2015-01-18 23:07:12 +00:00
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#!/usr/bin/perl -w
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=encoding utf8
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=head1 Design of GNU Parallel
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This document describes design decisions made in the development of
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GNU B<parallel> and the reasoning behind them. It will give an
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overview of why some of the code looks like it does, and help new
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maintainers understand the code better.
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2015-01-20 21:08:52 +00:00
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=head2 One file program
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GNU B<parallel> is a Perl script in a single file. It is object
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oriented, but contrary to normal Perl scripts each class is not in its
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own file. This is due to user experience: The goal is that in a pinch
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the user will be able to get GNU B<parallel> working simply by copying
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a single file: No need messing around with environment variables like
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PERL5LIB.
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=head2 Old Perl style
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GNU B<parallel> uses some old, deprecated constructs. This is due to a
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goal of being able to run on old installations. Currently the target
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is CentOS 3.9 and Perl 5.8.0.
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=head2 Exponentially back off
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GNU B<parallel> busy waits. This is because the reason why a job is
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not started may be due to load average, and thus it will not make
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sense to wait for a job to finish. Instead the load average must be
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2015-04-09 23:20:51 +00:00
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checked again. Load average is not the only reason: --timeout has a
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similar problem.
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2015-01-20 21:08:52 +00:00
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To not burn up too up too much CPU GNU B<parallel> sleeps
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exponentially longer and longer if nothing happens, maxing out at 1
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second.
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=head2 Shell compatibility
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It is a goal to have GNU B<parallel> work equally well in any
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shell. However, in practice GNU B<parallel> is being developed in
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B<bash> and thus testing in other shells is limited to reported bugs.
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When an incompatibility is found there is often not an easy fix:
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Fixing the problem in B<csh> often breaks it in B<bash>. In these
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cases the fix is often to use a small Perl script and call that.
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2015-01-18 23:07:12 +00:00
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=head2 Job slots
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The easiest way to explain what GNU B<parallel> does is to assume that
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there are a number of job slots, and when a slot becomes available a
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job from the queue will be run in that slot. But originally GNU
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B<parallel> did not model job slots in the code. Job slots have been
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added to make it possible to use {%} as a replacement string.
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Job slots were added to the code in 20140522, but while the job
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sequence number can be computed in advance, the job slot can only be
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computed the moment a slot becomes available. So it has been
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implemented as a stack with lazy evaluation: Draw one from an empty
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stack and the stack is extended by one. When a job is done, push the
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available job slot back on the stack.
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This implementation also means that if you use remote executions, you
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cannot assume that a given job slot will remain on the same remote
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server. This goes double since number of job slots can be adjusted on
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the fly (by giving B<--jobs> a file name).
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2015-01-20 21:08:52 +00:00
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2015-01-18 23:07:12 +00:00
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=head2 Rsync protocol version
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B<rsync> 3.1.x uses protocol 31 which is unsupported by version
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2.5.7. That means that you cannot push a file to a remote system using
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B<rsync> protocol 31, if the remote system uses 2.5.7. B<rsync> does
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not automatically downgrade to protocol 30.
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GNU B<parallel> does not require protocol 31, so if the B<rsync>
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version is >= 3.1.0 then B<--protocol 30> is added to force newer
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B<rsync>s to talk to version 2.5.7.
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2015-02-22 14:09:26 +00:00
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=head2 Compression
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B<--compress> compresses the data in the temporary files. This is a
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bit tricky because there should be no files to clean up if GNU
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B<parallel> is killed by a power outage.
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GNU B<parallel> first selects a compress program. If the user has not
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selected one, the first of these that are in $PATH is used: B<lzop
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pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2>. They are sorted by
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speed on a 8 core machine.
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Schematically the setup is as follows:
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command started by parallel | compress > tmpfile
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cattail tmpfile | uncompress | parallel
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The setup is duplicated for both standard output (stdout) and standard
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error (stderr).
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GNU B<parallel> pipes output from the command run into the compress
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program which saves to a tmpfile. GNU B<parallel> records the pid of
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the compress program. At the same time a small perl script (called
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B<cattail> above) is started: It basically does B<cat> followed by
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B<tail -f>, but it also removes the tmpfile as soon as the first byte
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is read, and it continously checks if the pid of the compress program
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is dead. If the compress program is dead, B<cattail> reads the rest of
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tmpfile and exits.
