parallel: Implemented --number-of-cpus and --number-of-cores

Prepared man-page for parallel remote execution

parallel

@@ -21,14 +21,31 @@ Several lines will be run in parallel.
 
 =item I<command>
 
-Command to execute.  If B<command> or the following arguments contain {}
+Command to execute.  If B<command> or the following arguments contain
-every instance will be substituted with the input line. Setting a
+{} every instance will be substituted with the input line. Setting a
 command also invokes B<-f>.
 
 If B<command> is given, B<parallel> will behave similar to B<xargs>. If
 B<command> is not given B<parallel> will behave similar to B<cat | sh>.
 
 
+=item B<{}>
+
+Input line. This is the default replacement string and will normally
+be used for putting the argument in the command line. It can be
+changed with B<-I>.
+
+
+=item B<{.}> (not implemented)
+
+Input line without extension. This is a specialized replacement string
+with the extension removed. It will remove from the last B<.> till the
+end of line of each input line and replace {.} with the
+remaining. E.g. I<foo.jpg> becomes I<foo>. If the input line does
+not contain B<.> it will remain unchanged.
+
+{.} can be used the same places as {}.
+
 =item B<--null>
 
 =item B<-0>
@@ -80,11 +97,17 @@ Group output.  Output from each jobs is grouped together and is only
 printed when the command is finished. STDERR first followed by STDOUT.
 B<-g> is the default. Can be reversed with B<-u>.
 
+
 =item B<-I> I<string>
 
 Use the replacement string I<string> instead of {}.
 
 
+=item B<-U> I<string> (not implemented)
+
+Use the replacement string I<string> instead of {.} for input line without extension.
+
+
 =item B<--jobs> I<N>
 
 =item B<-j> I<N>
@@ -104,9 +127,10 @@ Run up to N jobs in parallel.  0 means as many as possible. Default is 10.
 
 =item B<-P> I<+N>
 
-Add N to the number of CPUs.  Run this many jobs in parallel. For
+Add N to the number of CPU cores.  Run this many jobs in parallel. For
 compute intensive jobs I<-j +0> is useful as it will run
-number-of-cpus jobs in parallel.
+number-of-cpu-cores jobs in parallel. See also
+--use-cpus-instead-of-cores.
 
 
 =item B<--jobs> I<-N>
@@ -117,8 +141,9 @@ number-of-cpus jobs in parallel.
 
 =item B<-P> I<-N>
 
-Subtract N from the number of CPUs.  Run this many jobs in parallel.
+Subtract N from the number of CPU cores.  Run this many jobs in parallel.
-If the evaluated number is less than 1 then 1 will be used.
+If the evaluated number is less than 1 then 1 will be used.  See also
+--use-cpus-instead-of-cores.
 
 
 =item B<--jobs> I<N>%
@@ -129,8 +154,9 @@ If the evaluated number is less than 1 then 1 will be used.
 
 =item B<-P> I<N>%
 
-Multiply N% with the number of CPUs.  Run this many jobs in parallel.
+Multiply N% with the number of CPU cores.  Run this many jobs in parallel.
-If the evaluated number is less than 1 then 1 will be used.
+If the evaluated number is less than 1 then 1 will be used.  See also
+--use-cpus-instead-of-cores.
 
 
 =item B<--keeporder>
@@ -141,6 +167,18 @@ Keep sequence of output same as the order of input. If jobs 1 2 3 4
 end in the sequence 3 1 4 2 the output will still be 1 2 3 4.
 
 
+=item B<--number-of-cpus>
+
+Print the number of CPUs and exit (used by B<parallel> itself to
+determine the number of CPUs on remote machines).
+
+
+=item B<--number-of-cores>
+
+Print the number of cores and exit (used by B<parallel> itself to determine the
+number of cores on remote machines).
+
+
 =item B<--quote>
 
 =item B<-q>
@@ -151,12 +189,133 @@ QUOTING. Most people will never need this.  Quoting is disabled by
 default.
 
 
+=item B<-S> I<[ncpu/]sshlogin[,[ncpu/]sshlogin]> (not implemented)
+
+=item B<--sshlogin> I<[ncpu/]sshlogin[,[ncpu/]sshlogin]> (not implemented)
+
+Distribute jobs to remote servers. The jobs will be run on a list of
+remote servers.  B<parallel> will determine the number of CPU cores on
+the remote servers and run the number of jobs as specified by -j.  If
+the number I<ncpu> is given B<parallel> will use this number for
+number of CPUs on the host. Normally I<ncpu> will not be needed.
+
+An I<sshlogin> is the string you would normally pass to SSH to login,
+e.g. I<server.example.com>, I<foo@server.example.com>, or I<"-l foo -p
+2222 server.example.com">. The sshlogin must not require a password.
+
+The sshlogin ':' is special, it means 'no ssh' and will therefore run
+on the local machine.
+
+To specify more sshlogins separate the sshlogins by comma or repeat
+the options multiple times.
+
+For examples: see B<--sshloginfile>.
+
+The remote host must have B<parallel> installed.
+
+
+=item B<--sshloginfile> I<filename> (not implemented)
+
+File with sshlogins. The file consists of sshlogins on separate
+lines. Empty lines and lines starting with '#' are ignored. Example:
+
+  server.example.com
+  username@server2.example.com
+  8/my-8-core-server.example.com
+  2/myusername@my-dualcore.example.net
+  # This server has SSH running on port 2222
+  -p 2222 server.example.net
+  4/-p 2222 quadserver.example.net
+  # Assume 16 cores on the local machine
+  16/:
+
+
 =item B<--silent>
 
 Silent.  The job to be run will not be printed. This is the default.
 Can be reversed with B<-v>.
 
