Changeset 209

Timestamp:

04/28/09 15:01:45 (7 months ago)

Author:

cholt

Message:

lock file update

Files:

• INSTALL (modified) (1 diff)
• MPI/mpi_maker (modified) (3 diffs)
• README (modified) (1 diff)
• lib/File/NFSLock.pm (modified) (3 diffs)
• lib/GI.pm (modified) (16 diffs)
• lib/ds_utility.pm (modified) (1 diff)
• lib/runlog.pm (modified) (1 diff)

INSTALL

@@ -86 +86 @@
-
-  a.  You will have to download the source code and complile it on your machine.
-.  If your using Mac OS-X you can do this
-by typing fink install glib
+ or Glib 2.0.  If your using Mac OS-X you
+can do this by typing fink install glib and fink install glib2-dev
-  b.  Change to the directory containing the Exonerate package to be compiled.
-  c.  To install exonerate in the directory /usr/local/exonerate, type:

MPI/mpi_maker

@@ -260 +260 @@
-               "again|a" =>\$OPT{again},
-               "quiet" =>\$main::quiet,
+               "no_thread" =>\$main::no_thread,
-               "CTL" => sub {GI::generate_control_files() if($rank == $root); MPI_Finalize(); exit(0);},
-               "help|?" => sub {print $usage if($rank == $root); MPI_Finalize(); exit(0)}
@@ -343 +344 @@
-   #---main code for distribution of mpi data starts here
-
-
+do 
-   my $thr = threads->create(\&node_thread);
-   my $go_mpi_status = 1;
-1;
+($main::no_thread) ? 0 : 1; #set to true for threads false for no threads
-
-   while($go_mpi_status){
@@ -818 +819 @@
-   my $tier;
-   my $chunk;
+
+   if($main::no_thread){ #pause and return if no thread is needed
+       $t_need_flag = 0;
+       return;
+   }
+
-   $t_need_flag = 1;
-

README

@@ -35 +35 @@
-    *Augustus 2.0 or higher (augustus.gobics.de)
-    *GeneMark.hmm-E 3.9 or higher (exon.biology.gatech.edu)
-
+2.6 or higher 
-
-To install mpi_maker, you must have an mpi package installed, try the

lib/File/NFSLock.pm

@@ -133 +133 @@
-      time() + $self->{blocking_timeout} : 0;
-
-  ### remove an old lockfile if it is older than the stale_timeout
-  if( -e $self->{lock_file} &&
-      $self->{stale_lock_timeout} > 0 &&
-      time() - (stat _)[9] > $self->{stale_lock_timeout} ){
-    unlink $self->{lock_file};
-  }
-
-  while (1) {
+    ### remove an old lockfile if it is older than the stale_timeout
+    if( -e $self->{lock_file} &&
+        $self->{stale_lock_timeout} > 0 &&
+        time() - (stat _)[9] > $self->{stale_lock_timeout} ){
+        unlink $self->{lock_file};
+    }
+
-    ### open the temporary file
-    $self->create_magic
@@ -161 +161 @@
-    ### If lock exists and is readable, see who is mooching on the lock
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-    }
-
@@ -434 +432 @@
-  ### hard link to the actual file which will bring it up to date
-  return ( link( $file, $rand_file) && unlink($rand_file) );
+}
+
+sub refresh {
+  my $self = shift;
+
+  $errstr = undef;
+  my $rand_file = $self->{rand_file};
+  my $file = $self->{lock_file};
+  $self->{lock_line} = "$HOSTNAME $self->{lock_pid} ".time()." ".int(rand()*10000)."\n";
+  local *_FH;
+  open (_FH,">$rand_file") or do { $errstr = "Couldn't open \"$rand_file\" [$!]"; return undef; };
+  print _FH $self->{lock_line};
+  close _FH;
+
+  my $err;
+  system("mv $rand_file $file") && ($err = "ERROR: Could not refresh lock\n");
+  unlink($rand_file) if(-e $rand_file);
+  die $err if($err);
+
+  return 1;
-}
-

