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parallel: If --block is left out, --pipepart will use a block size that will result in 10 jobs per jobslot.
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parent
d570ec2d20
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51f212e548
42
src/parallel
42
src/parallel
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@ -120,17 +120,30 @@ $Global::JobQueue = JobQueue->new(
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$number_of_args,\@Global::transfer_files,\@Global::ret_files);
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if($opt::pipepart) {
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if($opt::roundrobin) {
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# Compute size of -a
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if(not $opt::blocksize or $opt::roundrobin) {
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# --block not set =>
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# compute reasonable value giving 10 jobs per jobslot
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# --roundrobin => divide equally between jobslots
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my $size = 0;
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# Compute size of -a
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$size += -s $_ for @opt::a;
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# Compute $Global::max_jobs_running
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$Global::dummy_jobs = 1;
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for my $sshlogin (values %Global::host) {
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$sshlogin->max_jobs_running();
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}
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$Global::max_jobs_running or ::die_bug("Global::max_jobs_running not set");
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# Set --blocksize = size / no of proc
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$opt::blocksize = 1 + $size / $Global::max_jobs_running;
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$Global::max_jobs_running or
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::die_bug("Global::max_jobs_running not set");
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if($opt::roundrobin) {
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# Run in total $job_slots jobs
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# Set --blocksize = size / no of proc
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$Global::blocksize = 1 + int($size / $Global::max_jobs_running);
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} else {
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# Run in total $job_slots*10 jobs
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# Set --blocksize = size / no of proc / 10
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$Global::blocksize = 1 +
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int($size / $Global::max_jobs_running / 10);
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}
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}
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@Global::cat_partials = map { pipe_part_files($_) } @opt::a;
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# Unget the empty arg as many times as there are parts
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@ -215,7 +228,7 @@ sub pipe_part_files {
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}
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my $header = find_header(\$buf,open_or_exit($file));
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# find positions
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my @pos = find_split_positions($file,$opt::blocksize,length $header);
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my @pos = find_split_positions($file,$Global::blocksize,length $header);
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# Make @cat_partials
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my @cat_partials = ();
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for(my $i=0; $i<$#pos; $i++) {
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@ -230,7 +243,7 @@ sub find_header {
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# $fh = filehandle to read from
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# Uses:
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# $opt::header
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# $opt::blocksize
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# $Global::blocksize
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# Returns:
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# $header string
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my ($buf_ref, $fh) = @_;
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@ -239,7 +252,7 @@ sub find_header {
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if($opt::header eq ":") { $opt::header = "(.*\n)"; }
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# Number = number of lines
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$opt::header =~ s/^(\d+)$/"(.*\n)"x$1/e;
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while(read($fh,substr($$buf_ref,length $$buf_ref,0),$opt::blocksize)) {
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while(read($fh,substr($$buf_ref,length $$buf_ref,0),$Global::blocksize)) {
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if($$buf_ref=~s/^($opt::header)//) {
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$header = $1;
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last;
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@ -318,7 +331,7 @@ sub spreadstdin {
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# read a record
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# Spawn a job and print the record to it.
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# Uses:
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# $opt::blocksize
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# $Global::blocksize
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# STDIN
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# $opt::r
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# $Global::max_lines
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@ -335,7 +348,7 @@ sub spreadstdin {
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my $chunk_number = 1;
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my $one_time_through;
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my $two_gb = 2**31-1;
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my $blocksize = $opt::blocksize;
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my $blocksize = $Global::blocksize;
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my $in = *STDIN;
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my $header = find_header(\$buf,$in);
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while(1) {
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@ -998,11 +1011,10 @@ sub parse_options {
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if(@opt::transfer_files) { push @Global::transfer_files, @opt::transfer_files; }
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if(not defined $opt::recstart and
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not defined $opt::recend) { $opt::recend = "\n"; }
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if(not defined $opt::blocksize) { $opt::blocksize = "1M"; }
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$opt::blocksize = multiply_binary_prefix($opt::blocksize);
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if($opt::blocksize > 2**31-1) {
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$Global::blocksize = multiply_binary_prefix($opt::blocksize || "1M");
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if($Global::blocksize > 2**31-1) {
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warning("--blocksize >= 2G causes problems. Using 2G-1.");
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$opt::blocksize = 2**31-1;
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$Global::blocksize = 2**31-1;
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}
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$opt::memfree = multiply_binary_prefix($opt::memfree);
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check_invalid_option_combinations();
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@ -5130,7 +5142,7 @@ sub compute_number_of_processes {
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$max_system_proc_reached and last;
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my $before_getting_arg = time;
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if(!$opt::roundrobin) {
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if(!$Global::dummy_jobs) {
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get_args_or_jobs() or last;
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}
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$wait_time_for_getting_args += time - $before_getting_arg;
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@ -1133,13 +1133,19 @@ B<--files> is often used with B<--pipe>.
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B<--pipe> maxes out at around 1 GB/s input, and 100 MB/s output. If
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performance is important use B<--pipepart>.
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See also: B<--recstart>, B<--recend>, B<--fifo>, B<--cat>, B<--pipepart>.
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See also: B<--recstart>, B<--recend>, B<--fifo>, B<--cat>,
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B<--pipepart>, B<--files>.
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=item B<--pipepart>
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Pipe parts of a physical file. B<--pipepart> works similar to
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B<--pipe>, but is much faster. It has a few limitations:
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B<--pipe>, but is much faster.
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If B<--block> is left out, B<--pipepart> will use a block size that
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will result in 10 jobs per jobslot.