 
+=item B<--transfer> (not implemented)
+
+Transfer files to remote servers. B<--transfer> is used with
+B<--sshlogin> when the arguments are files and should be transfered to
+the remote servers. The files will be transfered using B<rsync> and
+will be put relative to the default login dir. E.g.
+
+  echo foo/bar.txt | parallel \
+    --sshlogin server.example.com --transfer wc
+
+This will transfer the file I<foo/bar.txt> to the server
+I<server.example.com> to the file $HOME/foo/bar.txt before running
+B<wc foo/bar.txt> on I<server.example.com>.
+
+  echo /tmp/foo/bar.txt | parallel \
+    --sshlogin server.example.com --transfer wc
+
+This will transfer the file I<foo/bar.txt> to the server
+I<server.example.com> to the file /tmp/foo/bar.txt before running
+B<wc /tmp/foo/bar.txt> on I<server.example.com>.
+
+B<--transfer> is often used with B<--return> and B<--cleanup>.
+
+B<--transfer> is ignored when used with B<--sshlogin :> or when not used with B<--sshlogin>.
+
+
+=item B<--return> I<suffix> (not implemented)
+
+Transfer files from remote servers. B<--return> is used with
+B<--sshlogin> when the arguments are files on the remote servers. When
+processing is done the file with I<suffix> appended will be transfered
+from the remote server using B<rsync> and will be put relative to
+the default login dir. E.g.
+
+  echo foo/bar.txt | parallel \
+    --sshlogin server.example.com --return .out touch {}.out
+
+This will transfer the file I<$HOME/foo/bar.txt.out> from the server
+I<server.example.com> to the file I<foo/bar.txt.out> after running
+B<touch foo/bar.txt.out> on I<server.example.com>.
+
+  echo /tmp/foo/bar.txt | parallel \
+    --sshlogin server.example.com --return .out touch {}.out
+
+This will transfer the file I</tmp/foo/bar.txt.out> from the server
+I<server.example.com> to the file I</tmp/foo/bar.txt.out> after running
+B<touch /tmp/foo/bar.txt.out> on I<server.example.com>.
+
+Multiple files with different suffixes can be transfered by repeating
+the options multiple times:
+
+  echo /tmp/foo/bar.txt | \
+    parallel --sshlogin server.example.com \
+    --return .out --return .out2 touch {}.out {}.out2
+
+B<--return> is often used with B<--transfer> and B<--cleanup>.
+
+B<--return> is ignored when used with B<--sshlogin :> or when not used with B<--sshlogin>.
+
+
+=item B<--cleanup> (not implemented)
+
+Remove transfered files. B<--cleanup> will remove the transfered files
+on the remote server after processing is done.
+
+  find log -name '*gz' | parallel \
+    --sshlogin server.example.com --transfer --return .bz2 \
+    --cleanup "zcat {} | bzip -9 >{}.bz2"
+
+With B<--transfer> the file transfered to the remote server will be
+removed on the remote server.  Directories created will not be removed
+- even if they are empty.
+
+With B<--return> the file transfered from the remote server will be
+removed on the remote server.  Directories created will not be removed
+- even if they are empty.
+
+B<--cleanup> is ignored when not used with B<--transfer> or B<--return>.
+
+
 =item B<--ungroup>
 
 =item B<-u>
@@ -165,6 +324,16 @@ Ungroup output.  Output is printed as soon as possible. This may cause
 output from different commands to be mixed. Can be reversed with B<-g>.
 
 
+=item B<--use-cpus-instead-of-cores> (not implemented)
+
+Count the number of CPUs instead of cores. When computing how many
+jobs to run in parallel relative to the number of cores you can ask
+parallel to instead look at the number of CPUs. This will make sense
+for computers that have hyperthreading as two jobs running on one CPU
+with hyperthreading will run slower than two jobs running on two CPUs.
+Normal users will not need this option.
+
+
 =item B<-v>
 
 Verbose.  Print the job to be run on STDOUT. Can be reversed with
@@ -231,9 +400,9 @@ file:
 
 B<convert -geometry 120 foo.jpg thumb_foo.jpg>
 
-If the system has more than 1 CPU it can be run with number-of-cpus
+If the system has more than 1 CPU core it can be run with
-jobs in parallel (-j +0). This will do that for all jpg files in a
+number-of-cpu-cores jobs in parallel (-j +0). This will do that for
-directory:
+all jpg files in a directory:
 
 B<ls *.jpg | parallel -j +0 convert -geometry 120 {} thumb_{}>
 
@@ -257,6 +426,9 @@ is a better solution:
   find . -name '*.jpg' | parallel -j +0 convert -geometry 120 {} {}_thumb.jpg
   find . -name '*_thumb.jpg' | ren 's:/([^/]+)_thumb.jpg$:/thumb_$1:'
 
+(Not implemented) This will make files like ./foo/bar_thumb.jpg:
+
+B<find . -name '*.jpg' | parallel -j +0 convert -geometry 120 {} {.}_thumb.jpg>
 
 =head1 EXAMPLE 4: Substitution and redirection
 
@@ -342,6 +514,104 @@ B<(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel -k tra
 This will make sure the traceroute to foss.org.my will be printed
 first.
 
