sub processCnfDirectory {
  use Time::HiRes(gettimeofday);
  use File::Basename;
  my($path) = @_;
  my $pid;
  local $SIG{ALRM} = sub {
        $didTimeout=1;
        print OUTPUT "timeout";
        print "process id", $pid, "\n";
        kill 9, $pid;
       die "Timeout\n";
  };

  print( "working in: $path\n" );

  # append a trailing / if it's not there 
  $path .= '/' if($path !~ /\/$/);

  # loop through the files contained in the directory 
  for my $file (glob($path . '*')) {

    # check if the file is a directory 
    if( -d $file)
      # pass the directory to the routine ( recursion )
      processCnfDirectory($file);
    }
    elsif ($file =~ /.*\.cnf/)
    {
      print OUTPUT basename($file), ",";

      # run using the first solver
      $pid = fork;
      eval {
        $didTimeout=0;
        $start1=gettimeofday();
        alarm $timeout;
        #$pid = `$solver1 $file`;
        $result = `$solver1 $file`;
        waitpid($pid, 0);
      };
      alarm 0;
      $end1=gettimeofday();
      if($didTimeout == 0) {
        print OUTPUT $end1 - $start1;
      }
      print OUTPUT ",";

      # run using the second solver
      $pid = fork;
      eval {
        $didTimeout=0;
        $start2=gettimeofday();
        alarm $timeout;
        #$pid = `$solver2 $file`;
        $result = `$solver2 $file`;
        waitpid($pid, 0);
      };
     };
      alarm 0;
      $end2=gettimeofday();
      if($didTimeout == 0) {
        print OUTPUT $end2 - $start2;
      }
      print OUTPUT "\n";
    }
  }
}
[download]

Okay, you still don't need to use fork(). When you use backticks like that, perl runs that command in another process which you can kill - no fork() needed.

You may want to look at File::Find instead of glob. It makes this kind of thing easier.

I don't see what you are doing with $result, but one way is to capture the process ID from the shell:

$pid = `command && echo $$` ;

I suggest you take a step back and start again with File::Find. I think you've overcomplicated your solution.

You might also try to prevent the OOM issue in the "solver" instead.

I was using fork to obtain the pid. How would I obtain the pid without using fork so I can kill it?