move Grid library to a proper place. And update to OO moose

annotation/BILS/Grid/BilsGridRunner.pm

@@ -0,0 +1,76 @@
+package BilsGridRunner;
+
+use strict;
+use warnings;
+use Carp;
+use base qw (GridRunner);  ## really just for aesthetics
+use List::Util qw (shuffle);
+use FindBin;
+
+BEGIN {
+
+    ## find the path to the LSF_perl_lib directory.
+    foreach my $dir (@INC) {
+        if (-d "$dir/LSF_perl_lib") {
+            push (@INC, "$dir/LSF_perl_lib");
+            last;
+        }
+    }
+    ## find the path to the SLURM_perl_lib directory.
+    foreach my $dir (@INC) {
+        if (-d "$dir/SLURM_perl_lib") {
+            push (@INC, "$dir/SLURM_perl_lib");
+            last;
+        }
+    }
+}
+
+use Run_Bsub;
+use Cwd;
+
+####
+sub run_on_grid {
+    my ($args) = @_  ;
+
+    my (@cmds, $scheduler, $queueu);
+    if( ! defined($args->{cmds}) ) {print "No command provided.\n";exit;}    		 else{ @cmds = $args->{cmds}; }
+    if( ! defined($args->{scheduler})) {$scheduler="slurm"; print "Default scheduler used: $scheduler\n"} 		 else{ $scheduler = $args->{scheduler}; }
+    if( ! defined($args->{queueu})) {$queueu=undef;} 		 else{ $queueu = $args->{queueu}; }
+
+    @cmds = shuffle @cmds;
+
+    if($scheduler eq "slurm"){
+      &Run_Slurm::set_queue("normal");
+      &Run_Slurm::set_memory("4"); # 4 G of RAM
+      #&Run_Bsub::set_mount_test(cwd()); # only run on nodes with a verified mount
+      my @failed_cmds = &Run_Slurm::run(@cmds);
+    }
+    elsif($scheduler eq "lsf"){
+      &Run_Bsub::set_queue("normal");
+      &Run_Bsub::set_memory("4"); # 4 G of RAM
+      #&Run_Bsub::set_mount_test(cwd()); # only run on nodes with a verified mount
+      my @failed_cmds = &Run_Bsub::run(@cmds);
+    }
+    else{
+        print "Scheduler $scheduler not implemented yet. <slurm> and <lsf> are the only possible choice currently\n";
+    }
+
+    if (@failed_cmds) {
+
+        my $num_failed_cmds = scalar(@failed_cmds);
+
+        print STDERR "$num_failed_cmds commands failed during grid computing.\n";
+
+        return(&run_on_grid(@failed_cmds));
+
+    }
+    else {
+        print "All commands completed successfully on the computing grid.\n";
+        return(0);
+    }
+}
+
+####
+
+
+1;