+=head1 EXAMPLE 9: Using remote computers (not implemented)
+
+To run commands on a remote computer SSH needs to be set up and you
+must be able to login without entering a password (B<ssh-agent> may be
+handy).
+
+To run B<echo> on B<server.example.com>:
+
+  seq 1 10 | parallel --sshlogin server.example.com echo
+
+To run commands on more than one remote computer run:
+
+  seq 1 10 | parallel --sshlogin server.example.com,server2.example.net echo
+
+Or:
+
+  seq 1 10 | parallel --sshlogin server.example.com \
+    --sshlogin server2.example.net echo
+
+If the login username is I<foo> on I<server2.example.net> use:
+
+  seq 1 10 | parallel --sshlogin server.example.com \
+    --sshlogin foo@server2.example.net echo
+
+To distribute the commands to a list of machines, make a file
+I<mymachines> with all the machines:
+
+  server.example.com
+  foo@server2.example.com
+  server3.example.com
+
+Then run:
+
+  seq 1 10 | parallel --sshloginfile mymachines echo
+
+To include the local machine add the special sshlogin ':' to the list:
+
+  server.example.com
+  foo@server2.example.com
+  server3.example.com
+  :
+
+If the number of CPU cores on the remote servers is not identified
+correctly the number of CPU cores can be added in front. Here the
+server has 8 CPU cores.
+
+  seq 1 10 | parallel --sshlogin 8/server.example.com echo
+
+
+=head1 EXAMPLE 10: Transferring of files (not implemented)
+
+To recompress gzipped files with bzip2 using a remote server run:
+
+  find logs/ -name '*.gz' | \
+    parallel --sshlogin server.example.com \
+    --transfer "zcat {} | bzip2 -9 >{}.bz2"
+
+This will list the .gz-files in the I<logs> directory and all
+directories below. Then it will transfer the files to
+I<server.example.com> to the corresponding directory in
+I<$HOME/logs>. On I<server.example.com> the file will be recompressed
+using B<zcat> and B<bzip2> resulting in the corresponding file with
+the suffix I<.bz2>.
+
+If you want the file to be transfered back to the local machine add
+I<--return .bz2>:
+
+  find logs/ -name '*.gz' | \
+    parallel --sshlogin server.example.com \
+    --transfer --return .bz2 "zcat {} | bzip2 -9 >{}.bz2"
+
+After the recompressing is done the I<.bz2>-file is transfered back to
+the local machine.
+
+If you want to delete the transfered files on the remote machine add
+I<--cleanup>:
+
+  find logs/ -name '*.gz' | \
+    parallel --sshlogin server.example.com \
+    --transfer --return .bz2 --cleanup "zcat {} | bzip2 -9 >{}.bz2"
+
+If you want run one several servers add the servers to I<--sshlogin>
+either using ',' or separate I<--sshlogin>:
+
+  find logs/ -name '*.gz' | \
+    parallel --sshlogin server.example.com,server2.example.com \
+    --sshlogin server3.example.com \
+    --transfer --return .bz2 --cleanup "zcat {} | bzip2 -9 >{}.bz2"
+
+You can add the local machine using I<--sshlogin :>. This will disable the
+removing and transferring for the local machine only:
+
+  find logs/ -name '*.gz' | \
+    parallel --sshlogin server.example.com,server2.example.com \
+    --sshlogin server3.example.com \
+    --sshlogin : \
+    --transfer --return .bz2 --cleanup "zcat {} | bzip2 -9 >{}.bz2"
+
 
 =head1 QUOTING
 
@@ -439,7 +709,7 @@ So B<parallel>'s newline separation can be emulated with:
 B<cat | xargs -d "\n" -n1 I<command>>
 
 B<xargs> can run a given number of jobs in parallel, but has no
-support for running no_of_cpus jobs in parallel.
+support for running number-of-cpu-cores jobs in parallel.
 
 B<xargs> has no support for grouping the output, therefore output may
 run together, e.g. the first half of a line is from one process and
@@ -512,25 +782,17 @@ hard, as all foreground processes get the INT from the shell.
 If there are nomore jobs (STDIN is closed) then make sure to
 distribute the arguments evenly if running -X.
 
-Distibute jobs to computers with different speeds/no_of_cpu using ssh
+Distibute jobs to computers with different speeds/number-of-cpu-cores using ssh
 ask the computers how many cpus they have and spawn appropriately
 according to -j setting. Reuse ssh connection (-M and -S)
 http://www.semicomplete.com/blog/geekery/distributed-xargs.html?source=rss20
 http://code.google.com/p/ppss/wiki/Manual2
 
-=head2 -S
+http://www.gnu.org/software/pexec/
 
--S sshlogin[,sshlogin]
 
-sshlogin is [user@]host or filename with list of sshlogin
 
-What about copying data to remote host? Have an option that says the
+Where will '>' be run? Local or remote? Where ever is easier.
-argument is a file that should be copied.
-
-What about copying data from remote host? Have an option that says
-the argument is a file that should be copied.
-
-Where will '>' be run? Local or remote?
 