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B<--pipepart> has a few limitations:
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=over 3
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@ -2866,7 +2872,7 @@ Or if the regexps are fixed strings:
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grep -F -f regexps.txt bigfile
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There are 2 limiting factors: CPU and disk I/O. CPU is easy to
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measure: If the grep takes >90% CPU (e.g. when running top), then the
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measure: If the B<grep> takes >90% CPU (e.g. when running top), then the
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CPU is a limiting factor, and parallelization will speed this up. If
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not, then disk I/O is the limiting factor, and depending on the disk
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system it may be faster or slower to parallelize. The only way to know
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@ -2876,23 +2882,23 @@ If the CPU is the limiting factor parallelization should be done on the regexps:
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cat regexp.txt | parallel --pipe -L1000 --round-robin grep -f - bigfile
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If a line matches multiple regexps, the line may be duplicated. The command
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will start one grep per CPU and read bigfile one time per CPU,
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but as that is done in parallel, all reads except the first will be
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cached in RAM. Depending on the size of regexp.txt it may be faster to
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use --block 10m instead of -L1000. If regexp.txt is too big to fit in
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RAM, remove --round-robin and adjust -L1000. This will cause bigfile
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to be read more times.
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If a line matches multiple regexps, the line may be duplicated. The
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command will start one B<grep> per CPU and read I<bigfile> one time
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per CPU, but as that is done in parallel, all reads except the first
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will be cached in RAM. Depending on the size of I<regexp.txt> it may
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be faster to use B<--block 10m> instead of B<-L1000>. If I<regexp.txt>
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is too big to fit in RAM, remove B<--round-robin> and adjust
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B<-L1000>. This will cause I<bigfile> to be read more times.
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Some storage systems perform better when reading multiple chunks in
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parallel. This is true for some RAID systems and for some network file
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systems. To parallelize the reading of bigfile:
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systems. To parallelize the reading of I<bigfile>:
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parallel --pipepart --block 100M -a bigfile -k grep -f regexp.txt
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This will split bigfile into 100MB chunks and run grep on each of
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these chunks. To parallelize both reading of bigfile and regexp.txt
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combine the two using --fifo:
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This will split I<bigfile> into 100MB chunks and run B<grep> on each of
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these chunks. To parallelize both reading of I<bigfile> and I<regexp.txt>
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combine the two using B<--fifo>:
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parallel --pipepart --block 100M -a bigfile --fifo cat regexp.txt \
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\| parallel --pipe -L1000 --round-robin grep -f - {}
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@ -4860,8 +4866,9 @@ it also uses rsync with ssh.
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=head1 SEE ALSO
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B<ssh>(1), B<rsync>(1), B<find>(1), B<xargs>(1), B<dirname>(1),
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B<make>(1), B<pexec>(1), B<ppss>(1), B<xjobs>(1), B<prll>(1),
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B<dxargs>(1), B<mdm>(1)
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B<ssh>(1), B<ssh-agent>(1), B<sshpass>(1), B<ssh-copy-id>(1),
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B<rsync>(1), B<find>(1), B<xargs>(1), B<dirname>(1), B<make>(1),
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B<pexec>(1), B<ppss>(1), B<xjobs>(1), B<prll>(1), B<dxargs>(1),
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B<mdm>(1)
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=cut
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@ -1819,7 +1819,7 @@
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<p>When using <b>--cat</b>, <b>--pipepart</b>, or when a job is run on a remote machine, the command is wrapped with helper scripts. <b>-vv</b> shows all of this.</p>
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<pre><code> parallel -vv --pipepart wc :::: num30000</code></pre>
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<pre><code> parallel -vv --pipepart --block 1M wc :::: num30000</code></pre>
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<p>Output:</p>
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@ -1816,7 +1816,7 @@ When using B<--cat>, B<--pipepart>, or when a job is run on a remote
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machine, the command is wrapped with helper scripts. B<-vv> shows all
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of this.
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parallel -vv --pipepart wc :::: num30000
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parallel -vv --pipepart --block 1M wc :::: num30000
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Output:
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@ -596,6 +596,16 @@ echo '### bug #34422: parallel -X --eta crashes with div by zero'
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# We do not care how long it took
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seq 2 | stdout parallel -X --eta echo | grep -E -v 'ETA:.*AVG'
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echo '**'
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echo '### --pipepart autoset --block => 10*joblots'
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seq 1000 > /run/shm/parallel$$;
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parallel -j2 -k --pipepart echo {#} :::: /run/shm/parallel$$;
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rm /run/shm/parallel$$
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echo '**'
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EOF
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echo '### 1 .par file from --files expected'
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@ -1638,5 +1638,32 @@ Computers / CPU cores / Max jobs to run
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1:local / 8 / 2
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Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
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echo '**'
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**
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echo '### --pipepart autoset --block => 10*joblots'
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### --pipepart autoset --block => 10*joblots
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seq 1000 > /run/shm/parallel$$; parallel -j2 -k --pipepart echo {#} :::: /run/shm/parallel$$; rm /run/shm/parallel$$
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1
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2
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3
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4
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5
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6
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7
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8
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9
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10
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11
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12
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13
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14
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15
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16
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17
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18
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19
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20
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echo '**'
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**
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### 1 .par file from --files expected
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0
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@ -846,7 +846,7 @@ _
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parallel --env _ -S $SERVER1 'echo $VAR; my_func2' ::: bar
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/bin/bash: my_func2: command not found
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parallel -vv --pipepart wc :::: num30000
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parallel -vv --pipepart --block 1M wc :::: num30000
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<num30000 perl -e 'while(@ARGV) { sysseek(STDIN,shift,0) || die; $left = shift; while($read = sysread(STDIN,$buf, ($left > 131072 ? 131072 : $left))){ $left -= $read; syswrite(STDOUT,$buf); } }' 0 0 0 168894 | (wc)
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30000 30000 168894
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my_func3() {
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