Implemented --tty as the old default of assigning a tty to the first

job causes problems.
Cleanup if --workdir <> . did not work. Fixed.

README

@@ -6,7 +6,7 @@ Please send problems and feedback to bug-parallel@gnu.org.
 = Presentation of GNU Parallel =
 
 GNU Parallel is a shell tool for executing jobs in parallel using one
-or more machines. A job is typically a single command or a small
+or more computers. A job is typically a single command or a small
 script that has to be run for each of the lines in the input. The
 typical input is a list of files, a list of hosts, a list of users, or
 a list of tables.

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.67 for parallel 20101206.
+# Generated by GNU Autoconf 2.67 for parallel 20101220.
 #
 # Report bugs to <bug-parallel@gnu.org>.
 #
@@ -551,8 +551,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='parallel'
 PACKAGE_TARNAME='parallel'
-PACKAGE_VERSION='20101206'
+PACKAGE_VERSION='20101220'
-PACKAGE_STRING='parallel 20101206'
+PACKAGE_STRING='parallel 20101220'
 PACKAGE_BUGREPORT='bug-parallel@gnu.org'
 PACKAGE_URL=''
 
@@ -1168,7 +1168,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures parallel 20101206 to adapt to many kinds of systems.
+\`configure' configures parallel 20101220 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1234,7 +1234,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of parallel 20101206:";;
+     short | recursive ) echo "Configuration of parallel 20101220:";;
    esac
   cat <<\_ACEOF
 
@@ -1301,7 +1301,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-parallel configure 20101206
+parallel configure 20101220
 generated by GNU Autoconf 2.67
 
 Copyright (C) 2010 Free Software Foundation, Inc.
@@ -1318,7 +1318,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by parallel $as_me 20101206, which was
+It was created by parallel $as_me 20101220, which was
 generated by GNU Autoconf 2.67.  Invocation command line was
 
   $ $0 $@
@@ -2133,7 +2133,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='parallel'
- VERSION='20101206'
+ VERSION='20101220'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2684,7 +2684,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by parallel $as_me 20101206, which was
+This file was extended by parallel $as_me 20101220, which was
 generated by GNU Autoconf 2.67.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2746,7 +2746,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-parallel config.status 20101206
+parallel config.status 20101220
 configured by $0, generated by GNU Autoconf 2.67,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([parallel], [20101206], [bug-parallel@gnu.org])
+AC_INIT([parallel], [20101220], [bug-parallel@gnu.org])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_FILES([

doc/FUTURE_IDEAS

@@ -1,3 +1,6 @@
+cleanup of transferred files in workdir fixed.
+-T implemented as ssh/rsync sometimes hang due to getting a tty.
+
 Til QUOTING:
 
 FN="two  spaces"
@@ -309,7 +312,8 @@ distribute the arguments evenly if running -X.
 
 =head1 options
 
-One char options not used: A F G K O Q R T Z
+One char options not used: A F G K O Q R T Z c f
+-T terminal
 
 =head1 sem
 

doc/release_new_version

@@ -22,7 +22,7 @@ rm -fr autom4te.cache aclocal.m4 config.h config.h.in config.log Makefile.in mis
 rm -rf src/Makefile.in
 autoreconf --install -W gnu
 ./configure
-make && sudo make install
+make -j && sudo make install
 
 == Testsuite ==
 
@@ -89,9 +89,14 @@ https://savannah.gnu.org/news/approve.php?group=parallel
 
 http://www.gnu.org/software/parallel/
 http://www.gnu.org/software/parallel/man.html
+http://www.gnu.org/software/parallel/sql.html
+http://www.gnu.org/software/parallel/sem.html
+http://www.gnu.org/software/parallel/niceload.html
 
-pod2html src/parallel > ../parallel-web/parallel/man.html
+pod2html src/parallel.pod > ../parallel-web/parallel/man.html
 pod2html src/sql > ../parallel-web/parallel/sql.html
+pod2html src/niceload > ../parallel-web/parallel/niceload.html
+pod2html src/sem.pod > ../parallel-web/parallel/sem.html
 cd ../parallel-web/parallel
 cvs up
 cvs ci
@@ -125,11 +130,13 @@ cc:Peter Simons <simons@cryp.to>, Sandro Cazzaniga <kharec@mandriva.org>,
    Andrew McFague <amcfague@wgen.net>, Steven M. Christensen <sunfreeware@gmail.com>,
    Chris Howey <howeyc@gmail.com>, Fethican Coşkuner <fethicanc@gmail.com>,
    Rogério Brito <rbrito@ime.usp.br>, Jonathan Palardy <jonathan.palardy@gmail.com>,
-   Koen Vervloesem <koen@vervloesem.eu>, R. Tyler Croy <tyler@monkeypox.org>
+   Koen Vervloesem <koen@vervloesem.eu>, R. Tyler Croy <tyler@monkeypox.org>,
+   ryoichiro.suzuki@gmail.com,kerick@shiftedbit.net,
+   Christian Faulhammer <fauli@gentoo.org>
 