 
 Parallelize so this can be done:
@@ -609,6 +871,8 @@ GetOptions("debug|D" => \$::opt_D,
 	   "quote|q" => \$::opt_q,
 	   "I=s" => \$::opt_I,
 	   "jobs|j=s" => \$::opt_P,
+	   "number-of-cpus" => \$::opt_number_of_cpus,
+	   "number-of-cores" => \$::opt_number_of_cores,
 	   # xargs-compatibility - implemented, man, unittest
 	   "max-procs|P=s" => \$::opt_P,
 	   "delimiter|d=s" => \$::opt_d,
@@ -674,6 +938,8 @@ if(defined $::opt_i and $::opt_i) { $Global::replacestring = $::opt_i; }
 if(defined $::opt_E and $::opt_E) { $Global::end_of_file_string = $::opt_E; }
 if(defined $::opt_n and $::opt_n) { $Global::max_number_of_args = $::opt_n; }
 if(defined $::opt_h) { die_usage(); }
+if(defined $::opt_number_of_cpus) { print no_of_cpus(),"\n"; exit(0); }
+if(defined $::opt_number_of_cores) { print no_of_cores(),"\n"; exit(0); }
 if(defined $::opt_version) { version(); exit(0); }
 
 if(defined $::opt_a) {
@@ -735,7 +1001,15 @@ sub generate_command_line {
     }
 
     my $number_of_args = 0;
+    # max number of lines (-L) =
+    # number_of_read_lines = 0
     while (defined($next_arg = get_next_arg())) {
+	# if defined max_number_of_lines {
+	# number_of_read_lines++
+	# if $next_arg =~ /\w$/ number_of_read_lines-- (Trailing blanks cause an
+	    # input line to be logically continued on the next input line.)
+	# if number_of_read_lines > max_number_of_lines
+	    # last
 	push (@quoted_args, $next_arg);
 	$number_of_args++;
 	if(not $Global::xargs and not $Global::Xargs) {
@@ -1013,9 +1287,16 @@ sub user_requested_processes {
     return $processes;
 }
 
+sub no_of_cores {
+    # TODO This should return number of cores and not the number of CPUs
+    return no_of_cpus(@_);
+}
+
 sub no_of_cpus {
     if(not $Global::no_of_cpus) {
-	my $no_of_cpus = (no_of_cpus_gnu_linux() || no_of_cpus_solaris());
+	my $no_of_cpus = (no_of_cpus_darwin()
+			  || no_of_cpus_gnu_linux()
+			  || no_of_cpus_solaris());
 	if($no_of_cpus) {
 	    $Global::no_of_cpus = $no_of_cpus;
 	} else {
@@ -1039,6 +1320,11 @@ sub no_of_cpus_gnu_linux {
     return $no_of_cpus;
 }
 
+sub no_of_cpus_darwin {
+    my $no_of_cpus = `sysctl -n hw.ncpu 2>/dev/null`;
+    return $no_of_cpus;
+}
+
 sub no_of_cpus_solaris {
     if(-x "/usr/sbin/psrinfo") {
 	my @psrinfo = `/usr/sbin/psrinfo`;
@@ -1372,16 +1658,21 @@ sub my_memory_usage {
     use strict;
     use FileHandle;
 
+
     my $pid = $$;
-    my $fh = FileHandle->new("</proc/$pid/stat");
+    if(-e "/proc/$pid/stat") {
+	my $fh = FileHandle->new("</proc/$pid/stat");
 
-    my $data = <$fh>;
+	my $data = <$fh>;
-    chomp $data;
+	chomp $data;
-    $fh->close;
+	$fh->close;
 
-    my @procinfo = split(/\s+/,$data);
+	my @procinfo = split(/\s+/,$data);
 
-    return $procinfo[22];
+	return $procinfo[22];
+    } else {
+	return 0;
+    }
 }
 
