in reply to missing values when using Parallel::ForkManager

G'day plagent,

You haven't shown the code that actually generates the report. That makes it rather difficult to troubleshoot.

The actual output you show has staggered columns. This suggests to me that data for various columns is either whitespace or empty strings. The latter could be the result of an uninitialized value being treated as "". The warnings pragma will alert you to this.

Other potential issues include:

If one or more of those suggestions and guesses lead to a solution, that's great. If not, you'll need to post more code for us to help you further. Also include any output from the two pragmata I mentioned: given they're both lexically scoped, it's important to show where in your code that you've included them.

-- Ken

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Re^2: missing values when using Parallel::ForkManager
by plagent (Novice) on Jul 06, 2015 at 05:38 UTC
    Thanks, Ken. I updated the source code, and hope this light version will explain my trouble. In fact, there was complaint from running the above code. It is "Use of uninitialized value $count". The code of this line is 
    my $count = $result_buffer->{$id}->{$pwm};

    [download]
    The missing value here indicates that this piece of code 
     my $count = count_pwm_num($pwm,$seq_1,$seq_2);

    [download]
    did not perform its function when parameters were transferred here. $pwm is from list @ciona_pwm_array. Because after executing those lines, the result will catch either 1 or 0, 
    if($count != 0) {
     $output_temp_handle->print($id);
     $output_temp_handle->print("\t$pwm\t1\n");
}
else {
     $output_temp_handle->print($id);
     $output_temp_handle->print("\t$pwm\t0\n");
}

    [download]
    However, as shown in result table, several values were missed from certain rows, (row c missed value 1 in column B, row b missed value 1 in column A. The missing values have no specific pattern, and it seems randomly lost. I doubted for some reason it did not execute this code 
    $pm->start and next PWM;

    [download]
    But I do not know why. Thanks.
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      I wrote a mini code for this problem which replicates my puzzle. 
      #!/usr/bin/perl

use strict;
use Parallel::ForkManager;

my $pm = Parallel::ForkManager->new(10);

foreach my $j (1..100) {
    LINKS:
    for my $i (1..10) {
        $pm->start and next LINKS;
        my $num = count($i);
        print $num,"\t";
        $pm->finish;
    }
    print "\n";
    $pm->wait_all_children;
}

sub count {
    my $num = shift;
    return $num + 1;
}

      [download]
      I expected each row should generate ten numbers from 2 to 11. However, several rows will miss values. Even worse, several rows output 11 numbers instead of 10 numbers, and have replicate, for example, 10 appear twice. Why?
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[d/l]

        I don't get any missed numbers; I always get 2..11. I moved the wait_all_children() line above the line that prints a newline so that the output is clearer and more consistent: 

        2       3       4       5       6       7       9       8       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       10      9       8     
+  11
2       3       4       5       6       7       9       10      11    
+  8
2       3       4       5       6       7       9       8       11    
+  10
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       9       11      8     
+  10
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       8       9       7       11    
+  10
2       3       4       5       6       7       9       10      8     
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       8       9       7       11    
+  10
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       8       9       10      7     
+  11
2       3       4       5       6       7       8       10      9     
+  11
2       3       4       5       6       7       9       10      8     
+  11
2       3       4       5       6       7       8       9       11    
+  10
2       3       4       5       6       7       9       10      8     
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       8       9       10    
+  11
2       3       4       5       6       7       9       10      8     
+  11

        [download]

        Doing things in parallel means that you can't guarantee in what order they will finish. Sometimes one process takes a bit longer than the others and so the numbers appear "out of order".

        - tye        

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