Index: /trunk/cleanup.php =================================================================== --- /trunk/cleanup.php (revision 34) +++ /trunk/cleanup.php (revision 35) @@ -44,19 +44,10 @@ write_log( "$me: debug db=$db; requestID=$requestID" ); - $us3_link = mysql_connect( $dbhost, $user, $passwd ); + $us3_link = mysqli_connect( $dbhost, $user, $passwd, $db ); if ( ! $us3_link ) { - write_log( "$me: could not connect: $dbhost, $user, $passwd" ); + write_log( "$me: could not connect: $dbhost, $user, $passwd, $db" ); mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" ); - return( -1 ); - } - - $result = mysql_select_db( $db, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: could not select DB $db" ); - mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" ); return( -1 ); } @@ -65,20 +56,20 @@ $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID=$requestID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { write_log( "$me: Bad query: $query" ); - mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) ); + mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result ); + list( $email_address, $investigatorGUID, $editXMLFilename ) = mysqli_fetch_array( $result ); $query = "SELECT personID FROM people " . "WHERE personGUID='$investigatorGUID'"; - $result = mysql_query( $query, $us3_link ); - - list( $personID ) = mysql_fetch_array( $result ); + $result = mysqli_query( $us3_link, $query ); + + list( $personID ) = mysqli_fetch_array( $result ); $query = "SELECT clusterName, submitTime, queueStatus, method " . @@ -87,13 +78,13 @@ "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID"; - $result = mysql_query( $query, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); + $result = mysqli_query( $us3_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - if ( mysql_num_rows( $result ) == 0 ) + if ( mysqli_num_rows( $result ) == 0 ) { write_log( "$me: US3 Table error - No records for requestID: $requestID" ); @@ -101,5 +92,5 @@ } - list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result ); + list( $cluster, $submittime, $queuestatus, $jobtype ) = mysqli_fetch_array( $result ); // Get the GFAC ID @@ -107,18 +98,19 @@ "WHERE HPCAnalysisRequestID=$requestID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { write_log( "$me: Bad query: $query" ); - mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) ); + mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result ); + list( $HPCAnalysisResultID, $gfacID ) = mysqli_fetch_array( $result ); // Get data from global GFAC DB then insert it into US3 DB - $result = mysql_select_db( $gDB, $gfac_link ); +/* + $result = mysqli_select_db( $gfac_link, $gDB ); if ( ! $result ) @@ -128,9 +120,10 @@ return( -1 ); } + */ $query = "SELECT status, cluster, id FROM analysis " . "WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { @@ -140,5 +133,5 @@ } - list( $status, $cluster, $id ) = mysql_fetch_array( $result ); + list( $status, $cluster, $id ) = mysqli_fetch_array( $result ); $is_us3iab = preg_match( "/us3iab/", $cluster ); @@ -156,26 +149,26 @@ "WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); - mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) ); + $result = mysqli_query( $gfac_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); + mail_to_user( "fail", "Internal error " . mysqli_error( $gfac_link ) ); return( -1 ); } - list( $analysisID ) = mysql_fetch_array( $result ); + list( $analysisID ) = mysqli_fetch_array( $result ); // Get the request guid (LIMS submit dir name) $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID = $requestID "; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - } - - list( $requestGUID ) = mysql_fetch_array( $result ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + } + + list( $requestGUID ) = mysqli_fetch_array( $result ); $output_dir = "$submit_dir/$requestGUID"; @@ -254,10 +247,10 @@ "WHERE analysisID = $analysisID " . "ORDER BY time "; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -268,7 +261,7 @@ "Processed: $now\n\n" . "Queue Messages\n\n" ; - if ( mysql_num_rows( $result ) > 0 ) - { - while ( list( $message, $time ) = mysql_fetch_array( $result ) ) + if ( mysqli_num_rows( $result ) > 0 ) + { + while ( list( $message, $time ) = mysqli_fetch_array( $result ) ) $message_log .= "$time $message\n"; } @@ -277,10 +270,10 @@ "WHERE analysisID = $analysisID "; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -288,6 +281,6 @@ "WHERE gfacID='$gfacID' "; - $result = mysql_query( $query, $gfac_link ); - list( $queue_msg ) = mysql_fetch_array( $result ); + $result = mysqli_query( $gfac_link, $query ); + list( $queue_msg ) = mysqli_fetch_array( $result ); // But let's allow for investigation of other large stdout and/or stderr @@ -306,10 +299,10 @@ $query = "DELETE from analysis WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -322,5 +315,5 @@ $message_filename = "$output_dir/$db-$requestID-messages.txt"; file_put_contents( $message_filename, $message_log, FILE_APPEND ); - // mysql_close( $gfac_link ); + // mysqli_close( $gfac_link ); ///////// @@ -328,15 +321,15 @@ $query = "UPDATE HPCAnalysisResult SET " . - "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " . - "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "', " . + "stderr='" . mysqli_real_escape_string( $us3_link, $stderr ) . "', " . + "stdout='" . mysqli_real_escape_string( $us3_link, $stdout ) . "', " . "queueStatus='completed' " . "WHERE HPCAnalysisResultID=$HPCAnalysisResultID"; - $result = mysql_query( $query, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) ); + $result = mysqli_query( $us3_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query:\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -345,10 +338,10 @@ $query = "DELETE from analysis WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -429,9 +422,9 @@ "mgroupcount = {$otherdata['groupcount']} " . "WHERE HPCAnalysisResultID=$HPCAnalysisResultID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); } @@ -450,26 +443,30 @@ $modelGUID = $noise_data[ 'modelGUID' ]; $noiseGUID = $noise_data[ 'noiseGUID' ]; + $editGUID = '00000000-0000-0000-0000-000000000000'; + if ( isset( $model_data[ 'editGUID' ] ) ) + $editGUID = $model_data[ 'editGUID' ]; $query = "INSERT INTO noise SET " . "noiseGUID='$noiseGUID'," . "modelGUID='$modelGUID'," . - "editedDataID=1, " . + "editedDataID=" . + "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," . "modelID=1, " . "noiseType='$type'," . "description='$desc'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; // Add later after all files are processed: editDataID, modelID - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $id = mysql_insert_id( $us3_link ); + $id = mysqli_insert_id( $us3_link ); $file_type = "noise"; $noiseIDs[] = $id; @@ -498,18 +495,18 @@ "mrecsGUID='$mrecGUID'," . "description='$desc'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; // Add later after all files are processed: editDataID, modelID - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $id = mysql_insert_id( $us3_link ); + $id = mysqli_insert_id( $us3_link ); $file_type = "mrecs"; $mrecsIDs[] = $id; @@ -543,16 +540,16 @@ "meniscus='$meniscus'," . "variance='$variance'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; - - $result = mysql_query( $query, $us3_link ); + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; + + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query " . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $modelID = mysql_insert_id( $us3_link ); + $modelID = mysqli_insert_id( $us3_link ); $id = $modelID; $file_type = "model"; @@ -560,5 +557,5 @@ $query = "INSERT INTO modelPerson SET " . "modelID=$modelID, personID=$personID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); } @@ -571,10 +568,10 @@ "resultID=$id"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -595,10 +592,10 @@ "WHERE noiseID=$noiseID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -615,10 +612,10 @@ "WHERE mrecsID=$mrecsID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -633,12 +630,12 @@ $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID = $requestID "; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); } -// list( $requestGUID ) = mysql_fetch_array( $result ); +// list( $requestGUID ) = mysqli_fetch_array( $result ); // // chdir( "$submit_dir/$requestGUID" ); @@ -651,5 +648,5 @@ // exec( "rm -rf $gfacID" ); - mysql_close( $us3_link ); + mysqli_close( $us3_link ); ///////// @@ -725,5 +722,7 @@ { $limshost = gethostname(); - if ( ! preg_match( "/\./", $limshost ) ) + if ( preg_match( "/scyld/", $limshost ) ) + $limshost = 'alamo.uthscsa.edu'; + else if ( ! preg_match( "/\./", $limshost ) ) $limshost = $limshost . $org_domain; } @@ -870,9 +869,31 @@ global $me; global $db; + global $dbhost; global $status; $is_us3iab = preg_match( "/us3iab/", $cluster ); $is_jetstr = preg_match( "/jetstream/", $cluster ); - - // Figure out remote directory + $limshost = $dbhost; + $stderr = ''; + $stdout = ''; + $tarfile = ''; + + if ( $limshost == 'localhost' ) + { // If DB host is local host, get full LIMS host name + $limshost = gethostname(); + if ( preg_match( "/scyld/", $limshost ) ) + $limshost = 'alamo.uthscsa.edu'; + else if ( ! preg_match( "/\./", $limshost ) ) + $limshost = $limshost . $org_domain; + } + + if ( preg_match( "/alamo/", $limshost ) && + preg_match( "/alamo/", $cluster ) ) + { // If both LIMS and cluster are alamo, set up local transfers + $is_us3iab = 1; + if ( ! preg_match( "/\/local/", $work_remote ) ) + $work_remote = $work_remote . "/local"; + } + + // Figure out job's remote (or local) work directory $remoteDir = sprintf( "$work_remote/$db-%06d", $requestID ); //write_log( "$me: is_us3iab=$is_us3iab remoteDir=$remoteDir" ); @@ -891,5 +912,5 @@ $lworkdir = "/N/us3_cluster/work/local"; } - $cmd = "ssh us3@$clushost 'ls -d $lworkdir' 2/dev/null"; + $cmd = "ssh us3@$clushost 'ls -d $lworkdir' 2>/dev/null"; exec( $cmd, $output, $stat ); $work_remote = $output[ 0 ]; @@ -934,5 +955,5 @@ } else - { + { // Is US3IAB or alamo-to-alamo, so just change to local work directory $pwd = chdir( "$remoteDir" ); write_log( "$me: IS US3IAB: pwd=$pwd $remoteDir"); @@ -942,13 +963,34 @@ // Write the files to gfacDB + $secwait = 10; + $num_try = 0; + while ( ! file_exists( "stderr" ) && $num_try < 3 ) + { // Do waits and retries to let stderr appear + sleep( $secwait ); + $num_try++; + $secwait *= 2; +write_log( "$me: not-exist-stderr: num_try=$num_try" ); + } + + $lense = 0; if ( file_exists( "stderr" ) ) - { // Filter stderr to not have libnnls debug lines -// exec( "mv stderr stderr+nnls", $output, $stat ); -// exec( "grep -vi nnls stderr+nnls >stderr", $output, $stat ); + { + $lense = filesize( "stderr" ); + if ( $lense > 1000000 ) + { // Replace exceptionally large stderr with smaller version + exec( "mv stderr stderr-orig", $output, $stat ); + exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat ); + exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat ); + exec( "cat stderr-h stderr-t >stderr", $output, $stat ); + } $stderr = file_get_contents( "stderr" ); } else + { $stderr = ""; + } + if ( file_exists( "stdout" ) ) $stdout = file_get_contents( "stdout" ); + $fn1_tarfile = "analysis-results.tar"; $fn2_tarfile = "output/" . $fn1_tarfile; @@ -958,38 +1000,38 @@ $tarfile = file_get_contents( $fn2_tarfile ); - $lense = strlen( $stderr ); - if ( $lense > 1000000 ) - { // Replace exceptionally large stderr with smaller version - exec( "mv stderr stderr-orig", $output, $stat ); - exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat ); - exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat ); - exec( "cat stderr-h stderr-t >stderr", $output, $stat ); - $stderr = file_get_contents( "stderr" ); - } -$lent = strlen( $tarfile ); -write_log( "$me: tarfile size: $lent"); +// $lense = strlen( $stderr ); +// if ( $lense > 1000000 ) +// { // Replace exceptionally large stderr with smaller version +// exec( "mv stderr stderr-orig", $output, $stat ); +// exec( "head -n 5000 stderr-orig >stderr-h", $output, $stat ); +// exec( "tail -n 5000 stderr-orig >stderr-t", $output, $stat ); +// exec( "cat stderr-h stderr-t >stderr", $output, $stat ); +// $stderr = file_get_contents( "stderr" ); +// } $lene = strlen( $stderr ); write_log( "$me: stderr size: $lene (was $lense)"); $leno = strlen( $stdout ); write_log( "$me: stdout size: $leno"); -$estarf=mysql_real_escape_string($tarfile,$gfac_link); +$lent = strlen( $tarfile ); +write_log( "$me: tarfile size: $lent"); + $esstde = mysqli_real_escape_string( $gfac_link, $stderr ); + $esstdo = mysqli_real_escape_string( $gfac_link, $stdout ); + $estarf = mysqli_real_escape_string( $gfac_link, $tarfile ); +$lene = strlen($esstde); +write_log( "$me: es-stderr size: $lene"); +$leno = strlen($esstdo); +write_log( "$me: es-stdout size: $leno"); $lenf = strlen($estarf); -write_log( "$me: es-tarfile size: $lenf"); -$esstdo=mysql_real_escape_string($stdout,$gfac_link); -$leno = strlen($esstdo); -write_log( "$me: es-stdout size: $leno"); -$esstde=mysql_real_escape_string($stderr,$gfac_link); -$lene = strlen($esstde); -write_log( "$me: es-stderr size: $lene"); +write_log( "$me: es-tarfile size: $lenf"); $query = "UPDATE analysis SET " . - "stderr='" . mysql_real_escape_string( $stderr, $gfac_link ) . "'," . - "stdout='" . mysql_real_escape_string( $stdout, $gfac_link ) . "'," . - "tarfile='" . mysql_real_escape_string( $tarfile, $gfac_link ) . "'"; - - $result = mysql_query( $query, $gfac_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + "stderr='" . $esstde . "'," . + "stdout='" . $esstdo . "'," . + "tarfile='" . $estarf . "'"; + + $result = mysqli_query( $gfac_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); echo "Bad query\n"; return( -1 ); Index: /trunk/cleanup_gfac.php =================================================================== --- /trunk/cleanup_gfac.php (revision 34) +++ /trunk/cleanup_gfac.php (revision 35) @@ -41,19 +41,10 @@ write_log( "$me: debug db=$db; requestID=$requestID" ); - $us3_link = mysql_connect( $dbhost, $user, $passwd ); + $us3_link = mysqli_connect( $dbhost, $user, $passwd, $db ); if ( ! $us3_link ) { - write_log( "$me: could not connect: $dbhost, $user, $passwd" ); - mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" ); - return( -1 ); - } - - $result = mysql_select_db( $db, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: could not select DB $db" ); - mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" ); + write_log( "$me: could not connect: $dbhost, $user, $passwd, $db" ); + mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $db" ); return( -1 ); } @@ -62,20 +53,20 @@ $query = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID=$requestID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { write_log( "$me: Bad query: $query" ); - mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) ); - return( -1 ); - } - - list( $email_address, $investigatorGUID, $editXMLFilename ) = mysql_fetch_array( $result ); + mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) ); + return( -1 ); + } + + list( $email_address, $investigatorGUID, $editXMLFilename ) = mysqli_fetch_array( $result ); $query = "SELECT personID FROM people " . "WHERE personGUID='$investigatorGUID'"; - $result = mysql_query( $query, $us3_link ); - - list( $personID ) = mysql_fetch_array( $result ); + $result = mysqli_query( $us3_link, $query ); + + list( $personID ) = mysqli_fetch_array( $result ); /* @@ -90,13 +81,13 @@ "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID"; - $result = mysql_query( $query, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - return( -1 ); - } - - if ( mysql_num_rows( $result ) == 0 ) + $result = mysqli_query( $us3_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + return( -1 ); + } + + if ( mysqli_num_rows( $result ) == 0 ) { write_log( "$me: US3 Table error - No records for requestID: $requestID" ); @@ -104,5 +95,5 @@ } - list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result ); + list( $cluster, $submittime, $queuestatus, $jobtype ) = mysqli_fetch_array( $result ); // Get the GFAC ID @@ -110,24 +101,22 @@ "WHERE HPCAnalysisRequestID=$requestID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { write_log( "$me: Bad query: $query" ); - mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) ); - return( -1 ); - } - - list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result ); + mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) ); + return( -1 ); + } + + list( $HPCAnalysisResultID, $gfacID ) = mysqli_fetch_array( $result ); //////// // Get data from global GFAC DB and insert it into US3 