From 47aa8d94d3ddff39295966cee67ce884c98be8da Mon Sep 17 00:00:00 2001 From: Chris Dyer Date: Fri, 27 Jan 2012 14:49:08 -0500 Subject: rename vest to dpmert (dynamic programming mert), rename variables and types to correspond to standard geometric concepts --- vest/parallelize.pl | 423 ---------------------------------------------------- 1 file changed, 423 deletions(-) delete mode 100755 vest/parallelize.pl (limited to 'vest/parallelize.pl') diff --git a/vest/parallelize.pl b/vest/parallelize.pl deleted file mode 100755 index 7d0365cc..00000000 --- a/vest/parallelize.pl +++ /dev/null @@ -1,423 +0,0 @@ -#!/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 Cwd qw/ abs_path cwd getcwd /; -use File::Temp qw/ tempfile /; -use Getopt::Long; -use IPC::Open2; -use strict; -use POSIX ":sys_wait_h"; - -use File::Basename; -my $myDir = dirname(__FILE__); -print STDERR __FILE__." -> $myDir\n"; -push(@INC, $myDir); -require "libcall.pl"; - -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"; - } -} -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 $fn"; - unchecked_output("$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); - check_call(@cmd) if $mkdir; - } - return $base.$ext; -} - -my $abscwd=abs_path(&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=check_output("which $prog"); - chomp $cmd; - die "$prog not found - $cmd" unless $cmd; -} -#$cmd=abs_path($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=check_output("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; - $errordir=abs_path($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 = check_output("dirname $0"); chomp $mydir; -my $sentserver = "$mydir/sentserver"; -my $sentclient = "$mydir/sentclient"; -my $host = check_output("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'; - return unchecked_output("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. -my $pid = fork; -if ($pid == 0) { # child - sleep 8; # give other thread time to start sentserver - $script = "$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; - } - } - } - print STDERR "CHILD PROCESSES SPAWNED ... WAITING\n"; - for my $p (@pids) { - waitpid($p, 0); - } -} else { -# my $todo = "$sentserver -k $key $multiflag $port "; - my $todo = "$sentserver -k $key $multiflag $port $stay_alive_flag "; - if ($verbose){ print STDERR "Running: $todo\n"; } - check_call($todo); - print STDERR "Call to $sentserver returned.\n"; - cleanup(); - exit(0); -} - -sub numof_live_jobs { - if ($use_fork) { - die "not implemented"; - } else { - # We can probably continue decoding if the qstat error is only temporary - my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat"))); - return ($#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=){ - 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; - } - my $pid = fork; - if ($pid == 0) { - my ($fh, $scr_name) = get_temp_script(); - print $fh $script; - close $fh; - my $todo = "/bin/bash -xeo pipefail $scr_name 1> $outfile 2> $errorfile"; - print STDERR "EXEC: $todo\n"; - my $out = check_output("$todo"); - unlink $scr_name or warn "Failed to remove $scr_name"; - exit 0; - } else { - push @pids, $pid; - } -} - -sub get_temp_script { - my ($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 = check_output("basename $0"); chomp $name; - print << "Help"; - -usage: $name [options] - - Automatic black-box parallelization of commands. - -options: - - --use-fork - Instead of using qsub, use fork. - - -e, --error-dir - Retain output files from jobs in , 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 -} -- cgit v1.2.3