parallel/doc/FUTURE_IDEAS

BUG:
(echo echo a ; echo ; echo echo b) | parallel -k


Dont start:

* load
* memory free | head -n 2 | awk \{print\ \$4+\$6+\$7\}
* swap
* seek

vmstat\ 1\ 2\ \|\ tail\ -n1\ \|\ awk\ \{print\\\ \\\$7*\\\$8\}


Video 30. 36. 41. 48


# GNU Parallel 20110522 - The Pakistan Release

I am Ole Tange. I am the author of GNU Parallel.

So far GNU Parallel has been focused on replacing a single
for-loop. The Pakistan release introduces a way to replace nested
loops.

# NESTED FOR LOOPS

As example I will use the image manipulation program 'convert' from
ImageMagick. This command will convert foo.png to jpg with a size of
800 and JPEG-quality of 95.

convert -resize 800 -quality 95 foo.png foo_800_q95.jpg

With a for-loop it can be done on a list of files:

for file in *.png ; do
  convert -resize 800 -quality 95 $file ${file%.*}_800_q95.jpg
done

This is the kind of loops GNU Parallel is good at replacing:

parallel convert -resize 800 -quality 95 {} {.}_800_q95.jpg ::: *.png


To get the images in 3 different JPEG-qualities you can use a nested for-loop:

for qual in 25 50 95 ; do
  for file in *.png ; do
    convert -resize 800 -quality $qual $file ${file%.*}_800_q${qual}.jpg
  done
done

With GNU Parallel 'Pakistan' you can do this:

parallel convert -resize 800 -quality {2} {1} {1.}_800_q{2}.jpg ::: *.png ::: 25 50 95

The new is that you can use the ::: multiple times. GNU Parallel will
then generate all the combinations and execute the command with these.
The {1} and {2} will be replaced by the relevant input source.

To get the 3 different JPEG-qualities in 2 different sizes you can
nest the for-loop even further:

for size in 800 30 ; do
  for qual in 25 50 95 ; do
    for file in *.png ; do
      convert -resize $size -quality $qual $file ${file%.*}_${size}_q${qual}.jpg
    done
  done
done

With GNU Parallel 'Pakistan' you can do this:

parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg ::: *.png ::: 25 50 95 ::: 800 30

GNU Parallel will again generate all the combinations of the input
sources and run the jobs in parallel.

You can also provide the arguments in a file. This will do the same as above:

(echo 25; echo 50; echo 95) > qualities
ls *.png > png-files
(echo 800; echo 30) > sizes
parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg :::: png-files qualities sizes

But you can even mix triple and quad colon. These will do the same:

parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg :::: png-files ::: 25 50 95 ::: 800 30

parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg :::: png-files ::: 25 50 95 :::: sizes

The special file '-' reads from standard input. This will do the same as above:

ls *.png | parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg :::: - ::: 25 50 95 :::: sizes

This is probably one of the ways you will use this feature as that can easily be combined with find:

find . -name '*.png' | \
parallel convert -resize {3} -quality {2} {1} {1.}_{3}_q{2}.jpg :::: - ::: 25 50 95 :::: sizes

# Thank you for watching
#
# If you like GNU Parallel:
# * Post this video on forums/blogs/Twitter/Facebook/Linkedin
# * Join the mailing list http://lists.gnu.org/mailman/listinfo/parallel
# * Request or write a review for your favourite blog or magazine
# * Request or build a package for your favourite distribution
# * Invite me for your next conference (Contact http://ole.tange.dk)
#
# If GNU Parallel saves you money:
# * (Have your company) donate to FSF https://my.fsf.org/donate/
#
# If you use GNU Parallel for a publication please cite:
# O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login:
# The USENIX Magazine, February 2011:42-47.
#
# Find GNU Parallel at http://www.gnu.org/software/parallel/


Postkort:
- Forside kun figur
- Bagside:
  - Logo med figur - evt gnu.org/s/parallel
  - kort grå tekst, der forklarer hvad det er.
  - Eet eksempel: parallel gzip ::: *
  - Link til video. http://nd.gd/0s 

GNU parallel is a UNIX-tool for running commands in parallel.
To gzip all files running one job per CPU write:
  parallel gzip ::: *
Watch the intro video to learn more: http://nd.gd/0s
Or read more about GNU parallel: www.gnu.org/s/parallel

job->start():
$jobslot = Global::jobslot->$sshlogin

sub get_jobslot {
    my $sshlogin = shift;
    my $jobslot_id = pop @Global::jobslots{$sshlogin};
    if not defined $jobslot_id {
       $jobslot_id = ++$Global::max_jobslot_id;
    }
    return $jobslot_id;
}

sub release_jobslot {
    my $sshlogin = shift;
    my $jobslot_id = shift;
    push @Global::jobslots{$sshlogin}, $jobslot_id;
}

