Provided by:
parallel_20141022+ds1-1_all 
NAME
parallel - build and execute shell command lines from standard input in
parallel
SYNOPSIS
parallel [options] [command [arguments]] < list_of_arguments
parallel [options] [command [arguments]] ( ::: arguments | ::::
argfile(s) ) ...
parallel --semaphore [options] command
#!/usr/bin/parallel --shebang [options] [command [arguments]]
DESCRIPTION
GNU parallel is a shell tool for executing jobs in parallel using one
or more computers. A job can be 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. A job can also be a command that reads from a pipe. GNU
parallel can then split the input into blocks and pipe a block into
each command in parallel.
If you use xargs and tee today you will find GNU parallel very easy to
use as GNU parallel is written to have the same options as xargs. If
you write loops in shell, you will find GNU parallel may be able to
replace most of the loops and make them run faster by running several
jobs in parallel.
GNU parallel makes sure output from the commands is the same output as
you would get had you run the commands sequentially. This makes it
possible to use output from GNU parallel as input for other programs.
For each line of input GNU parallel will execute command with the line
as arguments. If no command is given, the line of input is executed.
Several lines will be run in parallel. GNU parallel can often be used
as a substitute for xargs or cat | bash.
Reader's guide
Start by watching the intro videos for a quick introduction:
http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
Then look at the EXAMPLEs after the list of OPTIONS. That will give you
an idea of what GNU parallel is capable of.
Then spend an hour walking through the tutorial (man
parallel_tutorial). Your command line will love you for it.
Finally you may want to look at the rest of this manual if you have
special needs not already covered.
OPTIONS
command Command to execute. If command or the following arguments
contain replacement strings (such as {}) every instance will
be substituted with the input.
If command is given, GNU parallel solve the same tasks as
xargs. If command is not given GNU parallel will behave
similar to cat | sh.
The command must be an executable, a script, a composed
command, or a function.
If it is a Bash function you need to export -f the function
first. To use aliases copy the full environment as described
under --env and use env_parallel instead of parallel.
If it is a zsh function you will need to use this helper
function exportf to export and to set $PARALLEL_SHELL to bash:
function exportf (){
export $(echo $1)="`whence -f $1 | sed -e "s/$1 //" `"
}
function my_func(){
echo $1;
echo "hello";
}
exportf my_func
PARALLEL_SHELL=/bin/bash parallel "my_func {}" ::: 1 2
The command cannot contain the character \257 (macron: X).
{} Input line. This replacement string will be replaced by a full
line read from the input source. The input source is normally
stdin (standard input), but can also be given with -a, :::, or
::::.
The replacement string {} can be changed with -I.
If the command line contains no replacement strings then {}
will be appended to the command line.
{.} Input line without extension. This replacement string will be
replaced by the input with the extension removed. If the input
line contains . after the last / the last . till the end of
the string will be removed and {.} will be replaced with the
remaining. E.g. foo.jpg becomes foo, subdir/foo.jpg becomes
subdir/foo, sub.dir/foo.jpg becomes sub.dir/foo, sub.dir/bar
remains sub.dir/bar. If the input line does not contain . it
will remain unchanged.
The replacement string {.} can be changed with --er.
To understand replacement strings see {}.
{/} Basename of input line. This replacement string will be
replaced by the input with the directory part removed.
The replacement string {/} can be changed with
--basenamereplace.
To understand replacement strings see {}.
{//} Dirname of input line. This replacement string will be
replaced by the dir of the input line. See dirname(1).
The replacement string {//} can be changed with
--dirnamereplace.
To understand replacement strings see {}.
{/.} Basename of input line without extension. This replacement
string will be replaced by the input with the directory and
extension part removed. It is a combination of {/} and {.}.
The replacement string {/.} can be changed with
--basenameextensionreplace.
To understand replacement strings see {}.
{#} (alpha testing)
Sequence number of the job to run. This replacement string
will be replaced by the sequence number of the job being run.
It contains the same number as $PARALLEL_SEQ.
The replacement string {#} can be changed with --seqreplace.
To understand replacement strings see {}.
{%} (alpha testing)
Job slot number. This replacement string will be replaced by
the job's slot number between 1 and number of jobs to run in
parallel. There will never be 2 jobs running at the same time
with the same job slot number.
The replacement string {%} can be changed with --slotreplace.
To understand replacement strings see {}.
{n} Argument from input source n or the n'th argument. This
positional replacement string will be replaced by the input
from input source n (when used with -a or ::::) or with the
n'th argument (when used with -N). If n is negative it refers
to the n'th last argument.
To understand replacement strings see {}.
{n.} Argument from input source n or the n'th argument without
extension. It is a combination of {n} and {.}.
This positional replacement string will be replaced by the
input from input source n (when used with -a or ::::) or with
the n'th argument (when used with -N). The input will have the
extension removed.
To understand positional replacement strings see {n}.
{n/} Basename of argument from input source n or the n'th argument.
It is a combination of {n} and {/}.
This positional replacement string will be replaced by the
input from input source n (when used with -a or ::::) or with
the n'th argument (when used with -N). The input will have the
directory (if any) removed.
To understand positional replacement strings see {n}.
{n//} Dirname of argument from input source n or the n'th argument.
It is a combination of {n} and {//}.
This positional replacement string will be replaced by the dir
of the input from input source n (when used with -a or ::::)
or with the n'th argument (when used with -N). See dirname(1).
To understand positional replacement strings see {n}.
{n/.} Basename of argument from input source n or the n'th argument
without extension. It is a combination of {n}, {/}, and {.}.
This positional replacement string will be replaced by the
input from input source n (when used with -a or ::::) or with
the n'th argument (when used with -N). The input will have the
directory (if any) and extension removed.
To understand positional replacement strings see {n}.
{=perl expression=}
Replace with calculated perl expression. $_ will contain the
same as {}. After evaluating perl expression $_ will be used
as the value. It is recommended to only change $_ but you have
full access to all of GNU parallel's internal functions and
data structures.
The {=perl expression=} must be given as a single string.
See also: --rpl --parens
{=n perl expression=}
Positional equivalent to {= perl expression =}. To understand
positional replacement strings see {n}.
See also: {= perl expression =} {n}.
::: arguments
Use arguments from the command line as input source instead of
stdin (standard input). Unlike other options for GNU parallel
::: is placed after the command and before the arguments.
The following are equivalent:
(echo file1; echo file2) | parallel gzip
parallel gzip ::: file1 file2
parallel gzip {} ::: file1 file2
parallel --arg-sep ,, gzip {} ,, file1 file2
parallel --arg-sep ,, gzip ,, file1 file2
parallel ::: "gzip file1" "gzip file2"
To avoid treating ::: as special use --arg-sep to set the
argument separator to something else. See also --arg-sep.
stdin (standard input) will be passed to the first process
run.
If multiple ::: are given, each group will be treated as an
input source, and all combinations of input sources will be
generated. E.g. ::: 1 2 ::: a b c will result in the
combinations (1,a) (1,b) (1,c) (2,a) (2,b) (2,c). This is
useful for replacing nested for-loops.
::: and :::: can be mixed. So these are equivalent:
parallel echo {1} {2} {3} ::: 6 7 ::: 4 5 ::: 1 2 3
parallel echo {1} {2} {3} :::: <(seq 6 7) <(seq 4 5) :::: <(seq 1 3)
parallel -a <(seq 6 7) echo {1} {2} {3} :::: <(seq 4 5) :::: <(seq 1 3)
parallel -a <(seq 6 7) -a <(seq 4 5) echo {1} {2} {3} ::: 1 2 3
seq 6 7 | parallel -a - -a <(seq 4 5) echo {1} {2} {3} ::: 1 2 3
seq 4 5 | parallel echo {1} {2} {3} :::: <(seq 6 7) - ::: 1 2 3
:::: argfiles
Another way to write -a argfile1 -a argfile2 ...
::: and :::: can be mixed.
See -a, ::: and --xapply.
--null
-0 Use NUL as delimiter. Normally input lines will end in \n
(newline). If they end in \0 (NUL), then use this option. It
is useful for processing arguments that may contain \n
(newline).
--arg-file input-file
-a input-file
Use input-file as input source. If you use this option, stdin
(standard input) is given to the first process run.
Otherwise, stdin (standard input) is redirected from
/dev/null.
If multiple -a are given, each input-file will be treated as
an input source, and all combinations of input sources will be
generated. E.g. The file foo contains 1 2, the file bar
contains a b c. -a foo -a bar will result in the combinations
(1,a) (1,b) (1,c) (2,a) (2,b) (2,c). This is useful for
replacing nested for-loops.
See also --xapply and {n}.
--arg-file-sep sep-str
Use sep-str instead of :::: as separator string between
command and argument files. Useful if :::: is used for
something else by the command.
See also: ::::.
--arg-sep sep-str
Use sep-str instead of ::: as separator string. Useful if :::
is used for something else by the command.
Also useful if you command uses ::: but you still want to read
arguments from stdin (standard input): Simply change --arg-sep
to a string that is not in the command line.
See also: :::.
--bar Show progress as a progress bar. In the bar is shown: % of
jobs completed, estimated seconds left, and number of jobs
started.
It is compatible with zenity:
seq 1000 | parallel -j30 --bar '(echo {};sleep 0.1)' 2>
>(zenity --progress --auto-kill) | wc
--basefile file
--bf file
file will be transferred to each sshlogin before a jobs is
started. It will be removed if --cleanup is active. The file
may be a script to run or some common base data needed for the
jobs. Multiple --bf can be specified to transfer more
basefiles. The file will be transferred the same way as
--transfer.
--basenamereplace replace-str
--bnr replace-str
Use the replacement string replace-str instead of {/} for
basename of input line.
--basenameextensionreplace replace-str
--bner replace-str
Use the replacement string replace-str instead of {/.} for
basename of input line without extension.
--bg Run command in background thus GNU parallel will not wait for
completion of the command before exiting. This is the default
if --semaphore is set.
See also: --fg, man sem.
Implies --semaphore.
--bibtex Print the BibTeX entry for GNU parallel and disable citation
notice.
--block size
--block-size size
Size of block in bytes. The size can be postfixed with K, M,
G, T, P, k, m, g, t, or p which would multiply the size with
1024, 1048576, 1073741824, 1099511627776, 1125899906842624,
1000, 1000000, 1000000000, 1000000000000, or 1000000000000000
respectively.
GNU parallel tries to meet the block size but can be off by
the length of one record. For performance reasons size should
be bigger than a single record.
size defaults to 1M.
See --pipe for use of this.
--cat Create a temporary file with content. Normally --pipe will
give data to the program on stdin (standard input). With --cat
GNU parallel will create a temporary file with the name in {},
so you can do: parallel --pipe --cat wc {}.
See also --fifo.
--cleanup
Remove transferred files. --cleanup will remove the
transferred files 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 --transfer the file transferred to the remote computer
will be removed on the remote computer. Directories created
will not be removed - even if they are empty.
With --return the file transferred from the remote computer
will be removed on the remote computer. Directories created
will not be removed - even if they are empty.
--cleanup is ignored when not used with --transfer or
--return.
--colsep regexp
-C regexp
Column separator. The input will be treated as a table with
regexp separating the columns. The n'th column can be access
using {n} or {n.}. E.g. {3} is the 3rd column.
--colsep implies --trim rl.
regexp is a Perl Regular Expression:
http://perldoc.perl.org/perlre.html
--compress
Compress temporary files. If the output is big and very
compressible this will take up less disk space in $TMPDIR and
possibly be faster due to less disk I/O.
GNU parallel will try lzop, pigz, gzip, pbzip2, plzip, bzip2,
lzma, lzip, xz in that order, and use the first available.
--compress-program prg
--decompress-program prg
Use prg for (de)compressing temporary files. It is assumed
that prg -dc will decompress stdin (standard input) to stdout
(standard output) unless --decompress-program is given.
--ctrlc Sends SIGINT to tasks running on remote computers thus killing
them.
--delimiter delim
-d delim Input items are terminated by the specified character. Quotes
and backslash are not special; every character in the input is
taken literally. Disables the end-of-file string, which is
treated like any other argument. This can be used when the
input consists of simply newline-separated items, although it
is almost always better to design your program to use --null
where this is possible. The specified delimiter may be a
single character, a C-style character escape such as \n, or an
octal or hexadecimal escape code. Octal and hexadecimal
escape codes are understood as for the printf command.
Multibyte characters are not supported.
--dirnamereplace replace-str
--dnr replace-str
Use the replacement string replace-str instead of {//} for
dirname of input line.
-E eof-str
Set the end of file string to eof-str. If the end of file
string occurs as a line of input, the rest of the input is
ignored. If neither -E nor -e is used, no end of file string
is used.
--delay secs
Delay starting next job secs seconds. GNU parallel will pause
secs seconds after starting each job. secs can be less than 1
seconds.
--dry-run
Print the job to run on stdout (standard output), but do not
run the job. Use -v -v to include the ssh/rsync wrapping if
the job would be run on a remote computer. Do not count on
this literaly, though, as the job may be scheduled on another
computer or the local computer if : is in the list.
--eof[=eof-str]
-e[eof-str]
This option is a synonym for the -E option. Use -E instead,
because it is POSIX compliant for xargs while this option is
not. If eof-str is omitted, there is no end of file string.
If neither -E nor -e is used, no end of file string is used.
--env var (alpha testing)
Copy environment variable var. This will copy var to the
environment that the command is run in. This is especially
useful for remote execution.
In Bash var can also be a Bash function - just remember to
export -f the function, see command.
The variable '_' is special. It will copy all enviroment
variables except for the ones mentioned in
~/.parallel/ignored_vars.
