/usr/share/arc/SGEmod.pm is in nordugrid-arc-arex 5.4.2-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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require Exporter;
our @ISA = qw(Exporter);
our @EXPORT_OK = qw(get_lrms_info get_lrms_options_schema);
use POSIX qw(floor ceil);
# force locale LANG to POSIX see bug #3314
$ENV{LANG}="POSIX";
use LogUtils;
use XML::Simple qw(:strict);
use strict;
our $path;
our $options;
our $lrms_info = {};
# status of nodes and queues
our %node_stats = ();
# all running jobs, indexed by job-ID and task-ID
our %running_jobs = ();
# all waiting jobs, indexed by job-ID
our %waiting_jobs = ();
# Switch to choose between codepaths for SGE 6.x (the default) and SGE 5.x
our $compat_mode;
our $sge_type;
our $sge_version;
our $cpudistribution;
our @queue_names;
our $queuedjobs = 0;
our $queuedcpus = 0;
our $max_jobs;
our $max_u_jobs;
our %user_total_jobs;
our %user_waiting_jobs;
our $log = LogUtils->getLogger(__PACKAGE__);
##########################################
# Public interface
##########################################
sub get_lrms_options_schema {
return {
'sge_root' => '',
'sge_bin_path' => '',
'sge_cell' => '*',
'sge_qmaster_port' => '*',
'sge_execd_port' => '*',
'queues' => {
'*' => {
'users' => [ '' ],
'sge_queues' => '*',
'sge_jobopts' => '*'
}
},
'jobs' => [ '' ]
};
}
sub get_lrms_info($) {
$options = shift;
lrms_init();
type_and_version();
run_qconf();
run_qstat();
require Data::Dumper; import Data::Dumper qw(Dumper);
#print STDERR Dumper(\%node_stats);
#print STDERR Dumper(\%running_jobs);
#print STDERR Dumper(\%waiting_jobs);
cluster_info();
my %qconf = %{$options->{queues}};
for my $qname ( keys %qconf ) {
queue_info($qname);
}
my $jids = $options->{jobs};
jobs_info($jids);
for my $qname ( keys %qconf ) {
my $users = $qconf{$qname}{users};
users_info($qname,$users);
}
# recycle memory
%running_jobs = ();
%waiting_jobs = ();
nodes_info();
return $lrms_info
}
##########################################
# Private subs
##########################################
#
# Generic function to process the ouptut of an external program. The callback
# function will be invoked with a file descriptor receiving the standard output
# of the external program as it's first argument.
#
sub run_callback {
my ($command, $callback, @extraargs) = @_;
my ($executable) = split ' ', $command;
$log->error("Not an executable: $executable")
unless (-x "$executable");
local *QQ;
$log->error("Failed creating pipe from: $command: $!")
unless open QQ, "$command |";
&$callback(*QQ, @extraargs);
close QQ;
my $exitcode = $? >> 8;
$log->info("Failed running command (exit code $exitcode): $command")
if $?;
return ! $?;
}
#
# Generic function to process the ouptut of an external program. The callback
# function will be invoked for each line of output from the external program.
#
sub loop_callback {
my ($command, $callback) = @_;
return run_callback($command, sub {
my $fh = shift;
my $line;
chomp $line and &$callback($line) while defined ($line = <$fh>);
});
}
#
# Determine SGE variant and version.
# Set compatibility mode if necessary.
#
sub type_and_version {
run_callback("$path/qstat -help", sub {
my $fh = shift;
my ($firstline) = <$fh>;
($sge_type, $sge_version) = split " ", $firstline;
});
$compat_mode = 0; # version 6.x assumed
if ($sge_type !~ /GE/ or not $sge_version) {
$log->error("Cannot indentify SGE version from output of '$path/qstat -help': $sge_type $sge_version");
} elsif ($sge_version =~ /^5\./ or $sge_version =~ /^pre6.0/) {
$compat_mode = 1;
$log->info("Using SGE 5.x compatibility mode");
}
}
#
# Processes an array task definition (i.e.: '3,4,6-8,10-20:2')
# and returns the number of individual tasks
#
sub count_array_spec($) {
my $count = 0;
for my $spec (split ',', shift) {
# handles expressions like '6-10:2' and '6-10' and '6'
return 0 unless $spec =~ '^(\d+)(?:-(\d+)(?::(\d+))?)?$';
my ($lower,$upper,$step) = ($1,$2,$3);
$upper = $lower unless defined $upper;
$step = 1 unless $step;
$count += 1 + floor(abs($upper-$lower)/$step);
}
return $count;
}
#
# this block contains the functions used to parse the output of qstat
#
{
# shared variables
my $line; # used to keep the most recently line read from qstat
my $currentjobid = undef;
my $currentqueue = undef;
my $currentnode = undef;
#### Regular expression matching a queue line, like:
# libero@compute-3-7.local BPC 0/8 4.03 lx24-amd64 S
# all.q@hyper.uio.no BIP 0/0/1 0.00 lx24-x86
# all.q@compute-14-19.local BIPC 0/8 -NA- lx24-amd64 Adu
# corvus.q BICP 0/16 99.99 solaris64 aAdu
my $queue_regex = '^\s*(\S+)\s+\w+\s+(?:(\d+)/)?(\d+)/(\d+)\s+(\S+)\s+\S+(?:\s+(\w+))?\s*$';
#### Regular expression matching complex lines from qstat -F
# hl:num_proc=1
# hl:mem_total=1009.523M
# qf:qname=shar
# qf:hostname=squark.uio.no
my $complex_regex = '\s+(\w\w:\w+)=(.*)\s*';