Test sshlogins in parallel. Assume parallel is in path

seq 1 10 | parallel -I {o} 'seq 1 255 | parallel echo ssh -oNoHostAuthenticationForLocalhost=true 127.0.{o}.{}' >/tmp/sshloginfile
seq 1 1000 | parallel --sshloginfile /tmp/sshloginfile echo

ssh -F /tmp/
 
Example:
Chop mbox into emails
Parallel sort

codecoverage

Testsuite: sem without ~/.parallel

Til QUOTING:

FN="two  spaces"
echo 1 | parallel -q echo {} "$FN"
# Prints 2 spaces between 'two' and 'spaces'

-q will not work with composed commands as it will quote the ; as
well. So composed commands have to be quoted by hand:

# Using export:
FN2="two  spaces"
export FN2
echo 1 | parallel echo {} \"\$FN2\" \; echo \"\$FN2\" {}
# Prints 2 spaces between 'two' and 'spaces'

# Without export:
FN3="two  spaces"
echo 1 | parallel echo {} \""$FN3"\" \; echo \'"$FN3"\' {}

# By quoting the space in the variable
FN4='two\ \ spaces'
echo 1 | parallel echo {} $FN4 \; echo $FN4 {}



= Bug? ==

locate .gz | parallel -X find {} -size +1000 -size -2000 | parallel --workdir ... -S .. --trc {/}.bz2 'zcat {} | bzip2 > {/}.bz2'


== Compare ==

http://code.google.com/p/spawntool/
http://code.google.com/p/push/

== Bug? ==

.parallel/config with --long-options

time find . -type f | parallel -j+0 --eta -S..,: --progress --trc {}.gz gzip  {}

== SQL ==

Example with %0a as newline
sql :my_postgres?'\dt %0a SELECT * FROM users'

cat ~/.sql/aliases | parallel --colsep '\s' sql {1} '"select 0.14+3;" | grep -q 3.14 || (echo dead: {1}; exit 1)'

== FEX ==

fex syntax for splitting fields
http://www.semicomplete.com/projects/fex/
sql :foo 'select * from bar' | parallel --fex '|{1,2}' do_stuff {2} {1}


--autocolsep: Læs alle linjer.
Prøv fastlængde: Find tegn, som står i alle linjer på de samme pladser. Risiko for falske pos
Prøv fieldsep: Find eet tegn, som optræder det samme antal gange i alle linjer (tab sep)
Prøv klyngesep: Find den samme klynge tegn, som står samme antal gange i alle linjer (' | ' sep)
Fjern whitespace før og efter colonne

hvis der er n af tegn A og 2n af tegn B, så

  a | b | c

Simpleste: tab sep

for hver linje
  max,min count for hver char

for hver char
  if max == min :
    potentiel
    min_potentiel = min(min_potentiel,min)

for potentiel:
  if min % min_potentiel = 0: sepchars += potentiel,no of sepchars += min / min_potentiel

colsep = [sepchars]{no_of_sepchars}


# TODO max_line_length on remote
# TODO compute how many can be transferred within max_line_length

=head1 YouTube video --pipe

cp parallel.fasta  parallel.mbox lucene.tar

# GNU Parallel 20110205 - The FOSDEM Release

I assume you already know GNU Parallel. If not watch the intro video first.

GNU Parallel has so far worked similar to xargs. But the FOSDEM
release of GNU Parallel introduces the new --pipe option. It makes GNU
Parallel work similar to tee.

tee pipes a copy of the output to a file and a copy to another
program.

seq 1 5 | tee myfile | wc

Here it pipes a copy to the file myfile and to the command word count (wc).

cat myfile

and we can see the content is what we expected.

The pipe option of GNU Parallel splits data into records and pipes a
block of records into a program:

seq 1 5 | parallel --pipe -N1 cat';' echo foo

Here we pipe each number to the command cat and print foo after
running cat.

GNU Parallel does this in parallel starting one process per cpu so the
order may be different because one command may finish before another.

# RECORD SEPARATORS

GNU Parallel splits on record separators.

seq 1 5 | parallel --pipe --recend '\n' -N1 cat';' echo foo

This is the example we saw before: the record separator is \n and
--recend will keep the record separator at the end of the record.