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As most compress programs write out a header when they start, the
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tmpfile in practice is unlinked after around 40 ms.
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2015-01-18 23:07:12 +00:00
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=head2 Wrapping
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The command given by the user can be wrapped in multiple
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templates. Templates can be wrapped in other templates.
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=over 15
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=item --shellquote
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echo <<shell double quoted input>>
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=item --nice I<pri>
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\nice -n I<pri> $shell -c <<shell quoted input>>
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The \ is needed to avoid using the builtin nice command, which does not
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support -n in B<tcsh>. B<$shell -c> is needed to nice composed commands
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command.
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=item --cat
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(cat > {}; <<input>> {}; perl -e '$bash=shift; $csh=shift; for(@ARGV)
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{unlink;rmdir;} if($bash=~s/h//) {exit$bash;} exit$csh;' "$?h"
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"$status" {});
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2015-05-20 19:09:33 +00:00
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{} is set to $PARALLEL_TMP which is a tmpfile. The Perl script saves
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the exit value, unlinks the tmpfile, and returns the exit value - no
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matter if the shell is B<bash> (using $?) or B<*csh> (using $status).
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2015-01-18 23:07:12 +00:00
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=item --fifo
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2015-05-20 19:09:33 +00:00
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perl -e '($s,$c,$f) = @ARGV;
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system "mkfifo", $f;
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$pid = fork || exec $s, "-c", $c;
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open($o,">",$f) || die $!;
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while(sysread(STDIN,$buf,32768)){
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syswrite $o, $buf;
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}
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close $o;
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waitpid $pid,0;
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unlink $f;
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exit $?/256;' $shell <<input>> $PARALLEL_TMP
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This is an elaborate way of: mkfifo {}; run <<input>> in the
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background using $shell; copying STDIN to {}; waiting for background
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to complete; remove {} and exit with the exit code from <<input>>.
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2015-05-20 19:09:33 +00:00
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It is made this way to be compatible with B<*csh>.
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2015-01-18 23:07:12 +00:00
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=item --sshlogin I<sln>
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ssh I<sln> <<shell quoted input>>
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=item --transfer
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( ssh I<sln> mkdir -p ./I<workdir>;rsync --protocol 30 -rlDzR -essh ./{} I<sln>:./I<workdir> ); <<input>>
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Read about B<--protocol 30> in the section B<Rsync protocol version>.
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=item --basefile
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<<todo>>
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=item --return I<file>
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<<input>>; _EXIT_status=$?; mkdir -p I<workdir>; rsync --protocol 30 --rsync-path=cd\ ./I<workdir>\;\ rsync -rlDzR -essh I<sln>:./I<file> ./I<workdir>; exit $_EXIT_status;
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The B<--rsync-path=cd ...> is needed because old versions of B<rsync>
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do not support B<--no-implied-dirs>.
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The B<$_EXIT_status> trick is to postpone the exit value. This makes it
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incompatible with B<*csh> and should be fixed in the future. Maybe a
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wrapping 'sh -c' is enough?
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=item --cleanup
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<<input>> _EXIT_status=$?; <<return>>
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ssh I<sln> \(rm\ -f\ ./I<workdir>/{}\;\ rmdir\ ./I<workdir>\ \>\&/dev/null\;\); exit $_EXIT_status;
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B<$_EXIT_status>: see B<--return> above.
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=item --pipe
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sh -c 'dd bs=1 count=1 of=I<tmpfile> 2>/dev/null'; test ! -s "I<tmpfile>" && rm -f "I<tmpfile>" && exec true; (cat I<tmpfile>; rm I<tmpfile>; cat - ) | ( <<input>> );
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This small wrapper makes sure that <<input>> will never be run if
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there is no data. B<sh -c> is needed to hide stderr if the user's
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shell is B<csh> (which cannot hide stderr).