 sub my_size {

parallel.1

@@ -124,7 +124,7 @@
 .\" ========================================================================
 .\"
 .IX Title "PARALLEL 1"
-.TH PARALLEL 1 "2010-03-06" "perl v5.10.1" "User Contributed Perl Documentation"
+.TH PARALLEL 1 "2010-04-13" "perl v5.10.1" "User Contributed Perl Documentation"
 .\" For nroff, turn off justification.  Always turn off hyphenation; it makes
 .\" way too many mistakes in technical documents.
 .if n .ad l
@@ -144,12 +144,26 @@ or \fBcat | sh\fR.
 Several lines will be run in parallel.
 .IP "\fIcommand\fR" 9
 .IX Item "command"
-Command to execute.  If \fBcommand\fR or the following arguments contain {}
+Command to execute.  If \fBcommand\fR or the following arguments contain
-every instance will be substituted with the input line. Setting a
+{} every instance will be substituted with the input line. Setting a
 command also invokes \fB\-f\fR.
 .Sp
 If \fBcommand\fR is given, \fBparallel\fR will behave similar to \fBxargs\fR. If
 \&\fBcommand\fR is not given \fBparallel\fR will behave similar to \fBcat | sh\fR.
+.IP "\fB{}\fR" 9
+.IX Item "{}"
+Input line. This is the default replacement string and will normally
+be used for putting the argument in the command line. It can be
+changed with \fB\-I\fR.
+.IP "\fB{.}\fR (not implemented)" 9
+.IX Item "{.} (not implemented)"
+Input line without extension. This is a specialized replacement string
+with the extension removed. It will remove from the last \fB.\fR till the
+end of line of each input line and replace {.} with the
+remaining. E.g. \fIfoo.jpg\fR becomes \fIfoo\fR. If the input line does
+not contain \fB.\fR it will remain unchanged.
+.Sp
+{.} can be used the same places as {}.
 .IP "\fB\-\-null\fR" 9
 .IX Item "--null"
 .PD 0
@@ -205,6 +219,9 @@ printed when the command is finished. \s-1STDERR\s0 first followed by \s-1STDOUT
 .IP "\fB\-I\fR \fIstring\fR" 9
 .IX Item "-I string"
 Use the replacement string \fIstring\fR instead of {}.
+.IP "\fB\-U\fR \fIstring\fR (not implemented)" 9
+.IX Item "-U string (not implemented)"
+Use the replacement string \fIstring\fR instead of {.} for input line without extension.
 .IP "\fB\-\-jobs\fR \fIN\fR" 9
 .IX Item "--jobs N"
 .PD 0
@@ -226,9 +243,10 @@ Run up to N jobs in parallel.  0 means as many as possible. Default is 10.
 .IP "\fB\-P\fR \fI+N\fR" 9
 .IX Item "-P +N"
 .PD
-Add N to the number of CPUs.  Run this many jobs in parallel. For
+Add N to the number of \s-1CPU\s0 cores.  Run this many jobs in parallel. For
 compute intensive jobs \fI\-j +0\fR is useful as it will run
-number-of-cpus jobs in parallel.
+number-of-cpu-cores jobs in parallel. See also
+\&\-\-use\-cpus\-instead\-of\-cores.
 .IP "\fB\-\-jobs\fR \fI\-N\fR" 9
 .IX Item "--jobs -N"
 .PD 0
@@ -239,8 +257,9 @@ number-of-cpus jobs in parallel.
 .IP "\fB\-P\fR \fI\-N\fR" 9
 .IX Item "-P -N"
 .PD
-Subtract N from the number of CPUs.  Run this many jobs in parallel.
+Subtract N from the number of \s-1CPU\s0 cores.  Run this many jobs in parallel.
-If the evaluated number is less than 1 then 1 will be used.
+If the evaluated number is less than 1 then 1 will be used.  See also
+\&\-\-use\-cpus\-instead\-of\-cores.
 .IP "\fB\-\-jobs\fR \fIN\fR%" 9
 .IX Item "--jobs N%"
 .PD 0
@@ -251,8 +270,9 @@ If the evaluated number is less than 1 then 1 will be used.
 .IP "\fB\-P\fR \fIN\fR%" 9
 .IX Item "-P N%"
 .PD
-Multiply N% with the number of CPUs.  Run this many jobs in parallel.
+Multiply N% with the number of \s-1CPU\s0 cores.  Run this many jobs in parallel.
-If the evaluated number is less than 1 then 1 will be used.
+If the evaluated number is less than 1 then 1 will be used.  See also
+\&\-\-use\-cpus\-instead\-of\-cores.
 .IP "\fB\-\-keeporder\fR" 9
 .IX Item "--keeporder"
 .PD 0
@@ -261,6 +281,14 @@ If the evaluated number is less than 1 then 1 will be used.
 .PD
 Keep sequence of output same as the order of input. If jobs 1 2 3 4
 end in the sequence 3 1 4 2 the output will still be 1 2 3 4.
+.IP "\fB\-\-number\-of\-cpus\fR" 9
+.IX Item "--number-of-cpus"
+Print the number of CPUs and exit (used by \fBparallel\fR itself to
+determine the number of CPUs on remote machines).
+.IP "\fB\-\-number\-of\-cores\fR" 9
+.IX Item "--number-of-cores"
+Print the number of cores and exit (used by \fBparallel\fR itself to determine the
+number of cores on remote machines).
 .IP "\fB\-\-quote\fR" 9
 .IX Item "--quote"
 .PD 0
@@ -271,10 +299,137 @@ Quote \fBcommand\fR.  This will quote the command line so special
 characters are not interpreted by the shell. See the section