-Subject: GNU Parallel 20101202 released
+Subject: GNU Parallel 20101222 released
 
-GNU Parallel 20101202 has been released. It is available for
+GNU Parallel 20101222 has been released. It is available for
 download at: http://ftp.gnu.org/gnu/parallel/
 
 New in this release:
@@ -146,13 +153,26 @@ New in this release:
 * Implemented --nice set the niceness of jobs running both locally and
   remotely.
 
+* Implemented --dry-run to print the job without running it.
+
+* Implemented --tty as the old default of assigning a tty to the first
+  job causes problems.
+
 * Review with focus on clusters. Thanks to Taylor Gillespie
   http://www.unixpronews.com/unixpronews-49-20101019GNUParallelSpeedUpProcessingWithMulticoresClusters.html
 
+* Review with focus on protein similarity. 
+  http://kevinformatics.tumblr.com/post/2142473893/cluster-like-computing-using-gnu-parallel
+
+* Review in Spanish.
+  http://gr3p.com/2010/12/gnu-parallel-acelera-tus-scripts-en-linux
+
+* Quite a few bug fixes and man page updates.
+
 = About GNU Parallel =
 
 GNU Parallel is a shell tool for executing jobs in parallel using one
-or more machines. A job is typically a single command or a small
+or more computers. A job is typically a single command or a small
 script that has to be run for each of the lines in the input. The
 typical input is a list of files, a list of hosts, a list of users, a
 list of URLs, or a list of tables.

src/Makefile.am

@@ -18,21 +18,21 @@ niceload.1: niceload Makefile
 	pod2man --release='$(PACKAGE_VERSION)' --center='$(PACKAGE_NAME)' \
 		--section=1 $(srcdir)/niceload > $(srcdir)/niceload.1
 
-parallel.html: parallel Makefile
+parallel.html: parallel Makefile sem
-	pod2html $(srcdir)/parallel > $(srcdir)/parallel.html
+	./sem --fg --id pod2html pod2html $(srcdir)/parallel.pod > $(srcdir)/parallel.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-sem.html: sem.pod Makefile
+sem.html: sem.pod Makefile sem
-	pod2html $(srcdir)/sem.pod > $(srcdir)/sem.html
+	./sem --fg --id pod2html pod2html $(srcdir)/sem.pod > $(srcdir)/sem.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-sql.html: sql Makefile
+sql.html: sql Makefile sem
-	pod2html $(srcdir)/sql > $(srcdir)/sql.html
+	./sem --fg --id pod2html pod2html $(srcdir)/sql > $(srcdir)/sql.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-niceload.html: niceload Makefile
+niceload.html: niceload Makefile sem
-	pod2html $(srcdir)/niceload > $(srcdir)/niceload.html
+	./sem --fg --id pod2html pod2html $(srcdir)/niceload > $(srcdir)/niceload.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
 sem: parallel
 	ln -fs parallel sem

src/Makefile.in

@@ -463,21 +463,21 @@ niceload.1: niceload Makefile
 	pod2man --release='$(PACKAGE_VERSION)' --center='$(PACKAGE_NAME)' \
 		--section=1 $(srcdir)/niceload > $(srcdir)/niceload.1
 
-parallel.html: parallel Makefile
+parallel.html: parallel Makefile sem
-	pod2html $(srcdir)/parallel > $(srcdir)/parallel.html
+	./sem --fg --id pod2html pod2html $(srcdir)/parallel.pod > $(srcdir)/parallel.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-sem.html: sem.pod Makefile
+sem.html: sem.pod Makefile sem
-	pod2html $(srcdir)/sem.pod > $(srcdir)/sem.html
+	./sem --fg --id pod2html pod2html $(srcdir)/sem.pod > $(srcdir)/sem.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-sql.html: sql Makefile
+sql.html: sql Makefile sem
-	pod2html $(srcdir)/sql > $(srcdir)/sql.html
+	./sem --fg --id pod2html pod2html $(srcdir)/sql > $(srcdir)/sql.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
-niceload.html: niceload Makefile
+niceload.html: niceload Makefile sem
-	pod2html $(srcdir)/niceload > $(srcdir)/niceload.html
+	./sem --fg --id pod2html pod2html $(srcdir)/niceload > $(srcdir)/niceload.html
-	rm -f $(srcdir)/pod2htm*
+	./sem --fg --id pod2html rm -f $(srcdir)/pod2htm*
 
