host_file option for mpi

MGEScan · Feb 17, 2016 · b585b28 · b585b28
1 parent 0f5f812
commit b585b28
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Showing 3 changed files with 26 additions and 5 deletions.
diff --git a/mgescan/ltr/find_ltr.pl b/mgescan/ltr/find_ltr.pl
@@ -40,6 +40,12 @@
 my $RANGE_BIN=500;         # range in the bin
 my $FLANKING_LEN=20;
 
+my $debug, $host_file, $hf_option;
+$debug = $ENV{'MGESCAN_DEBUG'};
+$host_file = "";
+$hf_option = "";
+$host_file = $ENV{'MGESCAN_HOME'}."/host_file" if -f $ENV{'MGESCAN_HOME'}."/host_file";
+$host_file = $ENV{'MGESCAN_SRC'}."/host_file" if -f $ENV{'MGESCAN_SRC'}."/host_file";
 
 ###################################################
 # HMM for domain
@@ -191,7 +197,8 @@ sub call_find_ltr_for_each_chr{   #$genome_dir, $main_dir, $ltr_dir, $ltr_data_d
 	#print("mkdir ".$_[3]);   
 	if ($nmpi) {
 		my $mpi_program = $program_dir."/../mpi_mgescan";
-		my $mpi_option = "-mca btl ^openib"; # ignore finding infiniteband
+		$hf_option = "-hostfile $host_file " if ($host_file != "");
+		my $mpi_option = $hf_option."-mca btl ^openib"; # ignore finding infiniteband
 		my $prg_name = "ltr";
 		my $command = "mpirun -n ".$nmpi." ".$mpi_option." ".$mpi_program." --prg ".$prg_name." --genome ".$_[0]." --data ".$_[3]." --hmmerv ".$hmmerv;
 		# mpirun -n 1 -mca btl ^openib /nfs/nfs4/home/lee212/github/mgescan/mgescan/ltr/../mpi_mgescan --prg ltr --genome /scratch/lee212/test-results/mgescan2/ltr/dmelanogaster/genome/ --data /scratch/lee212/test-results/mgescan2/ltr/dmelanogaster/ltr/ltr/ --hmmerv 3

diff --git a/mgescan/ltr/find_ltr_pair.pl b/mgescan/ltr/find_ltr_pair.pl
@@ -44,6 +44,13 @@
 my $chr_name;
 my $run_hmm;
 
+my $debug, $host_file, $hf_option;
+$debug = $ENV{'MGESCAN_DEBUG'};
+$host_file = "";
+$hf_option = "";
+$host_file = $ENV{'MGESCAN_HOME'}."/host_file" if -f $ENV{'MGESCAN_HOME'}."/host_file";
+$host_file = $ENV{'MGESCAN_SRC'}."/host_file" if -f $ENV{'MGESCAN_SRC'}."/host_file";
+
 ###################################################
 # HMM for domain
 ###################################################
@@ -127,7 +134,8 @@ sub call_find_ltr_for_each_chr{   #$genome_dir, $main_dir, $ltr_dir, $ltr_data_d
 	system("mkdir ".$_[3]);   
 	if ($nmpi) {
 		my $mpi_program = $program_dir."/../mpi_mgescan";
-		my $mpi_option = "-mca btl ^openib"; # ignore finding infiniteband
+		$hf_option = "-hostfile $host_file " if ($host_file != "");
+		my $mpi_option = $hf_option."-mca btl ^openib"; # ignore finding infiniteband
 		my $prg_name = "ltr";
 		my $command = "mpirun -n ".$nmpi." ".$mpi_option." ".$mpi_program." --prg ".$prg_name." --genome ".$_[0]." --data ".$_[3]." --hmmerv ".$hmmerv;
 		system($command);

diff --git a/mgescan/nonltr/run_MGEScan.pl b/mgescan/nonltr/run_MGEScan.pl
@@ -25,8 +25,12 @@
 my $nmpi;
 my $host = hostname;
 
-my $debug;
+my $debug, $host_file, $hf_option;
 $debug = $ENV{'MGESCAN_DEBUG'};
+$host_file = "";
+$hf_option = "";
+$host_file = $ENV{'MGESCAN_HOME'}."/host_file" if -f $ENV{'MGESCAN_HOME'}."/host_file";
+$host_file = $ENV{'MGESCAN_SRC'}."/host_file" if -f $ENV{'MGESCAN_SRC'}."/host_file";
 
 print "\n\n";
 GetOptions(
@@ -87,7 +91,8 @@
 #
 if ($nmpi) {
 	my $mpi_program = $program_dir."/../mpi_mgescan";
-	my $mpi_option = "-mca btl ^openib"; # ignore finding infiniteband
+	$hf_option = "-hostfile $host_file " if ($host_file != "");
+	my $mpi_option = $hf_option."-mca btl ^openib"; # ignore finding infiniteband
 	my $command = "mpirun -n ".$nmpi." ".$mpi_option." ".$mpi_program." --prg nonltr --genome ".$plus_dna_dir." --data ".$plus_out_dir." --hmmerv ".$hmmerv;
 	system($command);
 } else {
@@ -128,7 +133,8 @@
 invert_seq($plus_dna_dir, $minus_dna_dir);
 if ($nmpi) {
 	my $mpi_program = $program_dir."/../mpi_mgescan";
-	my $mpi_option = "-mca btl ^openib"; # ignore finding infiniteband
+	$hf_option = "-hostfile $host_file " if ($host_file != "");
+	my $mpi_option = $hf_option."-mca btl ^openib"; # ignore finding infiniteband
 	my $command = "mpirun -n ".$nmpi." ".$mpi_option." ".$mpi_program." --prg nonltr --genome ".$minus_dna_dir." --data ".$minus_out_dir." --hmmerv ".$hmmerv;
 	system($command);
 } else {