#### Regular expressions matching jobs (for SGE version 6.x), like:
# 4518 2.71756 brkhrt_5ch whe042 r 08/20/2008 10:50:23 4
# 1602 2.59942 runmain_4_ user1 r 08/13/2008 22:42:17 1 21
# 1872 2.59343 test_GG1 otherusr Eqw 08/05/2008 17:36:45 1 4,6-8:1
# 7539 7.86785 methane_i user11 qw 06/26/2008 11:16:52 4
#### Assume job name column is exactly 10 characters wide.
my $jobid_prio_name_regex6 = '(\d+)\s+[.\d]+\s+\S.{9}';
my $user_state_date_regex6 = '(\S+)\s+(\w+)\s+(\d\d/\d\d/\d{4} \d\d:\d\d:\d\d)';
my $slots_tid_regex6 = '(\d+)(?:\s+(\d+))?'; # for running jobs
my $slots_taskdef_regex6 = '(\d+)(?:\s+([:\-\d,]+))?'; # for queued jobs
my $base_regex6 = '^\s*'.$jobid_prio_name_regex6.' '.$user_state_date_regex6;
my $running_regex6 = $base_regex6.'\s+'.$slots_tid_regex6.'\s*$';
my $waiting_regex6 = $base_regex6.'\s+'.$slots_taskdef_regex6.'\s*$';
#### Regular expressions matching jobs (for SGE version 5.x), like:
# 217 0 submit.tem lemlib r 07/21/2008 09:55:32 MASTER
# 0 submit.tem lemlib r 07/21/2008 09:55:32 SLAVE
# 27 0 exam.sh c01p01 r 02/03/2006 16:40:49 MASTER 2
# 0 exam.sh c01p01 r 02/03/2006 16:40:49 SLAVE 2
# 254 0 CPMD baki qw 08/14/2008 10:12:29
# 207 0 STDIN adi qw 08/15/2008 17:23:37 2-10:2
#### Assume job name column is exactly 10 characters wide.
my $jobid_prio_name_regex5 = '(?:(\d+)\s+)?[.\d]+\s+\S.{9}';
my $user_state_date_regex5 = '(\S+)\s+(\w+)\s+(\d\d/\d\d/\d{4} \d\d:\d\d:\d\d)';
my $master_tid_regex5 = '(MASTER|SLAVE)(?:\s+(\d+))?'; # for running jobs
my $taskdef_regex5 = '(?:\s+([:\-\d,]+))?'; # for queued jobs
my $base_regex5 = '^\s*'.$jobid_prio_name_regex5.' '.$user_state_date_regex5;
my $running_regex5 = $base_regex5.'\s+'.$master_tid_regex5.'\s*$';
my $waiting_regex5 = $base_regex5.$taskdef_regex5.'\s*$';
sub run_qstat {
my $command = "$path/qstat -u '*'";
$command .= $compat_mode ? " -F" : " -f";
die unless run_callback($command, \&qstat_parser_callback);
}
sub qstat_parser_callback {
my $fh = shift;
# validate header line
$line = <$fh>;
return unless defined $line; # if there was no output
my @hdr = split ' ',$line;
$log->error("qstat header line not recognized")
unless ($hdr[0] eq 'queuename');
$line = <$fh>;
while (defined $line and $line =~ /^--------------/) {
handle_queue($fh);
handle_running_jobs($fh);
}
return unless defined $line; # if there are no waiting jobs
$line = <$fh>; $log->error("Unexpected line from qstat") unless $line =~ /############/;
$line = <$fh>; $log->error("Unexpected line from qstat") unless $line =~ /PENDING JOBS/;
$line = <$fh>; $log->error("Unexpected line from qstat") unless $line =~ /############/;
$line = <$fh>;
handle_waiting_jobs($fh);
# there should be no lines left
$log->error("Cannot parse qstat output line: $line")
if defined $line;
}
sub handle_queue {
my $fh = shift;
$line = <$fh>;
if (defined $line and $line =~ /$queue_regex/) {
my ($qname,$used,$total,$load,$flags) = ($1,$3,$4,$5,$6||'');
$line = <$fh>;
if (not $compat_mode) {
($currentqueue, $currentnode) = split '@',$qname,2;
unless ($currentnode) {
$log->error("Queue name of the form 'queue\@host' expected. Got: $qname");
}
} else {
$currentqueue = $qname;
# parse complexes to extract hostname
while (defined $line and $line =~ /$complex_regex/) {
$currentnode = $2 if $1 eq 'qf:hostname';
$line = <$fh>;
}
$log->warning("Could not extract hostname for queue $qname") unless $currentnode;