 sem: parallel
 	ln -fs parallel sem

src/parallel

@@ -142,6 +142,7 @@ sub get_options_from_array {
 	 "workdir|W=s" => \$::opt_workdir,
 	 "tmpdir=s" => \$::opt_tmpdir,
 	 "tempdir=s" => \$::opt_tmpdir,
+	 "tty|T" => \$::opt_tty,
 	 "halt-on-error|H=s" => \$::opt_halt_on_error,
 	 "retries=i" => \$::opt_retries,
 	 "dry-run|dryrun" => \$::opt_dryrun,
@@ -192,7 +193,7 @@ sub get_options_from_array {
 sub parse_options {
     # Returns: N/A
     # Defaults:
-    $Global::version = 20101217;
+    $Global::version = 20101220;
     $Global::progname = 'parallel';
     $Global::debug = 0;
     $Global::verbose = 0;
@@ -234,7 +235,9 @@ sub parse_options {
     if(defined $::opt_U) { $Global::replace{'{.}'} = $::opt_U; }
     if(defined $::opt_i and $::opt_i) { $Global::replace{'{}'} = $::opt_i; }
     if(defined $::opt_basenamereplace) { $Global::replace{'{/}'} = $::opt_basenamereplace; }
-    if(defined $::opt_basenameextensionreplace) { $Global::replace{'{/.}'} = $::opt_basenameextensionreplace; }
+    if(defined $::opt_basenameextensionreplace) {
+	$Global::replace{'{/.}'} = $::opt_basenameextensionreplace;
+    }
     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_N and $::opt_N) { $Global::max_number_of_args = $::opt_N; }
@@ -245,8 +248,12 @@ sub parse_options {
     if(defined $::opt_arg_sep) { $Global::arg_sep = $::opt_arg_sep; }
     if(defined $::opt_arg_file_sep) { $Global::arg_file_sep = $::opt_arg_file_sep; }
     if(defined $::opt_number_of_cpus) { print SSHLogin::no_of_cpus(),"\n"; wait_and_exit(0); }
-    if(defined $::opt_number_of_cores) { print SSHLogin::no_of_cores(),"\n"; wait_and_exit(0); }
+    if(defined $::opt_number_of_cores) {
-    if(defined $::opt_max_line_length_allowed) { print CommandMaxLength::real_max_length(),"\n"; wait_and_exit(0); }
+	print SSHLogin::no_of_cores(),"\n"; wait_and_exit(0);
+    }
+    if(defined $::opt_max_line_length_allowed) {
+	print Limits::Command::real_max_length(),"\n"; wait_and_exit(0);
+    }
     if(defined $::opt_version) { version(); wait_and_exit(0); }
     if(defined $::opt_show_limits) { show_limits(); }
     if(defined @::opt_sshlogin) { @Global::sshlogin = @::opt_sshlogin; }
@@ -258,6 +265,16 @@ sub parse_options {
     if(defined $::opt_fg) { $Global::semaphore = 1; }
     if(defined $::opt_bg) { $Global::semaphore = 1; }
     if(defined $::opt_wait) { $Global::semaphore = 1; }
+    if(defined $::opt_tty) {
+	# Defaults for --tty: -j1 -u
+	# Can be overridden with -jXXX -g
+	if(not defined $::opt_P) {
+	    $::opt_P = 1;
+	}
+	if(not defined $::opt_g) {
+	    $Global::grouped = 0;
+	}
+    }
     if(defined @::opt_trc) {
 	push @Global::ret_files, @::opt_trc;
 	$::opt_transfer = 1;
@@ -625,7 +642,7 @@ sub init_run_jobs {
     }
 }
 
-sub login_and_host {
+sub __login_and_host {
     # Returns:
     #   login@hostname
     my $sshlogin = shift;
@@ -1383,10 +1400,10 @@ sub dec_jobs_running {
     $self->{'jobs_running'}--;
 }
 