To copy Bash arrays you need an importer function, as Bash
arrays cannot be exported:
import_array () {
local func=$1; shift;
export $func='() {
'"$(for arr in $@; do
declare -p $arr|sed '1s/declare -./&g/'
done)"'
}'
}
declare -A assoc='([one]="1" [two]="2")'
declare -a indexed='([0]="one" [1]="two")'
import_array my_importer assoc indexed
parallel --env my_importer \
'my_importer; echo "{}" "${indexed[{}]}" "${assoc[${indexed[{}]}]}"' ::: "${!indexed[@]}"
To copy the full environment use this function (e.g. by
putting it in .bashrc):
env_parallel() {
export parallel_bash_environment='() {
'"$(echo "shopt -s expand_aliases 2>/dev/null"; alias;typeset -p | grep -vFf <(readonly; echo GROUPS; echo FUNCNAME; echo DIRSTACK; echo _; echo PIPESTATUS; echo USERNAME) | grep -v BASH_;typeset -f)"'
}'
# Run as: env_parallel [normal parallel options]
`which parallel` "$@"
unset parallel_bash_environment
}
# call as:
env_parallel [normal parallel options]
See also: --record-env.
--eta Show the estimated number of seconds before finishing. This
forces GNU parallel to read all jobs before starting to find
the number of jobs. GNU parallel normally only reads the next
job to run. Implies --progress.
--fg Run command in foreground thus GNU parallel will wait for
completion of the command before exiting.
See also --bg, man sem.
Implies --semaphore.
--fifo Create a temporary fifo with content. Normally --pipe will
give data to the program on stdin (standard input). With
--fifo GNU parallel will create a temporary fifo with the name
in {}, so you can do: parallel --pipe --fifo wc {}.
Beware: If data is not read from the fifo, the job will block
forever.
See also --cat.
--filter-hosts
Remove down hosts. For each remote host: check that login
through ssh works. If not: do not use this host.
Currently you can not put --filter-hosts in a profile,
$PARALLEL, /etc/parallel/config or similar. This is because
GNU parallel uses GNU parallel to compute this, so you will
get an infinite loop. This will likely be fixed in a later
release.
--gnu Behave like GNU parallel. This option historically took
precedence over --tollef. The --tollef option is now retired,
and therefore may not be used. --gnu is kept for
compatibility.
--group Group output. Output from each jobs is grouped together and is
only printed when the command is finished. stderr (standard
error) first followed by stdout (standard output). This takes
some CPU time. In rare situations GNU parallel takes up lots
of CPU time and if it is acceptable that the outputs from
different commands are mixed together, then disabling grouping
with -u can speedup GNU parallel by a factor of 10.
--group is the default. Can be reversed with -u.
See also: --line-buffer --ungroup
--help
-h Print a summary of the options to GNU parallel and exit.
--halt-on-error val
--halt val
How should GNU parallel terminate if one of more jobs fail?
0 Do not halt if a job fails. Exit status will be the
number of jobs failed. This is the default.
1 Do not start new jobs if a job fails, but complete the
running jobs including cleanup. The exit status will be
the exit status from the last failing job.
2 Kill off all jobs immediately and exit without cleanup.
The exit status will be the exit status from the
failing job.
1-99% If val% of the jobs fail and minimum 3: Do not start
new jobs, but complete the running jobs including
cleanup. The exit status will be the exit status from
the last failing job.
--header regexp
Use regexp as header. For normal usage the matched header
(typically the first line: --header '.*\n') will be split
using --colsep (which will default to '\t') and column names
can be used as replacement variables: {column name}.
For --pipe the matched header will be prepended to each
output.
--header : is an alias for --header '.*\n'.
If regexp is a number, it will match that many lines.
-I replace-str
Use the replacement string replace-str instead of {}.
--replace[=replace-str]
-i[replace-str]
This option is a synonym for -Ireplace-str if replace-str is
specified, and for -I{} otherwise. This option is deprecated;
use -I instead.
--joblog logfile
Logfile for executed jobs. Save a list of the executed jobs to
logfile in the following TAB separated format: sequence
number, sshlogin, start time as seconds since epoch, run time
in seconds, bytes in files transferred, bytes in files
returned, exit status, signal, and command run.
To convert the times into ISO-8601 strict do:
perl -a -F"\t" -ne 'chomp($F[2]=`date -d \@$F[2] +%FT%T`);
print join("\t",@F)'
See also --resume.
--jobs N
-j N
--max-procs N
-P N Number of jobslots. Run up to N jobs in parallel. 0 means as
many as possible. Default is 100% which will run one job per
CPU core.
If --semaphore is set default is 1 thus making a mutex.
--jobs +N
-j +N
--max-procs +N
-P +N Add N to the number of CPU cores. Run this many jobs in
parallel. See also --use-cpus-instead-of-cores.
--jobs -N
-j -N
--max-procs -N
-P -N Subtract N from the number of CPU cores. Run this many jobs
in parallel. If the evaluated number is less than 1 then 1
will be used. See also --use-cpus-instead-of-cores.
--jobs N%
-j N%
--max-procs N%
-P N% Multiply N% with the number of CPU cores. Run this many jobs
in parallel. See also --use-cpus-instead-of-cores.
--jobs procfile
-j procfile
--max-procs procfile
-P procfile
Read parameter from file. Use the content of procfile as
parameter for -j. E.g. procfile could contain the string 100%
or +2 or 10. If procfile is changed when a job completes,
procfile is read again and the new number of jobs is computed.
If the number is lower than before, running jobs will be
allowed to finish but new jobs will not be started until the
wanted number of jobs has been reached. This makes it
possible to change the number of simultaneous running jobs
while GNU parallel is running.
--keep-order
-k Keep sequence of output same as the order of input. Normally
the output of a job will be printed as soon as the job
completes. Try this to see the difference:
parallel -j4 sleep {}\; echo {} ::: 2 1 4 3
parallel -j4 -k sleep {}\; echo {} ::: 2 1 4 3
If used with --onall or --nonall the output will grouped by
sshlogin in sorted order.
-L max-lines
When used with --pipe: Read records of max-lines.
When used otherwise: Use at most max-lines nonblank input
lines per command line. Trailing blanks cause an input line
to be logically continued on the next input line.
-L 0 means read one line, but insert 0 arguments on the
command line.
Implies -X unless -m, --xargs, or --pipe is set.
--max-lines[=max-lines]
-l[max-lines]
When used with --pipe: Read records of max-lines.
When used otherwise: Synonym for the -L option. Unlike -L,
the max-lines argument is optional. If max-lines is not
specified, it defaults to one. The -l option is deprecated
since the POSIX standard specifies -L instead.
-l 0 is an alias for -l 1.
Implies -X unless -m, --xargs, or --pipe is set.
--line-buffer
Buffer output on line basis. --group will keep the output
together for a whole job. --ungroup allows output to mixup
with half a line coming from one job and half a line coming
from another job. --line-buffer fits between these two: GNU
parallel will print a full line, but will allow for mixing
lines of different jobs.
--line-buffer takes more CPU power than than both --group and
--ungroup, but can be faster than --group if the CPU is not
the limiting factor.
See also: --group --ungroup
--load max-load
Do not start new jobs on a given computer unless the number of
running processes on the computer is less than max-load. max-
load uses the same syntax as --jobs, so 100% for one per CPU
is a valid setting. Only difference is 0 which is interpreted
as 0.01.
--controlmaster
-M Use ssh's ControlMaster to make ssh connections faster. Useful
if jobs run remote and are very fast to run. This is disabled
for sshlogins that specify their own ssh command.
--xargs Multiple arguments. Insert as many arguments as the command
line length permits.
If {} is not used the arguments will be appended to the line.
If {} is used multiple times each {} will be replaced with all
the arguments.
Support for --xargs with --sshlogin is limited and may fail.
See also -X for context replace. If in doubt use -X as that
will most likely do what is needed.
-m Multiple arguments. Insert as many arguments as the command
line length permits. If multiple jobs are being run in
parallel: distribute the arguments evenly among the jobs. Use
-j1 to avoid this.
If {} is not used the arguments will be appended to the line.
If {} is used multiple times each {} will be replaced with all
the arguments.
Support for -m with --sshlogin is limited and may fail.
See also -X for context replace. If in doubt use -X as that
will most likely do what is needed.
--minversion version
Print the version GNU parallel and exit. If the current
version of GNU parallel is less than version the exit code is
255. Otherwise it is 0.
This is useful for scripts that depend on features only
available from a certain version of GNU parallel.
--nonall (beta testing)
--onall with no arguments. Run the command on all computers
given with --sshlogin but take no arguments. GNU parallel will
log into --jobs number of computers in parallel and run the
job on the computer. -j adjusts how many computers to log into
in parallel.
This is useful for running the same command (e.g. uptime) on a
list of servers.
--onall (beta testing)
Run all the jobs on all computers given with --sshlogin. GNU
parallel will log into --jobs number of computers in parallel
and run one job at a time on the computer. The order of the
jobs will not be changed, but some computers may finish before
others. -j adjusts how many computers to log into in parallel.
When using --group the output will be grouped by each server,
so all the output from one server will be grouped together.
--output-as-files
--outputasfiles
--files Instead of printing the output to stdout (standard output) the
output of each job is saved in a file and the filename is then
printed.
--pipe
--spreadstdin
Spread input to jobs on stdin (standard input). Read a block
of data from stdin (standard input) and give one block of data
as input to one job.
The block size is determined by --block. The strings
--recstart and --recend tell GNU parallel how a record starts
and/or ends. The block read will have the final partial record
removed before the block is passed on to the job. The partial
record will be prepended to next block.
If --recstart is given this will be used to split at record
start.
If --recend is given this will be used to split at record end.
If both --recstart and --recend are given both will have to
match to find a split position.
If neither --recstart nor --recend are given --recend defaults
to '\n'. To have no record separator use --recend "".
--files is often used with --pipe.
See also: --recstart, --recend, --fifo, --cat, --pipepart.
--pipepart (beta testing)
Pipe parts of a physical file. --pipepart works similar to
--pipe, but is much faster. It has a few limitations:
* The file must be a physical (seekable) file and must be
given using -a or ::::.
* Record counting (-N) and line counting (-L/-l) do not work.
--plain Ignore any --profile, $PARALLEL, and ~/.parallel/config to get
full control on the command line (used by GNU parallel
internally when called with --sshlogin).
--plus Activate additional replacement strings: {+/} {+.} {+..}
{+...} {..} {...} {/..} {/...}. The idea being that '{+foo}'
matches the opposite of '{foo}' and {} = {+/}/{/} = {.}.{+.} =
{+/}/{/.}.{+.} = {..}.{+..} = {+/}/{/..}.{+..} = {...}.{+...}
= {+/}/{/...}.{+...}
--progress
Show progress of computations. List the computers involved in
the task with number of CPU cores detected and the max number
of jobs to run. After that show progress for each computer:
number of running jobs, number of completed jobs, and
percentage of all jobs done by this computer. The percentage
will only be available after all jobs have been scheduled as
GNU parallel only read the next job when ready to schedule it
- this is to avoid wasting time and memory by reading
everything at startup.
By sending GNU parallel SIGUSR2 you can toggle turning on/off
--progress on a running GNU parallel process.
See also --eta.
--max-args=max-args
-n max-args
Use at most max-args arguments per command line. Fewer than
max-args arguments will be used if the size (see the -s
option) is exceeded, unless the -x option is given, in which
case GNU parallel will exit.
-n 0 means read one argument, but insert 0 arguments on the
command line.
Implies -X unless -m is set.
--max-replace-args=max-args
-N max-args
Use at most max-args arguments per command line. Like -n but
also makes replacement strings {1} .. {max-args} that
represents argument 1 .. max-args. If too few args the {n}
will be empty.
-N 0 means read one argument, but insert 0 arguments on the
command line.
This will set the owner of the homedir to the user:
tr ':' '\n' < /etc/passwd | parallel -N7 chown {1} {6}
Implies -X unless -m or --pipe is set.
When used with --pipe -N is the number of records to read.
This is somewhat slower than --block.
--max-line-length-allowed
Print the maximal number of characters allowed on the command
line and exit (used by GNU parallel itself to determine the
line length on remote computers).
--number-of-cpus
Print the number of physical CPUs and exit (used by GNU
parallel itself to determine the number of physical CPUs on
remote computers).
--number-of-cores
Print the number of CPU cores and exit (used by GNU parallel
itself to determine the number of CPU cores on remote
computers).
--no-notice
Do not display citation notice. A citation notice is printed
on stderr (standard error) only if stderr (standard error) is
a terminal, the user has not specified --no-notice, and the
user has not run --bibtex once.
--nice niceness
Run the command at this niceness. For simple commands you can
just add nice in front of the command. But if the command
consists of more sub commands (Like: ls|wc) then prepending
nice will not always work. --nice will make sure all sub
commands are niced.
--interactive
-p Prompt the user about whether to run each command line and
read a line from the terminal. Only run the command line if
the response starts with 'y' or 'Y'. Implies -t.
--parens parensstring
Use to define start and end parenthesis for {= perl expression
=}. The left and the right parenthesis can be multiple
characters and are assumed to be the same length. The default
is {==} giving {= as the start parenthesis and =} as the end
parenthesis.
Another useful setting is ,,,, which would make both
parenthesis ,,:
parallel --parens ,,,, echo foo is ,,s/I/O/g,, ::: FII
See also: --rpl {= perl expression =}
--profile profilename
-J profilename
Use profile 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 computer and a different
profile for running jobs on remote computers. See the section
PROFILE FILES for examples.
profilename corresponds to the file ~/.parallel/profilename.
You can give multiple profiles by repeating --profile. If
parts of the profiles conflict, the later ones will be used.
Default: config
--quote
-q Quote command. This will quote the command line so special
characters are not interpreted by the shell. See the section
QUOTING. Most people will never need this. Quoting is
disabled by default.
--no-run-if-empty
-r If the stdin (standard input) only contains whitespace, do not
run the command.
If used with --pipe this is slow.
--noswap Do not start new jobs on a given computer if there is both
swap-in and swap-out activity.
The swap activity is only sampled every 10 seconds as the
sampling takes 1 second to do.
Swap activity is computed as (swap-in)*(swap-out) which in
practice is a good value: swapping out is not a problem,
swapping in is not a problem, but both swapping in and out
usually indicates a problem.