lib/GI.pm

@@ -5 +5 @@
-
-use strict;
-
+
+
-use Exporter;
-use FileHandle;
@@ -41 +42 @@
-use maker::sens_spec;
-use File::NFSLock;
+use threads;
-
-@ISA = qw(
@@ -796 +798 @@
-   my $CTL_OPT     = shift;
-   my $LOG         = shift;
-
-
+
+
+
+
+
-   my $hmm = $CTL_OPT->{gmhmm};
-   
@@ -807 +812 @@
-   $LOG->add_entry("STARTED", $out_file, "");   
-
+
-   my $command  = $exe;
-   $command .= " -m $hmm";
+   $command .= " -g $gm";
+   $command .= " -p $pro";
-   $command .= " -o $out_file";
-   $command .= " $in_file";
@@ -1262 +1270 @@
-   #copy db to local tmp dir and run xdformat or formatdb
-   if ((! @{[<$tmp_db.x?d*>]} || ! @{[<$tmp_db.?sq*>]}) && (! -e $blast_finished)) {
-
+undef
-           copy($db, $tmp_db) if(! -e $tmp_db);
-           dbformat($formater, $tmp_db, 'blastn');
@@ -1508 +1516 @@
-   #copy db to local tmp dir and run xdformat or format db 
-   if ((! @{[<$tmp_db.x?d*>]} || ! @{[<$tmp_db.?sq*>]}) && (! -e $blast_finished) ) {
-
+undef
-           copy($db, $tmp_db) if(! -e $tmp_db);
-           dbformat($formater, $tmp_db, 'blastx');
@@ -1766 +1774 @@
-   #copy db to local tmp dir and run xdformat or formatdb
-   if ((! @{[<$tmp_db.x?d*>]} || ! @{[<$tmp_db.?sq*>]}) && (! -e $blast_finished) ) {
-
+undef
-           copy($db, $tmp_db) if(! -e $tmp_db);
-           dbformat($formater, $tmp_db, 'tblastx');
@@ -2061 +2069 @@
-
-   return $the_void;
+}
+#-----------------------------------------------------------------------------
+#refreshes the maker directory lock every 30 seconds
+sub maintain_lock {
+   my $lock  = shift;
+
+   while(1){
+       sleep 30;
+       $lock->refresh;
+   }
-}
-#-----------------------------------------------------------------------------
@@ -2182 +2200 @@
-                  'qrna',
-                  'fathom',
+                  'probuild'
-                 );
-
@@ -2398 +2417 @@
-   push (@infiles, 'snap') if (grep (/snap/, @{$CTL_OPT{_run}}));
-   push (@infiles, 'gmhmme3') if (grep (/genemark/, @{$CTL_OPT{_run}}));
+   push (@infiles, 'probuild') if (grep (/genemark/, @{$CTL_OPT{_run}}));
-   push (@infiles, 'augustus') if (grep (/augustus/, @{$CTL_OPT{_run}})); 
-   push (@infiles, 'fgenesh') if (grep (/fgenesh/, @{$CTL_OPT{_run}}));
@@ -2556 +2576 @@
-        if(! -d $CTL_OPT{out_base});
-
+   #--check if another instance of maker is running, if not lock the directory
+   my $check;
+   if(-e $CTL_OPT{out_base}."/.maker_lock.NFSLock"){
+       warn "WARNING: Lock found, maker may already be running.\n".
+           "Checking for other instance.\n\n";
+       $check = 1;
+   }
+
+   #lock must be global or it is detroyed outside of block
+   if($LOCK = new File::NFSLock($CTL_OPT{out_base}."/.maker_lock", 'EX', 40, 40)){
+       warn "Everything seems ok!!\n\n" if($check);
+
+       my $thr = threads->create(\&maintain_lock, $LOCK); 
+       $thr->detach;
+   }
+   else{
+       die "ERROR: Another instance of maker is already running for this dataset\n";
+   }
+   
+
-   #--set up optional global TMP
-   if($CTL_OPT{TMP}){
@@ -2576 +2616 @@
-   my %O = (@_) ? @_ : set_defaults();
-   my $ev = 1 if($main::eva);
+   my $log = 1 if(@_);
-
-   #--build opts.ctl file
-   open (OUT, "> $dir/eval_opts.ctl") if($ev);
-
+
+
-   print OUT "#-----Genome (Required for De-Novo Annotation)\n" if(!$ev);
-   print OUT "#-----Genome (Required if not internal to GFF3 file)\n" if($ev);
@@ -2626 +2668 @@
-   print OUT "fgenesh_par_file:$O{fgenesh_par_file} #Fgenesh parameter file\n";
-   print OUT "model_gff:$O{model_gff} #gene models from an external gff3 file (annotation pass-through)\n" if(!$ev);
-model
+pred
-   print OUT "\n";
-   print OUT "#-----Other Annotation Type Options (features maker doesn't recognize)\n" if(!$ev);
@@ -2662 +2704 @@
-   #--build bopts.ctl file
-   open (OUT, "> $dir/eval_bopts.ctl") if($ev);
-
+
+
-   print OUT "#-----BLAST and Exonerate Statistics Thresholds\n";
-   print OUT "blast_type:$O{blast_type} #set to 'wublast' or 'ncbi'\n";
@@ -2697 +2740 @@
-   #--build maker_exe.ctl file
-   open (OUT, "> $dir/eval_exe.ctl") if($ev);
-
+
+
-   print OUT "#-----Location of Executables Used by Maker/Evaluator\n";
-   print OUT "formatdb:$O{formatdb} #location of NCBI formatdb executable\n";
@@ -2719 +2763 @@
-   print OUT "qrna:$O{qrna} #location of qrna executable (not yet implemented)\n";
-   print OUT "fathom:$O{fathom} #location of fathom executable (not yet implemented)\n";
+   print OUT "probuild:$O{probuild} #location of probuild executable (required for genemark)\n";
-   close(OUT);    
-}

lib/ds_utility.pm

@@ -124 +124 @@
-sub add_entry {
-   my $self = shift;
-
+
+
+
+
+
+
+
+
+
-
-   open(my $IN, ">>", $self->{log});

lib/runlog.pm

@@ -506 +506 @@
-
-                my ($te) = $CTL_OPTIONS{repeat_protein} =~ /([^\/]+)$/;
-
-
-
-
+
+
+
+
+
+
-                foreach my $f (@f){
-                    push (@files, $f) if (-f $f);
-                    push (@dirs, $f) if (-d $f);
-                }
+
-            }
-