Beefy Boxes and Bandwidth Generously Provided by pair Networks
Perl Monk, Perl Meditation
 
PerlMonks  

Re^5: Reading HUGE file multiple times

by BrowserUk (Pope)
on Apr 28, 2013 at 13:45 UTC ( #1031069=note: print w/ replies, xml ) Need Help??


in reply to Re^4: Reading HUGE file multiple times
in thread Reading HUGE file multiple times

I think the reason is it's writing data line as a hash name and the data line can have 300.000 characters.

No, it's not.

At least, if your description of the file is accurate it isn't.

This bit of the code: $Library_Index{<$Library>} = tell(ARGV), reads the IDs and constructs the hash.

And this bit: scalar <$Library> reads and discards the long data lines.

However, Now I think I see the problem with your version of the code.

This bit:until eof(); of the line iterates until the file is read, except that you forgot to put the filehandle $Library in the parens, so the program will never end because it is testing the end-of-file condition of a different file which will never be true.

Change the line to:

$Library_Index{<$Library>} = tell(ARGV), scalar <$Library> until eof($ +Library);

And see how long it takes.


With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.


Comment on Re^5: Reading HUGE file multiple times
Select or Download Code
Re^6: Reading HUGE file multiple times
by Anonymous Monk on Apr 28, 2013 at 14:16 UTC

    Ups, replied in a wrong place.

    I tried the new code and it works really fast. Problem is there is an error with tell and it's all -1. Would be nice if I could just have ENST04000413399 as and ID but it does not mater that much. From Dumper

    $VAR32564 = -1; $VAR32565 = '>ENST04000413399 ';
      Problem is there is an error with tell and it's all -1.

      D'oh! I made the same mistake you did; I forgot to change ARGV for $Library. The line should read:

      $Library_Index{<$Library>} = tell($library), scalar <$Library> until e +of($Library);

      I tested the write-the-index-to-disc code with a file containing 17,000 id/record pairs with 300,000 data records (5.2GB).

      This creates the index and writes it to disc:

      #! perl -slw use strict; use Storable qw[ store ]; print time; my %idx; $idx{ <> } = tell( STDIN ), scalar <> until eof STDIN; store \%idx, '1031021.idx' or die $!; print time;

      The whole process takes a little over 3 minutes:

      C:\test>1031021-i.pl <1031021.dat 1367160156 1367160362 C:\test>dir 1031021* 28/04/2013 15:30 193 1031021-i.pl 28/04/2013 15:04 5,272,940,608 1031021.dat 28/04/2013 15:46 316,385 1031021.idx 28/04/2013 15:29 374 1031021.pl

      And this code loads that index from disk (<1 second) and the reads 1000 random records (26 seconds) using it:

      #! perl -slw use strict; use Storable qw[ retrieve ]; print time; my $idx = retrieve '1031021.idx' or die $!; print time; open DAT, '+<', '1031021.dat' or die $!; for( 1 .. 1000 ) { my( $id, $offset ) = each %$idx; seek DAT, $offset, 0; my $vid = <DAT>; die 'mismatch' unless $id eq $vid; my $data = <DAT>; } close DAT; print time;

      Run:

      C:\test>1031021.pl 1367160624 1367160624 1367160651

      With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
      Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
      "Science is about questioning the status quo. Questioning authority".
      In the absence of evidence, opinion is indistinguishable from prejudice.
        Perfect! Works like a charm and is blazing fast comparing to initial read method. Thanks so much for your help.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://1031069]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others chilling in the Monastery: (5)
As of 2014-07-14 01:56 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    When choosing user names for websites, I prefer to use:








    Results (254 votes), past polls