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=item --tmux
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2015-02-23 21:32:34 +00:00
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mkfifo I<tmpfile.tmx>;
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tmux -S <tmpfile.tms> new-session -s pI<PID> -d 'sleep .2' >&/dev/null;
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tmux -S <tmpfile.tms> new-window -t pI<PID> -n <<shell quoted input>> \(<<shell quoted input>>\)\;\ perl\ -e\ \'while\(\$t++\<3\)\{\ print\ \$ARGV\[0\],\"\\n\"\ \}\'\ \$\?h/\$status\ \>\>\ I<tmpfile.tmx>\&echo\ <<shell double quoted input>>\;echo\ \Job\ finished\ at:\ \`date\`\;sleep\ 10;
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exec perl -e '$/="/";$_=<>;$c=<>;unlink $ARGV; /(\d+)h/ and exit($1);exit$c' I<tmpfile.tmx>
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First a FIFO is made (.tmx). It is used for communicating exit
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value. Next a new tmux session is made. This may fail if there is
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already a session, so the output is ignored. If all job slots finish
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at the same time, then B<tmux> will close the session. A temporary
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socket is made (.tms) to avoid a race condition in B<tmux>. It is
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cleaned up when GNU B<parallel> finishes.
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The input is used as the name of the windows in B<tmux>. When the job
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2015-02-23 21:32:34 +00:00
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inside B<tmux> finishes, the exit value is printed to the FIFO (.tmx).
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This FIFO is opened by B<perl> outside B<tmux>, and B<perl> then
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removes the FIFO. B<Perl> blocks until the first value is read from
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the FIFO, and this value is used as exit value.
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To make it compatible with B<csh> and B<bash> the exit value is
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printed as: $?h/$status and this is parsed by B<perl>.
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Works in B<csh>.
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There is a bug that makes it necessary to print the exit value 3
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times.
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Another bug in B<tmux> requires the length of the tmux title and
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command to not have certain limits. When inside these limits, 75 '\ '
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are added to the title to force it to be outside the limits.
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You can map the bad limits using:
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2015-04-22 22:15:23 +00:00
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perl -e 'sub r { int(rand(shift)).($_[0] && "\t".r(@_)) } print map { r(@ARGV)."\n" } 1..10000' 1600 1500 90 |
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perl -ane '$F[0]+$F[1]+$F[2] < 2037 and print ' |
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parallel --colsep '\t' --tagstring '{1}\t{2}\t{3}' tmux -S /tmp/p{%}-'{=3 $_="O"x$_ =}' \
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new-session -d -n '{=1 $_="O"x$_ =}' true'\ {=2 $_="O"x$_ =};echo $?;rm -f /tmp/p{%}-O*'
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perl -e 'sub r { int(rand(shift)).($_[0] && "\t".r(@_)) } print map { r(@ARGV)."\n" } 1..10000' 17000 17000 90 |
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parallel --colsep '\t' --tagstring '{1}\t{2}\t{3}' \
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tmux -S /tmp/p{%}-'{=3 $_="O"x$_ =}' new-session -d -n '{=1 $_="O"x$_ =}' true'\ {=2 $_="O"x$_ =};echo $?;rm /tmp/p{%}-O*'
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> value.csv 2>/dev/null
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R -e 'a<-read.table("value.csv");X11();plot(a[,1],a[,2],col=a[,3]+5,cex=0.1);Sys.sleep(1000)'
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For B<tmux 1.8> 17000 can be lowered to 2100.
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The interesting areas are title 0..1000 with (title + whole command)
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in 996..1127 and 9331..9636.
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2015-01-18 23:07:12 +00:00
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=back
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The ordering of the wrapping is important:
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=over 5
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=item *
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B<--nice>/B<--cat>/B<--fifo> should be done on the remote machine
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=item *
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B<--pipepart>/B<--pipe> should be done on the local machine inside B<--tmux>
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=back
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2015-03-03 00:05:36 +00:00
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=head2 --block-size adjustment
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Every time GNU B<parallel> detects a record bigger than
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B<--block-size> it increases the block size by 30%. A small
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B<--block-size> gives very poor performance; by exponentially
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increasing the block size performance will not suffer.
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2015-03-16 18:51:08 +00:00
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=head2 Convenience options --nice --basefile --transfer --return
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--cleanup --tmux --group --compress --cat --fifo --workdir
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These are all convenience options that make it easier to do a
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task. But more importantly: They are tested to work on corner cases,
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too. Take B<--nice> as an example:
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nice parallel command ...
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will work just fine. But when run remotely, you need to move the nice
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command so it is being run on the server:
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2015-04-09 23:20:51 +00:00
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parallel -S server nice command ...