DB - // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd ); - - $result = mysql_select_db( $gDB, $gfac_link ); - - if ( ! $result ) - { - write_log( "$me: Could not connect to DB $gDB" ); + $gfac_link = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB ); + + if ( ! $gfac_link ) + { + write_log( "$me: Could not connect to DB $dbhost : $gDB" ); mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" ); return( -1 ); @@ -137,5 +126,5 @@ "WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { @@ -145,5 +134,5 @@ } - $num_rows = mysql_num_rows( $result ); + $num_rows = mysqli_num_rows( $result ); if ( $num_rows == 0 ) { @@ -156,5 +145,5 @@ //} - list( $status, $cluster, $id ) = mysql_fetch_array( $result ); + list( $status, $cluster, $id ) = mysqli_fetch_array( $result ); //write_log( "$me: db=$db; requestID=$requestID; status=$status; cluster=$cluster" ); @@ -176,14 +165,14 @@ "WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); - mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) ); - return( -1 ); - } - - $num_rows = mysql_num_rows( $result ); + $result = mysqli_query( $gfac_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); + mail_to_user( "fail", "Internal error " . mysqli_error( $gfac_link ) ); + return( -1 ); + } + + $num_rows = mysqli_num_rows( $result ); if ( $num_rows == 0 ) { @@ -192,5 +181,5 @@ } - list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result ); + list( $analysisID, $stderr, $stdout, $tarfile ) = mysqli_fetch_array( $result ); if ( strlen( $tarfile ) > 0 ) @@ -209,10 +198,10 @@ "WHERE analysisID = $analysisID " . "ORDER BY time "; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -226,8 +215,8 @@ $need_finish = ( $status == 'COMPLETE' ); - if ( mysql_num_rows( $result ) > 0 ) + if ( mysqli_num_rows( $result ) > 0 ) { $time_msg = time(); - while ( list( $message, $time ) = mysql_fetch_array( $result ) ) + while ( list( $message, $time ) = mysqli_fetch_array( $result ) ) { //write_log( "$me: message=$message" ); @@ -263,10 +252,10 @@ "WHERE analysisID = $analysisID "; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } @@ -274,13 +263,13 @@ $query = "SELECT stdout, stderr, status, queue_msg FROM analysis " . "WHERE gfacID='$gfacID' "; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); try { // What if this is too large? - list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result ); + list( $stdout, $stderr, $status, $queue_msg ) = mysqli_fetch_array( $result ); } catch ( Exception $e ) { - write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) ); + write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysqli_error( $gfac_link ) ); // Just go ahead and clean up } @@ -301,10 +290,10 @@ $query = "DELETE from analysis WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { // Just log it and continue - write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) ); } write_log( "$me: GFAC DB entry deleted" ); @@ -316,12 +305,12 @@ $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID = $requestID "; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); } - list( $requestGUID ) = mysql_fetch_array( $result ); + list( $requestGUID ) = mysqli_fetch_array( $result ); $output_dir = "$submit_dir/$requestGUID"; write_log( "$me: Output dir determined: $output_dir" ); @@ -334,5 +323,5 @@ $message_filename = "$output_dir/$db-$requestID-messages.txt"; file_put_contents( $message_filename, $message_log, FILE_APPEND ); - // mysql_close( $gfac_link ); + // mysqli_close( $gfac_link ); write_log( "$me: *messages.txt written" ); @@ -341,14 +330,14 @@ $query = "UPDATE HPCAnalysisResult SET " . - "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " . - "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' " . + "stderr='" . mysqli_real_escape_string( $us3_link, $stderr ) . "', " . + "stdout='" . mysqli_real_escape_string( $us3_link, $stdout ) . "' " . "WHERE HPCAnalysisResultID=$HPCAnalysisResultID"; - $result = mysql_query( $query, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) ); + $result = mysqli_query( $us3_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query:\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -442,9 +431,9 @@ "mgroupcount = {$otherdata['groupcount']} " . "WHERE HPCAnalysisResultID=$HPCAnalysisResultID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); } @@ -463,26 +452,30 @@ $modelGUID = $noise_data[ 'modelGUID' ]; $noiseGUID = $noise_data[ 'noiseGUID' ]; + $editGUID = '00000000-0000-0000-0000-000000000000'; + if ( isset( $model_data[ 'editGUID' ] ) ) + $editGUID = $model_data[ 'editGUID' ]; $query = "INSERT INTO noise SET " . "noiseGUID='$noiseGUID'," . "modelGUID='$modelGUID'," . - "editedDataID=2, " . + "editedDataID=" . + "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," . "modelID=1, " . "noiseType='$type'," . "description='$desc'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; // Add later after all files are processed: editDataID, modelID - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $id = mysql_insert_id( $us3_link ); + $id = mysqli_insert_id( $us3_link ); $file_type = "noise"; $noiseIDs[] = $id; @@ -490,5 +483,5 @@ // Keep track of modelGUIDs for later, when we replace them $modelGUIDs[ $id ] = $modelGUID; -//write_log( "$me: noise file inserted into DB : id=$id" ); +//write_log( "$me: noise file inserted into DB : id=$id modelGUID=$modelGUID" ); } @@ -512,18 +505,18 @@ "mrecsGUID='$mrecGUID'," . "description='$desc'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; // Add later after all files are processed: editDataID, modelID - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $id = mysql_insert_id( $us3_link ); + $id = mysqli_insert_id( $us3_link ); $file_type = "mrecs"; $mrecsIDs[] = $id; @@ -560,16 +553,16 @@ "meniscus='$meniscus'," . "variance='$variance'," . - "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'"; - - $result = mysql_query( $query, $us3_link ); + "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'"; + + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query " . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } - $modelID = mysql_insert_id( $us3_link ); + $modelID = mysqli_insert_id( $us3_link ); $id = $modelID; $file_type = "model"; @@ -577,5 +570,5 @@ $query = "INSERT INTO modelPerson SET " . "modelID=$modelID, personID=$personID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); //write_log( "$me: model file inserted into DB : id=$id" ); } @@ -586,10 +579,10 @@ "resultID=$id"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -611,10 +604,10 @@ "WHERE noiseID=$noiseID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -633,10 +626,10 @@ "WHERE mrecsID=$mrecsID"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) ); + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) ); return( -1 ); } @@ -651,12 +644,12 @@ $query = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " . "WHERE HPCAnalysisRequestID = $requestID "; - $result = mysql_query( $query, $us3_link ); - - if ( ! $result ) - { - write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) ); - } - - list( $requestGUID ) = mysql_fetch_array( $result ); + $result = mysqli_query( $us3_link, $query ); + + if ( ! $result ) + { + write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) ); + } + + list( $requestGUID ) = mysqli_fetch_array( $result ); chdir( "$submit_dir/$requestGUID" ); @@ -669,5 +662,5 @@ // exec( "rm -rf $gfacID" ); - mysql_close( $us3_link ); + mysqli_close( $us3_link ); ///////// Index: /trunk/cluster_status.php =================================================================== --- /trunk/cluster_status.php (revision 34) +++ /trunk/cluster_status.php (revision 35) @@ -22,5 +22,6 @@ } -exit(); +//exit(); +exit(0); // Get the cluster status @@ -115,8 +116,7 @@ //echo " $cluster $queued, $status, $running\n"; - $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd ); - $result = mysql_select_db( $gDB, $gfac_link ); - - if ( ! $result ) + $gfac_link = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB ); + + if ( ! $gfac_link ) { write_log( "$self: Could not connect to DB $gDB" ); @@ -126,14 +126,14 @@ $query = "SELECT * FROM cluster_status WHERE cluster='$cluster'"; - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gfac_link ) ); - echo "$self: Query failed $query - " . mysql_error( $gfac_link ) . "\n"; + write_log( "$self: Query failed $query - " . mysqli_error( $gfac_link ) ); + echo "$self: Query failed $query - " . mysqli_error( $gfac_link ) . "\n"; exit(); } - $rows = mysql_num_rows( $result ); + $rows = mysqli_num_rows( $result ); if ( $rows == 0 ) // INSERT @@ -154,10 +154,10 @@ } - $result = mysql_query( $query, $gfac_link ); + $result = mysqli_query( $gfac_link, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gfac_link ) ); - echo "$self: Query failed $query - " . mysql_error( $gfac_link ) . "\n"; + write_log( "$self: Query failed $query - " . mysqli_error( $gfac_link ) ); + echo "$self: Query failed $query - " . mysqli_error( $gfac_link ) . "\n"; } } @@ -182,6 +182,8 @@ else { - $clusters = array( "alamo", "lonestar5", "stampede", "comet", - "stampede2-b", "jetstream", "jureca", "jacinto-b" ); +// $clusters = array( "alamo", "lonestar5", "comet", +// "stampede2", "jetstream", "jureca", "jacinto" ); + $clusters = array( "alamo", "lonestar5", "comet", + "stampede2", "jetstream" ); } @@ -238,8 +240,8 @@ break; } - case 'stampede': - { - $host = "us3@stampede.tacc.utexas.edu"; - $qstat = `ssh $host '/usr/local/bin/showq 2>&1|grep "Total Jobs"'`; + case 'stampede2': + { + $host = "us3@stampede2.tacc.utexas.edu"; + $qstat = `ssh $host '/usr/local/bin/showq 2>/dev/null|grep "Total Jobs"'`; $sparts = preg_split( '/\s+/', $qstat ); $tot = $sparts[ 2 ]; @@ -251,21 +253,8 @@ break; } - case 'stampede2': - { - $host = "us3@stampede2.tacc.utexas.edu"; - $qstat = `ssh $host '/usr/local/bin/showq 2>&1|grep "Total Jobs"'`; - $sparts = preg_split( '/\s+/', $qstat ); - $tot = $sparts[ 2 ]; - $run = $sparts[ 5 ]; - $que = $sparts[ 8 ]; - $sta = "up"; - if ( $tot == '' || $tot == '0' ) - $sta = "down"; - break; - } case 'lonestar5': { $host = "us3@ls5.tacc.utexas.edu"; - $qstat = `ssh $host '/usr/local/bin/showq 2>&1|grep "Total Jobs"'`; + $qstat = `ssh $host '/usr/local/bin/showq 2>/dev/null|grep "Total Jobs"'`; $sparts = preg_split( '/\s+/', $qstat ); $tot = $sparts[ 2 ]; @@ -280,6 +269,6 @@ { $run = $sparts[ 5 ]; -// $que = $sparts[ 8 ]; - $que = $sparts[ 11 ]; + $que = $sparts[ 8 ]; +// $que = $sparts[ 11 ]; } break; @@ -288,27 +277,20 @@ { $host = "us3@comet.sdsc.edu"; - $qstat = `ssh $host '/usr/bin/sinfo -s -p compute -o "%a %F" |tail -1'`; - $sparts = preg_split( '/\s+/', $qstat ); - $sta = $sparts[ 0 ]; - $knts = $sparts[ 1 ]; - $sparts = preg_split( '/\//', $knts ); - $run = $sparts[ 0 ]; - $que = $sparts[ 1 ]; - if ( $sta == "" ) - $sta = "down"; - break; - } - case 'gordon': - { - $host = "us3@gordon.sdsc.edu"; - $qstat = `ssh $host '/opt/torque/bin/qstat -B 2>&1|tail -1'`; - $sparts = preg_split( '/\s+/', $qstat ); - $que = $sparts[ 3 ]; - $run = $sparts[ 4 ]; - $sta = $sparts[ 10 ]; - if ( $sta == "Active" ) - $sta = "up"; + //$qstat = `ssh $host '/usr/bin/sinfo -s -p compute -o "%a %F" |tail -1'`; + $qstat = `ssh $host '/home/us3/scripts/cstat 2>&1'`; + $sparts = preg_split( '/\s+/', $qstat ); + $tot = $sparts[ 1 ]; + $run = '0'; + $que = '0'; + $sta = "up"; + if ( $tot == '' || $tot == '0' ) + { + $sta = "down"; + } else - $sta = "down"; + { + $run = $sparts[ 3 ]; + $que = $sparts[ 5 ]; + } break; } Index: /trunk/gridctl.php =================================================================== --- /trunk/gridctl.php (revision 34) +++ /trunk/gridctl.php (revision 35) @@ -20,10 +20,11 @@ // Get data from global GFAC DB -$gLink = mysql_connect( $dbhost, $guser, $gpasswd ); - -if ( ! mysql_select_db( $gDB, $gLink ) ) -{ - write_log( "$self: Could not select DB $gDB - " . mysql_error() ); +$gLink = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB ); + +if ( ! $gLink ) +{ + write_log( "$self: Could not select DB $gDB - " . mysqli_error() ); mail_to_admin( "fail", "Internal Error: Could not select DB $gDB" ); + sleep(300); exit(); } @@ -31,29 +32,33 @@ $query = "SELECT gfacID, us3_db, cluster, status, queue_msg, " . "UNIX_TIMESTAMP(time), time from analysis"; -$result = mysql_query( $query, $gLink ); +$result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); - mail_to_admin( "fail", "Query failed $query\n" . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); + mail_to_admin( "fail", "Query failed $query\n" . mysqli_error( $gLink ) ); exit(); } -if ( mysql_num_rows( $result ) == 0 ) +if ( mysqli_num_rows( $result ) == 0 ) { //write_log( "$self: analysis read got numrows==0" ); exit(); // Nothing to do } +//write_log( "$loghdr gfac-analysis rows $nrows" ); $me_devel = preg_match( "/class_devel/", $class_dir ); +//echo "me_devel=$me_devel class_dir=$class_dir\n"; while ( list( $gfacID, $us3_db, $cluster, $status, $queue_msg, $time, $updateTime ) - = mysql_fetch_array( $result ) ) + = mysqli_fetch_array( $result ) ) { // If this entry does not match class/class_devel, skip processing +//echo " gfacID=$gfacID gf_status=$status\n"; if ( preg_match( "/US3-A/i", $gfacID ) ) { // For thrift, job and gridctl must match $job_devel = preg_match( "/US3-ADEV/i", $gfacID ); +//echo " THR: job_devel=$job_devel\n"; if ( ( $me_devel && !$job_devel ) || ( !$me_devel && $job_devel ) ) @@ -65,4 +70,5 @@ else if ( $me_devel ) { // Local (us3iab/-local) and class_devel: skip processing +//echo " LOC: me_devel=$me_devel\n"; continue; } @@ -99,4 +105,5 @@ //write_log( "$loghdr status_in=$status_in" ); $status = aira_status( $gfacID, $status_in ); +//echo "$loghdr status_in=$status_in status_ex=$status\n"; if($status != $status_in ) write_log( "$loghdr Set to $status from $status_in" ); @@ -110,4 +117,5 @@ if ( $status_gw == 'COMPLETE' ) $status = $status_gw; +//echo "$loghdr status_gw=$status_gw status=$status\n"; //write_log( "$loghdr non-AThrift status=$status status_gw=$status_gw" ); } @@ -119,4 +127,5 @@ if ( $status_gw == 'COMPLETE' || $status == 'UNKNOWN' ) $status = $status_gw; +//echo "$loghdr status_lo=$status\n"; //write_log( "$loghdr Local status=$status status_gw=$status_gw" ); } @@ -130,9 +139,9 @@ $query2 = "UPDATE analysis SET status='ERROR' WHERE gfacID='$gfacID'"; - $result2 = mysql_query( $query2, $gLink ); + $result2 = mysqli_query( $gLink, $query2 ); $status = 'ERROR'; if ( ! $result2 ) - write_log( "$loghdr Query failed $query2 - " . mysql_error( $gLink ) ); + write_log( "$loghdr Query failed $query2 - " . mysqli_error( $gLink ) ); } @@ -200,4 +209,5 @@ } } +mysqli_close( $gLink ); exit(); @@ -235,8 +245,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='SUBMIT_TIMEOUT' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -271,8 +281,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='FAILED' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -311,8 +321,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='RUN_TIMEOUT' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -349,8 +359,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='FAILED' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -397,8 +407,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='DATA_TIMEOUT' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -445,8 +455,8 @@ mail_to_admin( "hang", "$message - id: $gfacID" ); $query = "UPDATE analysis SET status='FAILED' WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); update_queue_messages( $message ); @@ -477,17 +487,17 @@ // Double check that the gfacID exists $query = "SELECT count(*) FROM analysis WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); - mail_to_admin( "fail", "Query failed $query\n" . mysql_error( $gLink ) ); - return; - } - - list( $count ) = mysql_fetch_array( $result ); - -if ($count==0) -write_log( "$loghdr count = $count gfacID = $gfacID" ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); + mail_to_admin( "fail", "Query failed $query\n" . mysqli_error( $gLink ) ); + return; + } + + list( $count ) = mysqli_fetch_array( $result ); + +//if ($count==0) +//write_log( "$loghdr count = $count gfacID = $gfacID" ); if ( $count == 0 ) return; @@ -597,7 +607,7 @@ } - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) - write_log( "$loghdr Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$loghdr Query failed $query - " . mysqli_error( $gLink ) ); if ( $message != 'NONE' ) @@ -619,20 +629,10 @@ global $loghdr; - $us3_link = mysql_connect( $dbhost, $user, $passwd ); + $us3_link = mysqli_connect( $dbhost, $user, $passwd, $us3_db ); if ( ! $us3_link ) { - write_log( "$loghdr could not connect: $dbhost, $user, $passwd" ); - mail_to_admin( "fail", "Could not connect to $dbhost" ); - return 0; - } - - - $result = mysql_select_db( $us3_db, $us3_link ); - - if ( ! $result ) - { - write_log( "$loghdr could not select DB $us3_db" ); - mail_to_admin( "fail", "Could not select DB $us3_db, $dbhost, $user, $passwd" ); + write_log( "$loghdr could not connect: $dbhost, $user, $passwd, $us3_db" ); + mail_to_admin( "fail", "Could not connect to $dbhost : $us3_db" ); return 0; } @@ -640,15 +640,15 @@ $query = "SELECT HPCAnalysisRequestID, UNIX_TIMESTAMP(updateTime) " . "FROM HPCAnalysisResult WHERE gfacID='$gfacID'"; - $result = mysql_query( $query, $us3_link ); + $result = mysqli_query( $us3_link, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $us3_link ) ); - mail_to_admin( "fail", "Query failed $query\n" . mysql_error( $us3_link ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $us3_link ) ); + mail_to_admin( "fail", "Query failed $query\n" . mysqli_error( $us3_link ) ); return 0; } - list( $requestID, $updateTime ) = mysql_fetch_array( $result ); - mysql_close( $us3_link ); + list( $requestID, $updateTime ) = mysqli_fetch_array( $result ); + mysqli_close( $us3_link ); return $requestID; @@ -859,5 +859,4 @@ //write_log( "$self result: $result" ); -/////////////////////////////////////////////////////////////////// $secwait = 2; $num_try = 0; @@ -870,13 +869,9 @@ write_log( "$me: num_try=$num_try secwait=$secwait" ); } -/////////////////////////////////////////////////////////////////// -// if ( $result == "" || -// preg_match( "/^qstat: Unknown/", $result ) || -// preg_match( "/ssh_exchange_id/", $result ) ) + if ( preg_match( "/^qstat: Unknown/", $result ) || preg_match( "/ssh_exchange_id/", $result ) ) { - write_log( "$self get_local_status: Local job $gfacID unknown" ); -//write_log( "$self get_local_status: result=$result" ); + write_log( "$self get_local_status: Local job $gfacID unknown result=$result" ); return 'UNKNOWN'; } @@ -937,20 +932,20 @@ $query = "SELECT id FROM analysis " . "WHERE gfacID = '$gfacID' "; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); - return; - } - list( $analysisID ) = mysql_fetch_array( $result ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); + return; + } + list( $analysisID ) = mysqli_fetch_array( $result ); // Insert message into queue_message table $query = "INSERT INTO queue_messages SET " . - "message = '" . mysql_real_escape_string( $message, $gLink ) . "', " . + "message = '" . mysqli_real_escape_string( $gLink, $message ) . "', " . "analysisID = '$analysisID' "; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: Query failed $query - " . mysql_error( $gLink ) ); + write_log( "$self: Query failed $query - " . mysqli_error( $gLink ) ); return; } @@ -966,29 +961,19 @@ global $us3_db; - $us3_link = mysql_connect( $dbhost, $user, $passwd ); + $us3_link = mysqli_connect( $dbhost, $user, $passwd, $us3_db ); if ( ! $us3_link ) { write_log( "$self: could not connect: $dbhost, $user, $passwd" ); - mail_to_admin( "fail", "Could not connect to $dbhost" ); + mail_to_admin( "fail", "Could not connect to $dbhost : $us3_db" ); return 0; } - - $result = mysql_select_db( $us3_db, $us3_link ); - - if ( ! $result ) - { - write_log( "$self: could not select DB $us3_db" ); - mail_to_admin( "fail", "Could not select DB $us3_db, $dbhost, $user, $passwd" ); - return 0; - } - $query = "UPDATE HPCAnalysisResult SET " . - "lastMessage='" . mysql_real_escape_string( $message, $us3_link ) . "'" . + "lastMessage='" . mysqli_real_escape_string( $us3_link, $message ) . "'" . "WHERE gfacID = '$gfacID' "; - mysql_query( $query, $us3_link ); - mysql_close( $us3_link ); + mysqli_query( $us3_link, $query ); + mysqli_close( $us3_link ); } @@ -1173,4 +1158,5 @@ } +//if ( $status != 'SUBMITTED' ) //write_log( "$loghdr status/_in/_gw/_ex=$status/$status_in/$status_gw/$status_ex" ); if ( $status != $status_gw ) Index: /trunk/manage-us3-pipe.php =================================================================== --- /trunk/manage-us3-pipe.php (revision 34) +++ /trunk/manage-us3-pipe.php (revision 35) @@ -55,18 +55,11 @@ // We need the gfacID - $resource = mysql_connect( $dbhost, $user, $passwd ); + $resource = mysqli_connect( $dbhost, $user, $passwd, $db ); if ( ! $resource ) { - write_log( "$self process(): Could not connect to MySQL - " . mysql_error() ); + write_log( "$self process(): Could not connect to MySQL - " . mysqli_error($resource) ); write_log( "$self process(): original msg - $msg" ); return; - } - - if ( ! mysql_select_db( $db, $resource ) ) - { - write_log( "$self: Could not select DB $db " . mysql_error( $resource ) ); - write_log( "$self process(): original msg - $msg" ); - return; } @@ -76,5 +69,5 @@ "LIMIT 1"; - $result = mysql_query( $query, $resource ); + $result = mysqli_query( $resource, $query ); if ( ! $result ) @@ -86,6 +79,6 @@ // Set flags for Airavata/Thrift and "Finished..." - list( $gfacID ) = mysql_fetch_row( $result ); - mysql_close( $resource ); + list( $gfacID ) = mysqli_fetch_row( $result ); + mysqli_close( $resource ); $is_athrift = preg_match( "/^US3-A/i", $gfacID ); @@ -164,15 +157,9 @@ global $self; - $resource = mysql_connect( $dbhost, $user, $passwd ); + $resource = mysqli_connect( $dbhost, $user, $passwd, $db ); if ( ! $resource ) { - write_log( "$self: Could not connect to DB" ); - return; - } - - if ( ! mysql_select_db( $db, $resource ) ) - { - write_log( "$self: Could not select DB $db " . mysql_error( $resource ) ); + write_log( "$self: Could not connect to DB $db " . mysqli_error( $resource ) ); return; } @@ -183,5 +170,5 @@ "LIMIT 1"; - $result = mysql_query( $query, $resource ); + $result = mysqli_query( $resource, $query ); if ( ! $result ) @@ -191,5 +178,5 @@ } - list( $resultID ) = mysql_fetch_row( $result ); + list( $resultID ) = mysqli_fetch_row( $result ); $query = "UPDATE HPCAnalysisResult SET "; @@ -219,9 +206,9 @@ } - $query .