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Remove code related to MPI
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bosborne committed Dec 5, 2011
1 parent 5577f09 commit b047cb4
Showing 1 changed file with 1 addition and 29 deletions.
30 changes: 1 addition & 29 deletions lib/Bio/Tools/Run/Phylo/Phyml.pm
Expand Up @@ -198,7 +198,6 @@ map { $models3->{'aa'}->{$_} = 1 }
-opt_topology => boolean [1] -opt_topology => boolean [1]
-opt_lengths => boolean [1] -opt_lengths => boolean [1]
-no_memory_check => boolean [1] -no_memory_check => boolean [1]
-mpi => boolean [1]
-program_name => string -program_name => string
=cut =cut
Expand All @@ -221,8 +220,7 @@ sub new {
$freq, $kappa, $invar, $category_number, $freq, $kappa, $invar, $category_number,
$alpha, $tree, $opt_topology, $opt_lengths, $alpha, $tree, $opt_topology, $opt_lengths,
$opt, $search, $rand_start, $rand_starts, $opt, $search, $rand_start, $rand_starts,
$rand_seed, $no_memory_check, $bootstrap, $mpi, $rand_seed, $no_memory_check, $bootstrap, $program_name
$program_name
) )
= $self->_rearrange( = $self->_rearrange(
[ [
Expand All @@ -245,7 +243,6 @@ sub new {
RAND_SEED RAND_SEED
NO_MEMORY_CHECK NO_MEMORY_CHECK
BOOTSTRAP BOOTSTRAP
MPI
PROGRAM_NAME PROGRAM_NAME
) )
], ],
Expand All @@ -271,7 +268,6 @@ sub new {
$self->rand_seed($rand_seed) if $rand_seed; $self->rand_seed($rand_seed) if $rand_seed;
$self->no_memory_check($no_memory_check) if $no_memory_check; $self->no_memory_check($no_memory_check) if $no_memory_check;
$self->bootstrap($bootstrap) if $bootstrap; $self->bootstrap($bootstrap) if $bootstrap;
$self->mpi($mpi) if $mpi;
$self->program_name($program_name) if $program_name; $self->program_name($program_name) if $program_name;


return $self; return $self;
Expand Down Expand Up @@ -903,29 +899,6 @@ sub no_memory_check {
return $self->{_no_memory_check} || 0; return $self->{_no_memory_check} || 0;
} }


=head2 mpi
Title : mpi
Usage : $factory->mpi(1);
Function:
Returns : boolean (defaults to false)
Args : None to get, integer to set.
=cut

sub mpi {
my ( $self, $value ) = @_;
if ( defined($value) ) {
if ($value) {
$self->{_mpi} = 1;
}
else {
$self->{_mpi} = 0;
}
}
return $self->{_mpi} || 0;
}

=head2 bootstrap =head2 bootstrap
Title : bootstrap Title : bootstrap
Expand Down Expand Up @@ -957,7 +930,6 @@ sub _run {
my ( $self, $file ) = @_; my ( $self, $file ) = @_;


my $exe = $self->executable || return; my $exe = $self->executable || return;
$exe .= '-mpi' if $self->mpi;


my $command; my $command;
my $output_stat_file; my $output_stat_file;
Expand Down

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