fixed conflicts

1 files changed, 423 insertions, 0 deletions

diff --git a/training/utils/parallelize.pl b/training/utils/parallelize.pl
new file mode 100755
index 00000000..4197e0e5
--- /dev/null
+++ b/training/utils/parallelize.pl
@@ -0,0 +1,423 @@
+#!/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 $workdir = '.';
+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,
+      "workdir=s" => \$workdir,
+      "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, $filename) = tempfile( "$workdir/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
+}