#!/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. #TODO: if -j 1, run immediately, not via sentserver? possible differences in environment might make debugging harder #ANNOYANCE: if input is shorter than -j n lines, or at the very last few lines, repeatedly sleeps. time cut down to 15s from 60s my $SCRIPT_DIR; BEGIN { use Cwd qw/ abs_path /; use File::Basename; $SCRIPT_DIR = dirname(abs_path($0)); push @INC, $SCRIPT_DIR, "$SCRIPT_DIR/../environment"; } use LocalConfig; use File::Temp qw/ tempfile /; use Getopt::Long; use IPC::Open2; use strict; use POSIX ":sys_wait_h"; use Cwd qw(getcwd); my $tailn=5; # +0 = concatenate all the client logs. 5 = last 5 lines 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 $numnodes = 8; my $user = $ENV{"USER"}; my $pmem = "9g"; my $basep=50300; my $randp=300; my $tryp=50; my $no_which; my $no_cd; my $DEBUG=$ENV{DEBUG}; print STDERR "DEBUG=$DEBUG output enabled.\n" if $DEBUG; my $verbose = 1; sub verbose { if ($verbose) { print STDERR @_,"\n"; } } sub debug { if ($DEBUG) { my ($package, $filename, $line) = caller; print STDERR "DEBUG: $filename($line): ",join(' ',@_),"\n"; } } sub abspath($) { my $p=shift; my $a=`readlink -f $p`; chomp $a; $a } my $is_shell_special=qr.[ \t\n\\><|&;"'`~*?{}$!()].; my $shell_escape_in_quote=qr.[\\"\$`!].; sub escape_shell { my ($arg)=@_; return undef unless defined $arg; return '""' unless $arg; if ($arg =~ /$is_shell_special/) { $arg =~ s/($shell_escape_in_quote)/\\$1/g; return "\"$arg\""; } return $arg; } sub preview_files { my ($l,$skipempty,$footer,$n)=@_; $n=$tailn unless defined $n; my @f=grep { ! ($skipempty && -z $_) } @$l; my $fn=join(' ',map {escape_shell($_)} @f); my $cmd="tail -n $n $fn"; `$cmd`.($footer?"\nNONEMPTY FILES:\n$fn\n":""); } sub prefix_dirname($) { #like `dirname but if ends in / then return the whole thing local ($_)=@_; if (/\/$/) { $_; } else { s#/[^/]$##; $_ ? $_ : ''; } } sub ensure_final_slash($) { local ($_)=@_; m#/$# ? $_ : ($_."/"); } sub extend_path($$;$$) { my ($base,$ext,$mkdir,$baseisdir)=@_; if (-d $base) { $base.="/"; } else { my $dir; if ($baseisdir) { $dir=$base; $base.='/' unless $base =~ /\/$/; } else { $dir=prefix_dirname($base); } my @cmd=("/bin/mkdir","-p",$dir); system(@cmd) if $mkdir; } return $base.$ext; } my $abscwd=abspath(&getcwd); sub print_help; my $use_fork; my @pids; # Process command-line options unless (GetOptions( "stay-alive" => \$stay_alive, "recycle-clients" => \$recycle_clients, "error-dir=s" => \$errordir, "multi-line" => \$multiline, "file=s" => \@files_to_stage, "use-fork" => \$use_fork, "verbose" => \$verbose, "jobs=i" => \$numnodes, "pmem=s" => \$pmem, "baseport=i" => \$basep, # "iport=i" => \$randp, #for short name -i "no-which!" => \$no_which, "no-cd!" => \$no_cd, "tailn=s" => \$tailn, ) && scalar @ARGV){ print_help(); die "bad options."; } my $cmd = ""; my $prog=shift; if ($no_which) { $cmd=$prog; } else { $cmd=`which $prog`; chomp $cmd; die "$prog not found - $cmd" unless $cmd; } #$cmd=abspath($cmd); for my $arg (@ARGV) { $cmd .= " ".escape_shell($arg); } die "Please specify a command to parallelize\n" if $cmd eq ''; my $cdcmd=$no_cd ? '' : ("cd ".escape_shell($abscwd)."\n"); my $executable = $cmd; $executable =~ s/^\s*(\S+)($|\s.*)/$1/; $executable=`basename $executable`; chomp $executable; print STDERR "Parallelizing ($numnodes ways): $cmd\n\n"; # create -e dir and save .sh use File::Temp qw/tempdir/; unless ($errordir) { $errordir=tempdir("$executable.XXXXXX",CLEANUP=>1); } if ($errordir) { my $scriptfile=extend_path("$errordir/","$executable.sh",1,1); -d $errordir || die "should have created -e dir $errordir"; open SF,">",$scriptfile || die; print SF "$cdcmd$cmd\n"; close SF; chmod 0755,$scriptfile; $errordir=abspath($errordir); &verbose("-e dir: $errordir"); } # 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; # find open port srand; my $port = 