}
if ($currentnode) {
# Was this node not listed with qhost -xml ?
if (not exists $node_stats{$currentnode} or
not exists $node_stats{$currentnode}{totalcpus}) {
# Node name may have been truncated by qstat -f
if (length $qname >= 30) {
# Try to match it with a node already listed by qhost -xml
my @fullnames = grep { length($_) >= length($currentnode)
and $_ =~ m/^\Q$currentnode\E/
} grep { exists $node_stats{$_}{totalcpus}
} keys %node_stats;
$currentnode = $fullnames[0] if @fullnames == 1;
}
# Node name may have been truncated by qhost -xml
for (my $name = $currentnode; length $name >= 24; chop $name) {
$currentnode = $name if exists $node_stats{$name}
and exists $node_stats{$name}{totalcpus}
}
}
if (not exists $node_stats{$currentnode} or
not exists $node_stats{$currentnode}{totalcpus}) {
$log->warning("Queue $currentqueue\@$currentnode cannot be matched"
." with a hostname listed by qhost -xml");
}
$node_stats{$currentnode}{load} = $load unless $load eq '-NA-';
$node_stats{$currentnode}{runningslots} ||= 0; # will be counted later
$node_stats{$currentnode}{queues}{$currentqueue}
= {usedslots=>$used, totalslots=>$total, suspslots=>'0', flags=>$flags};
}
}
}
# Running jobs in a queue instance
sub handle_running_jobs {
my $fh = shift;
my $regex = $compat_mode ? $running_regex5 : $running_regex6;
while (defined $line and $line =~ /$regex/) {
if (not $compat_mode) { ### SGE v 6.x ###
my ($jobid,$user,$slots,$taskid) = ($1,$2,$5,$6);
$taskid = 0 unless $taskid; # 0 is an invalid task id
# Index running jobs by job-ID and task-ID
my $task = $running_jobs{$jobid}{$taskid} || {};
$running_jobs{$jobid}{$taskid} = $task;
$user_total_jobs{$user}++;
$task->{user} = $user;
$task->{state} = $3;
$task->{date} = $4;
$task->{queue} = $currentqueue;
$task->{nodes}{$currentnode} = $slots;
$task->{slots} += $slots;
if ($task->{state} =~ /[sST]/) {
$node_stats{$currentnode}{queues}{$currentqueue}{suspslots} += $slots;
} else {
$node_stats{$currentnode}{runningslots} += $slots;
}
} else { ### SGE 5.x, pre 6.0 ###
my ($jobid,$user,$role,$taskid) = ($1,$2,$5,$6);
$taskid = 0 unless $taskid; # 0 is an invalid task id
if ($role eq 'MASTER' and not defined $jobid) {
$log->error("Cannot parse qstat output line: $line");
} elsif (not defined $jobid) {
$jobid = $currentjobid;
} else {
$currentjobid = $jobid;
}
# Index running jobs by job-ID and task-ID
my $task = $running_jobs{$jobid}{$taskid} || {};
$running_jobs{$jobid}{$taskid} = $task;
if ($role eq 'MASTER') { # each job has one MASTER
$user_total_jobs{$user}++;
$task->{user} = $user;
$task->{state} = $3;
$task->{date} = $4;
$task->{queue} = $currentqueue;
$task->{slots}++;
$task->{nodes}{$currentnode}++;
$task->{is_parallel} = 0;
if ($task->{state} =~ /[sST]/) {
$node_stats{$currentnode}{queues}{$currentqueue}{suspslots}++;
} else {
$node_stats{$currentnode}{runningslots}++;
}
} elsif (not $task->{is_parallel}) { # Fist SLAVE following the MASTER
$task->{is_parallel} = 1; # Don't count this SLAVE
} else { # Other SLAVEs, resume counting
$task->{slots}++;
$task->{nodes}{$currentnode}++;
if ($task->{state} =~ /[sST]/) {
$node_stats{$currentnode}{queues}{$currentqueue}{suspslots}++;
} else {
$node_stats{$currentnode}{runningslots}++;
}
}
}
last unless defined ($line = <$fh>);
}
}
sub handle_waiting_jobs {
my $fh = shift;
my $rank = 1;
my $regex = $compat_mode ? $waiting_regex5 : $waiting_regex6;
while (defined $line and $line =~ /$regex/) {
if (not $compat_mode) { ### SGE v 6.x ###
my ($jobid,$user,$taskdef) = ($1,$2,$6);
my $ntasks = $taskdef ? count_array_spec($taskdef) : 1;
unless ($ntasks) {
$log->error("Failed parsing task definition: $taskdef");
}
$waiting_jobs{$jobid}{user} = $user;
$waiting_jobs{$jobid}{state} = $3;
$waiting_jobs{$jobid}{date} = $4;
$waiting_jobs{$jobid}{slots} = $5;
$waiting_jobs{$jobid}{tasks} += $ntasks;
$waiting_jobs{$jobid}{rank} = $rank;
$user_total_jobs{$user} += $ntasks;
$user_waiting_jobs{$user} += $ntasks;
$rank += $ntasks;
} else { ### SGE 5.x, pre 6.0 ###
my ($jobid,$user,$taskdef) = ($1,$2,$5);
my $ntasks = $taskdef ? count_array_spec($taskdef) : 1;
unless ($ntasks) {
$log->error("Failed parsing task definition: $taskdef");
