers = "From: $org_name Admin<$admin_email>" . "\n";
572 $headers .= "Cc: $org_name Admin<$admin_email>" . "\n";
573
574 // Set the reply address
575 $headers .= "Reply-To: $org_name<$admin_email>" . "\n";
576 $headers .= "Return-Path: $org_name<$admin_email>" . "\n";
577
578 // Try to avoid spam filters
579 $now = time();
580 $headers .= "Message-ID: <" . $now . "cleanup@$dbhost>\n";
581 $headers .= "X-Mailer: PHP v" . phpversion() . "\n";
582 $headers .= "MIME-Version: 1.0" . "\n";
583 $headers .= "Content-Transfer-Encoding: 8bit" . "\n";
584
585 $subject = "UltraScan Job Notification - $subj_status - " . substr( $gfacID, 0, 16 );
586 $message = "
587 Your UltraScan job is complete:
588
589 Submission Time : $submittime
590 Analysis ID : $gfacID
591 RunID : $runID
592 EditID : $editID
593 Data Type : $dataType
594 Cell/Channel/Wl : $cell / $channel / $wl
595 Status : $queuestatus
596 Cluster : $cluster
597 Job Type : $jobtype
598 GFAC Status : $status
599 ";
600
601 // This would change to ( $status != 'COMPLETE' ) or something like that.
602 if ( $type != "success" ) $message .= "Error Message : $msg\n";
603
604 // Handle the error case where an error occurs before fetching the
605 // user's email address
606 if ( $email_address == "" ) $email_address = $admin_email;
607
608 mail( $email_address, $subject, $message, $headers );
609}
610
611function parse_xml( $xml, $type )
612{
613 $parser = new XMLReader();
614 $parser->xml( $xml );
615
616 $results = array();
617
618 while ( $parser->read() )
619 {
620 if ( $parser->name == $type )
621 {
622 while ( $parser->moveToNextAttribute() )
623 {
624 $results[ $parser->name ] = $parser->value;
625 }
626
627 break;
628 }
629 }
630
631 $parser->close();
632 return $results;
633}
634
635// Function to get information about the current job GFAC
636function get_gfac_message( $gfacID )
637{
638 global $serviceURL;
639 global $me;
640
641 $hex = "[0-9a-fA-F]";
642 if ( ! preg_match( "/^US3-Experiment/i", $gfacID ) &&
643 ! preg_match( "/^US3-$hex{8}-$hex{4}-$hex{4}-$hex{4}-$hex{12}$/", $gfacID ) )
644 {
645 // Then it's not a GFAC job
646 return false;
647 }
648
649 $url = "$serviceURL/jobstatus/$gfacID";
650 try
651 {
652 $post = new HttpRequest( $url, HttpRequest::METH_GET );
653 $http = $post->send();
654 $xml = $post->getResponseBody();
655 }
656 catch ( HttpException $e )
657 {
658 write_log( "$me: Job status not available - $gfacID" );
659 return false;
660 }
661
662 // Parse the result
663 $gfac_message = parse_message( $xml );
664
665 return $gfac_message;
666}
667
668function parse_message( $xml )
669{
670 $status = "";
671 $gfac_message = "";
672
673 $parser = new XMLReader();
674 $parser->xml( $xml );
675
676 $results = array();
677
678 while( $parser->read() )
679 {
680 $type = $parser->nodeType;
681
682 if ( $type == XMLReader::ELEMENT )
683 $name = $parser->name;
684
685 else if ( $type == XMLReader::TEXT )
686 {
687 if ( $name == "status" )
688 $status = $parser->value;
689 else
690 $gfac_message = $parser->value;
691 }
692 }
693
694 $parser->close();
695 return $gfac_message;
696}
697
698function get_local_files( $gfac_link, $cluster, $requestID, $id, $gfacID )
699{
700 global $work;
701 global $work_remote;
702 global $me;
703 global $db;
704 global $status;
705
706 // Figure out local working directory
707 if ( ! is_dir( "$work/$gfacID" ) ) mkdir( "$work/$gfacID", 0770 );
708 $pwd = chdir( "$work/$gfacID" );
709
710 // Figure out remote directory
711 $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID );
712
713 // Get stdout, stderr, output/analysis-results.tar
714 $output = array();
715// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stdout . 2>&1";
716//
717// exec( $cmd, $output, $stat );
718// if ( $stat != 0 )
719// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
720//
721// $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
722// exec( $cmd, $output, $stat );
723// if ( $stat != 0 )
724// write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
725
726 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/output/analysis-results.tar . 2>&1";
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/stdout . 2>&1";
732 exec( $cmd, $output, $stat );
733 if ( $stat != 0 )
734 {
735 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
736 sleep( 10 );
737 write_log( "$me: RETRY" );
738 exec( $cmd, $output, $stat );
739 if ( $stat != 0 )
740 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
741 }
742
743 $cmd = "scp us3@$cluster.uthscsa.edu:$remoteDir/stderr . 2>&1";
744 exec( $cmd, $output, $stat );
745 if ( $stat != 0 )
746 {
747 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
748 sleep( 10 );
749 write_log( "$me: RETRY" );
750 exec( $cmd, $output, $stat );
751 if ( $stat != 0 )
752 write_log( "$me: Bad exec:\n$cmd\n" . implode( "\n", $output ) );
753 }
754
755 // Write the files to gfacDB
756
757 if ( file_exists( "stderr" ) ) $stderr = file_get_contents( "stderr" );
758 if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" );
759 if ( file_exists( "analysis-results.tar" ) )
760 $tarfile = file_get_contents( "analysis-results.tar" );
761
762 $query = "UPDATE analysis SET " .
763 "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," .
764 "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," .
765 "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'";
766
767 $result = mysql_query( $query, $gfac_link );
768
769 if ( ! $result )
770 {
771 write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
772 echo "Bad query\n";
773 return( -1 );
774 }
775}
776?>
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