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And this will again work just fine, as long as you are running a
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single command. When you are running a composed command you need nice
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to apply to the whole command, and it gets harder still:
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2015-04-09 23:20:51 +00:00
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parallel -S server -q nice bash -c 'command1 ...; command2 | command3'
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2015-03-16 18:51:08 +00:00
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It is not impossible, but by using B<--nice> GNU B<parallel> will do
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the right thing for you. Similarly when transferring files: It starts
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to get hard when the file names contain space, :, `, *, or other
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special characters.
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To run the commands in a B<tmux> session you basically just need to
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quote the command. For simple commands that is easy, but when commands
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contain special characters, it gets much harder to get right.
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B<--cat> and B<--fifo> are easy to do by hand, until you want to clean
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up the tmpfile and keep the exit code of the command.
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The real killer comes when you try to combine several of these: Doing
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that correctly for all corner cases is next to impossible to do by
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hard.
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2015-01-18 23:07:12 +00:00
|
|
|
=head2 Shell shock
|
|
|
|
|
|
|
|
The shell shock bug in B<bash> did not affect GNU B<parallel>, but the
|
|
|
|
solutions did. B<bash> first introduced functions in variables named:
|
|
|
|
I<BASH_FUNC_myfunc()> and later changed that to I<BASH_FUNC_myfunc%%>. When
|
|
|
|
transferring functions GNU B<parallel> reads off the function and changes
|
|
|
|
that into a function definition, which is copied to the remote system and
|
|
|
|
executed before the actual command is executed. Therefore GNU B<parallel>
|
|
|
|
needs to know how to read the function.
|
|
|
|
|
|
|
|
From version 20150122 GNU B<parallel> tries both the ()-version and
|
|
|
|
the %%-version, and the function definition works on both pre- and
|
|
|
|
post-shellshock versions of B<bash>.
|
|
|
|
|
|
|
|
|
|
|
|
=head2 Remote Ctrl-C and standard error (stderr)
|
|
|
|
|
2015-04-09 23:20:51 +00:00
|
|
|
If the user presses Ctrl-C the user expects jobs to stop. This works
|
2015-01-18 23:07:12 +00:00
|
|
|
out of the box if the jobs are run locally. Unfortunately it is not so
|
|
|
|
simple if the jobs are run remotely.
|
|
|
|
|
|
|
|
If remote jobs are run in a tty using B<ssh -tt>, then Ctrl-C works,
|
|
|
|
but all output to standard error (stderr) is sent to standard output
|
|
|
|
(stdout). This is not what the user expects.
|
|
|
|
|
|
|
|
If remote jobs are run without a tty using B<ssh> (without B<-tt>),
|
|
|
|
then output to standard error (stderr) is kept on stderr, but Ctrl-C
|
|
|
|
does not kill remote jobs. This is not what the user expects.
|
|
|
|
|
|
|
|
So what is needed is a way to have both. It seems the reason why
|
|
|
|
Ctrl-C does not kill the remote jobs is because the shell does not
|
|
|
|
propagate the hang-up signal from B<sshd>. But when B<sshd> dies, the
|
|
|
|
parent of the login shell becomes B<init> (process id 1). So by
|
|
|
|
exec'ing a Perl wrapper to monitor the parent pid and kill the child
|
|
|
|
if the parent pid becomes 1, then Ctrl-C works and stderr is kept on
|
|
|
|
stderr. The wrapper looks like this:
|
|
|
|
|
|
|
|
$SIG{CHLD} = sub { $done = 1; };
|
|
|
|
$pid = fork;
|
|
|
|
unless($pid) {
|
|
|
|
# Make own process group to be able to kill HUP it later
|
|
|
|
setpgrp;
|
|
|
|
exec $ENV{SHELL}, "-c", ($bashfunc."@ARGV");
|
|
|
|
die "exec: $!\n";
|
|
|
|
}
|
|
|
|
do {
|
|
|
|
# Parent is not init (ppid=1), so sshd is alive
|
|
|
|
# Exponential sleep up to 1 sec
|
|
|
|
$s = $s < 1 ? 0.001 + $s * 1.03 : $s;
|
|
|
|
select(undef, undef, undef, $s);
|
|
|
|
} until ($done || getppid == 1);
|
|
|
|
# Kill HUP the process group if job not done
|
|
|
|
kill(SIGHUP, -${pid}) unless $done;
|
|
|
|
wait;
|
|
|
|
exit ($?&127 ? 128+($?&127) : 1+$?>>8)
|
|
|
|
|
|
|
|
|
|
|
|
=head2 Transferring of variables and functions
|
|
|
|
|
2015-04-09 23:20:51 +00:00
|
|
|
Transferring of variables and functions given by B<--env> is done by
|
2015-02-22 14:09:26 +00:00
|
|
|
running a Perl script remotely that calls the actual command. The Perl
|
|
|
|
script sets $ENV{variable} to the correct value before exec'ing the a
|
|
|
|
shell that runs the function definition followed by the actual
|
|
|
|
command.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
B<env_parallel> (mentioned in the man page) copies the full current
|
|
|
|
environment into the environment variable
|
|
|
|
B<parallel_bash_environment>. This variable is picked up by GNU
|
|
|
|
B<parallel> and used to create the Perl script mentioned above.
