merge with upstream

1 files changed, 0 insertions, 423 deletions

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=<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;
-  }
-  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 <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
-}