}
# The number of slots is not available from qstat output.
$waiting_jobs{$jobid}{user} = $user;
$waiting_jobs{$jobid}{state} = $3;
$waiting_jobs{$jobid}{date} = $4;
$waiting_jobs{$jobid}{tasks} += $ntasks;
$waiting_jobs{$jobid}{rank} = $rank;
# SGE 5.x does not list number of slots. Assuming 1 slot per job!
$waiting_jobs{$jobid}{slots} = 1;
$user_total_jobs{$user} += $ntasks;
$user_waiting_jobs{$user} += $ntasks;
$rank += $ntasks;
}
last unless defined ($line = <$fh>);
}
}
} # end of qstat block
sub run_qconf {
# cpu distribution
$cpudistribution = '';
# qconf -sep deprecated therefore we are using qhost -xml
my $qhost_xml_output = `$path/qhost -xml` or $log->error("Failed listing licensed processors");
use XML::Simple qw(:strict);
my $xml = XMLin($qhost_xml_output, KeyAttr => { host => 'name' }, ForceArray => [ 'host' ]);
for my $h ( keys %{$xml->{host}} ) {
next if $h eq "global";
$node_stats{$h}{arch} =$xml->{host}{$h}{"hostvalue"}[0]{content};
$node_stats{$h}{totalcpus} = $xml->{host}{$h}{"hostvalue"}[1]{content};
}
my %cpuhash;
$cpuhash{$_->{totalcpus}}++ for values %node_stats;
while ( my ($cpus,$count) = each %cpuhash ) {
$cpudistribution .= "${cpus}cpu:$count " if $cpus > 0;
}
chop $cpudistribution;
# global limits
loop_callback("$path/qconf -sconf global", sub {
my $l = shift;
$max_jobs = $1 if $l =~ /^max_jobs\s+(\d+)/;
$max_u_jobs = $1 if $l =~ /^max_u_jobs\s+(\d+)/;
}) or $log->error("Failed listing global configurations");
# list all queues
loop_callback("$path/qconf -sql", sub {
push @queue_names, shift
}) or $log->error("Failed listing all queues");
chomp @queue_names;
}
sub req_limits ($) {
my $line = shift;
my ($reqcputime, $reqwalltime);
while ($line =~ /[sh]_cpu=(\d+)/g) {
$reqcputime = $1 if not $reqcputime or $reqcputime > $1;
}
while ($line =~ /[sh]_rt=(\d+)/g) {
$reqwalltime = $1 if not $reqwalltime or $reqwalltime > $1;
}
return ($reqcputime, $reqwalltime);
}
sub lrms_init() {
$ENV{SGE_ROOT} = $options->{sge_root} || $ENV{SGE_ROOT};
$log->error("could not determine SGE_ROOT") unless $ENV{SGE_ROOT};
$ENV{SGE_CELL} = $options->{sge_cell} || $ENV{SGE_CELL} || 'default';
$ENV{SGE_QMASTER_PORT} = $options->{sge_qmaster_port} if $options->{sge_qmaster_port};
$ENV{SGE_EXECD_PORT} = $options->{sge_execd_port} if $options->{sge_execd_port};
for (split ':', $ENV{PATH}) {
$ENV{SGE_BIN_PATH} = $_ and last if -x "$_/qsub";
}
$ENV{SGE_BIN_PATH} = $options->{sge_bin_path} || $ENV{SGE_BIN_PATH};
$log->error("SGE executables not found") unless -x "$ENV{SGE_BIN_PATH}/qsub";
$path = $ENV{SGE_BIN_PATH};
}
sub cluster_info () {
my $lrms_cluster = {};
# add this cluster to the info tree
$lrms_info->{cluster} = $lrms_cluster;
# Figure out SGE type and version
$lrms_cluster->{lrms_glue_type} = "sungridengine";
$lrms_cluster->{lrms_type} = $sge_type;
$lrms_cluster->{lrms_version} = $sge_version;
$lrms_cluster->{cpudistribution} = $cpudistribution;
$lrms_cluster->{totalcpus} += $_->{totalcpus} || 0 for values %node_stats;