--record-env
Record current environment variables in
~/.parallel/ignored_vars. This is useful before using --env _.
See also --env.
--recstart startstring
--recend endstring
If --recstart is given startstring will be used to split at
record start.
If --recend is given endstring will be used to split at record
end.
If both --recstart and --recend are given the combined string
endstringstartstring will have to match to find a split
position. This is useful if either startstring or endstring
match in the middle of a record.
If neither --recstart nor --recend are given then --recend
defaults to '\n'. To have no record separator use --recend "".
--recstart and --recend are used with --pipe.
Use --regexp to interpret --recstart and --recend as regular
expressions. This is slow, however.
--regexp Use --regexp to interpret --recstart and --recend as regular
expressions. This is slow, however.
--remove-rec-sep
--removerecsep
--rrs Remove the text matched by --recstart and --recend before
piping it to the command.
Only used with --pipe.
--results prefix
--res prefix
Save the output into files. The files will be stored in a
directory tree rooted at prefix. Within this directory tree,
each command will result in two files: prefix/<ARGS>/stdout
and prefix/<ARGS>/stderr, where <ARGS> is a sequence of
directories representing the header of the input source (if
using --header :) or the number of the input source and
corresponding values.
E.g:
parallel --header : --results foo echo {a} {b} ::: a I II ::: b III IIII
will generate the files:
foo/a/I/b/III/stderr
foo/a/I/b/III/stdout
foo/a/I/b/IIII/stderr
foo/a/I/b/IIII/stdout
foo/a/II/b/III/stderr
foo/a/II/b/III/stdout
foo/a/II/b/IIII/stderr
foo/a/II/b/IIII/stdout
and
parallel --results foo echo {1} {2} ::: I II ::: III IIII
will generate the files:
foo/1/I/2/III/stderr
foo/1/I/2/III/stdout
foo/1/I/2/IIII/stderr
foo/1/I/2/IIII/stdout
foo/1/II/2/III/stderr
foo/1/II/2/III/stdout
foo/1/II/2/IIII/stderr
foo/1/II/2/IIII/stdout
See also --files, --header, --joblog.
--resume Resumes from the last unfinished job. By reading --joblog or
the --results dir GNU parallel will figure out the last
unfinished job and continue from there. As GNU parallel only
looks at the sequence numbers in --joblog then the input, the
command, and --joblog all have to remain unchanged; otherwise
GNU parallel may run wrong commands.
See also --joblog, --results, --resume-failed.
--resume-failed
Retry all failed and resume from the last unfinished job. By
reading --joblog GNU parallel will figure out the failed jobs
and run those again. After that it will resume last unfinished
job and continue from there. As GNU parallel only looks at the
sequence numbers in --joblog then the input, the command, and
--joblog all have to remain unchanged; otherwise GNU parallel
may run wrong commands.
See also --joblog, --resume.
--retries n
If a job fails, retry it on another computer on which it has
not failed. Do this n times. If there are fewer than n
computers in --sshlogin GNU parallel will re-use all the
computers. This is useful if some jobs fail for no apparent
reason (such as network failure).
--return filename
Transfer files from remote computers. --return is used with
--sshlogin when the arguments are files on the remote
computers. When processing is done the file filename will be
transferred from the remote computer using 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 $HOME/foo/bar.out from the
computer server.example.com to the file foo/bar.out after
running touch foo/bar.out on server.example.com.
echo /tmp/foo/bar.txt | parallel \
--sshlogin server.example.com --return {.}.out touch {.}.out
This will transfer the file /tmp/foo/bar.out from the computer
server.example.com to the file /tmp/foo/bar.out after running
touch /tmp/foo/bar.out on server.example.com.
Multiple files can be transferred by repeating the options
multiple times:
echo /tmp/foo/bar.txt | \
parallel --sshlogin server.example.com \
--return {.}.out --return {.}.out2 touch {.}.out {.}.out2
--return is often used with --transfer and --cleanup.
--return is ignored when used with --sshlogin : or when not
used with --sshlogin.
--round-robin
--round Normally --pipe will give a single block to each instance of
the command. With --round-robin all blocks will at random be
written to commands already running. This is useful if the
command takes a long time to initialize.
--keep-order will not work with --round-robin as it is
impossible to track which input block corresponds to which
output.
--rpl 'tag perl expression'
Use tag as a replacement string for perl expression. This
makes it possible to define your own replacement strings. GNU
parallel's 7 replacement strings are implemented as:
--rpl '{} '
--rpl '{#} 1 $_=$job->seq()'
--rpl '{%} 1 $_=$job->slot()'
--rpl '{/} s:.*/::'
--rpl '{//} $Global::use{"File::Basename"} ||= eval "use File::Basename; 1;"; $_ = dirname($_);'
--rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
--rpl '{.} s:\.[^/.]+$::'
If the user defined replacement string starts with '{' it can
also be used as a positional replacement string (like {2.}).
It is recommended to only change $_ but you have full access
to all of GNU parallel's internal functions and data
structures.
Here are a few examples:
Remove 2 extensions (e.g. .tar.gz)
--rpl '{..} s:\.[^/.]+$::;s:\.[^/.]+$::;'
Keep only the extension
--rpl '{ext} s:.*\.::'
Is the job sequence even or odd?
--rpl '{odd} $_=$job->seq()%2?"odd":"even"'
See also: {= perl expression =} --parens
--max-chars=max-chars
-s max-chars
Use at most max-chars characters per command line, including
the command and initial-arguments and the terminating nulls at
the ends of the argument strings. The largest allowed value
is system-dependent, and is calculated as the argument length
limit for exec, less the size of your environment. The
default value is the maximum.
Implies -X unless -m is set.
--show-limits
Display the limits on the command-line length which are
imposed by the operating system and the -s option. Pipe the
input from /dev/null (and perhaps specify --no-run-if-empty)
if you don't want GNU parallel to do anything.
--semaphore
Work as a counting semaphore. --semaphore will cause GNU
parallel to start command in the background. When the number
of simultaneous jobs is reached, GNU parallel will wait for
one of these to complete before starting another command.
--semaphore implies --bg unless --fg is specified.
--semaphore implies --semaphorename `tty` unless
--semaphorename is specified.
Used with --fg, --wait, and --semaphorename.
The command sem is an alias for parallel --semaphore.
See also man sem.
--semaphorename name
--id name
Use name as the name of the semaphore. Default is the name of
the controlling tty (output from tty).
The default normally works as expected when used
interactively, but when used in a script name should be set.
$$ or my_task_name are often a good value.
The semaphore is stored in ~/.parallel/semaphores/
Implies --semaphore.
See also man sem.
--semaphoretimeout secs
If the semaphore is not released within secs seconds, take it
anyway.
Implies --semaphore.
See also man sem.
--seqreplace replace-str
Use the replacement string replace-str instead of {#} for job
sequence number.
--shebang
--hashbang
GNU parallel can be called as a shebang (#!) command as the
first line of a script. The content of the file will be
treated as inputsource.
Like this:
#!/usr/bin/parallel --shebang -r traceroute
foss.org.my
debian.org
freenetproject.org
--shebang must be set as the first option.
On FreeBSD env is needed:
#!/usr/bin/env -S parallel --shebang -r traceroute
foss.org.my
debian.org
freenetproject.org
--shebang-wrap
GNU parallel can parallelize scripts by wrapping the shebang
line. If the program can be run like this:
cat arguments | parallel the_program
then the script can be changed to:
#!/usr/bin/parallel --shebang-wrap /the/original/parser --with-options
E.g.
#!/usr/bin/parallel --shebang-wrap /usr/bin/python
If the program can be run like this:
cat data | parallel --pipe the_program
then the script can be changed to:
#!/usr/bin/parallel --shebang-wrap --pipe /the/original/parser --with-options
E.g.
#!/usr/bin/parallel --shebang-wrap --pipe /usr/bin/perl -w
--shebang-wrap must be set as the first option.
--shellquote
Does not run the command but quotes it. Useful for making
quoted composed commands for GNU parallel.
--skip-first-line
Do not use the first line of input (used by GNU parallel
itself when called with --shebang).
--sshdelay secs
Delay starting next ssh by secs seconds. GNU parallel will
pause secs seconds after starting each ssh. secs can be less
than 1 seconds.
-S [ncpu/]sshlogin[,[ncpu/]sshlogin[,...]]
--sshlogin [ncpu/]sshlogin[,[ncpu/]sshlogin[,...]]
Distribute jobs to remote computers. The jobs will be run on a
list of remote computers. GNU parallel will determine the
number of CPU cores on the remote computers and run the number
of jobs as specified by -j. If the number ncpu is given GNU
parallel will use this number for number of CPU cores on the
host. Normally ncpu will not be needed.
An sshlogin is of the form:
[sshcommand [options]] [username@]hostname
The sshlogin must not require a password.
The sshlogin ':' is special, it means 'no ssh' and will
therefore run on the local computer.
The sshlogin '..' is special, it read sshlogins from
~/.parallel/sshloginfile
The sshlogin '-' is special, too, it read sshlogins from stdin
(standard input).
To specify more sshlogins separate the sshlogins by comma or
repeat the options multiple times.
For examples: see --sshloginfile.
The remote host must have GNU parallel installed.
--sshlogin is known to cause problems with -m and -X.
--sshlogin is often used with --transfer, --return, --cleanup,
and --trc.
--sshloginfile filename (beta testing)
--slf filename (beta testing)
File with sshlogins. The file consists of sshlogins on
separate lines. Empty lines and lines starting with '#' are
ignored. Example:
server.example.com
username@server2.example.com
8/my-8-core-server.example.com
2/my_other_username@my-dualcore.example.net
# This server has SSH running on port 2222
ssh -p 2222 server.example.net
4/ssh -p 2222 quadserver.example.net
# Use a different ssh program
myssh -p 2222 -l myusername hexacpu.example.net
# Use a different ssh program with default number of cores
//usr/local/bin/myssh -p 2222 -l myusername hexacpu.example.net
# Use a different ssh program with 6 cores
6//usr/local/bin/myssh -p 2222 -l myusername hexacpu.example.net
# Assume 16 cores on the local computer
16/:
When using a different ssh program the last argument must be
the hostname.
Multiple --sshloginfile are allowed.
GNU parallel will first look for the file in current dir; if
that fails it look for the file in ~/.parallel.
The sshloginfile '..' is special, it read sshlogins from
~/.parallel/sshloginfile
The sshloginfile '.' is special, it read sshlogins from
/etc/parallel/sshloginfile
The sshloginfile '-' is special, too, it read sshlogins from
stdin (standard input).
If the sshloginfile is changed it will be re-read when a job
finishes though at most once per second. This makes it
possible to add and remove hosts while running.
This can be used to have a daemon that updates the
sshloginfile to only contain servers that are up:
cp original.slf tmp2.slf
while [ 1 ] ; do
nice parallel --nonall -j0 -k --slf original.slf --tag echo | perl 's/\t$//' > tmp.slf
if diff tmp.slf tmp2.slf; then
mv tmp.slf tmp2.slf
fi
sleep 10
done &
parallel --slf tmp2.slf ...
--slotreplace replace-str
Use the replacement string replace-str instead of {%} for job
slot number.
--silent Silent. The job to be run will not be printed. This is the
default. Can be reversed with -v.
--tty Open terminal tty. If GNU 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. -j1), not buffer the output
(i.e. -u), and it will open a tty for the job. When the job is
done, the next job will get the tty.
--tag Tag lines with arguments. Each output line will be prepended
with the arguments and TAB (\t). When combined with --onall or
--nonall the lines will be prepended with the sshlogin
instead.
--tag is ignored when using -u.
--tagstring str
Tag lines with a string. Each output line will be prepended
with str and TAB (\t). str can contain replacement strings
such as {}.
--tagstring is ignored when using -u, --onall, and --nonall.
--tmpdir dirname
Directory for temporary files. GNU parallel normally buffers
output into temporary files in /tmp. By setting --tmpdir you
can use a different dir for the files. Setting --tmpdir is
equivalent to setting $TMPDIR.
--tmux Use tmux for output. Start a tmux session and run each job in
a window in that session. No other output will be produced.
--timeout val
Time out for command. If the command runs for longer than val
seconds it will get killed with SIGTERM, followed by SIGTERM
200 ms later, followed by SIGKILL 200 ms later.
If val is followed by a % then the timeout will dynamically be
computed as a percentage of the median average runtime. Only
values > 100% will make sense.
--verbose
-t Print the job to be run on stderr (standard error).
See also -v, -p.
--transfer
Transfer files to remote computers. --transfer is used with
--sshlogin when the arguments are files and should be
transferred to the remote computers. The files will be
transferred using rsync and will be put relative to the
default work dir. If the path contains /./ the remaining path
will be relative to the work dir. E.g.
echo foo/bar.txt | parallel \
--sshlogin server.example.com --transfer wc
This will transfer the file foo/bar.txt to the computer
server.example.com to the file $HOME/foo/bar.txt before
running wc foo/bar.txt on server.example.com.
echo /tmp/foo/bar.txt | parallel \
--sshlogin server.example.com --transfer wc
This will transfer the file foo/bar.txt to the computer
server.example.com to the file /tmp/foo/bar.txt before running
wc /tmp/foo/bar.txt on server.example.com.
--transfer is often used with --return and --cleanup.
--transfer is ignored when used with --sshlogin : or when not
used with --sshlogin.
--trc filename
Transfer, Return, Cleanup. Short hand for:
--transfer --return filename --cleanup
--trim <n|l|r|lr|rl>
Trim white space in input.
n No trim. Input is not modified. This is the default.
l Left trim. Remove white space from start of input. E.g. "
a bc " -> "a bc ".
r Right trim. Remove white space from end of input. E.g. " a
bc " -> " a bc".
lr
rl Both trim. Remove white space from both start and end of
input. E.g. " a bc " -> "a bc". This is the default if
--colsep is used.