-sub set_jobs_running {
+#sub set_jobs_running {
-    my $self = shift;
+#    my $self = shift;
-    $self->{'jobs_running'} = 0;
+#    $self->{'jobs_running'} = shift;
-}
+#}
 
 sub set_maxlength {
     my $self = shift;
@@ -2378,8 +2395,8 @@ sub sshcleanup {
 		join(" ",map { ::shell_quote_scalar($workdir."/".$_) } @subworkdirs);
 	}
 	my $relpath = ($file !~ m:^/:); # Is the path relative?
-	my $cleandir = ($relpath ? $workdir : "");
+	my $cleandir = ($relpath ? $workdir."/" : "");
-	$cleancmd .= "$sshcmd $serverlogin rm -f ".::shell_quote_scalar($file.$removeworkdir).";";
+	$cleancmd .= "$sshcmd $serverlogin rm -f ".::shell_quote_scalar($cleandir.$file.$removeworkdir).";";
     }
     return $cleancmd;
 }
@@ -2499,7 +2516,7 @@ sub start {
 	# Re-open to avoid complaining
 	open STDIN, "<&", $Global::original_stdin
 	    or die "Can't dup \$Global::original_stdin: $!";
-    } elsif (not $Global::tty_taken and -c "/dev/tty" and
+    } elsif ($::opt_tty and not $Global::tty_taken and -c "/dev/tty" and
 	     open(DEVTTY, "/dev/tty")) {
 	# Give /dev/tty to the command if no one else is using it
 	$pid = ::open3("<&DEVTTY", ">&STDOUT", ">&STDERR", $command) ||
@@ -3238,7 +3255,6 @@ sub get {
 	    } else {
 		push @out_record, Arg->new("");
 	    }
-	    
 	}
 	return \@out_record;
     } else {

src/parallel.pod

@@ -246,18 +246,18 @@ Implies B<--semaphore>.
 =item B<--cleanup>
 
 Remove transferred files. B<--cleanup> will remove the transferred files
-on the remote server after processing is done.
+on the remote computer 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 transferred to the remote server will be
+With B<--transfer> the file transferred to the remote computer will be
-removed on the remote server.  Directories created will not be removed
+removed on the remote computer.  Directories created will not be removed
 - even if they are empty.
 
-With B<--return> the file transferred from the remote server will be
+With B<--return> the file transferred from the remote computer will be
-removed on the remote server.  Directories created will not be removed
+removed on the remote computer.  Directories created will not be removed
 - even if they are empty.
 
 B<--cleanup> is ignored when not used with B<--transfer> or B<--return>.
@@ -493,12 +493,12 @@ Implies B<-X> unless B<-m> is set.
 
 =item B<--load> I<max-load> (experimental)
 
-Do not start new jobs on a given machine unless the load is less than
+Do not start new jobs on a given computer unless the load is less than
 I<max-load>. I<max-load> uses the same syntax as B<--jobs>, so I<100%>
 is a valid setting.
 
 The load average is only sampled every 10 seconds to avoid stressing
-small machines.
+small computers.
 
 
 =item B<--controlmaster> (experimental)
@@ -610,8 +610,8 @@ with 'y' or 'Y'.  Implies B<-t>.
 
 Use profile I<profilename> for options. This is useful if you want to
 have multiple profiles. You could have one profile for running jobs in
-parallel on the local machine and a different profile for running jobs
+parallel on the local computer and a different profile for running jobs
-on remote machines. See the section PROFILE FILES for examples.
+on remote computers. See the section PROFILE FILES for examples.
 
 I<profilename> corresponds to the file ~/.parallel/I<profilename>.
 
@@ -644,23 +644,23 @@ reason (such as network failure).
 
 =item B<--return> I<filename>
 
-Transfer files from remote servers. B<--return> is used with
+Transfer files from remote computers. B<--return> is used with
-B<--sshlogin> when the arguments are files on the remote servers. When
+B<--sshlogin> when the arguments are files on the remote computers. When
 processing is done the file I<filename> will be transferred
-from the remote server using B<rsync> and will be put relative to
+from the remote computer 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<$HOME/foo/bar.out> from the server
+This will transfer the file I<$HOME/foo/bar.out> from the computer
 I<server.example.com> to the file I<foo/bar.out> after running
 B<touch foo/bar.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.out> from the server
+This will transfer the file I</tmp/foo/bar.out> from the computer
 I<server.example.com> to the file I</tmp/foo/bar.out> after running
 B<touch /tmp/foo/bar.out> on I<server.example.com>.
 
@@ -742,9 +742,9 @@ when called with B<--shebang>).
 