But if what your records start with a record separator? Here is a
fast-a file:

cat parallel.fasta

Every record start with a >. To keep that with the record you use
--recstart:

cat parallel.fasta | parallel --pipe --recstart '>' -N1 cat';' echo foo

But what if you have both? mbox files is an example that has both an
ending and starting separator:

cat parallel.mbox |
parallel --pipe --recend '\n\n' --recstart 'From ' -N1 cat';' echo foo | less   #

The two newlines are staying with the email before and the From_ stays with the next record.

GNU Parallel cannot guarantee the first record will start with record
separator and it cannot guarantee the last record will end with record
separator. You will simply get what is first and last.

But GNU Parallel _does_ guarantee that it will only split at record
separators.

# NUMBER OF RECORDS

So far we have used -N1. This tells GNU Parallel to pipe one record to
the program.

seq 1 5 | parallel --pipe -N1 cat';' echo foo

But we can choose any amount:

seq 1 5 | parallel --pipe -N3 cat';' echo foo

This will pipe blocks of 3 records into cat and if there is not enough the last will only get two.

# BLOCKSIZE

However, using -N is inefficient. It is faster to pipe a full block into the program.

cat /usr/share/dict/words | parallel --pipe --blocksize 500k wc

We here tell GNU Parallel to split on \n and pipe blocks of 500 KB to
wc. 1 MB is the default:

cat /usr/share/dict/words | parallel --pipe wc

If you just have a bunch of bytes you often do not care about the
record separator. To split input into chunks you can disable the
--recend

ls -l lucene.tar
cat lucene.tar | parallel --pipe --recend '' -k gzip > lucene.tar.gz

GNU Parallel will then split the input into 1 MB blocks; pipe that to
gzip and -k will make sure the order of the output is kept before
saving to the tar.gz file.

The beauty of gzip is that if you concatenate two gzip files it is a
valid gzip file. To test this:

tar tvzf lucene.tar.gz #

# OUTPUT AS FILE

Sometimes the output of GNU Parallel cannot be mixed in a single stream like this:

seq 1 10 | shuf | parallel --pipe -N 3 sort -n

As you can see each block of 3 is sorted but the whole output is not sorted.

GNU Parallel can give the output in file. GNU Parallel will the list the
files created:

seq 1 10 | shuf | parallel --pipe --files -N 3 sort -n

Each of these files contains a sorted block:

cat

Sort has -m to merge sorted files into a sorted stream

seq 1 10 | shuf | parallel --pipe --files -N 3 sort -n | parallel -mj1 sort -nm

-m will append all the files behind the sort command and the -j1 will
make sure we only run one command. The only part missing now is
cleaning up by removing the temporary files. We can do that by
appending rm

seq 1 10 | shuf | parallel --pipe --files -N 3 sort -n |
parallel -mj1 sort -nm {} ";"rm {}


# Thank you for watching
#
# If you like GNU Parallel:
# * Post this video on forums/blogs/Twitter/Facebook/Linkedin
# * Join the mailing list http://lists.gnu.org/mailman/listinfo/parallel
# * Request or write a review for your favourite magazine
# * Request or build a package for your favourite distribution
# * Invite me for your next conference (Contact http://ole.tange.dk)
#
# If GNU Parallel saves you money:
# * (Have your company) donate to FSF https://my.fsf.org/donate/
#
# If you use GNU Parallel for a publication please cite:
# O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login:
# The USENIX Magazine, February 2011:42-47.
#
# Find GNU Parallel at http://www.gnu.org/software/parallel/



=head1 YouTube video2

Converting of WAV files to MP3 using GNU Parallel

# Run one jobs per CPU core
# For 'foo.wav' call the output file 'foo.mp3'

find music-files -type f | parallel -j+0 lame {} -o {.}.mp3

# Run one jobs per CPU core
# Run on local computer + 2 remote computers
# Give us progress information
# For 'foo.wav' call the output file 'foo.mp3'

find music-files -type f | parallel -j+0 -S :,server1,server2 \
--eta --trc {.}.mp3 lame {} -o {.}.mp3

# Colsep
# sem
# --retry

(echo a1.txt; echo b1.txt; echo c1.txt; echo a2.txt; echo b2.txt; echo c2.txt;)| \
parallel -X -N 3 my-program --file={}

(echo a1.txt; echo b1.txt; echo c1.txt; echo d1.txt; echo e1.txt; echo f1.txt;)| \
parallel -X my-program --file={}

# First job controls the tty
# -u needed because output should not be saved for later

find . -type f | parallel -uXj1 vim
find . -type f | parallel -uXj1 emacs

# If you have 1000 files only one contains 'foobar'
# stop when this one is found

find . -type f | parallel  grep -l foobar | head -1


# To test a list of hosts are up and pingable save this
# to a file called machinesup

#!/usr/bin/parallel --shebang --no-run-if-empty ping -c 3 {} >/dev/null 2>&1

google.com
yahoo.com
nowhere.gone

# Then:
#   chmod 755 machinesup
#   ./machinesup || echo Some machines are down



=head1 YouTube video

GNU Parallel is a tool with lots of uses in shell. Every time you use
xargs or a for-loop GNU Parallel can probably do that faster, safer
and more readable.