--ungroup
-u Ungroup output. Output is printed as soon as possible and by
passes GNU parallel internal processing. This may cause output
from different commands to be mixed thus should only be used
if you do not care about the output. Compare these:
parallel -j0 'sleep {};echo -n start{};sleep {};echo {}end'
::: 1 2 3 4
parallel -u -j0 'sleep {};echo -n start{};sleep {};echo {}end'
::: 1 2 3 4
It also disables --tag. GNU parallel outputs faster with -u.
Compare the speed of these:
parallel seq ::: 300000000 >/dev/null
parallel -u seq ::: 300000000 >/dev/null
parallel --line-buffer seq ::: 300000000 >/dev/null
Can be reversed with --group.
See also: --line-buffer --group
--extensionreplace replace-str
--er replace-str
Use the replacement string replace-str instead of {.} for
input line without extension.
--use-cpus-instead-of-cores
Count the number of physical CPUs instead of CPU cores. When
computing how many jobs to run simultaneously relative to the
number of CPU cores you can ask GNU parallel to instead look
at the number of physical CPUs. This will make sense for
computers that have hyperthreading as two jobs running on one
CPU with hyperthreading will run slower than two jobs running
on two physical CPUs. Some multi-core CPUs can run faster if
only one thread is running per physical CPU. Most users will
not need this option.
-v Verbose. Print the job to be run on stdout (standard output).
Can be reversed with --silent. See also -t.
Use -v -v to print the wrapping ssh command when running
remotely.
--version
-V Print the version GNU parallel and exit.
--workdir mydir
--wd mydir
Files transferred using --transfer and --return will be
relative to mydir on remote computers, and the command will be
executed in the dir mydir.
The special mydir value ... will create working dirs under
~/.parallel/tmp/ on the remote computers. If --cleanup is
given these dirs will be removed.
The special mydir value . uses the current working dir. If
the current working dir is beneath your home dir, the value .
is treated as the relative path to your home dir. This means
that if your home dir is different on remote computers (e.g.
if your login is different) the relative path will still be
relative to your home dir.
To see the difference try:
parallel -S server pwd ::: ""
parallel --wd . -S server pwd ::: ""
parallel --wd ... -S server pwd ::: ""
--wait Wait for all commands to complete.
Implies --semaphore.
See also man sem.
-X Multiple arguments with context replace. Insert as many
arguments as the command line length permits. If multiple jobs
are being run in parallel: distribute the arguments evenly
among the jobs. Use -j1 to avoid this.
If {} is not used the arguments will be appended to the line.
If {} is used as part of a word (like pic{}.jpg) then the
whole word will be repeated. If {} is used multiple times each
{} will be replaced with the arguments.
Normally -X will do the right thing, whereas -m can give
unexpected results if {} is used as part of a word.
Support for -X with --sshlogin is limited and may fail.
See also -m.
--exit
-x Exit if the size (see the -s option) is exceeded.
--xapply Read multiple input sources like xapply. If multiple input
sources are given, one argument will be read from each of the
input sources. The arguments can be accessed in the command as
{1} .. {n}, so {1} will be a line from the first input source,
and {6} will refer to the line with the same line number from
the 6th input source.
Compare these two:
parallel echo {1} {2} ::: 1 2 3 ::: a b c
parallel --xapply echo {1} {2} ::: 1 2 3 ::: a b c
Arguments will be recycled if one input source has more
arguments than the others:
parallel --xapply echo {1} {2} {3} ::: 1 2 ::: I II III ::: a b c d e f g
See also --header.
EXAMPLE: Working as xargs -n1. Argument appending
GNU parallel can work similar to xargs -n1.
To compress all html files using gzip run:
find . -name '*.html' | parallel gzip --best
If the file names may contain a newline use -0. Substitute FOO BAR with
FUBAR in all files in this dir and subdirs:
find . -type f -print0 | parallel -q0 perl -i -pe 's/FOO BAR/FUBAR/g'
Note -q is needed because of the space in 'FOO BAR'.
EXAMPLE: Reading arguments from command line
GNU parallel can take the arguments from command line instead of stdin
(standard input). To compress all html files in the current dir using
gzip run:
parallel gzip --best ::: *.html
To convert *.wav to *.mp3 using LAME running one process per CPU core
run:
parallel lame {} -o {.}.mp3 ::: *.wav
EXAMPLE: Inserting multiple arguments
When moving a lot of files like this: mv *.log destdir you will
sometimes get the error:
bash: /bin/mv: Argument list too long
because there are too many files. You can instead do:
ls | grep -E '\.log$' | parallel mv {} destdir
This will run mv for each file. It can be done faster if mv gets as
many arguments that will fit on the line:
ls | grep -E '\.log$' | parallel -m mv {} destdir
EXAMPLE: Context replace
To remove the files pict0000.jpg .. pict9999.jpg you could do:
seq -w 0 9999 | parallel rm pict{}.jpg
You could also do:
seq -w 0 9999 | perl -pe 's/(.*)/pict$1.jpg/' | parallel -m rm
The first will run rm 10000 times, while the last will only run rm as
many times needed to keep the command line length short enough to avoid
Argument list too long (it typically runs 1-2 times).
You could also run:
seq -w 0 9999 | parallel -X rm pict{}.jpg
This will also only run rm as many times needed to keep the command
line length short enough.
EXAMPLE: Compute intensive jobs and substitution
If ImageMagick is installed this will generate a thumbnail of a jpg
file:
convert -geometry 120 foo.jpg thumb_foo.jpg
This will run with number-of-cpu-cores jobs in parallel for all jpg
files in a directory:
ls *.jpg | parallel convert -geometry 120 {} thumb_{}
To do it recursively use find:
find . -name '*.jpg' | parallel convert -geometry 120 {} {}_thumb.jpg
Notice how the argument has to start with {} as {} will include path
(e.g. running convert -geometry 120 ./foo/bar.jpg thumb_./foo/bar.jpg
would clearly be wrong). The command will generate files like
./foo/bar.jpg_thumb.jpg.
Use {.} to avoid the extra .jpg in the file name. This command will
make files like ./foo/bar_thumb.jpg:
find . -name '*.jpg' | parallel convert -geometry 120 {} {.}_thumb.jpg
EXAMPLE: Substitution and redirection
This will generate an uncompressed version of .gz-files next to the
.gz-file:
parallel zcat {} ">"{.} ::: *.gz
Quoting of > is necessary to postpone the redirection. Another solution
is to quote the whole command:
parallel "zcat {} >{.}" ::: *.gz
Other special shell characters (such as * ; $ > < | >> <<) also need to
be put in quotes, as they may otherwise be interpreted by the shell and
not given to GNU parallel.
EXAMPLE: Composed commands
A job can consist of several commands. This will print the number of
files in each directory:
ls | parallel 'echo -n {}" "; ls {}|wc -l'
To put the output in a file called <name>.dir:
ls | parallel '(echo -n {}" "; ls {}|wc -l) > {}.dir'
Even small shell scripts can be run by GNU parallel:
find . | parallel 'a={}; name=${a##*/}; upper=$(echo "$name" | tr
"[:lower:]" "[:upper:]"); echo "$name - $upper"'
ls | parallel 'mv {} "$(echo {} | tr "[:upper:]" "[:lower:]")"'
Given a list of URLs, list all URLs that fail to download. Print the
line number and the URL.
cat urlfile | parallel "wget {} 2>/dev/null || grep -n {} urlfile"
Create a mirror directory with the same filenames except all files and
symlinks are empty files.
cp -rs /the/source/dir mirror_dir; find mirror_dir -type l | parallel
-m rm {} '&&' touch {}
Find the files in a list that do not exist
cat file_list | parallel 'if [ ! -e {} ] ; then echo {}; fi'
EXAMPLE: Calling Bash functions
If the composed command is longer than a line, it becomes hard to read.
In Bash you can use functions. Just remember to export -f the function.
doit() {
echo Doing it for $1
sleep 2
echo Done with $1
}
export -f doit
parallel doit ::: 1 2 3
doubleit() {
echo Doing it for $1 $2
sleep 2
echo Done with $1 $2
}
export -f doubleit
parallel doubleit ::: 1 2 3 ::: a b
To do this on remote servers you need to transfer the function using
--env:
parallel --env doit -S server doit ::: 1 2 3
parallel --env doubleit -S server doubleit ::: 1 2 3 ::: a b
If your environment (aliases, variables, and functions) is small you
can copy the full environment without having to export -f anything.
Just run this first:
env_parallel() {
export parallel_bash_environment='() {
'"$(echo "shopt -s expand_aliases 2>/dev/null"; alias;typeset -p | grep -vFf <(readonly; echo GROUPS; echo FUNCNAME; echo DIRSTACK; echo _; echo PIPESTATUS; echo USERNAME) | grep -v BASH_;typeset -f)"'
}'
# Run as: env_parallel parallel_bash_environment "2>/dev/null;" ...
`which parallel` "$@"
unset parallel_bash_environment
}
And then call as:
env_parallel doit ::: 1 2 3
env_parallel doubleit ::: 1 2 3 ::: a b
env_parallel -S server doit ::: 1 2 3
env_parallel -S server doubleit ::: 1 2 3 ::: a b
EXAMPLE: Function tester
To test a program with different parameters:
tester() {
if (eval "$@") >&/dev/null; then
perl -e 'printf "\033[30;102m[ OK ]\033[0m @ARGV\n"' "$@"
else
perl -e 'printf "\033[30;101m[FAIL]\033[0m @ARGV\n"' "$@"
fi
}
export -f tester
parallel tester my_program ::: arg1 arg2
parallel tester exit ::: 1 0 2 0
If my_program fails a red FAIL will be printed followed by the failing
command; otherwise a green OK will be printed followed by the command.
EXAMPLE: Removing file extension when processing files
When processing files removing the file extension using {.} is often
useful.
Create a directory for each zip-file and unzip it in that dir:
parallel 'mkdir {.}; cd {.}; unzip ../{}' ::: *.zip
Recompress all .gz files in current directory using bzip2 running 1 job
per CPU core in parallel:
parallel "zcat {} | bzip2 >{.}.bz2 && rm {}" ::: *.gz
Convert all WAV files to MP3 using LAME:
find sounddir -type f -name '*.wav' | parallel lame {} -o {.}.mp3
Put all converted in the same directory:
find sounddir -type f -name '*.wav' | parallel lame {} -o
mydir/{/.}.mp3
EXAMPLE: Removing two file extensions when processing files
If you have directory with tar.gz files and want these extracted in the
corresponding dir (e.g foo.tar.gz will be extracted in the dir foo) you
can do:
parallel --plus 'mkdir {..}; tar -C {..} -xf {}' ::: *.tar.gz
EXAMPLE: Download 10 images for each of the past 30 days
Let us assume a website stores images like:
http://www.example.com/path/to/YYYYMMDD_##.jpg
where YYYYMMDD is the date and ## is the number 01-10. This will
download images for the past 30 days:
parallel wget http://www.example.com/path/to/'$(date -d "today -{1}
days" +%Y%m%d)_{2}.jpg' ::: $(seq 30) ::: $(seq -w 10)
$(date -d "today -{1} days" +%Y%m%d) will give the dates in YYYYMMDD
with {1} days subtracted.
EXAMPLE: Copy files as last modified date (ISO8601) with added random digits
find . | parallel 'cp {} ../destdir/{= $a = int(10000*rand); $_ = `date
-r "$_" +%FT%T"$a"`; chomp; =}'
EXAMPLE: Digtal clock with "blinking" :
The : in a digital clock blinks. To make every other line have a ':'
and the rest a ' ' a perl expression is used to look at the 3rd input
source. If the value modudo 2 is 1: Use ":" otherwise use " ":
parallel -k echo {1}'{=3 $_=$_%2?":":" "=}'{2}{3} ::: {0..12} :::
{0..5} ::: {0..9}
EXAMPLE: Aggregating content of files
This:
parallel --header : echo x{X}y{Y}z{Z} \> x{X}y{Y}z{Z} \
::: X {1..5} ::: Y {01..10} ::: Z {1..5}
will generate the files x1y01z1 .. x5y10z5. If you want to aggregate
the output grouping on x and z you can do this:
parallel eval 'cat {=s/y01/y*/=} > {=s/y01//=}' ::: *y01*
For all values of x and z it runs commands like:
cat x1y*z1 > x1z1
So you end up with x1z1 .. x1z5 each containing the content of all
values of y.
EXAMPLE: Breadth first parallel web crawler/mirrorer
This script below will crawl and mirror a URL in parallel. It
downloads first pages that are 1 click down, then 2 clicks down, then
3; instead of the normal depth first, where the first link link on each
page is fetched first.
Run like this:
PARALLEL=-j100 ./parallel-crawl http://gatt.org.yeslab.org/
Remove the wget part if you only want a web crawler.
It works by fetching a page from a list of URLs and looking for links
in that page that are within the same starting URL and that have not
already been seen. These links are added to a new queue. When all the
pages from the list is done, the new queue is moved to the list of URLs
and the process is started over until no unseen links are found.
#!/bin/bash
# E.g. http://gatt.org.yeslab.org/
URL=$1
# Stay inside the start dir
BASEURL=$(echo $URL | perl -pe 's:#.*::; s:(//.*/)[^/]*:$1:')
URLLIST=$(mktemp urllist.XXXX)
URLLIST2=$(mktemp urllist.XXXX)
SEEN=$(mktemp seen.XXXX)
# Spider to get the URLs
echo $URL >$URLLIST
cp $URLLIST $SEEN
while [ -s $URLLIST ] ; do
cat $URLLIST |
parallel lynx -listonly -image_links -dump {} \; wget -qm -l1 -Q1 {} \; echo Spidered: {} \>\&2 |
perl -ne 's/#.*//; s/\s+\d+.\s(\S+)$/$1/ and do { $seen{$1}++ or print }' |
grep -F $BASEURL |
grep -v -x -F -f $SEEN | tee -a $SEEN > $URLLIST2
mv $URLLIST2 $URLLIST
done
rm -f $URLLIST $URLLIST2 $SEEN
EXAMPLE: Process files from a tar file while unpacking
If the files to be processed are in a tar file then unpacking one file
and processing it immediately may be faster than first unpacking all
files.
tar xvf foo.tgz | perl -ne 'print $l;$l=$_;END{print $l}' | parallel
echo
The Perl one-liner is needed to avoid race condition.
