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http://43.156.76.180:8026/YuuMJ/EukPhylo.git
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204 lines
9.8 KiB
Perl
204 lines
9.8 KiB
Perl
#!/usr/local/bin/perl -w
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#---------------------------------------------------------------------------------------------
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# **************************
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# ** SCRIPT DESCRIPTION **
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# **************************
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#
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# Daemon responsibility is to make sure that bioseq jobs were not lost; When running a query
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# in bioseq server, the first stage is taking place on the ibis server, then the cgi is
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# sending the job to the biocluster queue. Daemon is in charge of controlling this transfer.
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# Daemon runs forever and performs its checks every 5 seconds.
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# 1. Read the "queuing jobs" list, check the status for each job in the biocluster bioseq Q
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# 2. Decides which job should be removed from the queuing list and move to the running list:
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# This is done by a flag which should be found in the running directory, in case the job
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# began its run
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# 3. If a job is in Q status, output to the screen its position in the Q and the time that
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# passed since the beginning of the run.
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# $. If something went wrong: stop the run and output a system error to the user.
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#--------------------------------------------------------------------------------------------
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# REMARK: $server_name must be spelled:
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# Selecton, ConSurf, ConSeq - as it reads info from these directories
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# first: reads the bioseq Q. build a hash. key: the job number. value: stats. R or Q_<no>
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use lib "/bioseq/bioSequence_scripts_and_constants";
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use GENERAL_CONSTANTS;
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use BIOSEQUENCE_FUNCTIONS;
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use HandleQueue;
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use strict;
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my $queuing_jobs_list = GENERAL_CONSTANTS::QUEUING_JOBS;
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my $running_jobs_list = GENERAL_CONSTANTS::RUNNING_JOBS;
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my ($qsub_job_no, $server_name, $run_number, $time, $date, $dir_path, $dir_path_null, @all_lines_in_list, $user_email, $qsub_ans,$visited_index, $ans, $null_dir, $add_null, $cmd);
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$user_email = "";
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$add_null = "";
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my %runs_with_no_qsub = ();
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my %que_number_status = ();
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my @er_ans = ();
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my $ans_out_file = "checkjob.out";
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my $ans_err_file = "checkjob.err";
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my $i = 1;
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while ($i<2){ # a process that runs forever
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# read the queing list
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open LOG, ">>".GENERAL_CONSTANTS::DAEMON_LOG_FILE or die "could not open log GENERAL_CONSTANTS::DAEMON_LOG_FILE $!";
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open LIST, "+>>".$queuing_jobs_list or die "cannot open ".$queuing_jobs_list." for writing: $!";
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flock LIST, 2;
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seek LIST, 0, 0; #rewind the pointer to the beginning
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@all_lines_in_list = <LIST>; # read the contents into the array
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truncate LIST, 0; # remove all the information, The 0 represents the size of the file that we want
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foreach (@all_lines_in_list){
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chomp;
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#------------------------------------
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# getting the info for the queing job
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#------------------------------------
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if(/^(\d+) (\w+) (null_)?(\d+) (.+:\d+) (.+\-\d+)( visit\d+)?/){
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$qsub_job_no = $1;
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$server_name = $2;
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if ($3) {$null_dir = "null_";}
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else {$null_dir = "";}
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$run_number = $4;
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$time = $5;
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$date = $6;
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$dir_path = GENERAL_CONSTANTS::SERVERS_RESULTS_DIR.$server_name."/$run_number"."/";
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$dir_path_null = $dir_path;
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$dir_path_null = $dir_path ."nullModel/" if ($null_dir ne "");
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$add_null = "/nullModel" if ($null_dir ne "");
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#---------------------------------------
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# read the status of the Q in biocluster
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#---------------------------------------
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&HandleQueue::find_place_in_Q(\%que_number_status);
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if (exists $que_number_status{$qsub_job_no}){
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#---------------------------------
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# check if the job started running
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#---------------------------------
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if (-e $dir_path_null."qsub_ans.txt"){
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open QSUB_ANS, $dir_path_null."qsub_ans.txt";
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$qsub_ans = <QSUB_ANS>;
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close QSUB_ANS;
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if ($qsub_ans eq "OK"){
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#print "removing from list: $qsub_job_no $run_number and move it to run list\n";
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$_ = ""; # removing this line from the lines array
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unless (open RUN_LIST, ">>".$running_jobs_list)
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{print LOG "Could not open the file $running_jobs_list. reason: $!. report run $run_number is running\n";}
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flock RUN_LIST, 2;
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print RUN_LIST "$qsub_job_no $server_name ".$null_dir."$run_number $time $date\n";
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flock RUN_LIST, 8;
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close RUN_LIST;
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}
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else{
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$_ = ""; # removing this line from the lines array
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&report_error($qsub_job_no);
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}
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}
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#----------------------------------------------------------------------
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# jobs is in the Q, in Q status
