I tried repetition using Inline C. To ensure Inline C does not clobber file handles with MCE's IPC handles, I open file handles in Perl and pass file descriptors to C.
6 workers: 6.2x faster than Algorithm::Combinatorics on machines with 6 real-cores
use strict; use warnings; die "Not UNIX OS\n" if $^O eq 'MSWin32'; # usage: script.pl > out use Inline 'C' => Config => CCFLAGSEX => '-O2'; use Inline 'C' => <<'END_C'; #include <stdio.h> unsigned long c_repetition (int fd, float p0) { unsigned long c = 0; FILE *stream = fdopen(fd, "wb"); float p1,p2,p3,p4,p5,p6,p7,p8,p9,p10; for (p1=0; p1<=1; p1+=0.2){ for (p2=0; p2<=1; p2+=0.2){ for (p3=0; p3<=1; p3+=0.2){ for (p4=0; p4<=1; p4+=0.2){ for (p5=0; p5<=1; p5+=0.2){ for (p6=0; p6<=1; p6+=0.2){ for (p7=0; p7<=1; p7+=0.2){ for (p8=0; p8<=1; p8+=0.2){ for (p9=0; p9<=1; p9+=0.2){ for (p10=0; p10<=1; p10+=0.2){ //------------- fprintf(stream, "%0.1f\t%0 +.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t1 +.0\t1.0\n", p0,p1,p2,p3,p4,p5,p6,p7,p8,p9,p10); c++; //------------- } } } } } } } } } } fflush(stream); fclose(stream); return c; } END_C # Run on UNIX machines with 48+ GiB of RAM. # Otherwise, remove the -use_dev_shm argument. # Beware, consumes 18 GiB in temp dir. use MCE::Signal qw[ $tmp_dir -use_dev_shm ]; use Time::HiRes qw[ time ]; use MCE::Loop; use MCE::Shared; my $start = time; my $c_shared = MCE::Shared->scalar(0); MCE::Loop::init { max_workers => 6, chunk_size => 1 }; # loop through desired combinations mce_loop_s { my $p0 = $_; open my $fh, ">", "$tmp_dir/".MCE->chunk_id(); my $c = c_repetition(fileno($fh), $p0); close $fh; $c_shared->incrby($c); } 0.0, 1.0, 0.2, '%0.1f'; # p0: seq_beg, seq_end, seq_step, format MCE::Loop::finish(); system("cat $tmp_dir/[1-6]; rm -fr $tmp_dir"); printf STDERR "Took: %0.3f seconds [%ld]\n", time() - $start, $c_share +d->get();
36 workers: use-case for a 64-way box (32 real-cores + 32 hyper-threads)
This involves nested parallel loops, possible using MCE. The shared-counter variable increments fine no matter how many levels deep. Locking is handled automatically via the OO interface.
use strict; use warnings; die "Not UNIX OS\n" if $^O eq 'MSWin32'; # usage: script.pl > out use Inline 'C' => Config => CCFLAGSEX => '-O2'; use Inline 'C' => <<'END_C'; #include <stdio.h> unsigned long c_repetition (int fd, float p0, float p1) { unsigned long c = 0; FILE *stream = fdopen(fd, "wb"); float p2,p3,p4,p5,p6,p7,p8,p9,p10; for (p2=0; p2<=1; p2+=0.2){ for (p3=0; p3<=1; p3+=0.2){ for (p4=0; p4<=1; p4+=0.2){ for (p5=0; p5<=1; p5+=0.2){ for (p6=0; p6<=1; p6+=0.2){ for (p7=0; p7<=1; p7+=0.2){ for (p8=0; p8<=1; p8+=0.2){ for (p9=0; p9<=1; p9+=0.2){ for (p10=0; p10<=1; p10+=0.2){ //------------- fprintf(stream, "%0.1f\t%0.1f\ +t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t%0.1f\t1.0\t +1.0\n", p0,p1,p2,p3,p4,p5,p6,p7,p8,p9,p10); c++; //------------- } } } } } } } } } fflush(stream); fclose(stream); return c; } END_C # Run on UNIX machines with 48+ GiB of RAM. # Otherwise, remove the -use_dev_shm argument. # Beware, consumes 18 GiB in temp dir. use MCE::Signal qw[ $tmp_dir -use_dev_shm ]; use Time::HiRes qw[ time ]; use MCE::Loop; use MCE::Shared; my $start = time; my $c_shared = MCE::Shared->scalar(0); MCE::Loop::init { max_workers => 6, chunk_size => 1 }; # loop through desired combinations mce_loop_s { my $p0 = $_; MCE::Loop::init { max_workers => 6, chunk_size => 1 }; $tmp_dir .= "/".MCE->chunk_id(); mkdir $tmp_dir; mce_loop_s { my $p1 = $_; open my $fh, ">", "$tmp_dir/".MCE->chunk_id(); my $c = c_repetition(fileno($fh), $p0, $p1); close $fh; $c_shared->incrby($c); } 0.0, 1.0, 0.2, '%0.1f'; # p1: seq_beg, seq_end, seq_step, format MCE::Loop::finish(); } 0.0, 1.0, 0.2, '%0.1f'; # p0: seq_beg, seq_end, seq_step, format MCE::Loop::finish(); system("cat $tmp_dir/$_/[1-6]; rm -fr $tmp_dir/$_") for 1..6; printf STDERR "Took: %0.3f seconds [%ld]\n", time() - $start, $c_share +d->get();
Results: taken from a 4.2 GHz machine with 8 real-cores, hyper-threads disabled
Combinatorics : 459.752 seconds 6 workers : 74.394 seconds 36 workers : 58.021 seconds <- my CPU has 8 cores
Consuming 32 real-cores and a little more is possible on a 64-way box. Afterwards, one may use MCE or a parallel module of choice to process the output file in parallel.
Disclaimer: My Linux box is tuned to 4.2 GHz on all 8 cores. This is not common. What to take from this is that nested parallel loops is possible with care. On Linux, /dev/shm is beneficial for temporary storage.
Regards, Mario
In reply to Re^2: Parallelization of multiple nested loops
by marioroy
in thread Parallelization of multiple nested loops
by biosub
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