|
|
|
|
|
|
|
|
|
2015-04-09 23:20:51 +00:00
|
|
|
=head2 Base64 encoded bzip2
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
B<csh> limits words of commands to 1024 chars. This is often too little
|
|
|
|
when GNU B<parallel> encodes environment variables and wraps the
|
|
|
|
command with different templates. All of these are combined and quoted
|
|
|
|
into one single word, which often is longer than 1024 chars.
|
|
|
|
|
|
|
|
When the line to run is > 1000 chars, GNU B<parallel> therefore
|
|
|
|
encodes the line to run. The encoding B<bzip2>s the line to run,
|
|
|
|
converts this to base64, splits the base64 into 1000 char blocks (so B<csh>
|
|
|
|
does not fail), and prepends it with this Perl script that decodes,
|
|
|
|
decompresses and B<eval>s the line.
|
|
|
|
|
|
|
|
@GNU_Parallel=("use","IPC::Open3;","use","MIME::Base64");
|
|
|
|
eval "@GNU_Parallel";
|
|
|
|
|
|
|
|
$SIG{CHLD}="IGNORE";
|
|
|
|
# Search for bzip2. Not found => use default path
|
|
|
|
my $zip = (grep { -x $_ } "/usr/local/bin/bzip2")[0] || "bzip2";
|
|
|
|
# $in = stdin on $zip, $out = stdout from $zip
|
|
|
|
my($in, $out,$eval);
|
|
|
|
open3($in,$out,">&STDERR",$zip,"-dc");
|
|
|
|
if(my $perlpid = fork) {
|
|
|
|
close $in;
|
|
|
|
$eval = join "", <$out>;
|
|
|
|
close $out;
|
|
|
|
} else {
|
|
|
|
close $out;
|
|
|
|
# Pipe decoded base64 into 'bzip2 -dc'
|
|
|
|
print $in (decode_base64(join"",@ARGV));
|
|
|
|
close $in;
|
|
|
|
exit;
|
|
|
|
}
|
|
|
|
wait;
|
|
|
|
eval $eval;
|
|
|
|
|
|
|
|
Perl and B<bzip2> must be installed on the remote system, but a small
|
|
|
|
test showed that B<bzip2> is installed by default on all platforms
|
|
|
|
that runs GNU B<parallel>, so this is not a big problem.
|
|
|
|
|
|
|
|
The added bonus of this is that much bigger environments can now be
|
|
|
|
transferred as they will be below B<bash>'s limit of 131072 chars.
|
|
|
|
|
|
|
|
|
|
|
|
=head2 Which shell to use
|
|
|
|
|
|
|
|
Different shells behave differently. A command that works in B<tcsh>
|
|
|
|
may not work in B<bash>. It is therefore important that the correct
|
|
|
|
shell is used when GNU B<parallel> executes commands.
|
|
|
|
|
|
|
|
GNU B<parallel> tries hard to use the right shell. If GNU B<parallel>
|
|
|
|
is called from B<tcsh> it will use B<tcsh>. If it is called from
|
|
|
|
B<bash> it will use B<bash>. It does this by looking at the
|
|
|
|
(grand*)parent process: If the (grand*)parent process is a shell, use
|
|
|
|
this shell; otherwise look at the parent of this (grand*)parent. If
|
|
|
|
none of the (grand*)parents are shells, then $SHELL is used.
