Commit d385ed7c authored by Leo Gordon's avatar Leo Gordon
Browse files

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

parent 579e38a1
#!/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";
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