annotation/BILS/Grid/Bsub.pm

@@ -0,0 +1,153 @@
+package Bsub;
+
+use strict;
+use warnings;
+use File::Basename;
+use IPC::Cmd qw[can_run run];
+use Carp;
+use Moose;
+use BILS::Grid::GridRunner;
+
+extends 'GridRunner';
+
+has scheduler => ('is' => 'rw', isa => 'Str', default => 'LSF');
+
+# The BUILD method is called after an object is created.
+# Here it is used to set all different folders used to store logging
+sub BUILD {
+  can_run('bsub') or croak 'bsub command does not exist. Cannot run jobs!';
+}
+
+
+####
+sub _submit_job {
+    my $self = shift;
+    my $num_cmds_launched = shift;
+
+    my $num_cmds = $self->{num_cmds};
+    my $cmds_per_node = $self->{cmds_per_node};
+    my $cmds_list_aref = $self->{cmds_list};
+
+    my $log_dir = $self->{log_dir};
+    my $retvals_dir = $self->{retvals_dir};
+    my $cmds_dir = $self->{cmds_dir};
+    my $monitor_dir = $self->{monitor_dir};
+
+    my $orig_num_cmds_launched = $num_cmds_launched;
+
+
+    my $shell_script = "$cmds_dir/J$$.S${num_cmds_launched}.sh";
+    open (my $fh, ">$shell_script") or die $!;
+    print $fh "#!/bin/sh\n\n";
+
+    $self->_write_minimal_environment($fh);
+
+    my $num_cmds_written = 0;
+
+    my $monitor_started = "$monitor_dir/$num_cmds_launched.started";
+    my $monitor_finished = "$monitor_dir/$num_cmds_launched.finished";
+
+    my @cmd_indices_prepped;
+
+    while ($num_cmds_launched < $num_cmds && $num_cmds_written < $cmds_per_node) {
+        my $next_cmd_index = $num_cmds_launched; #always one less than the current index
+        my $cmd_string = $cmds_list_aref->[ $next_cmd_index ];
+
+        push (@cmd_indices_prepped, $next_cmd_index);
+
+    		my $retval_bin = int($next_cmd_index / $self->retval_bin_size());
+
+    		my $retval_subdir = "$retvals_dir/$retval_bin";
+    		unless (-d $retval_subdir) {
+    			mkdir $retval_subdir or die "Error, cannot mkdir $retval_subdir";
+    		}
+
+        print $fh "## Command index $next_cmd_index\n"
+            . "touch $monitor_started\n"
+            . "$cmd_string\n"
+            . 'echo $? >> ' . "$retval_subdir/entry_$next_cmd_index.ret\n\n";
+
+        $num_cmds_launched++;
+        $num_cmds_written++;
+    }
+
+    print $fh "\n"
+        . "rm -f $monitor_started\n"
+        . "touch $monitor_finished\n"
+        . "\n"
+        . "exit 0\n\n";
+
+
+    close $fh;
+    chmod (0775, $shell_script);
+
+    print "Submitting: $shell_script to bsub\n" if $self->verbose;
+
+
+    my $cmd = undef;
+    if($self->{queue}){
+      my $queue = $self->{queue};
+      my $cmd = "bsub -q $queue -e $shell_script.stderr -o $shell_script.stdout ";
+    }
+    else{
+      my $cmd = "bsub -e $shell_script.stderr -o $shell_script.stdout ";
+    }
+  	if (my $memory = $self->{memory}) {
+  		$cmd .= " -R \"rusage[mem=$memory]\" ";
+  	}
+	#if (my $mount_test = $self->{mount_test}) {
+#		$cmd .= " -E \"/broad/tools/NoArch/pkgs/local/checkmount $mount_test && [ -e $mount_test ]\" ";
+#	}
+    if (my $group = $self->{group}) {
+        $cmd .= " -G $group ";
+    }
+
+	   $cmd .= " $shell_script 2>&1 ";
+
+    my $job_id_text = `$cmd`;
+    # print STDERR "\n$job_id_text\n";
+
+    my $ret = $?;
+    if ($ret) {
+        print STDERR "BSUB failed to accept job: $cmd\n (ret $ret)\n";
+
+        unlink $shell_script; # cleanup, try again later
+
+        sleep(2*60); # sleep 2 minutes for now.  Give the system time to recuperate if a problem exists
+        return ($orig_num_cmds_launched);
+
+    }
+
+    else {
+
+        $shell_script = basename($shell_script);
+        open (my $logdir_jobsfh, ">>$log_dir/job_ids.txt") or die "Error, cannot open file $log_dir/job_ids.txt";
+        ## get the job ID and log it:
+        if ($job_id_text =~ /Job \<(\d+)\>/) {
+            my $job_id = $1;
+            print $logdir_jobsfh "$job_id\t$shell_script\n";
+            my $monitor_href = $self->{nodes_in_progress};
+            $monitor_href->{$monitor_finished} = $job_id;
+
+            $self->{job_id_to_cmd_indices}->{$job_id} = \@cmd_indices_prepped;
+            $self->{job_id_to_submission_time}->{$job_id} = time();
+
+        }
+        else {
+
+            die "Fatal error, couldn't extract Job ID from submission text: $job_id_text";
+
+        }
+        close $logdir_jobsfh;
+
+        # sleep($WAITTIME); # wait just a short while to give the system a few seconds to act on the submitted jobs.
+        return ($num_cmds_launched);
+    }
+
+}
+
+
+#no Moose;
+#__PACKAGE__->meta->make_immutable;
+;
+1