 =item B<--sshlogin> I<[ncpu/]sshlogin[,[ncpu/]sshlogin[,...]]>
 
-Distribute jobs to remote servers. The jobs will be run on a list of
+Distribute jobs to remote computers. The jobs will be run on a list of
-remote servers.  GNU B<parallel> will determine the number of CPU
+remote computers.  GNU B<parallel> will determine the number of CPU
-cores on the remote servers and run the number of jobs as specified by
+cores on the remote computers and run the number of jobs as specified by
 B<-j>.  If the number I<ncpu> is given GNU B<parallel> will use this
 number for number of CPU cores on the host. Normally I<ncpu> will not
 be needed.
@@ -803,6 +803,17 @@ Silent.  The job to be run will not be printed. This is the default.
 Can be reversed with B<-v>.
 
 
+=item B<--tty> (beta testing)
+
+=item B<-T> (beta testing)
+
+Open terminal tty. If GNU B<parallel> is used for starting an
+interactive program then this option may be needed. It will start only
+one job at a time (i.e. B<-j1>), not buffer the output (i.e. B<-u>),
+and it will open a tty for the job. When the job is done, the next job
+will get the tty.
+
+
 =item B<--tmpdir> I<dirname>
 
 Directory for temporary files. GNU B<parallel> normally buffers output
@@ -822,22 +833,22 @@ See also B<-v> and B<-p>.
 
 =item B<--transfer>
 
-Transfer files to remote servers. B<--transfer> is used with
+Transfer files to remote computers. B<--transfer> is used with
 B<--sshlogin> when the arguments are files and should be transferred to
-the remote servers. The files will be transferred using B<rsync> and
+the remote computers. The files will be transferred 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
+This will transfer the file I<foo/bar.txt> to the computer
 I<server.example.com> to the file I<$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
+This will transfer the file I<foo/bar.txt> to the computer
 I<server.example.com> to the file I</tmp/foo/bar.txt> before running
 B<wc /tmp/foo/bar.txt> on I<server.example.com>.
 
@@ -929,9 +940,9 @@ Print the version GNU B<parallel> and exit.
 =item B<-W> I<mydir> (beta testing)
 
 Files transferred using B<--transfer> and B<--return> will be relative
-to I<mydir> on remote machines, and the command will be executed in
+to I<mydir> on remote computers, and the command will be executed in
 that dir. The special workdir B<...> will create a workdir in
-B<~/.parallel/tmp/> on the remote machines and will be removed if
+B<~/.parallel/tmp/> on the remote computers and will be removed if
 using B<--cleanup>.
 
 
@@ -1323,16 +1334,16 @@ GNU B<parallel> will try to determine the number of CPU cores on each
 of the remote computers, so B<-j+0> will run one job per CPU core -
 even if the remote computers do not have the same number of CPU cores.
 
-If the number of CPU cores on the remote servers is not identified
+If the number of CPU cores on the remote computers is not identified
 correctly the number of CPU cores can be added in front. Here the
-server has 8 CPU cores.
+computer has 8 CPU cores.
 
   seq 1 10 | parallel --sshlogin 8/server.example.com echo
 
 
 =head1 EXAMPLE: Transferring of files
 
-To recompress gzipped files with B<bzip2> using a remote server run:
+To recompress gzipped files with B<bzip2> using a remote computer run:
 
   find logs/ -name '*.gz' | \
     parallel --sshlogin server.example.com \
@@ -1363,7 +1374,7 @@ computer and the files transferred from the remote computer:
     parallel --sshlogin server.example.com \
     --transfer --return {.}.bz2 --cleanup "zcat {} | bzip2 -9 >{.}.bz2"
 
-If you want run on several servers add the servers to I<--sshlogin>
+If you want run on several computers add the computers to I<--sshlogin>
 either using ',' or multiple I<--sshlogin>:
 
   find logs/ -name '*.gz' | \
@@ -1513,9 +1524,9 @@ same time:
 
 You can use GNU Parallel to start interactive programs like emacs or vi:
 
-B<cat filelist | parallel -uXj1 emacs>
+B<cat filelist | parallel -T -X emacs>
 
-B<cat filelist | parallel -uXj1 vi>
+B<cat filelist | parallel -T -X vi>
 
 If there are more files than will fit on a single command line, the
 editor will be started again with the remaining files.
@@ -1792,7 +1803,7 @@ Example: Profile for running a perl script before every command:
 Note how the $ and " need to be quoted using \.
 
 Example: Profile for running distributed jobs with B<nice> on the
-remote machines:
+remote computers:
 
   echo -S .. nice > ~/.parallel/dist
   parallel -J dist --trc {.}.bz2 bzip2 -9 ::: *
@@ -2385,14 +2396,14 @@ using GNU B<parallel>:
 ClusterSSH solves a different problem than GNU B<parallel>.
 