# Count used/free CPUs and queued jobs in the cluster
# Note: SGE has the concept of "slots", which roughly corresponds to
# concept of "cpus" in ARC (PBS) LRMS interface.
my $usedcpus = 0;
my $runningjobs = 0;
for my $tasks (values %running_jobs) {
for my $task (values %$tasks) {
$runningjobs++;
# Skip suspended jobs
$usedcpus += $task->{slots}
unless $task->{state} =~ /[sST]/;
}
}
for my $job (values %waiting_jobs) {
$queuedjobs += $job->{tasks};
$queuedcpus += $job->{tasks} * $job->{slots};
}
$lrms_cluster->{usedcpus} = $usedcpus;
$lrms_cluster->{queuedcpus} = $queuedcpus;
$lrms_cluster->{queuedjobs} = $queuedjobs;
$lrms_cluster->{runningjobs} = $runningjobs;
# List LRMS queues
#$lrms_cluster->{queue} = [ @queue_names ];
}
sub queue_info ($) {
my $qname = shift;
my $lrms_queue = {};
# add this queue to the info tree
$lrms_info->{queues}{$qname} = $lrms_queue;
# multiple (even overlapping) queues are supported.
my @qnames = ($qname);
# This code prepares for a scenario where grid jobs in a ComputingShare are
# submitted by a-rex to thout requesting specific queue. Jobs in can end up
# in several possible queues. This function should then try to agregate
# values over all the queues in a list.
# OBS: more work is needed to make this work
if ($options->{queues}{$qname}{sge_queues}) {
@qnames = split ' ', $options->{queues}{$qname}{sge_queues};
}
# NOTE:
# In SGE the relation between CPUs and slots is quite elastic. Slots is
# just one of the complexes that the SGE scheduler takes into account. It
# is quite possible (depending on configuration permits) to have more slots
# used by jobs than total CPUs on a node. On the other side, even if there
# are unused slots in a queue, jobs might be prevented to start because of
# some other constraints.
# queuestatus - will be negative only if all queue instances have a status
# flag set other than 'a'.
# queueused - sum of slots used by jobs, not including suspended jobs.
# queuetotal - sum of slots limited by the number of cpus on each node.
# queuefree - attempt to calculate free slots.
my $queuestatus = -1;
my $queuetotal = 0;
my $queuefree = 0;
my $queueused = 0;
for my $nodename (keys %node_stats) {
my $node = $node_stats{$nodename};
my $queues = $node->{queues};
next unless defined $queues;
my $nodetotal = 0; # number of slots on this node in the selected queues
my $nodemax = 0; # largest number of slots in any of the selected queues
my $nodefree = 0;
my $nodeused = 0;
for my $name (keys %$queues) {
next unless grep {$name eq $_} @qnames;
my $q = $queues->{$name};
$nodetotal += $q->{totalslots};
$nodemax = $q->{totalslots} if $nodemax < $q->{totalslots};
$nodeused += $q->{usedslots} - $q->{suspslots};
# Any flag on the queue implies that the queue is not taking more jobs.
$nodefree += $q->{totalslots} - $q->{usedslots} unless $q->{flags};
# The queue is healty if there is an instance in any other states
# than normal or (a)larm. See man qstat for the meaning of the flags.
$queuestatus = 1 unless $q->{flags} =~ /[dosuACDE]/;
}
# Cheating a bit here. SGE's scheduler would consider load averages
# among other things to decide if there are free slots.
if (defined $node->{totalcpus}) {
my $maxslots = $node->{totalcpus};
if ($nodetotal > $maxslots) {
$log->debug("Capping nodetotal ($nodename): $nodetotal > ".$maxslots);
$nodetotal = $maxslots;
}
if ($nodefree > $maxslots - $node->{runningslots}) {
$log->debug("Capping nodefree ($nodename): $nodefree > ".$maxslots." - ".$node->{runningslots});
$nodefree = $maxslots - $node->{runningslots};
$nodefree = 0 if $nodefree < 0;
}
} else {
$log->info("Node not listed by qhost -xml: $nodename");
}
$queuetotal += $nodetotal;
$queuefree += $nodefree;
$queueused += $nodeused;
}
$lrms_queue->{totalcpus} = $queuetotal;
#$lrms_queue->{freecpus} = $queuefree;
$lrms_queue->{running} = $queueused;
$lrms_queue->{status} = $queuestatus;
$lrms_queue->{MaxSlotsPerJob} = $queuetotal;
# settings in the config file override
my $qopts = $options->{queues}{$qname};
$lrms_queue->{totalcpus} = $qopts->{totalcpus} if $qopts->{totalcpus};
# reserve negative numbers for error states
$log->warning("Negative status for queue $qname: $lrms_queue->{status}")
if $lrms_queue->{status} < 0;