EXAMPLE: Rewriting a for-loop and a while-read-loop
for-loops like this:
(for x in `cat list` ; do
do_something $x
done) | process_output
and while-read-loops like this:
cat list | (while read x ; do
do_something $x
done) | process_output
can be written like this:
cat list | parallel do_something | process_output
For example: Find which host name in a list has IP address 1.2.3 4:
cat hosts.txt | parallel -P 100 host | grep 1.2.3.4
If the processing requires more steps the for-loop like this:
(for x in `cat list` ; do
no_extension=${x%.*};
do_something $x scale $no_extension.jpg
do_step2 <$x $no_extension
done) | process_output
and while-loops like this:
cat list | (while read x ; do
no_extension=${x%.*};
do_something $x scale $no_extension.jpg
do_step2 <$x $no_extension
done) | process_output
can be written like this:
cat list | parallel "do_something {} scale {.}.jpg ; do_step2 <{} {.}"
| process_output
EXAMPLE: Rewriting nested for-loops
Nested for-loops like this:
(for x in `cat xlist` ; do
for y in `cat ylist` ; do
do_something $x $y
done
done) | process_output
can be written like this:
parallel do_something {1} {2} :::: xlist ylist | process_output
Nested for-loops like this:
(for gender in M F ; do
for size in S M L XL XXL ; do
echo $gender $size
done
done) | sort
can be written like this:
parallel echo {1} {2} ::: M F ::: S M L XL XXL | sort
EXAMPLE: Finding the lowest difference between files
diff is good for finding differences in text files. diff | wc -l gives
an indication of the size of the difference. To find the differences
between all files in the current dir do:
parallel --tag 'diff {1} {2} | wc -l' ::: * ::: * | sort -nk3
This way it is possible to see if some files are closer to other files.
EXAMPLE: for-loops with column names
When doing multiple nested for-loops it can be easier to keep track of
the loop variable if is is named instead of just having a number. Use
--header : to let the first argument be an named alias for the
positional replacement string:
parallel --header : echo {gender} {size} ::: gender M F ::: size S M L XL XXL
This also works if the input file is a file with columns:
cat addressbook.tsv | parallel --colsep '\t' --header : echo {Name} {E-mail address}
EXAMPLE: Count the differences between all files in a dir
Using --results the results are saved in /tmp/diffcount*.
parallel --results /tmp/diffcount "diff -U 0 {1} {2} |tail -n +3 |grep -v '^@'|wc -l" ::: * ::: *
To see the difference between file A and file B look at the file
'/tmp/diffcount/1/A/2/B'.
EXAMPLE: Speeding up fast jobs
Starting a job on the local machine takes around 10 ms. This can be a
big overhead if the job takes very few ms to run. Often you can group
small jobs together using -X which will make the overhead less
significant. Compare the speed of these:
seq -w 0 9999 | parallel touch pict{}.jpg
seq -w 0 9999 | parallel -X touch pict{}.jpg
If your program cannot take multiple arguments, then you can use GNU
parallel to spawn multiple GNU parallels:
seq -w 0 999999 | parallel -j10 --pipe parallel -j0 touch pict{}.jpg
If -j0 normally spawns 252 jobs, then the above will try to spawn 2520
jobs. On a normal GNU/Linux system you can spawn 32000 jobs using this
technique with no problems. To raise the 32000 jobs limit raise
/proc/sys/kernel/pid_max to 4194303.
EXAMPLE: Using shell variables
When using shell variables you need to quote them correctly as they may
otherwise be split on spaces.
Notice the difference between:
V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
parallel echo ::: ${V[@]} # This is probably not what you want
and:
V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar)
parallel echo ::: "${V[@]}"
When using variables in the actual command that contains special
characters (e.g. space) you can quote them using '"$VAR"' or using "'s
and -q:
V="Here are two "
parallel echo "'$V'" ::: spaces
parallel -q echo "$V" ::: spaces
EXAMPLE: Group output lines
When running jobs that output data, you often do not want the output of
multiple jobs to run together. GNU parallel defaults to grouping the
output of each job, so the output is printed when the job finishes. If
you want full lines to be printed while the job is running you can use
--line-buffer. If you want output to be printed as soon as possible you
can use -u.
Compare the output of:
parallel traceroute ::: foss.org.my debian.org freenetproject.org
to the output of:
parallel --line-buffer traceroute ::: foss.org.my debian.org
freenetproject.org
and:
parallel -u traceroute ::: foss.org.my debian.org freenetproject.org
EXAMPLE: Tag output lines
GNU parallel groups the output lines, but it can be hard to see where
the different jobs begin. --tag prepends the argument to make that more
visible:
parallel --tag traceroute ::: foss.org.my debian.org freenetproject.org
--tag works with --line-buffer but not with -u:
parallel --tag --line-buffer traceroute ::: foss.org.my debian.org
freenetproject.org
Check the uptime of the servers in ~/.parallel/sshloginfile:
parallel --tag -S .. --nonall uptime
EXAMPLE: Keep order of output same as order of input
Normally the output of a job will be printed as soon as it completes.
Sometimes you want the order of the output to remain the same as the
order of the input. This is often important, if the output is used as
input for another system. -k will make sure the order of output will be
in the same order as input even if later jobs end before earlier jobs.
Append a string to every line in a text file:
cat textfile | parallel -k echo {} append_string
If you remove -k some of the lines may come out in the wrong order.
Another example is traceroute:
parallel traceroute ::: foss.org.my debian.org freenetproject.org
will give traceroute of foss.org.my, debian.org and freenetproject.org,
but it will be sorted according to which job completed first.
To keep the order the same as input run:
parallel -k traceroute ::: foss.org.my debian.org freenetproject.org
This will make sure the traceroute to foss.org.my will be printed
first.
A bit more complex example is downloading a huge file in chunks in
parallel: Some internet connections will deliver more data if you
download files in parallel. For downloading files in parallel see:
"EXAMPLE: Download 10 images for each of the past 30 days". But if you
are downloading a big file you can download the file in chunks in
parallel.
To download byte 10000000-19999999 you can use curl:
curl -r 10000000-19999999 http://example.com/the/big/file > file.part
To download a 1 GB file we need 100 10MB chunks downloaded and combined
in the correct order.
seq 0 99 | parallel -k curl -r \
{}0000000-{}9999999 http://example.com/the/big/file > file
EXAMPLE: Parallel grep
grep -r greps recursively through directories. On multicore CPUs GNU
parallel can often speed this up.
find . -type f | parallel -k -j150% -n 1000 -m grep -H -n STRING {}
This will run 1.5 job per core, and give 1000 arguments to grep.
EXAMPLE: Grepping n lines for m regular expressions.
The simplest solution to grep a big file for a lot of regexps is:
grep -f regexps.txt bigfile
Or if the regexps are fixed strings:
grep -F -f regexps.txt bigfile
There are 2 limiting factors: CPU and disk I/O. CPU is easy to measure:
If the grep takes >90% CPU (e.g. when running top), then the CPU is a
limiting factor, and parallelization will speed this up. If not, then
disk I/O is the limiting factor, and depending on the disk system it
may be faster or slower to parallelize. The only way to know for
certain is to measure.
If the CPU is the limiting factor parallelization should be done on the
regexps:
cat regexp.txt | parallel --pipe -L1000 --round-robin grep -f - bigfile
If a line matches multiple regexps, the line may be duplicated. The
command will start one grep per CPU and read bigfile one time per CPU,
but as that is done in parallel, all reads except the first will be
cached in RAM. Depending on the size of regexp.txt it may be faster to
use --block 10m instead of -L1000. If regexp.txt is too big to fit in
RAM, remove --round-robin and adjust -L1000. This will cause bigfile to
be read more times.
Some storage systems perform better when reading multiple chunks in
parallel. This is true for some RAID systems and for some network file
systems. To parallelize the reading of bigfile:
parallel --pipepart --block 100M -a bigfile -k grep -f regexp.txt
This will split bigfile into 100MB chunks and run grep on each of these
chunks. To parallelize both reading of bigfile and regexp.txt combine
the two using --fifo:
parallel --pipepart --block 100M -a bigfile --fifo cat regexp.txt \
\| parallel --pipe -L1000 --round-robin grep -f - {}
If a line matches multiple regexps, the line may be duplicated.
EXAMPLE: Using remote computers
To run commands on a remote computer SSH needs to be set up and you
must be able to login without entering a password (The commands ssh-
copy-id and ssh-agent may help you do that).
If you need to login to a whole cluster, you typically do not want to
accept the host key for every host. You want to accept them the first
time and be warned if they are ever changed. To do that:
# Add the servers to the sshloginfile
(echo servera; echo serverb) > .parallel/my_cluster
# Make sure .ssh/config exist
touch .ssh/config
cp .ssh/config .ssh/config.backup
# Disable StrictHostKeyChecking temporarily
(echo 'Host *'; echo StrictHostKeyChecking no) >> .ssh/config
parallel --slf my_cluster --nonall true
# Remove the disabling of StrictHostKeyChecking
mv .ssh/config.backup .ssh/config
The servers in .parallel/my_cluster are now added in .ssh/known_hosts.
To run echo on server.example.com:
seq 10 | parallel --sshlogin server.example.com echo
To run commands on more than one remote computer run:
seq 10 | parallel --sshlogin server.example.com,server2.example.net echo
Or:
seq 10 | parallel --sshlogin server.example.com \
--sshlogin server2.example.net echo
If the login username is foo on server2.example.net use:
seq 10 | parallel --sshlogin server.example.com \
--sshlogin foo@server2.example.net echo
If your list of hosts is server1-88.example.net with login foo:
seq 10 | parallel -Sfoo@server{1..88}.example.net echo
To distribute the commands to a list of computers, make a file
mycomputers with all the computers:
server.example.com
foo@server2.example.com
server3.example.com
Then run:
seq 10 | parallel --sshloginfile mycomputers echo
To include the local computer add the special sshlogin ':' to the list:
server.example.com
foo@server2.example.com
server3.example.com
:
GNU parallel will try to determine the number of CPU cores on each of
the remote computers, and 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 computers is not identified
correctly the number of CPU cores can be added in front. Here the
computer has 8 CPU cores.
seq 10 | parallel --sshlogin 8/server.example.com echo
EXAMPLE: Transferring of files
To recompress gzipped files with bzip2 using a remote computer run:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com \
--transfer "zcat {} | bzip2 -9 >{.}.bz2"
This will list the .gz-files in the logs directory and all directories
below. Then it will transfer the files to server.example.com to the
corresponding directory in $HOME/logs. On server.example.com the file
will be recompressed using zcat and bzip2 resulting in the
corresponding file with .gz replaced with .bz2.
If you want the resulting bz2-file to be transferred back to the local
computer add --return {.}.bz2:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com \
--transfer --return {.}.bz2 "zcat {} | bzip2 -9 >{.}.bz2"
After the recompressing is done the .bz2-file is transferred back to
the local computer and put next to the original .gz-file.
If you want to delete the transferred files on the remote computer add
--cleanup. This will remove both the file transferred to the remote
computer and the files transferred from the remote computer:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com \
--transfer --return {.}.bz2 --cleanup "zcat {} | bzip2 -9 >{.}.bz2"
If you want run on several computers add the computers to --sshlogin
either using ',' or multiple --sshlogin:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com,server2.example.com \
--sshlogin server3.example.com \
--transfer --return {.}.bz2 --cleanup "zcat {} | bzip2 -9 >{.}.bz2"
You can add the local computer using --sshlogin :. This will disable
the removing and transferring for the local computer only:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com,server2.example.com \
--sshlogin server3.example.com \
--sshlogin : \
--transfer --return {.}.bz2 --cleanup "zcat {} | bzip2 -9 >{.}.bz2"
Often --transfer, --return and --cleanup are used together. They can be
shortened to --trc:
find logs/ -name '*.gz' | \
parallel --sshlogin server.example.com,server2.example.com \
--sshlogin server3.example.com \
--sshlogin : \
--trc {.}.bz2 "zcat {} | bzip2 -9 >{.}.bz2"
With the file mycomputers containing the list of computers it becomes:
find logs/ -name '*.gz' | parallel --sshloginfile mycomputers \
--trc {.}.bz2 "zcat {} | bzip2 -9 >{.}.bz2"
If the file ~/.parallel/sshloginfile contains the list of computers the
special short hand -S .. can be used:
find logs/ -name '*.gz' | parallel -S .. \
--trc {.}.bz2 "zcat {} | bzip2 -9 >{.}.bz2"
EXAMPLE: Distributing work to local and remote computers
Convert *.mp3 to *.ogg running one process per CPU core on local
computer and server2:
parallel --trc {.}.ogg -S server2,: \
'mpg321 -w - {} | oggenc -q0 - -o {.}.ogg' ::: *.mp3
EXAMPLE: Running the same command on remote computers
To run the command uptime on remote computers you can do:
parallel --tag --nonall -S server1,server2 uptime
--nonall reads no arguments. If you have a list of jobs you want run on
each computer you can do:
parallel --tag --onall -S server1,server2 echo ::: 1 2 3
Remove --tag if you do not want the sshlogin added before the output.
If you have a lot of hosts use '-j0' to access more hosts in parallel.
EXAMPLE: Parallelizing rsync
rsync is a great tool, but sometimes it will not fill up the available
bandwidth. This is often a problem when copying several big files over
high speed connections.
