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parallel: Deal with {} as part of the command (not arg for the command).
This commit is contained in:
Ole Tange
parent
9493541236
commit
163712f709
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@ -236,8 +236,12 @@ Haiku of the month:
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New in this release:
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* A semibig refactoring of big functions. All non-trivial functions are now less than 100 lines. The refactoring makes this release beta quality.
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* GNU Parallel was cited in: Parallel post-processing with MPI-Bash http://dl.acm.org/citation.cfm?id=2691137
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* GNU Parallel was cited in: Distinguishing cause from effect using observational data: methods and benchmarks http://arxiv-web3.library.cornell.edu/pdf/1412.3773.pdf
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* GNU Parallel: Open Source For You (OSFY) magazine, October 2013 edition http://www.shakthimaan.com/posts/2014/11/27/gnu-parallel/news.html
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* コマンドを並列に実行するGNU parallelがとても便利 http://bicycle1885.hatenablog.com/entry/2014/08/10/143612
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145
src/parallel
145
src/parallel
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@ -2186,17 +2186,23 @@ sub progress {
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}
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sub get_job_with_sshlogin {
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# Input:
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# $sshlogin = which host should the job be run on?
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# Uses:
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# $opt::hostgroups
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# $Global::JobQueue
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# Returns:
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# next job object for $sshlogin if any available
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# $job = next job object for $sshlogin if any available
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my $sshlogin = shift;
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my $job = undef;
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my $job;
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if ($opt::hostgroups) {
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my @other_hostgroup_jobs = ();
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while($job = $Global::JobQueue->get()) {
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if($sshlogin->in_hostgroups($job->hostgroups())) {
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# Found a job for this hostgroup
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# Found a job to be run on a hostgroup of this
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# $sshlogin
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last;
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} else {
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# This job was not in the hostgroups of $sshlogin
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@ -2256,6 +2262,9 @@ sub get_job_with_sshlogin {
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sub __REMOTE_SSH__ {}
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sub read_sshloginfiles {
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# Read a list of --slf's
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# Input:
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# @files = files or symbolic file names to read
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# Returns: N/A
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for my $s (@_) {
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read_sshloginfile(expand_slf_shorthand($s));
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@ -2263,6 +2272,11 @@ sub read_sshloginfiles {
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}
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sub expand_slf_shorthand {
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# Expand --slf shorthand into a read file name
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# Input:
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# $file = file or symbolic file name to read
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# Returns:
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# $file = actual file name to read
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my $file = shift;
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if($file eq "-") {
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# skip: It is stdin
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@ -2283,6 +2297,11 @@ sub expand_slf_shorthand {
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}
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sub read_sshloginfile {
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# Read sshloginfile into @Global::sshlogin
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# Input:
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# $file = file to read
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# Uses:
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# @Global::sshlogin
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# Returns: N/A
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my $file = shift;
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my $close = 1;
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@ -2310,6 +2329,17 @@ sub read_sshloginfile {
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}
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sub parse_sshlogin {
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# Parse @Global::sshlogin into %Global::host.
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# Keep only hosts that are in one of the given ssh hostgroups.
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# Uses:
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# @Global::sshlogin
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# $Global::minimal_command_line_length
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# %Global::host
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# $opt::transfer
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# @opt::return
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# $opt::cleanup
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# @opt::basefile
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# @opt::trc
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# Returns: N/A
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my @login;
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if(not @Global::sshlogin) { @Global::sshlogin = (":"); }
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@ -2386,6 +2416,8 @@ sub parse_sshlogin {
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sub remote_hosts {
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# Return sshlogins that are not ':'
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# Uses:
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# %Global::host
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# Returns:
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# list of sshlogins with ':' removed
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return grep !/^:$/, keys %Global::host;
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@ -2394,6 +2426,9 @@ sub remote_hosts {
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sub setup_basefile {
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# Transfer basefiles to each $sshlogin
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# This needs to be done before first jobs on $sshlogin is run
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# Uses:
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# %Global::host
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# @opt::basefile
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# Returns: N/A
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my $cmd = "";
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my $rsync_destdir;
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@ -2416,6 +2451,9 @@ sub setup_basefile {
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sub cleanup_basefile {
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# Remove the basefiles transferred
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# Uses:
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# %Global::host
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# @opt::basefile
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# Returns: N/A
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my $cmd="";
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my $workdir = Job->new("")->workdir();
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@ -2431,9 +2469,58 @@ sub cleanup_basefile {
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}
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sub filter_hosts {
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# Remove down --sshlogins from active duty.
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# Find ncpus, ncores, maxlen, time-to-login for each host.