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# count the number of the daemon visits to it (not active at the moment)
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#----------------------------------------------------------------------
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else{
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# if the job was not accepted yet, we output the Q status to the user
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if (exists $runs_with_no_qsub{$run_number}){
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$runs_with_no_qsub{$run_number}++;
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$visited_index = $runs_with_no_qsub{$run_number};
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#$_ =~ s/visit\d+/visit$visited_index/;
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#$_.= "\n";
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}
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else{
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$runs_with_no_qsub{$run_number} = 1;
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#$_.= " visit1\n";
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}
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#print LOG "going to substruct time from $time $date\n";
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$ans = &BIOSEQUENCE_FUNCTIONS::subtract_time_from_now($time, $date);
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#print LOG $ans if ($ans ne "OK");
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#print LOG "reply from BIOSEQUENCE_FUNCTIONS::subtract_time_from_now : $ans\n";
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$ans = &GENERAL_CONSTANTS::print_Q_status_in_html($dir_path."output.html", $que_number_status{$qsub_job_no}, $ans, "none");
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print LOG $ans if ($ans ne "OK");
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#print LOG "reply from GENERAL_CONSTANTS::print_Q_status_in_html : $ans\n";
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}
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}
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#---------------------
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# jobs is not in the Q
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#---------------------
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elsif(!(exists $que_number_status{$qsub_job_no})){
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sleep 7; # maybe the run was just finished and the out files were not created yet.
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#-------------------------------------------------------------
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# if the run was deleted by the user - remove it from the list
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#-------------------------------------------------------------
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if (-e $dir_path."deleted_by_user"){
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$_ = "";
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}
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#-----------------------------------
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# check if it was not ended properly
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#-----------------------------------
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elsif (-e $dir_path_null."END_OK"){
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# this means that the run was finished through a normal procedure of the calculation methods
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$_ = ""; # removing this line from the lines array
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}
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#---------------------------------------------------------------------------------------------
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#if the job is not running, there will be an error when trying to check for it using "checkjob"
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#---------------------------------------------------------------------------------------------
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else{
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&HandleQueue::check_job($qsub_job_no, $null_dir.$run_number, $server_name, \@er_ans);
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print LOG $er_ans[0];
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if (exists $er_ans[1] && $er_ans[1] eq "error"){
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$_ = ""; # removing this line from the lines array
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&report_error($qsub_job_no);
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}
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}
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}
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}
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}
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# after reading the file, reprint the content to the list, only for lines which were not removed by the daemon
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foreach (@all_lines_in_list){
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if (/.+/){
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print LIST $_."\n";
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}
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}
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flock LIST, 8;
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close LIST;
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close LOG;
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sleep 5;
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$add_null = "";
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%que_number_status = ();
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@er_ans = ();
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}
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#----------------------------------
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## lock the HTML file, updating its status in the Q
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#sub print_Q_status_in_html{
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# my $html_file = shift;
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# my $_status = shift;
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# $html_file.="output.html";
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#
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# unless (open HTML, "+>>".$html_file) {
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# print LOG "Could not open file $html_file to update the status. Status is: $_status\n";}
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# else{
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# flock HTML, 2;
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# seek HTML, 0, 0; #rewind the pointer to the beginning
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# my @html_lines = <HTML>; # read the contents into the array
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# truncate HTML, 0; # remove all the information, The 0 represents the size of the file that we want
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# foreach (@html_lines){
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# if(/Your job status is: (.+)<\/font><br>/){
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# s/$1/$_status/;
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# last;
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# }
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# }
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# print HTML $_ foreach (@html_lines);
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# flock HTML, 8;
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# close HTML;
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# }
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#}
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#----------------------------------
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sub report_error{
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my $qsub_job_no = shift;
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print LOG "Terminating $run_number. ";
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$user_email = &HandleQueue::report_error_to_user($dir_path, $server_name, $run_number.$add_null, $run_number.$null_dir.".log", $run_number, "daemon.pl", $dir_path_null."output.html", $qsub_job_no);
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print LOG "output error message to: ".$dir_path_null."output.html to email: $user_email\n";
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}
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