 \&\s-1QUOTING\s0. Most people will never need this.  Quoting is disabled by
 default.
+.IP "\fB\-S\fR \fI[ncpu/]sshlogin[,[ncpu/]sshlogin]\fR (not implemented)" 9
+.IX Item "-S [ncpu/]sshlogin[,[ncpu/]sshlogin] (not implemented)"
+.PD 0
+.IP "\fB\-\-sshlogin\fR \fI[ncpu/]sshlogin[,[ncpu/]sshlogin]\fR (not implemented)" 9
+.IX Item "--sshlogin [ncpu/]sshlogin[,[ncpu/]sshlogin] (not implemented)"
+.PD
+Distribute jobs to remote servers. The jobs will be run on a list of
+remote servers.  \fBparallel\fR will determine the number of \s-1CPU\s0 cores on
+the remote servers and run the number of jobs as specified by \-j.  If
+the number \fIncpu\fR is given \fBparallel\fR will use this number for
+number of CPUs on the host. Normally \fIncpu\fR will not be needed.
+.Sp
+An \fIsshlogin\fR is the string you would normally pass to \s-1SSH\s0 to login,
+e.g. \fIserver.example.com\fR, \fIfoo@server.example.com\fR, or \fI\*(L"\-l foo \-p
+2222 server.example.com\*(R"\fR. The sshlogin must not require a password.
+.Sp
+The sshlogin ':' is special, it means 'no ssh' and will therefore run
+on the local machine.
+.Sp
+To specify more sshlogins separate the sshlogins by comma or repeat
+the options multiple times.
+.Sp
+For examples: see \fB\-\-sshloginfile\fR.
+.Sp
+The remote host must have \fBparallel\fR installed.
+.IP "\fB\-\-sshloginfile\fR \fIfilename\fR (not implemented)" 9
+.IX Item "--sshloginfile filename (not implemented)"
+File with sshlogins. The file consists of sshlogins on separate
+lines. Empty lines and lines starting with '#' are ignored. Example:
+.Sp
+.Vb 9
+\&  server.example.com
+\&  username@server2.example.com
+\&  8/my\-8\-core\-server.example.com
+\&  2/myusername@my\-dualcore.example.net
+\&  # This server has SSH running on port 2222
+\&  \-p 2222 server.example.net
+\&  4/\-p 2222 quadserver.example.net
+\&  # Assume 16 cores on the local machine
+\&  16/:
+.Ve
 .IP "\fB\-\-silent\fR" 9
 .IX Item "--silent"
 Silent.  The job to be run will not be printed. This is the default.
 Can be reversed with \fB\-v\fR.
+.IP "\fB\-\-transfer\fR (not implemented)" 9
+.IX Item "--transfer (not implemented)"
+Transfer files to remote servers. \fB\-\-transfer\fR is used with
+\&\fB\-\-sshlogin\fR when the arguments are files and should be transfered to
+the remote servers. The files will be transfered using \fBrsync\fR and
+will be put relative to the default login dir. E.g.
+.Sp
+.Vb 2
+\&  echo foo/bar.txt | parallel \e
+\&    \-\-sshlogin server.example.com \-\-transfer wc
+.Ve
+.Sp
+This will transfer the file \fIfoo/bar.txt\fR to the server
+\&\fIserver.example.com\fR to the file \f(CW$HOME\fR/foo/bar.txt before running
+\&\fBwc foo/bar.txt\fR on \fIserver.example.com\fR.
+.Sp
+.Vb 2
+\&  echo /tmp/foo/bar.txt | parallel \e
+\&    \-\-sshlogin server.example.com \-\-transfer wc
+.Ve
+.Sp
+This will transfer the file \fIfoo/bar.txt\fR to the server
+\&\fIserver.example.com\fR to the file /tmp/foo/bar.txt before running
+\&\fBwc /tmp/foo/bar.txt\fR on \fIserver.example.com\fR.
+.Sp
+\&\fB\-\-transfer\fR is often used with \fB\-\-return\fR and \fB\-\-cleanup\fR.
+.Sp
+\&\fB\-\-transfer\fR is ignored when used with \fB\-\-sshlogin :\fR or when not used with \fB\-\-sshlogin\fR.
+.IP "\fB\-\-return\fR \fIsuffix\fR (not implemented)" 9
+.IX Item "--return suffix (not implemented)"
+Transfer files from remote servers. \fB\-\-return\fR is used with
+\&\fB\-\-sshlogin\fR when the arguments are files on the remote servers. When
+processing is done the file with \fIsuffix\fR appended will be transfered
+from the remote server using \fBrsync\fR and will be put relative to
+the default login dir. E.g.
+.Sp
+.Vb 2
+\&  echo foo/bar.txt | parallel \e
+\&    \-\-sshlogin server.example.com \-\-return .out touch {}.out
+.Ve
+.Sp
+This will transfer the file \fI\f(CI$HOME\fI/foo/bar.txt.out\fR from the server
+\&\fIserver.example.com\fR to the file \fIfoo/bar.txt.out\fR after running
+\&\fBtouch foo/bar.txt.out\fR on \fIserver.example.com\fR.
+.Sp
+.Vb 2
+\&  echo /tmp/foo/bar.txt | parallel \e 
+\&    \-\-sshlogin server.example.com \-\-return .out touch {}.out
+.Ve
+.Sp
+This will transfer the file \fI/tmp/foo/bar.txt.out\fR from the server
+\&\fIserver.example.com\fR to the file \fI/tmp/foo/bar.txt.out\fR after running
+\&\fBtouch /tmp/foo/bar.txt.out\fR on \fIserver.example.com\fR.
+.Sp
+Multiple files with different suffixes can be transfered by repeating
+the options multiple times:
+.Sp
+.Vb 3
+\&  echo /tmp/foo/bar.txt | \e
+\&    parallel \-\-sshlogin server.example.com \e