If you have access to more computers through ssh, GNU Parallel makes
it easy to distribute jobs to these.

terminal2: ssh parallel@vh2.pi.dk
ssh parallel@vh2.pi.dk
 and

PS1="\[\e[7m\]GNU Parallel:\[\033[01;34m\]\w\[\033[00m\e[27m\]$ "
gunzip logs/*gz
rm -f logs/*bz2*
rm -rf zip/*[^p]
rm -rf dirs/*
rm -rf parallel-*bz2

xvidcap
ffmpeg -i 20100616_002.mp4 -ab 320k -ar 44100 speak.mp3
# Merge video using youtube
#ffmpeg -i speak.mp3 -i xvidcap.mpeg -target mpeg -hq -minrate 8000000 \
#-title "GNU Parallel" -author "Ole Tange" -copyright "(CC-By-SA) 2010" -comment "Intro video of GNU Parallel 20100616" videoaudio.mpg

# GNU PARALLEL - BASIC USAGE
# A GNU tool for parallelizing shell commands

## Ole Tange Author

# GET GNU PARALLEL
wget ftp://ftp.gnu.org/gnu/parallel/parallel-20100620.tar.bz2
tar xjf parallel-20100620.tar.bz2
cd parallel-20100620
./configure && make   ##
su
make install
exit
cd

## scp /usr/local/bin/parallel root@parallel:/usr/local/bin/


# YOUR FIRST PARALLEL JOBS
cd logs
du
/usr/bin/time gzip -1 *
## 24 sek - 22 sek
/usr/bin/time gunzip *
## 24 sek - 18
ls | time parallel gzip -1
## 17 sek - 10
ls | time parallel gunzip
## 25 sek - 19

# RECOMPRESS gz TO bz2
ls | time parallel gzip -1
ls *.gz | time parallel -j+0 --eta 'zcat {} | bzip2 -9 >{.}.bz2'
## Explain command line
## vis top local
## Man that is boring
## 2m41s - 2m - 3m35s

# RECOMPRESS gz TO bz2 USING local(:) AND REMOTE server1-4
ls *.gz |time parallel -j+0 --eta -Sserver1,server2,server3,server4,: \
--transfer --return {.}.bz2 --cleanup 'zcat {} | bzip2 -9 > {.}.bz2'
## Explain command line
## Explain server config
## vis top local
## vis top remote1-3
## 49 sek

# RECOMPRESS gz TO bz2 USING A SCRIPT ON local AND REMOTE server1-2,4
# (imagine the script is way more complex)
cp ../recompress /tmp
cat /tmp/recompress
ls *.gz |time parallel -j+0 --progress -Sserver1,server2,server4,: \
--trc {.}.bz2 --basefile /tmp/recompress '/tmp/recompress {} {.}.bz2'


# MAKING SMALL SCRIPTS
cd ../zip
ls -l
ls *.zip | parallel 'mkdir {.} && cd {.} && unzip ../{}' ###
ls -l

# GROUP OUTPUT
traceroute debian.org
traceroute debian.org & traceroute freenetproject.org  ###
(echo debian.org; echo freenetproject.org) | parallel traceroute ###

# KEEP ORDER
(echo debian.org; echo freenetproject.org) | parallel -k traceroute ###

# RUN MANY JOBS. USE OUTPUT
# Find the number of hosts responding to ping
ping -c 1 178.63.11.1
ping -c 1 178.63.11.1 | grep '64 bytes'
seq 1 255 | parallel -j255 ping -c 1 178.63.11.{} 2>&1 \
| grep '64 bytes' | wc -l
seq 1 255 | parallel -j0 ping -c 1 178.63.11.{} 2>&1 \
| grep '64 bytes' | wc -l

# MULTIPLE ARGUMENTS
# make dir: test-(1-5000).dir
cd ../dirs
rm -rf *; sync
seq 1 10 | parallel echo mkdir test-{}.dir
seq 1 5000 | time parallel mkdir test-{}.dir
## 15 sek

rm -rf *; sync
seq 1 10 | parallel -X echo mkdir test-{}.dir
seq 1 5000 | time parallel -X mkdir test-{}.dir