# Grid Engine has hard and soft limits for both CPU time and
# wall clock time. Nordugrid schema only has CPU time.
# The lowest of the 2 limits is returned by this code.
# This code breaks if there are some nodes with separate limits:
# h_rt 48:00:00,[cpt.uio.no=24:00:00]
my $command = "$path/qconf -sq @qnames";
loop_callback($command, sub {
my $l = shift;
if ($l =~ /^[sh]_rt\s+(\S+)/) {
return if $1 eq 'INFINITY';
my $timelimit;
if ($1 =~ /^(\d+):(\d+):(\d+)$/) {
my ($h,$m,$s) = ($1,$2,$3);
$timelimit = $s + 60 * ($m + 60 * $h);
} else {
$log->warning("Error extracting time limit from line: $l");
return;
}
if (not defined $lrms_queue->{maxwalltime}
or $lrms_queue->{maxwalltime} > $timelimit) {
$lrms_queue->{maxwalltime} = $timelimit;
}
}
elsif ($l =~ /^[sh]_cpu\s+(\S+)/) {
return if $1 eq 'INFINITY';
my $timelimit;
if ($1 =~ /^(\d+):(\d+):(\d+)$/) {
my ($h,$m,$s) = ($1,$2,$3);
$timelimit = $s + 60 * ($m + 60 * $h);
} else {
$log->warning("Error extracting time limit from line: $l");
return;
}
if (not defined $lrms_queue->{maxcputime}
or $lrms_queue->{maxcputime} > $timelimit) {
$lrms_queue->{maxcputime} = $timelimit;
}
}
}) or $log->error("Failed listing named queues");
# Grid Engine puts queueing jobs in single "PENDING" state pool,
# so here we report the total number queueing jobs in the cluster.
$lrms_queue->{queued} = $queuedjobs;
# nordugrid-queue-maxrunning
# nordugrid-queue-maxqueuable
# nordugrid-queue-maxuserrun
# The total max running jobs is the number of slots for this queue
$lrms_queue->{maxrunning} = $lrms_queue->{totalcpus};
# SGE has a global limit on total number of jobs, but not per-queue limit.
# This global limit gives an upper bound for maxqueuable and maxrunning
if ($max_jobs) {
$lrms_queue->{maxqueuable} = $max_jobs if $max_jobs;
$lrms_queue->{maxrunning} = $max_jobs if $lrms_queue->{maxrunning} > $max_jobs;
}
if (defined $max_u_jobs and defined $lrms_queue->{maxuserrun} and $lrms_queue->{maxuserrun} > $max_u_jobs) {
$lrms_queue->{maxuserrun} = $max_u_jobs;
}
}
sub jobs_info ($) {
# LRMS job IDs from Grid Manager
my $jids = shift;
my $lrms_jobs = {};
# add jobs to the info tree
$lrms_info->{jobs} = $lrms_jobs;
my ($job, @running, @queueing);
# loop through all requested jobs
for my $jid (@$jids) {
if (defined $running_jobs{$jid} and not defined $running_jobs{$jid}{0}) {
$log->warning("SGE job $jid is an array job. Unable to handle it");
} elsif (defined ($job = $running_jobs{$jid}{0})) {
push @running, $jid;
my $user = $job->{user};
$user_total_jobs{$user}++;
# OBS: it's assumed that jobs in this loop are not part of array
# jobs, which is true for grid jobs (non-array jobs have taskid 0)
if ($job->{state} =~ /[rt]/) {
# running or transfering
$lrms_jobs->{$jid}{status} = 'R';
} elsif ($job->{state} =~ /[sST]/) {
# suspended
$lrms_jobs->{$jid}{status} = 'S';
} else {
# Shouldn't happen
$lrms_jobs->{$jid}{status} = 'O';
push @{$lrms_jobs->{$jid}{comment}}, "Unexpected SGE state: $job->{state}";
$log->warning("SGE job $jid is in an unexpected state: $job->{state}");
}
# master node for parallel runs
my ($cluster_queue, $exec_host) = split '@', $job->{queue};
$lrms_jobs->{$jid}{nodes} = [ $exec_host ] if $exec_host;
$lrms_jobs->{$jid}{cpus} = $job->{slots};
} elsif (defined ($job = $waiting_jobs{$jid})) {
push @queueing, $jid;
$lrms_jobs->{$jid}{rank} = $job->{rank};
# Old SGE versions do not list the number of slots for queing jobs
$lrms_jobs->{$jid}{cpus} = $job->{slots} if not $compat_mode;