The following will start one rsync per big file in src-dir to dest-dir
on the server fooserver:
cd src-dir; find . -type f -size +100000 | parallel -v ssh fooserver
mkdir -p /dest-dir/{//}\;rsync -s -Havessh {} fooserver:/dest-dir/{}
The dirs created may end up with wrong permissions and smaller files
are not being transferred. To fix those run rsync a final time:
rsync -Havessh src-dir/ fooserver:/dest-dir/
If you are unable to push data, but need to pull them and the files are
called digits.png (e.g. 000000.png) you might be able to do:
seq -w 0 99 | parallel rsync -Havessh fooserver:src-path/*{}.png
destdir/
EXAMPLE: Use multiple inputs in one command
Copy files like foo.es.ext to foo.ext:
ls *.es.* | perl -pe 'print; s/\.es//' | parallel -N2 cp {1} {2}
The perl command spits out 2 lines for each input. GNU parallel takes 2
inputs (using -N2) and replaces {1} and {2} with the inputs.
Count in binary:
parallel -k echo ::: 0 1 ::: 0 1 ::: 0 1 ::: 0 1 ::: 0 1 ::: 0 1
Print the number on the opposing sides of a six sided die:
parallel --xapply -a <(seq 6) -a <(seq 6 -1 1) echo
parallel --xapply echo :::: <(seq 6) <(seq 6 -1 1)
Convert files from all subdirs to PNG-files with consecutive numbers
(useful for making input PNG's for ffmpeg):
parallel --xapply -a <(find . -type f | sort) -a <(seq $(find . -type
f|wc -l)) convert {1} {2}.png
Alternative version:
find . -type f | sort | parallel convert {} {#}.png
EXAMPLE: Use a table as input
Content of table_file.tsv:
foo<TAB>bar
baz <TAB> quux
To run:
cmd -o bar -i foo
cmd -o quux -i baz
you can run:
parallel -a table_file.tsv --colsep '\t' cmd -o {2} -i {1}
Note: The default for GNU parallel is to remove the spaces around the
columns. To keep the spaces:
parallel -a table_file.tsv --trim n --colsep '\t' cmd -o {2} -i {1}
EXAMPLE: Run the same command 10 times
If you want to run the same command with the same arguments 10 times in
parallel you can do:
seq 10 | parallel -n0 my_command my_args
EXAMPLE: Working as cat | sh. Resource inexpensive jobs and evaluation
GNU parallel can work similar to cat | sh.
A resource inexpensive job is a job that takes very little CPU, disk
I/O and network I/O. Ping is an example of a resource inexpensive job.
wget is too - if the webpages are small.
The content of the file jobs_to_run:
ping -c 1 10.0.0.1
wget http://example.com/status.cgi?ip=10.0.0.1
ping -c 1 10.0.0.2
wget http://example.com/status.cgi?ip=10.0.0.2
...
ping -c 1 10.0.0.255
wget http://example.com/status.cgi?ip=10.0.0.255
To run 100 processes simultaneously do:
parallel -j 100 < jobs_to_run
As there is not a command the jobs will be evaluated by the shell.
EXAMPLE: Processing a big file using more cores
To process a big file or some output you can use --pipe to split up the
data into blocks and pipe the blocks into the processing program.
If the program is gzip -9 you can do:
cat bigfile | parallel --pipe --recend '' -k gzip -9 >bigfile.gz
This will split bigfile into blocks of 1 MB and pass that to gzip -9 in
parallel. One gzip will be run per CPU core. The output of gzip -9 will
be kept in order and saved to bigfile.gz
gzip works fine if the output is appended, but some processing does not
work like that - for example sorting. For this GNU parallel can put the
output of each command into a file. This will sort a big file in
parallel:
cat bigfile | parallel --pipe --files sort | parallel -Xj1 sort -m {}
';' rm {} >bigfile.sort
Here bigfile is split into blocks of around 1MB, each block ending in
'\n' (which is the default for --recend). Each block is passed to sort
and the output from sort is saved into files. These files are passed to
the second parallel that runs sort -m on the files before it removes
the files. The output is saved to bigfile.sort.
GNU parallel's --pipe maxes out at around 100 MB/s because every byte
has to be copied through GNU parallel. But if bigfile is a real
(seekable) file GNU parallel can by-pass the copying and send the parts
directly to the program:
parallel --pipepart --block 100m -a bigfile --files sort | parallel
-Xj1 sort -m {} ';' rm {} >bigfile.sort
EXAMPLE: Running more than 250 jobs workaround
If you need to run a massive amount of jobs in parallel, then you will
likely hit the filehandle limit which is often around 250 jobs. If you
are super user you can raise the limit in /etc/security/limits.conf but
you can also use this workaround. The filehandle limit is per process.
That means that if you just spawn more GNU parallels then each of them
can run 250 jobs. This will spawn up to 2500 jobs:
cat myinput | parallel --pipe -N 50 --round-robin -j50 parallel -j50
your_prg
This will spawn up to 62500 jobs (use with caution - you need 64 GB RAM
to do this, and you may need to increase /proc/sys/kernel/pid_max):
cat myinput | parallel --pipe -N 250 --round-robin -j250 parallel -j250
your_prg
EXAMPLE: Working as mutex and counting semaphore
The command sem is an alias for parallel --semaphore.
A counting semaphore will allow a given number of jobs to be started in
the background. When the number of jobs are running in the background,
GNU sem will wait for one of these to complete before starting another
command. sem --wait will wait for all jobs to complete.
Run 10 jobs concurrently in the background:
for i in *.log ; do
echo $i
sem -j10 gzip $i ";" echo done
done
sem --wait
A mutex is a counting semaphore allowing only one job to run. This will
edit the file myfile and prepends the file with lines with the numbers
1 to 3.
seq 3 | parallel sem sed -i -e 'i{}' myfile
As myfile can be very big it is important only one process edits the
file at the same time.
Name the semaphore to have multiple different semaphores active at the
same time:
seq 3 | parallel sem --id mymutex sed -i -e 'i{}' myfile
EXAMPLE: Start editor with filenames from stdin (standard input)
You can use GNU parallel to start interactive programs like emacs or
vi:
cat filelist | parallel --tty -X emacs
cat filelist | parallel --tty -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.
EXAMPLE: Running sudo
sudo requires a password to run a command as root. It caches the
access, so you only need to enter the password again if you have not
used sudo for a while.
The command:
parallel sudo echo ::: This is a bad idea
is no good, as you would be prompted for the sudo password for each of
the jobs. You can either do:
sudo echo This
parallel sudo echo ::: is a good idea
or:
sudo parallel echo ::: This is a good idea
This way you only have to enter the sudo password once.
EXAMPLE: GNU Parallel as queue system/batch manager
GNU parallel can work as a simple job queue system or batch manager.
The idea is to put the jobs into a file and have GNU parallel read from
that continuously. As GNU parallel will stop at end of file we use tail
to continue reading:
true >jobqueue; tail -n+0 -f jobqueue | parallel
To submit your jobs to the queue:
echo my_command my_arg >> jobqueue
You can of course use -S to distribute the jobs to remote computers:
true >jobqueue; tail -f jobqueue | parallel -S ..
There is a a small issue when using GNU parallel as queue system/batch
manager: You have to submit JobSlot number of jobs before they will
start, and after that you can submit one at a time, and job will start
immediately if free slots are available. Output from the running or
completed jobs are held back and will only be printed when JobSlots
more jobs has been started (unless you use --ungroup or -u, in which
case the output from the jobs are printed immediately). E.g. if you
have 10 jobslots then the output from the first completed job will only
be printed when job 11 has started, and the output of second completed
job will only be printed when job 12 has started.
To use --eof to make GNU parallel exit, tail also needs to be forced to
exit:
tail -n+0 -f command-list.txt |
(parallel --eof=EXIT {}; echo Parallel is now done;
(seq 1000 >> command-list.txt &);
echo Done appending dummy data forcing tail to exit)
EXAMPLE: GNU Parallel as dir processor
If you have a dir in which users drop files that needs to be processed
you can do this on GNU/Linux (If you know what inotifywait is called on
other platforms file a bug report):
inotifywait -q -m -r -e MOVED_TO -e CLOSE_WRITE --format %w%f my_dir |
parallel -u echo
This will run the command echo on each file put into my_dir or subdirs
of my_dir.
You can of course use -S to distribute the jobs to remote computers:
inotifywait -q -m -r -e MOVED_TO -e CLOSE_WRITE --format %w%f my_dir |
parallel -S .. -u echo
If the files to be processed are in a tar file then unpacking one file
and processing it immediately may be faster than first unpacking all
files. Set up the dir processor as above and unpack into the dir.
Using GNU Parallel as dir processor has the same limitations as using
GNU Parallel as queue system/batch manager.
QUOTING
GNU parallel is very liberal in quoting. You only need to quote
characters that have special meaning in shell:
( ) $ ` ' " < > ; | \
and depending on context these needs to be quoted, too:
~ & # ! ? space * {
Therefore most people will never need more quoting than putting '\' in
front of the special characters.
Often you can simply put \' around every ':
perl -ne '/^\S+\s+\S+$/ and print $ARGV,"\n"' file
can be quoted:
parallel perl -ne \''/^\S+\s+\S+$/ and print $ARGV,"\n"'\' ::: file
However, when you want to use a shell variable you need to quote the
$-sign. Here is an example using $PARALLEL_SEQ. This variable is set by
GNU parallel itself, so the evaluation of the $ must be done by the sub
shell started by GNU parallel:
seq 10 | parallel -N2 echo seq:\$PARALLEL_SEQ arg1:{1} arg2:{2}
If the variable is set before GNU parallel starts you can do this:
VAR=this_is_set_before_starting
echo test | parallel echo {} $VAR
Prints: test this_is_set_before_starting
It is a little more tricky if the variable contains more than one space
in a row:
VAR="two spaces between each word"
echo test | parallel echo {} \'"$VAR"\'
Prints: test two spaces between each word
If the variable should not be evaluated by the shell starting GNU
parallel but be evaluated by the sub shell started by GNU parallel,
then you need to quote it:
echo test | parallel VAR=this_is_set_after_starting \; echo {} \$VAR
Prints: test this_is_set_after_starting
It is a little more tricky if the variable contains space:
echo test | parallel VAR='"two spaces between each word"' echo {}
\'"$VAR"\'
Prints: test two spaces between each word
$$ is the shell variable containing the process id of the shell. This
will print the process id of the shell running GNU parallel:
seq 10 | parallel echo $$
And this will print the process ids of the sub shells started by GNU
parallel.
seq 10 | parallel echo \$\$
If the special characters should not be evaluated by the sub shell then
you need to protect it against evaluation from both the shell starting
GNU parallel and the sub shell:
echo test | parallel echo {} \\\$VAR
Prints: test $VAR
GNU parallel can protect against evaluation by the sub shell by using
-q:
echo test | parallel -q echo {} \$VAR
Prints: test $VAR
This is particularly useful if you have lots of quoting. If you want to
run a perl script like this:
perl -ne '/^\S+\s+\S+$/ and print $ARGV,"\n"' file
It needs to be quoted like this:
ls | parallel perl -ne '/^\\S+\\s+\\S+\$/\ and\ print\ \$ARGV,\"\\n\"'
ls | parallel perl -ne \''/^\S+\s+\S+$/ and print $ARGV,"\n"'\'
Notice how spaces, \'s, "'s, and $'s need to be quoted. GNU parallel
can do the quoting by using option -q:
ls | parallel -q perl -ne '/^\S+\s+\S+$/ and print $ARGV,"\n"'
However, this means you cannot make the sub shell interpret special
characters. For example because of -q this WILL NOT WORK:
ls *.gz | parallel -q "zcat {} >{.}"
ls *.gz | parallel -q "zcat {} | bzip2 >{.}.bz2"
because > and | need to be interpreted by the sub shell.
If you get errors like:
sh: -c: line 0: syntax error near unexpected token
sh: Syntax error: Unterminated quoted string
sh: -c: line 0: unexpected EOF while looking for matching `''
sh: -c: line 1: syntax error: unexpected end of file
then you might try using -q.
If you are using bash process substitution like <(cat foo) then you may
try -q and prepending command with bash -c:
ls | parallel -q bash -c 'wc -c <(echo {})'
Or for substituting output:
ls | parallel -q bash -c 'tar c {} | tee >(gzip >{}.tar.gz) | bzip2
>{}.tar.bz2'
Conclusion: To avoid dealing with the quoting problems it may be easier
just to write a small script or a function (remember to export -f the
function) and have GNU parallel call that.
LIST RUNNING JOBS
If you want a list of the jobs currently running you can run:
killall -USR1 parallel
GNU parallel will then print the currently running jobs on stderr
(standard error).
COMPLETE RUNNING JOBS BUT DO NOT START NEW JOBS
If you regret starting a lot of jobs you can simply break GNU parallel,
but if you want to make sure you do not have half-completed jobs you
should send the signal SIGTERM to GNU parallel:
killall -TERM parallel
This will tell GNU parallel to not start any new jobs, but wait until
the currently running jobs are finished before exiting.
ENVIRONMENT VARIABLES
$PARALLEL_PID
The environment variable $PARALLEL_PID is set by GNU parallel
and is visible to the jobs started from GNU parallel. This
makes it possible for the jobs to communicate directly to GNU
parallel. Remember to quote the $, so it gets evaluated by
the correct shell.
Example: If each of the jobs tests a solution and one of jobs
finds the solution the job can tell GNU parallel not to start
more jobs by: kill -TERM $PARALLEL_PID. This only works on the
local computer.
$PARALLEL_SHELL (alpha testing)
Use this shell the shell for the commands run by GNU Parallel:
· $PARALLEL_SHELL. If undefined use:
· The shell that started GNU Parallel. If that cannot be
determined:
· $SHELL. If undefined use:
· /bin/sh
$PARALLEL_SEQ
$PARALLEL_SEQ will be set to the sequence number of the job
running. Remember to quote the $, so it gets evaluated by the
correct shell.
Example:
seq 10 | parallel -N2 echo seq:'$'PARALLEL_SEQ arg1:{1}
arg2:{2}
$TMPDIR Directory for temporary files. See: --tmpdir.
$PARALLEL
The environment variable $PARALLEL will be used as default
options for GNU parallel. If the variable contains special
shell characters (e.g. $, *, or space) then these need to be
to be escaped with \.
