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#!/usr/bin/env perl
# Author: Adam Lopez
#
# This script takes a command that processes input
# from stdin one-line-at-time, and parallelizes it
# on the cluster using David Chiang's sentserver/
# sentclient architecture.
#
# Prerequisites: the command *must* read each line
# without waiting for subsequent lines of input
# (for instance, a command which must read all lines
# of input before processing will not work) and
# return it to the output *without* buffering
# multiple lines.
use Getopt::Long;
use IPC::Open2;
use strict;
use POSIX ":sys_wait_h";
my $recycle_clients; # spawn new clients when previous ones terminate
my $stay_alive; # dont let server die when having zero clients
my $joblist = "";
my $errordir;
my $multiline;
my @files_to_stage;
my $verbose = 1;
my $numnodes;
my $user = $ENV{"USER"};
my $pmem = "2g";
sub print_help;
# Process command-line options
if (GetOptions(
"stay-alive" => \$stay_alive,
"recycle-clients" => \$recycle_clients,
"error-dir=s" => \$errordir,
"multi-line" => \$multiline,
"file=s" => \@files_to_stage,
"verbose" => \$verbose,
"jobs=i" => \$numnodes,
"pmem=s" => \$pmem
) == 0 || @ARGV == 0){
print_help();
}
my $cmd = "";
for my $arg (@ARGV){
if ($arg=~ /\s/){
$cmd .= "\"$arg\" ";
} else {
$cmd .= "$arg "
}
}
die "Please specify a command to parallelize\n" if $cmd eq '';
if ($errordir){
`mkdir -p $errordir`;
}
if ($verbose){ print STDERR "Parallelizing: $cmd\n\n"; }
# set cleanup handler
my @cleanup_cmds;
sub cleanup;
sub cleanup_and_die;
$SIG{INT} = "cleanup_and_die";
$SIG{TERM} = "cleanup_and_die";
$SIG{HUP} = "cleanup_and_die";
# other subs:
sub numof_live_jobs;
sub launch_job_on_node;
# vars
my $mydir = `dirname $0`; chomp $mydir;
my $sentserver = "$mydir/sentserver";
my $sentclient = "$mydir/sentclient";
my $host = `hostname`;
chomp $host;
my $executable = $cmd;
$executable =~ s/^\s*(\S+)($|\s.*)/$1/;
$executable=`basename $executable`;
chomp $executable;
# find open port
my $basep=50300;
my $randp=300;
my $tryp=50;
my $port = 50300+int(rand($randp));
my $endp=$port+$tryp;
if ($verbose){ print STDERR "Testing port $port...";}
while (`netstat -l 2>/dev/null | grep -q $port`){
if ($verbose){ print STDERR "port is busy\n";}
$port++;
if ($port > $endp){
die "Unable to find open port\n";
}
if ($verbose){ print STDERR "Testing port $port... "; }
}
if ($verbose){
print STDERR "port $port is available\n";
}
srand;
my $key = int(rand()*1000000);
my $multiflag = "";
if ($multiline){ $multiflag = "-m"; print STDERR "expecting multiline output.\n"; }
my $stay_alive_flag = "";
if ($stay_alive){ $stay_alive_flag = "--stay-alive"; print STDERR "staying alive while no clients are connected.\n"; }
my %node_count;
my $script = "";
# fork == one thread runs the sentserver, while the
# other spawns the sentclient commands.
if (my $pid = fork){
sleep 5; # give other thread time to start sentserver
$script .= "wait\n";
$script .= "$sentclient $host:$port:$key $cmd\n";
if ($verbose){
print STDERR "Client script:\n====\n";
print STDERR $script;
print STDERR "====\n";
}
for (my $jobn=0; $jobn<$numnodes; $jobn++){
launch_job_on_node(1);
}
if ($recycle_clients) {
my $ret;
my $livejobs;
while (1) {
$ret = waitpid($pid, WNOHANG);
#print STDERR "waitpid $pid ret = $ret \n";
if ($ret != 0) {last; } # break
$livejobs = numof_live_jobs();
if ($numnodes >= $livejobs ) { # a client terminated
print STDERR "num of requested nodes = $numnodes; num of currently live jobs = $livejobs; Client terminated - launching another.\n";
launch_job_on_node(1); # TODO: support named nodes
} else {
sleep (60);
}
}
}
waitpid($pid, 0);
cleanup();
} else {
# my $todo = "$sentserver -k $key $multiflag $port ";
my $todo = "$sentserver -k $key $multiflag $port $stay_alive_flag ";
if ($verbose){ print STDERR "Running: $todo\n"; }
my $rc = system($todo);
if ($rc){
die "Error: sentserver returned code $rc\n";
}
}
sub numof_live_jobs {
my @livejobs = grep(/$joblist/, split(/\n/, `qstat`));
return ($#livejobs + 1);
}
sub launch_job_on_node {
my $node = $_[0];
my $errorfile = "/dev/null";
my $outfile = "/dev/null";
unless (exists($node_count{$node})){
$node_count{$node} = 0;
}
my $node_count = $node_count{$node};
$node_count{$node}++;
my $clientname = $executable;
$clientname =~ s/^(.{4}).*$/$1/;
$clientname = "$clientname.$node.$node_count";
if ($errordir){
$errorfile = "$errordir/$clientname.ER";
$outfile = "$errordir/$clientname.OU";
}
my $todo = "qsub -l mem_free=9G -N $clientname -o $outfile -e $errorfile";
if ($verbose){ print STDERR "Running: $todo\n"; }
local(*QOUT, *QIN);
open2(\*QOUT, \*QIN, $todo);
print QIN $script;
close QIN;
while (my $jobid=<QOUT>){
chomp $jobid;
if ($verbose){ print STDERR "Launched client job: $jobid"; }
push(@cleanup_cmds, "`qdel $jobid 2> /dev/null`");
$jobid =~ s/^(\d+)(.*?)$/\1/g;
$jobid =~ s/^Your job (\d+) .*$/\1/;
print STDERR "short job id $jobid\n";
if ($joblist == "") { $joblist = $jobid; }
else {$joblist = $joblist . "\|" . $jobid; }
}
close QOUT;
}
sub cleanup_and_die {
cleanup();
die "\n";
}
sub cleanup {
if ($verbose){ print STDERR "Cleaning up...\n"; }
for $cmd (@cleanup_cmds){
if ($verbose){ print STDERR " $cmd\n"; }
eval $cmd;
}
if ($verbose){ print STDERR "Cleanup finished.\n"; }
}
sub print_help
{
my $name = `basename $0`; chomp $name;
print << "Help";
usage: $name [options]
Automatic black-box parallelization of commands.
options:
-e, --error-dir <dir>
Retain output files from jobs in <dir>, rather
than silently deleting them.
-m, --multi-line
Expect that command may produce multiple output
lines for a single input line. $name makes a
reasonable attempt to obtain all output before
processing additional inputs. However, use of this
option is inherently unsafe.
-v, --verbose
Print diagnostic informatoin on stderr.
-j, --jobs
Number of jobs to use.
-p, --pmem
pmem setting for each job.
Help
}
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