 ClusterSSH runs the same command with the same arguments on a list of
-machines - one per machine. This is typically used for administrating
+computers - one per computer. This is typically used for administrating
-several machines that are almost identical.
+several computers that are almost identical.
 
 GNU B<parallel> runs the same (or different) commands with different
-arguments in parallel possibly using remote machines to help
+arguments in parallel possibly using remote computers to help
-computing. If more than one machine is listed in B<-S> GNU B<parallel> may
+computing. If more than one computer is listed in B<-S> GNU B<parallel> may
 only use one of these (e.g. if there are 8 jobs to be run and one
-machine has 8 cores).
+computer has 8 cores).
 
 GNU B<parallel> can be used as a poor-man's version of ClusterSSH:
 

src/sem.pod

@@ -81,6 +81,17 @@ available.
   done
   sem --wait
 
+=head1 EXAMPLE: Protecting pod2html from itself
+
+pod2html creates two files: pod2htmd.tmp and pod2htmi.tmp which it
+does not clean up. It uses these two files for a short time. But if
+you run multiple pod2html in parallel (e.g. in a Makefile with make
+-j) you need to protect pod2html from running twice at the same
+time. B<sem> running as a mutex will do just that:
+
+  sem --fg --id pod2html pod2html foo.pod > foo.html
+  sem --fg --id pod2html rm -f pod2htmd.tmp pod2htmi.tmp
+
 
 =head1 BUGS
 

src/sql

@@ -528,7 +528,7 @@ $Global::Initfile && unlink $Global::Initfile;
 exit ($err);
 
 sub parse_options {
-    $Global::version = 20101206;
+    $Global::version = 20101220;
     $Global::progname = 'sql';
 
     # This must be done first as this may exec myself

testsuite/tests-to-run/test15.sh

@@ -91,7 +91,7 @@ echo 3 | xargs -P 1 -n 1 -a files cat -
 echo 'parallel Expect: 3 1 via psedotty  2'
 cat >/tmp/parallel-script-for-script <<EOF
 #!/bin/bash
-echo 3 | parallel -k -P 1 -n 1 -a files cat -
+echo 3 | parallel -T -k -P 1 -n 1 -a files cat -
 EOF
 chmod 755 /tmp/parallel-script-for-script
 echo via pseudotty | script -q -f -c /tmp/parallel-script-for-script /dev/null
@@ -102,7 +102,7 @@ echo 3 | xargs -I {} -P 1 -n 1 -a files cat {} -
 echo 'parallel Expect: 1 3 2 via pseudotty'
 cat >/tmp/parallel-script-for-script2 <<EOF
 #!/bin/bash
-echo 3 | parallel -k -I {} -P 1 -n 1 -a files cat {} -
+echo 3 | parallel -T -k -I {} -P 1 -n 1 -a files cat {} -
 EOF
 chmod 755 /tmp/parallel-script-for-script2
 echo via pseudotty | script -q -f -c /tmp/parallel-script-for-script2 /dev/null

testsuite/tests-to-run/test25.sh

@@ -13,7 +13,7 @@ parallel --argsep .--- -kv .--- 'echo a' 'echo b'
 echo '### Test stdin goes to first command only ("-" as argument)'
 cat >/tmp/parallel-script-for-script <<EOF
 #!/bin/bash
-echo via first cat |parallel -kv cat ::: - -
+echo via first cat |parallel -T -kv cat ::: - -
 EOF
 chmod 755 /tmp/parallel-script-for-script
 echo via pseudotty | script -q -f -c /tmp/parallel-script-for-script /dev/null
@@ -21,7 +21,7 @@ sleep 1
 echo '### Test stdin goes to first command only ("cat" as argument)'
 cat >/tmp/parallel-script-for-script2 <<EOF
 #!/bin/bash
-echo no output |parallel -kv ::: 'echo a' 'cat'
+echo no output |parallel -T -kv ::: 'echo a' 'cat'
 EOF
 chmod 755 /tmp/parallel-script-for-script2
 echo via pseudotty | script -q -f -c /tmp/parallel-script-for-script2 /dev/null