Example:
cat list | parallel -j1 -k -v ls
can be written as:
cat list | PARALLEL="-kvj1" parallel ls
cat list | parallel -j1 -k -v -S"myssh user@server" ls
can be written as:
cat list | PARALLEL='-kvj1 -S myssh\ user@server' parallel
echo
Notice the \ in the middle is needed because 'myssh' and
'user@server' must be one argument.
DEFAULT PROFILE (CONFIG FILE)
The global configuration file /etc/parallel/config, followed by user
configuration file ~/.parallel/config (formerly known as .parallelrc)
will be read in turn if they exist. Lines starting with '#' will be
ignored. The format can follow that of the environment variable
$PARALLEL, but it is often easier to simply put each option on its own
line.
Options on the command line take precedence, followed by the
environment variable $PARALLEL, user configuration file
~/.parallel/config, and finally the global configuration file
/etc/parallel/config.
Note that no file that is read for options, nor the environment
variable $PARALLEL, may contain retired options such as --tollef.
PROFILE FILES
If --profile set, GNU parallel will read the profile from that file
rather than the global or user configuration files. You can have
multiple --profiles.
Example: Profile for running a command on every sshlogin in
~/.ssh/sshlogins and prepend the output with the sshlogin:
echo --tag -S .. --nonall > ~/.parallel/n
parallel -Jn uptime
Example: Profile for running every command with -j-1 and nice
echo -j-1 nice > ~/.parallel/nice_profile
parallel -J nice_profile bzip2 -9 ::: *
Example: Profile for running a perl script before every command:
echo "perl -e '\$a=\$\$; print \$a,\" \",'\$PARALLEL_SEQ',\" \";';" > ~/.parallel/pre_perl
parallel -J pre_perl echo ::: *
Note how the $ and " need to be quoted using \.
Example: Profile for running distributed jobs with nice on the remote
computers:
echo -S .. nice > ~/.parallel/dist
parallel -J dist --trc {.}.bz2 bzip2 -9 ::: *
EXIT STATUS
If --halt-on-error 0 or not specified:
0 All jobs ran without error.
1-253 Some of the jobs failed. The exit status gives the number of
failed jobs
254 More than 253 jobs failed.
255 Other error.
If --halt-on-error 1 or 2: Exit status of the failing job.
DIFFERENCES BETWEEN GNU Parallel AND ALTERNATIVES
There are a lot programs with some of the functionality of GNU
parallel. GNU parallel strives to include the best of the functionality
without sacrificing ease of use.
SUMMARY TABLE
The following features are in some of the comparable tools:
Inputs
I1. Arguments can be read from stdin
I2. Arguments can be read from a file
I3. Arguments can be read from multiple files
I4. Arguments can be read from command line
I5. Arguments can be read from a table
I6. Arguments can be read from the same file using #! (shebang)
I7. Line oriented input as default (Quoting of special chars not
needed)
Manipulation of input
M1. Composed command
M2. Multiple arguments can fill up an execution line
M3. Arguments can be put anywhere in the execution line
M4. Multiple arguments can be put anywhere in the execution line
M5. Arguments can be replaced with context
M6. Input can be treated as complete execution line
Outputs
O1. Grouping output so output from different jobs do not mix
O2. Send stderr (standard error) to stderr (standard error)
O3. Send stdout (standard output) to stdout (standard output)
O4. Order of output can be same as order of input
O5. Stdout only contains stdout (standard output) from the command
O6. Stderr only contains stderr (standard error) from the command
Execution
E1. Running jobs in parallel
E2. List running jobs
E3. Finish running jobs, but do not start new jobs
E4. Number of running jobs can depend on number of cpus
E5. Finish running jobs, but do not start new jobs after first failure
E6. Number of running jobs can be adjusted while running
Remote execution
R1. Jobs can be run on remote computers
R2. Basefiles can be transferred
R3. Argument files can be transferred
R4. Result files can be transferred
R5. Cleanup of transferred files
R6. No config files needed
R7. Do not run more than SSHD's MaxStartups can handle
R8. Configurable SSH command
R9. Retry if connection breaks occasionally
Semaphore
S1. Possibility to work as a mutex
S2. Possibility to work as a counting semaphore
Legend
- = no
x = not applicable
ID = yes
As every new version of the programs are not tested the table may be
outdated. Please file a bug-report if you find errors (See REPORTING
BUGS).
parallel: I1 I2 I3 I4 I5 I6 I7 M1 M2 M3 M4 M5 M6 O1 O2 O3 O4 O5 O6 E1
E2 E3 E4 E5 E6 R1 R2 R3 R4 R5 R6 R7 R8 R9 S1 S2
xargs: I1 I2 - - - - - - M2 M3 - - - - O2 O3 - O5 O6 E1 - -
- - - - - - - - x - - - - -
find -exec: - - - x - x - - M2 M3 - - - - - O2 O3 O4 O5 O6 -
- - - - - - - - - - - - - - - x x
make -j: - - - - - - - - - - - - - O1 O2 O3 - x O6 E1 - -
- E5 - - - - - - - - - - - -
ppss: I1 I2 - - - - I7 M1 - M3 - - M6 O1 - - x - - E1 E2 ?E3
E4 - - R1 R2 R3 R4 - - ?R7 ? ? - -
pexec: I1 I2 - I4 I5 - - M1 - M3 - - M6 O1 O2 O3 - O5 O6 E1 - -
E4 - E6 R1 - - - - R6 - - - S1 -
xjobs: TODO - Please file a bug-report if you know what features xjobs
supports (See REPORTING BUGS).
prll: TODO - Please file a bug-report if you know what features prll
supports (See REPORTING BUGS).
dxargs: TODO - Please file a bug-report if you know what features
dxargs supports (See REPORTING BUGS).
mdm/middelman: TODO - Please file a bug-report if you know what
features mdm/middelman supports (See REPORTING BUGS).
xapply: TODO - Please file a bug-report if you know what features
xapply supports (See REPORTING BUGS).
paexec: TODO - Please file a bug-report if you know what features
paexec supports (See REPORTING BUGS).
ladon: TODO - Please file a bug-report if you know what features ladon
supports (See REPORTING BUGS).
ClusterSSH: TODO - Please file a bug-report if you know what features
ClusterSSH supports (See REPORTING BUGS).
DIFFERENCES BETWEEN xargs AND GNU Parallel
xargs offers some of the same possibilities as GNU parallel.
xargs deals badly with special characters (such as space, ' and "). To
see the problem try this:
touch important_file
touch 'not important_file'
ls not* | xargs rm
mkdir -p "My brother's 12\" records"
ls | xargs rmdir
You can specify -0 or -d "\n", but many input generators are not
optimized for using NUL as separator but are optimized for newline as
separator. E.g head, tail, awk, ls, echo, sed, tar -v, perl (-0 and \0
instead of \n), locate (requires using -0), find (requires using
-print0), grep (requires user to use -z or -Z), sort (requires using
-z).
So GNU parallel's newline separation can be emulated with:
cat | xargs -d "\n" -n1 command
xargs can run a given number of jobs in parallel, but has no support
for running number-of-cpu-cores jobs in parallel.
xargs has no support for grouping the output, therefore output may run
together, e.g. the first half of a line is from one process and the
last half of the line is from another process. The example Parallel
grep cannot be done reliably with xargs because of this. To see this in
action try:
parallel perl -e '\$a=\"1{}\"x10000000\;print\ \$a,\"\\n\"' '>' {} ::: a b c d e f
ls -l a b c d e f
parallel -kP4 -n1 grep 1 > out.par ::: a b c d e f
echo a b c d e f | xargs -P4 -n1 grep 1 > out.xargs-unbuf
echo a b c d e f | xargs -P4 -n1 grep --line-buffered 1 > out.xargs-linebuf
echo a b c d e f | xargs -n1 grep 1 > out.xargs-serial
ls -l out*
md5sum out*
xargs has no support for keeping the order of the output, therefore if
running jobs in parallel using xargs the output of the second job
cannot be postponed till the first job is done.
xargs has no support for running jobs on remote computers.
xargs has no support for context replace, so you will have to create
the arguments.
If you use a replace string in xargs (-I) you can not force xargs to
use more than one argument.
Quoting in xargs works like -q in GNU parallel. This means composed
commands and redirection require using bash -c.
ls | parallel "wc {} > {}.wc"
becomes (assuming you have 8 cores)
ls | xargs -d "\n" -P8 -I {} bash -c "wc {} > {}.wc"
and
ls | parallel "echo {}; ls {}|wc"
becomes (assuming you have 8 cores)
ls | xargs -d "\n" -P8 -I {} bash -c "echo {}; ls {}|wc"
DIFFERENCES BETWEEN find -exec AND GNU Parallel
find -exec offer some of the same possibilities as GNU parallel.
find -exec only works on files. So processing other input (such as
hosts or URLs) will require creating these inputs as files. find -exec
has no support for running commands in parallel.
DIFFERENCES BETWEEN make -j AND GNU Parallel
make -j can run jobs in parallel, but requires a crafted Makefile to do
this. That results in extra quoting to get filename containing newline
to work correctly.
make -j has no support for grouping the output, therefore output may
run together, e.g. the first half of a line is from one process and the
last half of the line is from another process. The example Parallel
grep cannot be done reliably with make -j because of this.
(Very early versions of GNU parallel were coincidently implemented
using make -j).
DIFFERENCES BETWEEN ppss AND GNU Parallel
ppss is also a tool for running jobs in parallel.
The output of ppss is status information and thus not useful for using
as input for another command. The output from the jobs are put into
files.
The argument replace string ($ITEM) cannot be changed. Arguments must
be quoted - thus arguments containing special characters (space '"&!*)
may cause problems. More than one argument is not supported. File names
containing newlines are not processed correctly. When reading input
from a file null cannot be used as a terminator. ppss needs to read the
whole input file before starting any jobs.
Output and status information is stored in ppss_dir and thus requires
cleanup when completed. If the dir is not removed before running ppss
again it may cause nothing to happen as ppss thinks the task is already
done. GNU parallel will normally not need cleaning up if running
locally and will only need cleaning up if stopped abnormally and
running remote (--cleanup may not complete if stopped abnormally). The
example Parallel grep would require extra postprocessing if written
using ppss.
For remote systems PPSS requires 3 steps: config, deploy, and start.
GNU parallel only requires one step.
EXAMPLES FROM ppss MANUAL
Here are the examples from ppss's manual page with the equivalent using
GNU parallel:
1 ./ppss.sh standalone -d /path/to/files -c 'gzip '
1 find /path/to/files -type f | parallel gzip
2 ./ppss.sh standalone -d /path/to/files -c 'cp "$ITEM"
/destination/dir '
2 find /path/to/files -type f | parallel cp {} /destination/dir
3 ./ppss.sh standalone -f list-of-urls.txt -c 'wget -q '
3 parallel -a list-of-urls.txt wget -q
4 ./ppss.sh standalone -f list-of-urls.txt -c 'wget -q "$ITEM"'
4 parallel -a list-of-urls.txt wget -q {}
5 ./ppss config -C config.cfg -c 'encode.sh ' -d /source/dir -m
192.168.1.100 -u ppss -k ppss-key.key -S ./encode.sh -n nodes.txt -o
/some/output/dir --upload --download ; ./ppss deploy -C config.cfg ;
./ppss start -C config
5 # parallel does not use configs. If you want a different username put
it in nodes.txt: user@hostname
5 find source/dir -type f | parallel --sshloginfile nodes.txt --trc
{.}.mp3 lame -a {} -o {.}.mp3 --preset standard --quiet
6 ./ppss stop -C config.cfg
6 killall -TERM parallel
7 ./ppss pause -C config.cfg
7 Press: CTRL-Z or killall -SIGTSTP parallel
8 ./ppss continue -C config.cfg
8 Enter: fg or killall -SIGCONT parallel
9 ./ppss.sh status -C config.cfg
9 killall -SIGUSR2 parallel
DIFFERENCES BETWEEN pexec AND GNU Parallel
pexec is also a tool for running jobs in parallel.
EXAMPLES FROM pexec MANUAL
Here are the examples from pexec's info page with the equivalent using
GNU parallel:
1 pexec -o sqrt-%s.dat -p "$(seq 10)" -e NUM -n 4 -c -- \
'echo "scale=10000;sqrt($NUM)" | bc'
1 seq 10 | parallel -j4 'echo "scale=10000;sqrt({})" | bc >
sqrt-{}.dat'
2 pexec -p "$(ls myfiles*.ext)" -i %s -o %s.sort -- sort
2 ls myfiles*.ext | parallel sort {} ">{}.sort"
3 pexec -f image.list -n auto -e B -u star.log -c -- \
'fistar $B.fits -f 100 -F id,x,y,flux -o $B.star'
3 parallel -a image.list \
'fistar {}.fits -f 100 -F id,x,y,flux -o {}.star' 2>star.log
4 pexec -r *.png -e IMG -c -o - -- \
'convert $IMG ${IMG%.png}.jpeg ; "echo $IMG: done"'
4 ls *.png | parallel 'convert {} {.}.jpeg; echo {}: done'
5 pexec -r *.png -i %s -o %s.jpg -c 'pngtopnm | pnmtojpeg'
5 ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {}.jpg'
6 for p in *.png ; do echo ${p%.png} ; done | \
pexec -f - -i %s.png -o %s.jpg -c 'pngtopnm | pnmtojpeg'
6 ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
7 LIST=$(for p in *.png ; do echo ${p%.png} ; done)
pexec -r $LIST -i %s.png -o %s.jpg -c 'pngtopnm | pnmtojpeg'
7 ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
8 pexec -n 8 -r *.jpg -y unix -e IMG -c \
'pexec -j -m blockread -d $IMG | \
jpegtopnm | pnmscale 0.5 | pnmtojpeg | \
pexec -j -m blockwrite -s th_$IMG'
8 Combining GNU parallel and GNU sem.
8 ls *jpg | parallel -j8 'sem --id blockread cat {} | jpegtopnm |' \
'pnmscale 0.5 | pnmtojpeg | sem --id blockwrite cat > th_{}'
8 If reading and writing is done to the same disk, this may be faster
as only one process will be either reading or writing:
8 ls *jpg | parallel -j8 'sem --id diskio cat {} | jpegtopnm |' \
'pnmscale 0.5 | pnmtojpeg | sem --id diskio cat > th_{}'
DIFFERENCES BETWEEN xjobs AND GNU Parallel
xjobs is also a tool for running jobs in parallel. It only supports
running jobs on your local computer.
xjobs deals badly with special characters just like xargs. See the
section DIFFERENCES BETWEEN xargs AND GNU Parallel.