if ($job->{state} =~ /E/) {
# DRMAA: SYSTEM_ON_HOLD ?
# TODO: query qacct for error msg
$lrms_jobs->{$jid}{status} = 'O';
} elsif ($job->{state} =~ /h/) {
# Job is on hold
$lrms_jobs->{$jid}{status} = 'H';
} elsif ($job->{state} =~ /w/ and $job->{state} =~ /q/) {
# Normally queued
$lrms_jobs->{$jid}{status} = 'Q';
} else {
# Shouldn't happen
$lrms_jobs->{$jid}{status} = 'O';
push @{$lrms_jobs->{$jid}{comment}}, "Unexpected SGE state: $job->{state}";
$log->warning("SGE job $jid is in an unexpected state: $job->{state}");
}
} else {
# The job has finished.
# Querying accounting system is slow, so we skip it for now.
# That will be done by scan-sge-jobs.
$log->debug("SGE job $jid has finished");
$lrms_jobs->{$jid}{status} = 'EXECUTED';
$lrms_jobs->{$jid}{comment} = [];
}
}
my $jid;
# Running jobs
$jid = undef;
my ($jidstr) = join ',', @running;
loop_callback("$path/qstat -j $jidstr", sub {
my $l = shift;
if ($l =~ /^job_number:\s+(\d+)/) {
$jid=$1;
}
elsif ($l =~ /^usage/) {
# OBS: array jobs have multiple 'usage' lines, one per runnig task
# Memory usage in kB
# SGE reports vmem and maxvmem.
# maxvmem chosen here
if ($l =~ /maxvmem=(\d+(?:\.\d+)?)\s*(\w)/) {
my $mult = 1024;
if ($2 eq "M") {$mult = 1024}
if ($2 eq "G") {$mult = 1024*1024}
$lrms_jobs->{$jid}{mem} = int($mult*$1);
}
# used cpu time in minutes
if ($l =~ /cpu=(?:(\d+):)?(\d+):(\d\d):(\d\d)/) {
my ($d,$h,$m,$s) = ($1||0,$2,$3,$4);
my $cputime = $s + 60*($m + 60*($h + 24*$d));
$lrms_jobs->{$jid}{cputime} = $cputime;
}
}
elsif ($l =~ /^hard resource_list/) {
my ($reqcputime, $reqwalltime) = req_limits($l);
$lrms_jobs->{$jid}{reqcputime} = $reqcputime if $reqcputime;
$lrms_jobs->{$jid}{reqwalltime} = $reqwalltime if $reqwalltime;
}
}) or $log->warning("Failed listing named jobs");
# Waiting jobs
$jidstr = join ',', @queueing;
$jid = undef;
loop_callback("$path/qstat -j $jidstr", sub {
my $l = shift;
if ($l =~ /^job_number:\s+(\d+)/) {
$jid=$1;
}
elsif ($l =~ /^hard resource_list/) {
my ($reqcputime, $reqwalltime) = req_limits($l);
$lrms_jobs->{$jid}{reqcputime} = $reqcputime if $reqcputime;
$lrms_jobs->{$jid}{reqwalltime} = $reqwalltime if $reqwalltime;
}
elsif ($l =~ /^\s*(cannot run because.*)/) {
# Reason for being held in queue
push @{$lrms_jobs->{$jid}{comment}}, "LRMS: $1";
}
# Look for error messages, often jobs pending in error state 'Eqw'
elsif ($l =~ /^error reason\s*\d*:\s*(.*)/) {
# for SGE version 6.x. Examples:
# error reason 1: can't get password entry for user "grid". Either the user does not exist or NIS error!
# error reason 1: 08/20/2008 13:40:27 [113794:25468]: error: can't chdir to /some/dir: No such file or directory
# error reason 1: fork failed: Cannot allocate memory
# 1: fork failed: Cannot allocate memory
push @{$lrms_jobs->{$jid}{comment}}, "SGE job state was Eqw. LRMS error message was: $1";
loop_callback("$path/qdel -fj $jidstr", sub {})
}
elsif ($l =~ /(job is in error state)/) {
# for SGE version 5.x.
push @{$lrms_jobs->{$jid}{comment}}, "SGE job state was Eqw. LRMS error message was: $1";
loop_callback("$path/qdel -fj $jidstr", sub {})
# qstat is not informative. qacct would be a bit more helpful with
# messages like:
# failed 1 : assumedly before job
# failed 28 : changing into working directory
}
}) or $log->warning("Failed listing named jobs");
}
sub users_info($$) {
my ($qname, $accts) = @_;
my $lrms_users = {};
# add users to the info tree
my $lrms_queue = $lrms_info->{queues}{$qname};
$lrms_queue->{users} = $lrms_users;