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# Uses:
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# %Global::host
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# $Global::minimal_command_line_length
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# $opt::use_cpus_instead_of_cores
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# Returns:
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# N/A
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my (%ncores, %ncpus, %time_to_login, %maxlen, %echo, @down_hosts);
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for (parallelized_host_filtering()) {
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my ($ncores_ref, $ncpus_ref, $time_to_login_ref, $maxlen_ref,
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$echo_ref, $down_hosts_ref) =
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parse_host_filtering(parallelized_host_filtering());
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%ncores = %$ncores_ref;
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%ncpus = %$ncpus_ref;
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%time_to_login = %$time_to_login_ref;
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%maxlen = %$maxlen_ref;
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%echo = %$echo_ref;
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@down_hosts = @$down_hosts_ref;
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delete @Global::host{@down_hosts};
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@down_hosts and ::warning("Removed @down_hosts\n");
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$Global::minimal_command_line_length = 8_000_000;
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while (my ($sshlogin, $obj) = each %Global::host) {
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if($sshlogin eq ":") { next }
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$ncpus{$sshlogin} or ::die_bug("ncpus missing: ".$obj->serverlogin());
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$ncores{$sshlogin} or ::die_bug("ncores missing: ".$obj->serverlogin());
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$time_to_login{$sshlogin} or ::die_bug("time_to_login missing: ".$obj->serverlogin());
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$maxlen{$sshlogin} or ::die_bug("maxlen missing: ".$obj->serverlogin());
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if($opt::use_cpus_instead_of_cores) {
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$obj->set_ncpus($ncpus{$sshlogin});
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} else {
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$obj->set_ncpus($ncores{$sshlogin});
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}
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$obj->set_time_to_login($time_to_login{$sshlogin});
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$obj->set_maxlength($maxlen{$sshlogin});
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$Global::minimal_command_line_length =
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::min($Global::minimal_command_line_length,
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int($maxlen{$sshlogin}/2));
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::debug("init", "Timing from -S:$sshlogin ncpus:",$ncpus{$sshlogin},
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" ncores:", $ncores{$sshlogin},
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" time_to_login:", $time_to_login{$sshlogin},
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" maxlen:", $maxlen{$sshlogin},
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" min_max_len:", $Global::minimal_command_line_length,"\n");
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}
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}
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sub parse_host_filtering {
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my (%ncores, %ncpus, %time_to_login, %maxlen, %echo, @down_hosts);
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for (@_) {
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chomp;
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my @col = split /\t/, $_;
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if(defined $col[6]) {
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@ -2455,7 +2542,6 @@ sub filter_hosts {
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# Remove sshlogin
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::debug("init", "--filtered $host\n");
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push(@down_hosts, $host);
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@down_hosts = uniq(@down_hosts);
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} elsif($col[6] eq "127") {
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# signal == 127: parallel not installed remote
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# Set ncpus and ncores = 1
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@ -2501,31 +2587,8 @@ sub filter_hosts {
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::die_bug("host check unmatched short jobline ($col[0]): $_");
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}
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}
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delete @Global::host{@down_hosts};
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@down_hosts and ::warning("Removed @down_hosts\n");
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$Global::minimal_command_line_length = 8_000_000;
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while (my ($sshlogin, $obj) = each %Global::host) {
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if($sshlogin eq ":") { next }
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$ncpus{$sshlogin} or ::die_bug("ncpus missing: ".$obj->serverlogin());
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$ncores{$sshlogin} or ::die_bug("ncores missing: ".$obj->serverlogin());
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$time_to_login{$sshlogin} or ::die_bug("time_to_login missing: ".$obj->serverlogin());
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$maxlen{$sshlogin} or ::die_bug("maxlen missing: ".$obj->serverlogin());
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if($opt::use_cpus_instead_of_cores) {
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$obj->set_ncpus($ncpus{$sshlogin});
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} else {
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$obj->set_ncpus($ncores{$sshlogin});
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}
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$obj->set_time_to_login($time_to_login{$sshlogin});
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$obj->set_maxlength($maxlen{$sshlogin});
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$Global::minimal_command_line_length =
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::min($Global::minimal_command_line_length,
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int($maxlen{$sshlogin}/2));
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::debug("init", "Timing from -S:$sshlogin ncpus:",$ncpus{$sshlogin},
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" ncores:", $ncores{$sshlogin},
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" time_to_login:", $time_to_login{$sshlogin},
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" maxlen:", $maxlen{$sshlogin},
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" min_max_len:", $Global::minimal_command_line_length,"\n");
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}
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@down_hosts = uniq(@down_hosts);
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return(\%ncores, \%ncpus, \%time_to_login, \%maxlen, \%echo, \@down_hosts);
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}
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sub parallelized_host_filtering {
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@ -6997,6 +7060,7 @@ sub new {
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}
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# Replace replacement strings with {= perl expr =}
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@command = merge_rpl_parts(@command);
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# Protect matching inside {= perl expr =}
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# by replacing {= and =} with \257< and \257>
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for(@command) {
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@ -7037,8 +7101,15 @@ sub new {
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}
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}
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}
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# Add {} if no replacement strings in @command
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my($replacecount_ref, $len_ref, @command) =
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replacement_counts_and_lengths(@command);
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if("@command" =~ /^\S*\257</) {
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# Replacement string is (part of) the command (and not just argument)
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# E.g. parallel {}, parallel my_{= s/_//=}, parallel {2}
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# Do no quote (Otherwise it will fail if the input contains spaces)
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$Global::noquote = 1;
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}
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return bless {
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'unget' => \@unget,
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@ -7093,7 +7164,7 @@ sub replacement_counts_and_lengths {
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# Count the number of different replacement strings.