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
This will do the right thing if called from:
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
=over 2
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
|
|
|
an interactive shell
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
|
|
|
a shell script
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
a Perl script in `` or using B<system> if called as a single string.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
=back
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
While these cover most cases, there are situations where it will fail:
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
#!/usr/bin/perl
|
|
|
|
|
|
|
|
system("parallel",'setenv a {}; echo $a',":::",2);
|
|
|
|
|
|
|
|
Here it depends on which shell is used to call the Perl script. If the
|
|
|
|
Perl script is called from B<tcsh> it will work just fine, but if it
|
2015-02-22 14:09:26 +00:00
|
|
|
is called from B<bash> it will fail, because the command B<setenv> is
|
|
|
|
not known to B<bash>.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
|
|
|
|
=head2 Quoting
|
|
|
|
|
|
|
|
Quoting is kept simple: Use \ for all special chars and ' for
|
|
|
|
newline. Whether a char is special depends on the shell and the
|
|
|
|
context. Luckily quoting a bit too many does not break things.
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
It is fast, but had the distinct disadvantage that if a string needs
|
|
|
|
to be quoted multiple times, the \'s double every time - increasing
|
|
|
|
the string length exponentially.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
|
|
|
|
=head2 --pipepart vs. --pipe
|
|
|
|
|
|
|
|
While B<--pipe> and B<--pipepart> look much the same to the user, they are
|
|
|
|
implemented very differently.
|
|
|
|
|
|
|
|
With B<--pipe> GNU B<parallel> reads the blocks from standard input
|
|
|
|
(stdin), which is then given to the command on standard input (stdin);
|
|
|
|
so every block is being processed by GNU B<parallel> itself. This is
|
|
|
|
the reason why B<--pipe> maxes out at around 100 MB/sec.
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
B<--pipepart>, on the other hand, first identifies at which byte
|
|
|
|
positions blocks start and how long they are. It does that by seeking
|
2015-01-18 23:07:12 +00:00
|
|
|
into the file by the size of a block and then reading until it meets
|
|
|
|
end of a block. The seeking explains why GNU B<parallel> does not know
|
|
|
|
the line number and why B<-L/-l> and B<-N> do not work.
|
|
|
|
|
|
|
|
With a reasonable block and file size this seeking is often more than
|
|
|
|
1000 faster than reading the full file. The byte positions are then
|
|
|
|
given to a small script that reads from position X to Y and sends
|
|
|
|
output to standard output (stdout). This small script is prepended to
|
|
|
|
the command and the full command is executed just as if GNU
|
|
|
|
B<parallel> had been in its normal mode. The script looks like this:
|
|
|
|
|
|
|
|
< file perl -e 'while(@ARGV) {
|
|
|
|
sysseek(STDIN,shift,0) || die;
|
|
|
|
$left = shift;
|
|
|
|
while($read = sysread(STDIN,$buf, ($left > 32768 ? 32768 : $left))){
|
|
|
|
$left -= $read; syswrite(STDOUT,$buf);
|
|
|
|
}
|
|
|
|
}' startbyte length_in_bytes
|
|
|
|
|
|
|
|
It delivers 1 GB/s per core.
|
|
|
|
|
|
|
|
Instead of the script B<dd> was tried, but many versions of B<dd> do
|
|
|
|
not support reading from one byte to another and might cause partial
|
2015-02-22 14:09:26 +00:00
|
|
|
data. See this for a surprising example:
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
yes | dd bs=1024k count=10 | wc
|
|
|
|
|
|
|
|
=head2 --jobs and --onall
|
|
|
|
|
|
|
|
When running the same commands on many servers what should B<--jobs>
|
|
|
|
signify? Is it the number of servers to run on in parallel? Is it the
|
|
|
|
number of jobs run in parallel on each server?
|
|
|
|
|
|
|
|
GNU B<parallel> lets B<--jobs> represent the number of servers to run
|
|
|
|
on in parallel. This is to make it possible to run a sequence of
|
|
|
|
commands (that cannot be parallelized) on each server, but run the
|
|
|
|
same sequence on multiple servers.