# freecpus
# queue length
#
# This is hard to implement correctly for a complex system such as SGE.
# Using simple estimate.
my $freecpus = 0;
foreach my $u ( @{$accts} ) {
if ($max_u_jobs) {
$user_total_jobs{$u} = 0 unless $user_total_jobs{$u};
$freecpus = $max_u_jobs - $user_total_jobs{$u};
$freecpus = $lrms_queue->{status}
if $lrms_queue->{status} < $freecpus;
} else {
$freecpus = $lrms_queue->{status};
}
$lrms_queue->{minwalltime} = 0;
$lrms_queue->{mincputime} = 0;
$lrms_users->{$u}{queuelength} = $user_waiting_jobs{$u} || 0;
$freecpus = 0 if $freecpus < 0;
if ($lrms_queue->{maxwalltime}) {
$lrms_users->{$u}{freecpus} = { $freecpus => $lrms_queue->{maxwalltime} };
} else {
$lrms_users->{$u}{freecpus} = { $freecpus => 0 }; # unlimited
}
}
}
sub run_qhost {
my ($host) = @_;
my $result = {};
#require Data::Dumper; import Data::Dumper qw(Dumper);
#print STDERR Dumper($host);
loop_callback("$path/qhost -F -h `echo $host | cut -d . -f 1` | grep '='", sub {
my $l = shift;
my ($prefix, $value ) = split ":", $l;
if ( $value =~ /^mem_total=(\d+(?:\.\d+)?)\s*(\w)/) {
my $mult = 1;
if ($2 eq "M") {$mult = 1024}
if ($2 eq "G") {$mult = 1024*1024}
$result->{$host}{pmem} = int($mult*$1);
}
elsif ( $value =~ /^virtual_total=(\d+(?:\.\d+)?)\s*(\w)/) {
my ($mult) = 1;
if ($2 eq "M") {$mult = 1024}
if ($2 eq "G") {$mult = 1024*1024}
$result->{$host}{vmem} = int($mult*$1);
}
elsif ( $value =~ /^m_socket=(\d+(?:\.\d+)?)/) {
$result->{$host}{nsock} = int($1);
}
}) or $log->error("Failed listing host attributes");
return $result;
}
sub check_host_state_na {
my ($host) = @_;
my $result;
loop_callback("$path/qstat -f | grep `echo $host | cut -d . -f 1`", sub {
my $l = shift;
if ( $l =~ /-NA-/) {
$result=1;
}
else {
$result=0;
}
}) or $log->error("Failed check host");
return $result;
}
sub nodes_info {
#require Data::Dumper; import Data::Dumper qw(Dumper);
my $lrms_nodes = {};
# add nodes to the info tree
$lrms_info->{nodes} = $lrms_nodes;
for my $host (keys %node_stats) {
my $node = $node_stats{$host};
my $queues = $node->{queues};
next unless defined $queues;
my $arc_queue = 0;
for my $qname1 (keys %$queues) {
for my $qname2 ( keys %{$options->{queues}}) {
if ($qname1 =~ $qname2 ) {$arc_queue = 1;}
}
}
if ($arc_queue == 0) {next;}
$lrms_nodes->{$host}{lcpus} = $node_stats{$host}{totalcpus};
$lrms_nodes->{$host}{slots} = $node_stats{$host}{totalcpus};
my $pmem;
my $vmem;
my $nsock;
if (check_host_state_na($host) != 1) {
$pmem = run_qhost($host);
$vmem = run_qhost($host);
$nsock = run_qhost($host);
$lrms_nodes->{$host}{pmem} = $pmem->{$host}{pmem};
$lrms_nodes->{$host}{vmem} = $vmem->{$host}{vmem};
$lrms_nodes->{$host}{nsock} = $nsock->{$host}{nsock};
$lrms_nodes->{$host}{isfree} = 1;
$lrms_nodes->{$host}{isavailable} = 1;
}
else {
$lrms_nodes->{$host}{pmem} = 0;
$lrms_nodes->{$host}{vmem} = 0;
$lrms_nodes->{$host}{nsock} = 0;
$lrms_nodes->{$host}{lcpus} = 0;
$lrms_nodes->{$host}{slots} = 0;
$lrms_nodes->{$host}{isfree} = 0;
$lrms_nodes->{$host}{isavailable} = 0;
}
# TODO
# $lrms_nodes->{$host}{tags} =
# $lrms_nodes->{$host}{release} =
#my %system = qw(lx Linux sol SunOS darwin Darwin);
#my %machine = qw(amd64 x86_64 x86 i686 ia64 ia64 ppc ppc sparc sparc sparc64 sparc64);
#if ($node_stats{$host}{arch} =~ /^(lx|sol|darwin)-(amd64|x86|ia64|ppc|sparc|sparc64)$/) {
# $lrms_nodes->{$host}{sysname} = $system{$1};
# $lrms_nodes->{$host}{machine} = $machine{$2};
#}
}
#print STDERR Dumper($lrms_nodes);
#print STDERR Dumper(%{$options->{queues}});
}
sub test {
LogUtils::level("VERBOSE");
require Data::Dumper; import Data::Dumper qw(Dumper);
$path = shift;
(%running_jobs,%waiting_jobs) = ();
get_lrms_info("");
print Dumper(\%node_stats,\%running_jobs,\%waiting_jobs);
}
#test('./test/6.0');
#test('./test/5.3');
#test($ARGV[0]);
1;
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