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# Find the lengths of context for context groups and non-context
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# groups.
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# If no {} found: add it to the @command
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# If no {} found in @command: add it to @command
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#
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# Input:
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# @command = command template
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@ -7111,8 +7182,8 @@ sub replacement_counts_and_lengths {
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for my $c (@cmd) {
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while($c =~ s/ \257<([^\257]*?)\257> /\000/x) {
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# %replacecount = { "perlexpr" => number of times seen }
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# e.g { "$_++" => 2 }
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$replacecount{$1} ++;
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# e.g { "s/a/b/" => 2 }
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$replacecount{$1}++;
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$sum++;
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}
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# Measure the length of the context around the {= perl expr =}
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@ -7133,13 +7204,13 @@ sub replacement_counts_and_lengths {
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# %replacecount = { "perlexpr" => number of times seen }
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# e.g { "$_++" => 2 }
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# But for tagstring we just need to mark it as seen
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$replacecount{$1}||=1;
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$replacecount{$1} ||= 1;
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}
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}
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if($opt::bar) {
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# If the command does not contain {} force it to be computed
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# as it is being used by --bar
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$replacecount{""}||=1;
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$replacecount{""} ||= 1;
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}
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$len{'context'} = 0+$contextlen;
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@ -7150,11 +7221,9 @@ sub replacement_counts_and_lengths {
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" Non: ", $len{'noncontext'}, " Ctxgrp: ", $len{'contextgroups'},
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" NonCtxGrp: ", $len{'noncontextgroups'}, "\n");
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if($sum == 0) {
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# Default command = {}
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# If not replacement string: append {}
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if(not @command) {
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# Default command = {}
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@command = ("\257<\257>");
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$Global::noquote = 1;
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} elsif(($opt::pipe or $opt::pipepart)
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and not $opt::fifo and not $opt::cat) {
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# With --pipe / --pipe-part you can have no replacement
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@ -30,7 +30,7 @@ echo '### Test bug #43376: {%} and {#} with --pipe'
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echo '**'
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echo '### {= and =} in different groups'
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echo '### {= and =} in different groups separated by space'
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parallel echo {= s/a/b/ =} ::: a
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parallel echo {= s/a/b/=} ::: a
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parallel echo {= s/a/b/=}{= s/a/b/=} ::: a
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@ -41,4 +41,15 @@ echo '### {= and =} in different groups'
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parallel echo {={= =} ::: a
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parallel echo {= {= =} ::: a
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parallel echo {= {= =} =} ::: a
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echo '**'
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echo '### {} as part of the command'
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echo p /bin/ls | parallel l{= s/p/s/ =}
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echo /bin/ls-p | parallel --colsep '-' l{=2 s/p/s/ =} {1}
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echo s /bin/ls | parallel l{}
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echo /bin/ls | parallel ls {}
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echo ls /bin/ls | parallel {}
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echo ls /bin/ls | parallel
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EOF
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@ -26,8 +26,8 @@ echo '### Test bug #43376: {%} and {#} with --pipe'
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1
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echo '**'
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**
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echo '### {= and =} in different groups'
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### {= and =} in different groups
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echo '### {= and =} in different groups separated by space'
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### {= and =} in different groups separated by space
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parallel echo {= s/a/b/ =} ::: a
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b
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parallel echo {= s/a/b/=} ::: a
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@ -48,3 +48,19 @@ b {=a
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{= a
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parallel echo {= {= =} =} ::: a
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{= a =}
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echo '**'
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**
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echo '### {} as part of the command'
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### {} as part of the command
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echo p /bin/ls | parallel l{= s/p/s/ =}
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/bin/ls
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echo /bin/ls-p | parallel --colsep '-' l{=2 s/p/s/ =} {1}
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/bin/ls
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echo s /bin/ls | parallel l{}
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/bin/ls
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echo /bin/ls | parallel ls {}
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/bin/ls
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echo ls /bin/ls | parallel {}
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/bin/ls
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echo ls /bin/ls | parallel
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/bin/ls
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