testsuite/tests-to-run/test47.sh

@@ -0,0 +1,170 @@
+#!/bin/bash
+
+SERVER1=parallel-server3
+SERVER2=parallel-server2
+
+# Minimal version of test17
+
+# Make sure sort order is the same
+export LANG=C
+
+echo '### Test --transfer --return --cleanup'
+
+rm -rf /tmp/parallel.file*
+stdout ssh $SERVER1 rm -rf 'tmp/parallel.file*'  '/tmp/parallel.file*'
+stdout ssh parallel@$SERVER2 rm -rf 'tmp/parallel.file*' '/tmp/parallel.file*'
+(seq 1 2) >/tmp/test17
+echo '# Create some weirdly files in /tmp'
+mkdir -p /tmp/parallel.file
+cat /tmp/test17 | parallel -k /bin/echo file{} '>'/tmp/parallel.file{}.file
+cat /tmp/test17 | parallel -k /bin/echo /tmp/parallel.file{}.file >/tmp/test17abs
+cat /tmp/test17 | parallel -k /bin/echo tmp/parallel.file{}.file >/tmp/test17rel
+
+echo '### --transfer - abspath'
+stdout ssh $SERVER1 'rm -rf /tmp/parallel.file*'
+stdout ssh parallel@$SERVER2 'rm -rf /tmp/parallel.file*'
+cat /tmp/test17abs | parallel -k --transfer --sshlogin $SERVER1,parallel@$SERVER2 cat {}";"rm {}
+# One of these should give the empty dir /tmp/parallel.file
+echo good if no file
+stdout ssh $SERVER1 ls '/tmp/parallel.file*'
+# The other: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*'
+
+echo '### --transfer - relpath'
+stdout ssh $SERVER1 'rm -rf tmp/parallel.file*' 
+stdout ssh parallel@$SERVER2 'rm -rf tmp/parallel.file*'
+cd /
+cat /tmp/test17rel | parallel -k --transfer --sshlogin $SERVER1,parallel@$SERVER2 cat {}";"rm {}
+# Should give: No such file or directory
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' 
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*'
+
+echo '### --transfer --cleanup - abspath'
+cat /tmp/test17abs | parallel -k --transfer --cleanup --sshlogin $SERVER1,parallel@$SERVER2 cat {}
+echo good if no file
+# Should give: No such file or directory
+stdout ssh $SERVER1 ls '/tmp/parallel.file*'
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*'
+
+echo '### --transfer --cleanup - relpath'
+cat /tmp/test17rel | parallel -k --transfer --cleanup --sshlogin $SERVER1,parallel@$SERVER2 cat {}
+# Should give: No such file or directory
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --return - abspath'
+rm -rf /tmp/parallel.file*out
+cat /tmp/test17abs | parallel -k --return {.}.out --sshlogin $SERVER1,parallel@$SERVER2 echo {} ">"{.}.out
+ls /tmp/parallel.file*out
+
+echo '### --return - relpath'
+rm -rf /tmp/parallel.file*out
+cat /tmp/test17rel | parallel -k --return {.}.out --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp/parallel.file ';'echo {} ">"{.}.out
+ls tmp/parallel.file*out
+
+echo '### --return - multiple files'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --return {.}.out --return {}.done \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'echo {} ">"{.}.out';'echo {} ">"{}.done';'
+ls tmp/parallel.file*out tmp/parallel.file*done
+
+echo '### --return --cleanup - abspath'
+rm -rf /tmp/parallel.file*out /tmp/parallel.file*done
+cat /tmp/test17abs | parallel -k --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp/parallel.file ';'echo {} ">"{.}.out';'echo {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls '/tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*' || echo OK
+
+echo '### --return --cleanup - relpath'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp/parallel.file ';'echo {} ">"{.}.out';'echo {} ">"{}.done';'
+ls tmp/parallel.file*out tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --return --cleanup - multiple returns'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp/parallel.file ';'echo {} ">"{.}.out';'echo {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --transfer --return --cleanup - abspath'
+rm -rf /tmp/parallel.file*out /tmp/parallel.file*done
+cat /tmp/test17abs | parallel -k --transfer --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls '/tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*' || echo OK
+
+
+echo '### --transfer --return --cleanup - relpath'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --transfer --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --transfer --return --cleanup - multiple files'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --transfer --return {.}.out --return {}.done --cleanup \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --trc - abspath'
+rm -rf /tmp/parallel.file*out /tmp/parallel.file*done
+cat /tmp/test17abs | parallel -k --trc {.}.out --trc {}.done \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls '/tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*' || echo OK
+
+echo '### --trc - relpath'
+rm -rf tmp/parallel.file*out tmp/parallel.file*done
+cat /tmp/test17rel | parallel -k --trc {.}.out --trc {}.done \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls tmp/parallel.file*out tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls 'tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls 'tmp/parallel.file*' || echo OK
+
+echo '### --trc - multiple files'
+rm -rf /tmp/parallel.file*out /tmp/parallel.file*done
+cat /tmp/test17abs | parallel -k --trc {.}.out --trc {}.done \
+  --sshlogin $SERVER1,parallel@$SERVER2 mkdir -p tmp ';'cat {} ">"{.}.out';'cat {} ">"{}.done';'
+ls /tmp/parallel.file*out /tmp/parallel.file*done
+echo good if no file
+stdout ssh $SERVER1 ls '/tmp/parallel.file*' || echo OK
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*' || echo OK
+
+echo '### --transfer --cleanup - multiple argument files'
+parallel -kv --transfer --cleanup -Sparallel@$SERVER2 cat {2} {1} :::: /tmp/test17rel <(sort -r /tmp/test17abs)
+# Should give: No such file or directory
+stdout ssh parallel@$SERVER2 ls '/tmp/parallel.file*' || echo OK
+