+\&    \-\-return .out \-\-return .out2 touch {}.out {}.out2
+.Ve
+.Sp
+\&\fB\-\-return\fR is often used with \fB\-\-transfer\fR and \fB\-\-cleanup\fR.
+.Sp
+\&\fB\-\-return\fR is ignored when used with \fB\-\-sshlogin :\fR or when not used with \fB\-\-sshlogin\fR.
+.IP "\fB\-\-cleanup\fR (not implemented)" 9
+.IX Item "--cleanup (not implemented)"
+Remove transfered files. \fB\-\-cleanup\fR will remove the transfered files
+on the remote server after processing is done.
+.Sp
+.Vb 3
+\&  find log \-name \*(Aq*gz\*(Aq | parallel \e
+\&    \-\-sshlogin server.example.com \-\-transfer \-\-return .bz2 \e
+\&    \-\-cleanup "zcat {} | bzip \-9 >{}.bz2"
+.Ve
+.Sp
+With \fB\-\-transfer\fR the file transfered to the remote server will be
+removed on the remote server.  Directories created will not be removed
+\&\- even if they are empty.
+.Sp
+With \fB\-\-return\fR the file transfered from the remote server will be
+removed on the remote server.  Directories created will not be removed
+\&\- even if they are empty.
+.Sp
+\&\fB\-\-cleanup\fR is ignored when not used with \fB\-\-transfer\fR or \fB\-\-return\fR.
 .IP "\fB\-\-ungroup\fR" 9
 .IX Item "--ungroup"
 .PD 0
@@ -283,6 +438,14 @@ Can be reversed with \fB\-v\fR.
 .PD
 Ungroup output.  Output is printed as soon as possible. This may cause
 output from different commands to be mixed. Can be reversed with \fB\-g\fR.
+.IP "\fB\-\-use\-cpus\-instead\-of\-cores\fR (not implemented)" 9
+.IX Item "--use-cpus-instead-of-cores (not implemented)"
+Count the number of CPUs instead of cores. When computing how many
+jobs to run in parallel relative to the number of cores you can ask
+parallel to instead look at the number of CPUs. This will make sense
+for computers that have hyperthreading as two jobs running on one \s-1CPU\s0
+with hyperthreading will run slower than two jobs running on two CPUs.
+Normal users will not need this option.
 .IP "\fB\-v\fR" 9
 .IX Item "-v"
 Verbose.  Print the job to be run on \s-1STDOUT\s0. Can be reversed with
@@ -344,9 +507,9 @@ file:
 .PP
 \&\fBconvert \-geometry 120 foo.jpg thumb_foo.jpg\fR
 .PP
-If the system has more than 1 \s-1CPU\s0 it can be run with number-of-cpus
+If the system has more than 1 \s-1CPU\s0 core it can be run with
-jobs in parallel (\-j +0). This will do that for all jpg files in a
+number-of-cpu-cores jobs in parallel (\-j +0). This will do that for
-directory:
+all jpg files in a directory:
 .PP
 \&\fBls *.jpg | parallel \-j +0 convert \-geometry 120 {} thumb_{}\fR
 .PP
@@ -373,6 +536,10 @@ is a better solution:
 \&  find . \-name \*(Aq*.jpg\*(Aq | parallel \-j +0 convert \-geometry 120 {} {}_thumb.jpg
 \&  find . \-name \*(Aq*_thumb.jpg\*(Aq | ren \*(Aqs:/([^/]+)_thumb.jpg$:/thumb_$1:\*(Aq
 .Ve
+.PP
+(Not implemented) This will make files like ./foo/bar_thumb.jpg:
+.PP
+\&\fBfind . \-name '*.jpg' | parallel \-j +0 convert \-geometry 120 {} {.}_thumb.jpg\fR
 .SH "EXAMPLE 4: Substitution and redirection"
 .IX Header "EXAMPLE 4: Substitution and redirection"
 This will compare all files in the dir to the file foo and save the
@@ -449,6 +616,127 @@ To keep the order the same as input run:
 .PP
 This will make sure the traceroute to foss.org.my will be printed
 first.
+.SH "EXAMPLE 9: Using remote computers (not implemented)"
+.IX Header "EXAMPLE 9: Using remote computers (not implemented)"
+To run commands on a remote computer \s-1SSH\s0 needs to be set up and you
+must be able to login without entering a password (\fBssh-agent\fR may be
+handy).
+.PP
+To run \fBecho\fR on \fBserver.example.com\fR:
+.PP
+.Vb 1
+\&  seq 1 10 | parallel \-\-sshlogin server.example.com echo
+.Ve
+.PP
+To run commands on more than one remote computer run:
+.PP
+.Vb 1
+\&  seq 1 10 | parallel \-\-sshlogin server.example.com,server2.example.net echo
+.Ve
+.PP
+Or:
+.PP
+.Vb 2
+\&  seq 1 10 | parallel \-\-sshlogin server.example.com \e
+\&    \-\-sshlogin server2.example.net echo
+.Ve
+.PP
+If the login username is \fIfoo\fR on \fIserver2.example.net\fR use:
+.PP
+.Vb 2
+\&  seq 1 10 | parallel \-\-sshlogin server.example.com \e
+\&    \-\-sshlogin foo@server2.example.net echo
+.Ve
+.PP
+To distribute the commands to a list of machines, make a file
+\&\fImymachines\fR with all the machines:
+.PP
+.Vb 3
+\&  server.example.com
+\&  foo@server2.example.com
+\&  server3.example.com
+.Ve
+.PP
+Then run:
+.PP
+.Vb 1
+\&  seq 1 10 | parallel \-\-sshloginfile mymachines echo
+.Ve
+.PP
+To include the local machine add the special sshlogin ':' to the list:
+.PP
+.Vb 4
+\&  server.example.com
+\&  foo@server2.example.com
+\&  server3.example.com
