136 lines
3.9 KiB
Perl
136 lines
3.9 KiB
Perl
#!/usr/bin/perl -w
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#
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# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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#
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# This file is part of Bowtie 2.
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#
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# Bowtie 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# Bowtie 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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#
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use strict;
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use warnings;
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use Getopt::Long;
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use FindBin qw($Bin);
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use lib "$Bin";
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use lib "$Bin/contrib";
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use Sim;
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use ForkManager;
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# Simulator configuration
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my %conf = (
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bowtie2_build => "bowtie2-build",
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bowtie2 => "bowtie2",
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bowtie2_build_debug => "bowtie2-build-debug",
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bowtie2_debug => "bowtie2-debug",
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tempdir => "/tmp",
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no_color => 1,
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small => 1
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);
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# Number of parallel processes to use
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my $cpus = 1;
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my $usage = qq!
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run.pl [options*]
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Options:
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--bowtie2 <path> Path to bowtie2 release binary
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--bowtie2-debug <path> Path to bowtie2 debug binary
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--bowtie2-build <path> Path to bowtie2-build release binary
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--bowtie2-build-debug <path> Path to bowtie2-build debug binary
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--tempdir <path> Put temporary files here
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--cases <int> Each thread runs around <int> cases (def: 5)
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--cpus <int> / -p <int> Run test cases in <int> threads at once
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--maxreads <int> Handle at most <int> reads per case
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--numrefs <int> Generate <int> refs per case
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--die-with-child Kill parent as soon as 1 child dies
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--no-die-with-child Don\'t kill parent as soon as 1 child dies
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--small Make small test cases
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--help Print this usage message
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!;
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my $help = 0;
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my $ncases = 5;
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my $dieWithChild = 1;
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GetOptions(
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"bowtie2=s" => \$conf{bowtie2},
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"bowtie2-debug=s" => \$conf{bowtie2_debug},
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"bowtie2-build=s" => \$conf{bowtie2_build},
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"bowtie2-build-debug=s" => \$conf{bowtie2_build_debug},
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"tempdir|tmpdir=s" => \$conf{tempdir},
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"cases-per-thread=i" => \$ncases,
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"small" => \$conf{small},
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"large" => sub { $conf{small} = 0 },
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"no-paired" => \$conf{no_paired},
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"color" => sub { $conf{no_color} = 0 },
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"no-color" => \$conf{no_color},
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"help" => \$help,
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"die-with-child" => \$dieWithChild,
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"no-die-with-child" => sub { $dieWithChild = 0 },
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"p|cpus=i" => \$cpus,
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"u|qupto|maxreads=i" => \$conf{maxreads},
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"numrefs|num-refs=i" => \$conf{numrefs},
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) || die "Bad options;";
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if($help) {
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print $usage;
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exit 0;
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}
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my $sim = Sim->new();
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my $pm = new Parallel::ForkManager($cpus);
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# Callback for when a child finishes so we can get its exit code
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my @childFailed = ();
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my @childFailedPid = ();
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$pm->run_on_finish(sub {
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my ($pid, $exit_code, $ident) = @_;
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if($exit_code != 0) {
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push @childFailed, $exit_code;
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push @childFailedPid, $pid;
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!$dieWithChild || die "Dying with child with PID $pid";
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}
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});
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my $totcases = $ncases * $cpus;
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for(1..$totcases) {
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my $childPid = $pm->start;
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if($childPid != 0) {
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next; # spawn the next child
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}
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$sim->nextCase(\%conf);
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$pm->finish;
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}
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$pm->wait_all_children;
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for(@childFailedPid) {
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print STDERR "Error message from child with pid $_:\n";
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my $fn = ".run.pl.child.$_";
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if(open(ER, $fn)) {
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print STDERR "---------\n";
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while(<ER>) {
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print STDERR $_;
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}
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print STDERR "---------\n";
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close(ER);
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} else {
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print STDERR "(could not open $fn)\n";
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}
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}
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print STDERR "PASSED\n";
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