testsuite/wanted-results/test19

@@ -85,7 +85,7 @@ parallel-server3 rsync --server --sender -lDrRze.iLsf --remove-source-files . ./
 'newline2.out
 parallel-server3 rsync --server --sender -lDrRze.iLsf --remove-source-files . ././tmp/parallel.file.'
 'newline2.out2
-parallel-server3 rm -f tmp/parallel.file.'
+parallel-server3 rm -f ./tmp/parallel.file.'
 'newline2; rmdir 2>/dev/null ./tmp
 -l parallel parallel-server2 rsync --server -lDErRze.iLsf . .
 parallel@parallel-server2 PARALLEL_SEQ=1;export PARALLEL_SEQ;PARALLEL_PID=00000;export PARALLEL_PID; cat tmp/parallel.file.'
@@ -97,7 +97,7 @@ parallel@parallel-server2 PARALLEL_SEQ=1;export PARALLEL_SEQ;PARALLEL_PID=00000;
 'newline1.out
 -l parallel parallel-server2 rsync --server --sender -lDrRze.iLsf --remove-source-files . ././tmp/parallel.file.'
 'newline1.out2
-parallel@parallel-server2 rm -f tmp/parallel.file.'
+parallel@parallel-server2 rm -f ./tmp/parallel.file.'
 'newline1; rmdir 2>/dev/null ./tmp
 ### Test use special ssh with > 9 simultaneous
 1

testsuite/wanted-results/test47

@@ -0,0 +1,127 @@
+### Test --transfer --return --cleanup
+# Create some weirdly files in /tmp
+### --transfer - abspath
+file1
+file2
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+ls: cannot access /tmp/parallel.file*: No such file or directory
+### --transfer - relpath
+file1
+file2
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+ls: cannot access tmp/parallel.file*: No such file or directory
+### --transfer --cleanup - abspath
+file1
+file2
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+ls: cannot access /tmp/parallel.file*: No such file or directory
+### --transfer --cleanup - relpath
+file1
+file2
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --return - abspath
+/tmp/parallel.file1.out
+/tmp/parallel.file2.out
+### --return - relpath
+tmp/parallel.file1.out
+tmp/parallel.file2.out
+### --return - multiple files
+tmp/parallel.file1.file.done
+tmp/parallel.file1.out
+tmp/parallel.file2.file.done
+tmp/parallel.file2.out
+### --return --cleanup - abspath
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+### --return --cleanup - relpath
+tmp/parallel.file1.file.done
+tmp/parallel.file1.out
+tmp/parallel.file2.file.done
+tmp/parallel.file2.out
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --return --cleanup - multiple returns
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --transfer --return --cleanup - abspath
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+### --transfer --return --cleanup - relpath
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --transfer --return --cleanup - multiple files
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --trc - abspath
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+### --trc - relpath
+tmp/parallel.file1.file.done
+tmp/parallel.file1.out
+tmp/parallel.file2.file.done
+tmp/parallel.file2.out
+good if no file
+ls: cannot access tmp/parallel.file*: No such file or directory
+OK
+### --trc - multiple files
+/tmp/parallel.file1.file.done
+/tmp/parallel.file1.out
+/tmp/parallel.file2.file.done
+/tmp/parallel.file2.out
+good if no file
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK
+### --transfer --cleanup - multiple argument files
+cat /tmp/parallel.file2.file tmp/parallel.file1.file
+file2
+file1
+cat /tmp/parallel.file1.file tmp/parallel.file2.file
+file1
+file2
+ls: cannot access /tmp/parallel.file*: No such file or directory
+OK