+\&  :
+.Ve
+.PP
+If the number of \s-1CPU\s0 cores on the remote servers is not identified
+correctly the number of \s-1CPU\s0 cores can be added in front. Here the
+server has 8 \s-1CPU\s0 cores.
+.PP
+.Vb 1
+\&  seq 1 10 | parallel \-\-sshlogin 8/server.example.com echo
+.Ve
+.SH "EXAMPLE 10: Transferring of files (not implemented)"
+.IX Header "EXAMPLE 10: Transferring of files (not implemented)"
+To recompress gzipped files with bzip2 using a remote server run:
+.PP
+.Vb 3
+\&  find logs/ \-name \*(Aq*.gz\*(Aq | \e
+\&    parallel \-\-sshlogin server.example.com \e
+\&    \-\-transfer "zcat {} | bzip2 \-9 >{}.bz2"
+.Ve
+.PP
+This will list the .gz\-files in the \fIlogs\fR directory and all
+directories below. Then it will transfer the files to
+\&\fIserver.example.com\fR to the corresponding directory in
+\&\fI\f(CI$HOME\fI/logs\fR. On \fIserver.example.com\fR the file will be recompressed
+using \fBzcat\fR and \fBbzip2\fR resulting in the corresponding file with
+the suffix \fI.bz2\fR.
+.PP
+If you want the file to be transfered back to the local machine add
+\&\fI\-\-return .bz2\fR:
+.PP
+.Vb 3
+\&  find logs/ \-name \*(Aq*.gz\*(Aq | \e
+\&    parallel \-\-sshlogin server.example.com \e
+\&    \-\-transfer \-\-return .bz2 "zcat {} | bzip2 \-9 >{}.bz2"
+.Ve
+.PP
+After the recompressing is done the \fI.bz2\fR\-file is transfered back to
+the local machine.
+.PP
+If you want to delete the transfered files on the remote machine add
+\&\fI\-\-cleanup\fR:
+.PP
+.Vb 3
+\&  find logs/ \-name \*(Aq*.gz\*(Aq | \e
+\&    parallel \-\-sshlogin server.example.com \e
+\&    \-\-transfer \-\-return .bz2 \-\-cleanup "zcat {} | bzip2 \-9 >{}.bz2"
+.Ve
+.PP
+If you want run one several servers add the servers to \fI\-\-sshlogin\fR
+either using ',' or separate \fI\-\-sshlogin\fR:
+.PP
+.Vb 4
+\&  find logs/ \-name \*(Aq*.gz\*(Aq | \e
+\&    parallel \-\-sshlogin server.example.com,server2.example.com \e
+\&    \-\-sshlogin server3.example.com \e
+\&    \-\-transfer \-\-return .bz2 \-\-cleanup "zcat {} | bzip2 \-9 >{}.bz2"
+.Ve
+.PP
+You can add the local machine using \fI\-\-sshlogin :\fR. This will disable the
+removing and transferring for the local machine only:
+.PP
+.Vb 5
+\&  find logs/ \-name \*(Aq*.gz\*(Aq | \e
+\&    parallel \-\-sshlogin server.example.com,server2.example.com \e
+\&    \-\-sshlogin server3.example.com \e
+\&    \-\-sshlogin : \e
+\&    \-\-transfer \-\-return .bz2 \-\-cleanup "zcat {} | bzip2 \-9 >{}.bz2"
+.Ve
 .SH "QUOTING"
 .IX Header "QUOTING"
 For more advanced use quoting may be an issue. The following will
@@ -541,7 +829,7 @@ So \fBparallel\fR's newline separation can be emulated with:
 \&\fBcat | xargs \-d \*(L"\en\*(R" \-n1 \f(BIcommand\fB\fR
 .PP
 \&\fBxargs\fR can run a given number of jobs in parallel, but has no
-support for running no_of_cpus jobs in parallel.
+support for running number-of-cpu-cores jobs in parallel.
 .PP
 \&\fBxargs\fR has no support for grouping the output, therefore output may
 run together, e.g. the first half of a line is from one process and
@@ -608,24 +896,15 @@ hard, as all foreground processes get the \s-1INT\s0 from the shell.
 If there are nomore jobs (\s-1STDIN\s0 is closed) then make sure to
 distribute the arguments evenly if running \-X.
 .PP
-Distibute jobs to computers with different speeds/no_of_cpu using ssh
+Distibute jobs to computers with different speeds/number\-of\-cpu\-cores using ssh
 ask the computers how many cpus they have and spawn appropriately
 according to \-j setting. Reuse ssh connection (\-M and \-S)
 http://www.semicomplete.com/blog/geekery/distributed\-xargs.html?source=rss20
 http://code.google.com/p/ppss/wiki/Manual2
-.SS "\-S"
-.IX Subsection "-S"
-\&\-S sshlogin[,sshlogin]
 .PP
-sshlogin is [user@]host or filename with list of sshlogin
+http://www.gnu.org/software/pexec/
 .PP
-What about copying data to remote host? Have an option that says the
+Where will '>' be run? Local or remote? Where ever is easier.
-argument is a file that should be copied.
-.PP
-What about copying data from remote host? Have an option that says
-the argument is a file that should be copied.
-.PP
-Where will '>' be run? Local or remote?
 .PP
 Parallelize so this can be done:
 mdm.screen find dir \-execdir mdm-run cmd {} \e;

unittest/actual-results/test15

@@ -25,6 +25,8 @@ replace
 replace
 replace
 replace
+replace
+replace
 include this
 include this
 include this

unittest/wanted-results/test15

@@ -25,6 +25,8 @@ replace
 replace
 replace
 replace
+replace
+replace
 include this
 include this
 include this