50300+int(rand($randp)); my $endp=$port+$tryp; sub listening_port_lines { my $quiet=$verbose?'':'2>/dev/null'; `netstat -a -n $quiet | grep LISTENING | grep -i tcp` } my $netstat=&listening_port_lines; if ($verbose){ print STDERR "Testing port $port...";} while ($netstat=~/$port/ || &listening_port_lines=~/$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"; } 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 = 0; my $script = ""; # fork == one thread runs the sentserver, while the # other spawns the sentclient commands. if (my $pid = fork) { sleep 8; # give other thread time to start sentserver $script = qq{wait $cdcmd$sentclient $host:$port:$key $cmd }; if ($verbose){ print STDERR "Client script:\n====\n"; print STDERR $script; print STDERR "====\n"; } for (my $jobn=0; $jobn<$numnodes; $jobn++){ launch_job(); } if ($recycle_clients) { my $ret; my $livejobs; while (1) { $ret = waitpid($pid, WNOHANG); #print STDERR "waitpid $pid ret = $ret \n"; last if ($ret != 0); $livejobs = numof_live_jobs(); if ($numnodes >= $livejobs ) { # a client terminated, OR # lines of input was less than -j print STDERR "num of requested nodes = $numnodes; num of currently live jobs = $livejobs; Client terminated - launching another.\n"; launch_job(); } else { sleep 15; } } } waitpid($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 $rc\n"; } } sub numof_live_jobs { if ($use_fork) { die "not implemented"; } else { my @livejobs = grep(/$joblist/, split(/\n/, `qstat`)); return ($#livejobs + 1); } } my (@errors,@outs,@cmds); sub launch_job { if ($use_fork) { return launch_job_fork(); } my $errorfile = "/dev/null"; my $outfile = "/dev/null"; $node_count++; my $clientname = $executable; $clientname =~ s/^(.{4}).*$/$1/; $clientname = "$clientname.$node_count"; if ($errordir){ $errorfile = "$errordir/$clientname.ER"; $outfile = "$errordir/$clientname.OU"; push @errors,$errorfile; push @outs,$outfile; } my $todo = qsub_args($pmem) . " -N $clientname -o $outfile -e $errorfile"; push @cmds,$todo; print STDERR "Running: $todo\n"; local(*QOUT, *QIN); open2(\*QOUT, \*QIN, $todo) or die "Failed to open2: $!"; print QIN $script; close QIN; while (my $jobid=<QOUT>){ chomp $jobid; if ($verbose){ print STDERR "Launched client job: $jobid"; } $jobid =~ s/^(\d+)(.*?)$/\1/g; $jobid =~ s/^Your job (\d+) .*$/\1/; print STDERR " short job id $jobid\n"; if ($verbose){ print STDERR "cd: $abscwd\n"; print STDERR "cmd: $cmd\n"; } if ($joblist == "") { $joblist = $jobid; } else {$joblist = $joblist . "\|" . $jobid; } my $cleanfn="`qdel $jobid 2> /dev/null`"; push(@cleanup_cmds, $cleanfn); } close QOUT; } sub launch_job_fork { my $errorfile = "/dev/null"; my $outfile = "/dev/null"; $node_count++; my $clientname = $executable; $clientname =~ s/^(.{4}).*$/$1/; $clientname = "$clientname.$node_count"; if ($errordir){ $errorfile = "$errordir/$clientname.ER"; $outfile = "$errordir/$clientname.OU"; push @errors,$errorfile; push @outs,$outfile; } if (my $pid = fork) { my ($fh, $scr_name) = get_temp_script(); print $fh $script; close $fh; my $todo = "/bin/sh $scr_name 1> $outfile 2> $errorfile"; print STDERR "EXEC: $todo\n"; my $out = `$todo`; print STDERR "RES: $out\n"; unlink $scr_name or warn "Failed to remove $scr_name"; exit 0; } } sub get_temp_script { my ($fh, $filename) = tempfile( "workXXXX", SUFFIX => '.sh'); return ($fh, $filename); } sub cleanup_and_die { cleanup(); die "\n"; } sub cleanup { print STDERR "Cleaning up...\n"; for $cmd (@cleanup_cmds){ print STDERR " Cleanup command: $cmd\n"; eval $cmd; } print STDERR "outputs:\n",preview_files(\@outs,1),"\n"; print STDERR "errors:\n",preview_files(\@errors,1),"\n"; print STDERR "cmd:\n",$cmd,"\n"; print STDERR " cat $errordir/*.ER\nfor logs.\n"; 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: --fork Instead of using qsub, use fork. -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 }