= "lastMessage='" . mysql_real_escape_string( $message ) . "'" . + $query .= "lastMessage='" . mysqli_real_escape_string( $resource, $message ) . "'" . "WHERE HPCAnalysisResultID=$resultID"; - mysql_query( $query, $resource ); - mysql_close( $resource ); + mysqli_query( $resource, $query ); + mysqli_close( $resource ); } @@ -242,8 +229,8 @@ // Get data from global GFAC DB - $gLink = mysql_connect( $dbhost, $guser, $gpasswd ); - if ( ! mysql_select_db( $gDB, $gLink ) ) - { - write_log( "$self: Could not select DB $gDB " . mysql_error( $gLink ) ); + $gLink = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB ); + if ( ! $gLink ) + { + write_log( "$self: Could not select DB $gDB " . mysqli_error( $gLink ) ); return; } @@ -260,9 +247,9 @@ { $query = "UPDATE analysis " . - "SET queue_msg='" . mysql_real_escape_string( $message ) . "' " . + "SET queue_msg='" . mysqli_real_escape_string( $gLink, $message ) . "' " . "WHERE gfacID='$gfacID'"; //write_log( "$self process(): updgf-u : status=$status" ); - mysql_query( $query, $gLink ); + mysqli_query( $gLink, $query ); } @@ -270,9 +257,9 @@ { $query = "UPDATE analysis SET status='$status', " . - "queue_msg='" . mysql_real_escape_string( $message ) . "' " . + "queue_msg='" . mysqli_real_escape_string( $gLink, $message ) . "' " . "WHERE gfacID='$gfacID'"; //write_log( "$self process(): updgf-s : status=$status" ); - mysql_query( $query, $gLink ); + mysqli_query( $gLink, $query ); } @@ -280,12 +267,12 @@ $query = "SELECT id FROM analysis " . "WHERE gfacID = '$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: bad query: $query " . mysql_error( $gLink ) ); - return; - } - - if ( mysql_num_rows( $result ) == 0 ) + write_log( "$self: bad query: $query " . mysqli_error( $gLink ) ); + return; + } + + if ( mysqli_num_rows( $result ) == 0 ) { write_log( "$self: can't find $gfacID in GFAC db" ); @@ -293,17 +280,17 @@ } - list( $aID ) = mysql_fetch_array( $result ); + list( $aID ) = mysqli_fetch_array( $result ); $query = "INSERT INTO queue_messages " . "SET analysisID = $aID, " . - "message = '" . mysql_real_escape_string( $message ) . "'"; - $result = mysql_query( $query, $gLink ); + "message = '" . mysqli_real_escape_string( $gLink, $message ) . "'"; + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: bad query: $query " . mysql_error( $gLink ) ); - return; - } - - mysql_close( $gLink ); + write_log( "$self: bad query: $query " . mysqli_error( $gLink ) ); + return; + } + + mysqli_close( $gLink ); } @@ -353,8 +340,8 @@ // Get data from global GFAC DB - $gLink = mysql_connect( $dbhost, $guser, $gpasswd ); - if ( ! mysql_select_db( $gDB, $gLink ) ) - { - write_log( "$self: Could not select DB $gDB " . mysql_error( $gLink ) ); + $gLink = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB ); + if ( ! $gLink ) + { + write_log( "$self: Could not connect to DB $gDB " . mysqli_error( $gLink ) ); return; } @@ -362,8 +349,8 @@ // Update message and update status to 'FINISHED' $query = "UPDATE analysis SET status='FINISHED', " . - "queue_msg='" . mysql_real_escape_string( $message ) . "' " . + "queue_msg='" . mysqli_real_escape_string( $gLink, $message ) . "' " . "WHERE gfacID='$gfacID'"; - mysql_query( $query, $gLink ); + mysqli_query( $gLink, $query ); write_log( "$self: Status FINISHED and 'Finished...' message updated" ); @@ -371,12 +358,12 @@ $query = "SELECT id FROM analysis " . "WHERE gfacID = '$gfacID'"; - $result = mysql_query( $query, $gLink ); + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: bad query: $query " . mysql_error( $gLink ) ); - return; - } - - if ( mysql_num_rows( $result ) == 0 ) + write_log( "$self: bad query: $query " . mysqli_error( $gLink ) ); + return; + } + + if ( mysqli_num_rows( $result ) == 0 ) { // write_log( "$self: can't find $gfacID in GFAC db" ); @@ -384,17 +371,17 @@ } - list( $aID ) = mysql_fetch_array( $result ); + list( $aID ) = mysqli_fetch_array( $result ); $query = "INSERT INTO queue_messages " . "SET analysisID = $aID, " . - "message = '" . mysql_real_escape_string( $message ) . "'"; - $result = mysql_query( $query, $gLink ); + "message = '" . mysqli_real_escape_string( $gLink, $message ) . "'"; + $result = mysqli_query( $gLink, $query ); if ( ! $result ) { - write_log( "$self: bad query: $query " . mysql_error( $gLink ) ); - return; - } - - mysql_close( $gLink ); + write_log( "$self: bad query: $query " . mysqli_error( $gLink ) ); + return; + } + + mysqli_close( $gLink ); } ?> Index: /trunk/runID_info.php =================================================================== --- /trunk/runID_info.php (revision 34) +++ /trunk/runID_info.php (revision 35) @@ -28,4 +28,5 @@ global $uses_airavata; +global $link; ?> @@ -62,4 +63,5 @@ function experiment_select( $select_name, $current_ID = NULL ) { + global $link; $myID = $_SESSION['id']; @@ -72,13 +74,13 @@ $users_clause . "ORDER BY lname, runID "; - $result = mysql_query( $query ) - or die( "Query failed : $query
" . mysql_error() ); - - if ( mysql_num_rows( $result ) == 0 ) return ""; + $result = mysqli_query( $link, $query ) + or die( "Query failed : $query
" . mysqli_error($link) ); + + if ( mysqli_num_rows( $result ) == 0 ) return ""; $text = "
\n" . "