# CALLING GNU PARALLEL FROM GNU PARALLEL
# make dir: top-(1-100)/sub-(1-100)
rm -rf *; sync
seq 1 100 | time parallel -I @@ \
'mkdir top-@@; seq 1 100 | parallel -X mkdir top-@@/sub-{}'
find | wc -l

cd
# Thank you for watching
#
# If you like GNU Parallel:
# * Post this video on your blog/Twitter/Facebook/Linkedin
# * Join the mailing list http://lists.gnu.org/mailman/listinfo/parallel
# * Request or write a review for your favourite magazine
# * Request or build a package for your favourite distribution
# * Invite me for your next conference (Contact http://ole.tange.dk)
#
# If GNU Parallel saves you money:
# * Donate to FSF https://my.fsf.org/donate/
#
# Find GNU Parallel at http://www.gnu.org/software/parallel/


# GIVE ME THE FIRST RESULT
(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel -H2 traceroute {}";false"

find . -type f | parallel -k -j150% -n 1000 -m grep -H -n STRING {}

(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel traceroute


=head1 IDEAS

Kan vi lave flere ssh'er, hvis vi venter lidt?
En ssh med 20% loss og 900 ms delay, så kan login nås på 15 sek.

Test if -0 works on filenames ending in '\n'


=head1 options

One char options not used: A F G K O Q R Z c f

=head1 sem

Parallelize so this can be done:
mdm.screen find dir -execdir mdm-run cmd {} \;
Maybe:
find dir -execdir par$ --communication-file /tmp/comfile cmd {} \;

find dir -execdir mutex -j4 -b cmd {} \;


=head1 Unlikely

Accept signal INT instead of TERM to complete current running jobs but
do not start new jobs. Print out the number of jobs waiting to
complete on STDERR. Accept sig INT again to kill now. This seems to be
hard, as all foreground processes get the INT from the shell.



# Gzip all files in parallel
parallel gzip ::: *

# Convert *.wav to *.mp3 using LAME running one process per CPU core:
parallel -j+0 lame {} -o {.}.mp3 ::: *.wav

# Make an uncompressed version of all *.gz
parallel zcat {} ">"{.} ::: *.gz

# Recompress all .gz files using bzip2 running 1 job per CPU core:
find . -name '*.gz' | parallel -j+0 "zcat {} | bzip2 >{.}.bz2 && rm {}"

# Create a directory for each zip-file and unzip it in that dir
parallel 'mkdir {.}; cd {.}; unzip ../{}' ::: *.zip

# Convert all *.mp3 in subdirs to *.ogg running
#   one process per CPU core on local computer and server2
find . -name '*.mp3' | parallel --trc {.}.ogg -j+0 -S server2,: \
         'mpg321 -w - {} | oggenc -q0 - -o {.}.ogg'

# Run mycmd on column 1-3 of each row of TAB separated values
parallel -a table_file.tsv --colsep '\t' mycmd -o {2} {3} -i {1}

# Run traceroute in parallel, but keep the output order the same
parallel -k traceroute ::: foss.org.my debian.org freenetproject.org


Test of signal passing through ssh
#!/bin/bash

SERVER1=parallel-server3
SERVER2=parallel-server2

export BG_PROC

start_remote_sleep() {
  parallel -D -u -S parallel@$SERVER2 sleep ::: 370 &
  BG_PROC=$!
  while ! ssh parallel@$SERVER2 ps -A -o cmd | grep -q '^sleep 370' ; do
    sleep 0.3
  done
}

stop_local_parallel() {
  kill -9 $BG_PROC
}

check_and_stop_remote_sleep() {
  ssh parallel@$SERVER2 ps -A -o cmd | grep '^sleep 370' 
  ssh parallel@$SERVER2 killall sleep
}

echo '### Test kill signals'
start_remote_sleep 2>/dev/null
kill -1 $BG_PROC
check_and_stop_remote_sleep

sub propagate_signal {
    my $signal = shift;
#    $signal = "KILL";
    ::debug("Sending $signal to ",keys %Global::running);
    kill $signal, keys %Global::running;
    if(defined $Global::original_sig{$signal}) {
	&{$Global::original_sig{$signal}};
    }
}

my %do_not_propagate = map { $_ => 1 } qw(TTOU TTIN CONT TSTP __WARN__ __DIE__);
for (keys %SIG) {
    $do_not_propagate{$_} and next;
    $SIG{$_} = eval 'sub { propagate_signal("'.$_.'"); };';
}