|
|
|
|
|
|
|
|
|
2015-01-20 21:08:52 +00:00
|
|
|
=head2 Buffering on disk
|
|
|
|
|
|
|
|
GNU B<parallel> buffers on disk in $TMPDIR using files, that are
|
|
|
|
removed as soon as they are created, but which are kept open. So even
|
|
|
|
if GNU B<parallel> is killed by a power outage, there will be no files
|
|
|
|
to clean up afterwards. Another advantage is that the file system is
|
|
|
|
aware that these files will be lost in case of a crash, so it does
|
|
|
|
not need to sync them to disk.
|
|
|
|
|
|
|
|
It gives the odd situation that a disk can be fully used, but there
|
|
|
|
are no visible files on it.
|
|
|
|
|
|
|
|
|
2015-01-18 23:07:12 +00:00
|
|
|
=head2 Disk full
|
|
|
|
|
|
|
|
GNU B<parallel> buffers on disk. If the disk is full data may be
|
|
|
|
lost. To check if the disk is full GNU B<parallel> writes a 8193 byte
|
2015-02-22 14:09:26 +00:00
|
|
|
file when a job finishes. If this file is written successfully, it is
|
|
|
|
removed immediately. If it is not written successfully, the disk is
|
2015-01-18 23:07:12 +00:00
|
|
|
full. The size 8193 was chosen because 8192 gave wrong result on some
|
|
|
|
file systems, whereas 8193 did the correct thing on all tested
|
|
|
|
filesystems.
|
|
|
|
|
2015-01-20 21:08:52 +00:00
|
|
|
|
2015-01-18 23:07:12 +00:00
|
|
|
=head2 Perl replacement strings, {= =}, and --rpl
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
The shorthands for replacement strings make a command look more
|
2015-01-18 23:07:12 +00:00
|
|
|
cryptic. Different users will need different replacement
|
|
|
|
strings. Instead of inventing more shorthands you get more more
|
|
|
|
flexible replacement strings if they can be programmed by the user.
|
|
|
|
|
|
|
|
The language Perl was chosen because GNU B<parallel> is written in
|
|
|
|
Perl and it was easy and reasonably fast to run the code given by the
|
|
|
|
user.
|
|
|
|
|
|
|
|
If a user needs the same programmed replacement string again and
|
|
|
|
again, the user may want to make his own shorthand for it. This is
|
|
|
|
what B<--rpl> is for. It works so well, that even GNU B<parallel>'s
|
|
|
|
own shorthands are implemented using B<--rpl>.
|
|
|
|
|
|
|
|
In Perl code the bigrams {= and =} rarely exist. They look like a
|
|
|
|
matching pair and can be entered on all keyboards. This made them good
|
|
|
|
candidates for enclosing the Perl expression in the replacement
|
|
|
|
strings. Another candidate ,, and ,, was rejected because they do not
|
|
|
|
look like a matching pair. B<--parens> was made, so that the users can
|
|
|
|
still use ,, and ,, if they like: B<--parens ,,,,>
|
|
|
|
|
|
|
|
Internally, however, the {= and =} are replaced by \257< and
|
|
|
|
\257>. This is to make it simple to make regular expressions: \257 is
|
2015-01-20 21:08:52 +00:00
|
|
|
disallowed on the command line, so when that is matched in a regular
|
|
|
|
expression, it is known that this is a replacement string.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
|
|
|
|
=head2 Test suite
|
|
|
|
|
|
|
|
GNU B<parallel> uses its own testing framework. This is mostly due to
|
|
|
|
historical reasons. It deals reasonably well with tests that are
|
|
|
|
dependent on how long a given test runs (e.g. more than 10 secs is a
|
|
|
|
pass, but less is a fail). It parallelizes most tests, but it is easy
|
|
|
|
to force a test to run as the single test (which may be important for
|
|
|
|
timing issues). It deals reasonably well with tests that fail
|
2015-02-22 14:09:26 +00:00
|
|
|
intermittently. It detects which tests failed and pushes these to the
|
|
|
|
top, so when running the test suite again, the tests that failed most
|
|
|
|
recently are run first.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
If GNU B<parallel> should adopt a real testing framework then those
|
|
|
|
elements would be important.
|
|
|
|
|
|
|
|
Since many tests are dependent on which hardware it is running on,
|
|
|
|
these tests break when run on a different hardware than what the test
|
|
|
|
was written for.
