post-mortem loader of worker memory usage information from the LSF

scripts/lsf_report.pl

+#!/usr/bin/env perl
+
+# Obtain bacct data for your pipeline from the LSF and store it in lsf_report table
+
+use strict;
+use warnings;
+use Getopt::Long;
+use Bio::EnsEMBL::Hive::URLFactory;
+
+my ($url, $infile, $lsf_user);
+
+GetOptions(
+           'url=s'                      => \$url,
+           'infile=s'                   => \$infile,
+           'lsf_user=s'                 => \$lsf_user,
+);
+
+unless( $url ) {
+    die "-url is an obligatory parameter for connecting to your database";
+}
+
+my $dba = Bio::EnsEMBL::Hive::URLFactory->fetch( $url );
+my $dbc = $dba->dbc();
+
+warn "Creating the 'lsf_report' table if it doesn't exist...\n";
+$dbc->do (qq{
+    CREATE TABLE IF NOT EXISTS lsf_report (
+        process_id       varchar(40) NOT NULL,
+        status           varchar(20) NOT NULL,
+        mem              varchar(20) NOT NULL,
+        swap             varchar(20) NOT NULL,
+        exception_status varchar(40) NOT NULL,
+
+        PRIMARY KEY (process_id)
+
+    ) ENGINE=InnoDB;
+});
+
+if( $infile ) {
+
+    warn "Parsing bacct file '$infile'...\n";
+
+} else {
+
+    warn "No bacct file given, finding out the time interval when the pipeline was run...\n";
+
+    my $sth_times = $dbc->prepare( 'SELECT min(born), max(died) FROM worker WHERE meadow_type="LSF"' );
+    $sth_times->execute();
+    my ($from_time, $to_time) = $sth_times->fetchrow_array();
+    $sth_times->finish();
+
+    $from_time=~s/[- ]/\//g;
+    $from_time=~s/:\d\d$//;
+    $to_time=~s/[- ]/\//g;
+    $to_time=~s/:\d\d$//;
+
+    warn "\tfrom=$from_time, to=$to_time\n";
+
+    $lsf_user = $lsf_user ? "-u $lsf_user" : '';
+    $infile = "bacct -C $from_time,$to_time $lsf_user -l |";
+
+    warn "Will run the following command to obtain bacct information: '$infile' (may take a few minutes)\n";
+}
+
+my $sth_replace = $dbc->prepare( 'REPLACE INTO lsf_report (process_id, status, mem, swap, exception_status) VALUES (?, ?, ?, ?, ?)' );
+{
+    local $/ = "------------------------------------------------------------------------------\n\n";
+    open(my $bacct_file, $infile);
+    my $record = <$bacct_file>; # skip the header
+
+    for my $record (<$bacct_file>) {
+        chomp $record;
+
+        # warn "RECORD:\n$record";
+
+        my @lines = split(/\n/, $record);
+        if( my ($process_id) = $lines[0]=~/^Job <(\d+(?:\[\d+\])?)>/) {
+
+            my $exception_status = '';
+            foreach (@lines) {
+                if(/^\s*EXCEPTION STATUS:\s*(.*?)\s*$/) {
+                    $exception_status = $1;
+                    $exception_status =~s/\s+/;/g;
+                }
+            }
+
+            my (@keys)   = split(/\s+/, $lines[@lines-2]);
+            my (@values) = split(/\s+/, $lines[@lines-1]);
+            my %usage = map { ($keys[$_] => $values[$_]) } (0..@keys-1);
+
+            #warn "PROC_ID=$process_id, STATUS=$usage{STATUS}, MEM=$usage{MEM}, SWAP=$usage{SWAP}, EXC_STATUS='$exception_status'\n";
+            $sth_replace->execute( $process_id, $usage{STATUS}, $usage{MEM}, $usage{SWAP}, $exception_status );
+        }
+    }
+
+    close $bacct_file;
+}
+$sth_replace->finish();
+warn "\nReport has been loaded into pipeline's lsf_report table. Enjoy.\n";
+