|
|
|
|
|
|
|
|
When most bugs are fixed a test is added, so this bug will not
|
2015-01-20 21:08:52 +00:00
|
|
|
reappear. It is, however, sometimes hard to create the environment in
|
|
|
|
which the bug shows up - especially if the bug only shows up
|
|
|
|
sometimes. One of the harder problems was to make a machine start
|
|
|
|
swapping without forcing it to its knees.
|
|
|
|
|
|
|
|
|
2015-02-22 14:09:26 +00:00
|
|
|
=head2 Median run time
|
2015-01-20 21:08:52 +00:00
|
|
|
|
|
|
|
Using a percentage for B<--timeout> causes GNU B<parallel> to compute
|
|
|
|
the median run time of a job. The median is a better indicator of the
|
|
|
|
expected run time than average, because there will often be outliers
|
|
|
|
taking way longer than the normal run time.
|
|
|
|
|
|
|
|
To avoid keeping all run times in memory, an implementation of
|
|
|
|
remedian was made (Rousseeuw et al).
|
|
|
|
|
|
|
|
|
|
|
|
=head2 Error messages and warnings
|
|
|
|
|
|
|
|
Error messages like: ERROR, Not found, and 42 are not very
|
|
|
|
helpful. GNU B<parallel> strives to inform the user:
|
|
|
|
|
|
|
|
=over 2
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
|
|
|
What went wrong?
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
|
|
|
Why did it go wrong?
|
|
|
|
|
|
|
|
=item *
|
|
|
|
|
|
|
|
What can be done about it?
|
|
|
|
|
|
|
|
=back
|
|
|
|
|
|
|
|
Unfortunately it is not always possible to predict the root cause of the error.
|
2015-01-18 23:07:12 +00:00
|
|
|
|
|
|
|
|
2015-01-21 21:24:23 +00:00
|
|
|
=head2 Computation of load
|
|
|
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2015-02-22 14:09:26 +00:00
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Contrary to the obvious B<--load> does not use load average. This is
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due to load average rising too slowly. Instead it uses B<ps> to list
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the number of jobs in running or blocked state (state D, O or R). This
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gives an instant load.
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2015-01-21 21:24:23 +00:00
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As remote calculation of load can be slow, a process is spawned to run
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B<ps> and put the result in a file, which is then used next time.
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2015-01-18 23:07:12 +00:00
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=head1 Ideas for new design
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=head2 Multiple processes working together
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Open3 is slow. Printing is slow. It would be good if they did not tie
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up ressources, but were run in separate threads.
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=head2 Transferring of variables and functions from zsh
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Transferring Bash functions to remote zsh works.
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Can parallel_bash_environment be used to import zsh functions?
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=head2 --rrs on remote using a perl wrapper
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... | perl -pe '$/=$recend$recstart;BEGIN{ if(substr($_) eq $recstart) substr($_)="" } eof and substr($_) eq $recend) substr($_)=""
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It ought to be possible to write a filter that removed rec sep on the
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fly instead of inside GNU B<parallel>. This could then use more cpus.
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Will that require 2x record size memory?
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Will that require 2x block size memory?
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=head1 Historical decisions
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=head2 --tollef
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You can read about the history of GNU B<parallel> on https://www.gnu.org/software/parallel/history.html
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B<--tollef> was included to make GNU B<parallel> switch compatible
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with the parallel from moreutils (which is made by Tollef Fog
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Heen). This was done so that users of that parallel easily could port
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their use to GNU B<parallel>: Simply set B<PARALLEL="--tollef"> and
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that would be it.
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But several distributions chose to make B<--tollef> global (by putting it
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into /etc/parallel/config), and that caused much confusion when people
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tried out the examples from GNU B<parallel>'s man page and these did
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not work. The users became frustrated because the distribution did
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not make it clear to them that it has made B<--tollef> global.
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So to lessen the frustration and the resulting support, B<--tollef>
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was obsoleted 20130222 and removed one year later.
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=head2 Transferring of variables and functions
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Until 20150122 variables and functions were transferred by looking at
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$SHELL to see whether the shell was a B<*csh> shell. If so the
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variables would be set using B<setenv>. Otherwise they would be set
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using B<=>. The caused the content of the variable to be repeated:
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echo $SHELL | grep "/t\{0,1\}csh" > /dev/null && setenv VAR foo ||
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export VAR=foo
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=cut
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