Here are the examples from xjobs's man page with the equivalent using
GNU parallel:
1 ls -1 *.zip | xjobs unzip
1 ls *.zip | parallel unzip
2 ls -1 *.zip | xjobs -n unzip
2 ls *.zip | parallel unzip >/dev/null
3 find . -name '*.bak' | xjobs gzip
3 find . -name '*.bak' | parallel gzip
4 ls -1 *.jar | sed 's/\(.*\)/\1 > \1.idx/' | xjobs jar tf
4 ls *.jar | parallel jar tf {} '>' {}.idx
5 xjobs -s script
5 cat script | parallel
6 mkfifo /var/run/my_named_pipe; xjobs -s /var/run/my_named_pipe & echo
unzip 1.zip >> /var/run/my_named_pipe; echo tar cf /backup/myhome.tar
/home/me >> /var/run/my_named_pipe
6 mkfifo /var/run/my_named_pipe; cat /var/run/my_named_pipe | parallel
& echo unzip 1.zip >> /var/run/my_named_pipe; echo tar cf
/backup/myhome.tar /home/me >> /var/run/my_named_pipe
DIFFERENCES BETWEEN prll AND GNU Parallel
prll is also a tool for running jobs in parallel. It does not support
running jobs on remote computers.
prll encourages using BASH aliases and BASH functions instead of
scripts. GNU parallel will never support running aliases (see why
http://www.perlmonks.org/index.pl?node_id=484296). However, scripts,
composed commands, or functions exported with export -f work just fine.
prll generates a lot of status information on stderr (standard error)
which makes it harder to use the stderr (standard error) output of the
job directly as input for another program.
Here is the example from prll's man page with the equivalent using GNU
parallel:
prll -s 'mogrify -flip $1' *.jpg
parallel mogrify -flip ::: *.jpg
DIFFERENCES BETWEEN dxargs AND GNU Parallel
dxargs is also a tool for running jobs in parallel.
dxargs does not deal well with more simultaneous jobs than SSHD's
MaxStartups. dxargs is only built for remote run jobs, but does not
support transferring of files.
DIFFERENCES BETWEEN mdm/middleman AND GNU Parallel
middleman(mdm) is also a tool for running jobs in parallel.
Here are the shellscripts of http://mdm.berlios.de/usage.html ported to
GNU parallel:
seq 19 | parallel buffon -o - | sort -n > result
cat files | parallel cmd
find dir -execdir sem cmd {} \;
DIFFERENCES BETWEEN xapply AND GNU Parallel
xapply can run jobs in parallel on the local computer.
Here are the examples from xapply's man page with the equivalent using
GNU parallel:
1 xapply '(cd %1 && make all)' */
1 parallel 'cd {} && make all' ::: */
2 xapply -f 'diff %1 ../version5/%1' manifest | more
2 parallel diff {} ../version5/{} < manifest | more
3 xapply -p/dev/null -f 'diff %1 %2' manifest1 checklist1
3 parallel --xapply diff {1} {2} :::: manifest1 checklist1
4 xapply 'indent' *.c
4 parallel indent ::: *.c
5 find ~ksb/bin -type f ! -perm -111 -print | xapply -f -v 'chmod a+x'
-
5 find ~ksb/bin -type f ! -perm -111 -print | parallel -v chmod a+x
6 find */ -... | fmt 960 1024 | xapply -f -i /dev/tty 'vi' -
6 sh <(find */ -... | parallel -s 1024 echo vi)
6 find */ -... | parallel -s 1024 -Xuj1 vi
7 find ... | xapply -f -5 -i /dev/tty 'vi' - - - - -
7 sh <(find ... |parallel -n5 echo vi)
7 find ... |parallel -n5 -uj1 vi
8 xapply -fn "" /etc/passwd
8 parallel -k echo < /etc/passwd
9 tr ':' '\012' < /etc/passwd | xapply -7 -nf 'chown %1 %6' - - - - - -
-
9 tr ':' '\012' < /etc/passwd | parallel -N7 chown {1} {6}
10 xapply '[ -d %1/RCS ] || echo %1' */
10 parallel '[ -d {}/RCS ] || echo {}' ::: */
11 xapply -f '[ -f %1 ] && echo %1' List | ...
11 parallel '[ -f {} ] && echo {}' < List | ...
DIFFERENCES BETWEEN paexec AND GNU Parallel
paexec can run jobs in parallel on both the local and remote computers.
paexec requires commands to print a blank line as the last output. This
means you will have to write a wrapper for most programs.
paexec has a job dependency facility so a job can depend on another job
to be executed successfully. Sort of a poor-man's make.
Here are the examples from paexec's example catalog with the equivalent
using GNU parallel:
1_div_X_run:
../../paexec -s -l -c "`pwd`/1_div_X_cmd" -n +1 <<EOF [...]
parallel echo {} '|' `pwd`/1_div_X_cmd <<EOF [...]
all_substr_run:
../../paexec -lp -c "`pwd`/all_substr_cmd" -n +3 <<EOF [...]
parallel echo {} '|' `pwd`/all_substr_cmd <<EOF [...]
cc_wrapper_run:
../../paexec -c "env CC=gcc CFLAGS=-O2 `pwd`/cc_wrapper_cmd" \
-n 'host1 host2' \
-t '/usr/bin/ssh -x' <<EOF [...]
parallel echo {} '|' "env CC=gcc CFLAGS=-O2 `pwd`/cc_wrapper_cmd" \
-S host1,host2 <<EOF [...]
# This is not exactly the same, but avoids the wrapper
parallel gcc -O2 -c -o {.}.o {} \
-S host1,host2 <<EOF [...]
toupper_run:
../../paexec -lp -c "`pwd`/toupper_cmd" -n +10 <<EOF [...]
parallel echo {} '|' ./toupper_cmd <<EOF [...]
# Without the wrapper:
parallel echo {} '| awk {print\ toupper\(\$0\)}' <<EOF [...]
DIFFERENCES BETWEEN map AND GNU Parallel
map sees it as a feature to have less features and in doing so it also
handles corner cases incorrectly. A lot of GNU parallel's code is to
handle corner cases correctly on every platform, so you will not get a
nasty surprise if a user for example saves a file called: My brother's
12" records.txt
map's example showing how to deal with special characters fails on
special characters:
echo "The Cure" > My\ brother\'s\ 12\"\ records
ls | map 'echo -n `gzip < "%" | wc -c`; echo -n '*100/'; wc -c < "%"' | bc
It works with GNU parallel:
ls | parallel 'echo -n `gzip < {} | wc -c`; echo -n '*100/'; wc -c < {}' | bc
And you can even get the file name prepended:
ls | parallel --tag '(echo -n `gzip < {} | wc -c`'*100/'; wc -c < {}) | bc'
map has no support for grouping. So this gives the wrong results
without any warnings:
parallel perl -e '\$a=\"1{}\"x10000000\;print\ \$a,\"\\n\"' '>' {} ::: a b c d e f
ls -l a b c d e f
parallel -kP4 -n1 grep 1 > out.par ::: a b c d e f
map -p 4 'grep 1' a b c d e f > out.map-unbuf
map -p 4 'grep --line-buffered 1' a b c d e f > out.map-linebuf
map -p 1 'grep --line-buffered 1' a b c d e f > out.map-serial
ls -l out*
md5sum out*
The documentation shows a workaround, but not only does that mix stdout
(standard output) with stderr (standard error) it also fails completely
for certain jobs (and may even be considered less readable):
parallel echo -n {} ::: 1 2 3
map -p 4 'echo -n % 2>&1 | sed -e "s/^/$$:/"' 1 2 3 | sort | cut -f2- -d:
map cannot handle bundled options: map -vp 0 echo this fails
map does not have an argument separator on the command line, but uses
the first argument as command. This makes quoting harder which again
may affect readability. Compare:
map -p 2 perl\\\ -ne\\\ \\\'/^\\\\S+\\\\s+\\\\S+\\\$/\\\ and\\\ print\\\ \\\$ARGV,\\\"\\\\n\\\"\\\' *
parallel -q perl -ne '/^\S+\s+\S+$/ and print $ARGV,"\n"' ::: *
map can do multiple arguments with context replace, but not without
context replace:
parallel --xargs echo 'BEGIN{'{}'}END' ::: 1 2 3
map does not set exit value according to whether one of the jobs
failed:
parallel false ::: 1 || echo Job failed
map false 1 || echo Never run
map requires Perl v5.10.0 making it harder to use on old systems.
map has no way of using % in the command (GNU Parallel has -I to
specify another replacement string than {}).
By design map is option incompatible with xargs, it does not have
remote job execution, a structured way of saving results, multiple
input sources, progress indicator, configurable record delimiter (only
field delimiter), logging of jobs run with possibility to resume,
keeping the output in the same order as input, --pipe processing, and
dynamically timeouts.
DIFFERENCES BETWEEN ladon AND GNU Parallel
ladon can run multiple jobs on files in parallel.
ladon only works on files and the only way to specify files is using a
quoted glob string (such as \*.jpg). It is not possible to list the
files manually.
As replacement strings it uses FULLPATH DIRNAME BASENAME EXT RELDIR
RELPATH
These can be simulated using GNU parallel by putting this in
~/.parallel/config:
--rpl 'FULLPATH $_=::shell_quote($_);chomp($_=qx{readlink -f $_});'
--rpl 'DIRNAME $_=::shell_quote(::dirname($_));chomp($_=qx{readlink -f $_});'
--rpl 'BASENAME s:.*/::;s:\.[^/.]+$::;'
--rpl 'EXT s:.*\.::'
--rpl 'RELDIR $_=::shell_quote($_);chomp(($_,$c)=qx{readlink -f $_;pwd});s:\Q$c/\E::;$_=::dirname($_);'
--rpl 'RELPATH $_=::shell_quote($_);chomp(($_,$c)=qx{readlink -f $_;pwd});s:\Q$c/\E::;'
ladon deals badly with filenames containing " and newline, and it fails
for output larger than 200k:
ladon '*' -- seq 36000 | wc
EXAMPLES FROM ladon MANUAL
It is assumed that the '--rpl's above are put in ~/.parallel/config and
that it is run under a shell that supports '**' globbing (such as zsh):
1 ladon "**/*.txt" -- echo RELPATH
1 parallel echo RELPATH ::: **/*.txt
2 ladon "~/Documents/**/*.pdf" -- shasum FULLPATH >hashes.txt
2 parallel shasum FULLPATH ::: ~/Documents/**/*.pdf >hashes.txt
3 ladon -m thumbs/RELDIR "**/*.jpg" -- convert FULLPATH -thumbnail
100x100^ -gravity center -extent 100x100 thumbs/RELPATH
3 parallel mkdir -p thumbs/RELDIR\; convert FULLPATH -thumbnail
100x100^ -gravity center -extent 100x100 thumbs/RELPATH ::: **/*.jpg
4 ladon "~/Music/*.wav" -- lame -V 2 FULLPATH DIRNAME/BASENAME.mp3
4 parallel lame -V 2 FULLPATH DIRNAME/BASENAME.mp3 ::: ~/Music/*.wav
DIFFERENCES BETWEEN ClusterSSH AND GNU Parallel
ClusterSSH solves a different problem than GNU parallel.
ClusterSSH opens a terminal window for each computer and using a master
window you can run the same command on all the computers. This is
typically used for administrating several computers that are almost
identical.
GNU parallel runs the same (or different) commands with different
arguments in parallel possibly using remote computers to help
computing. If more than one computer is listed in -S GNU parallel may
only use one of these (e.g. if there are 8 jobs to be run and one
computer has 8 cores).
GNU parallel can be used as a poor-man's version of ClusterSSH:
parallel --nonall -S server-a,server-b do_stuff foo bar
BUGS
Quoting of newline
Because of the way newline is quoted this will not work:
echo 1,2,3 | parallel -vkd, "echo 'a{}b'"
However, these will all work:
echo 1,2,3 | parallel -vkd, echo a{}b
echo 1,2,3 | parallel -vkd, "echo 'a'{}'b'"
echo 1,2,3 | parallel -vkd, "echo 'a'"{}"'b'"
Speed
Startup
GNU parallel is slow at starting up - around 250 ms the first time and
150 ms after that.
Job startup
Starting a job on the local machine takes around 10 ms. This can be a
big overhead if the job takes very few ms to run. Often you can group
small jobs together using -X which will make the overhead less
significant. Or you can run multiple GNU parallels as described in
EXAMPLE: Speeding up fast jobs.
SSH
When using multiple computers GNU parallel opens ssh connections to
them to figure out how many connections can be used reliably
simultaneously (Namely SSHD's MaxStartups). This test is done for each
host in serial, so if your --sshloginfile contains many hosts it may be
slow.
If your jobs are short you may see that there are fewer jobs running on
the remove systems than expected. This is due to time spent logging in
and out. -M may help here.
Disk access
A single disk can normally read data faster if it reads one file at a
time instead of reading a lot of files in parallel, as this will avoid
disk seeks. However, newer disk systems with multiple drives can read
faster if reading from multiple files in parallel.
If the jobs are of the form read-all-compute-all-write-all, so
everything is read before anything is written, it may be faster to
force only one disk access at the time:
sem --id diskio cat file | compute | sem --id diskio cat > file
If the jobs are of the form read-compute-write, so writing starts
before all reading is done, it may be faster to force only one reader
and writer at the time:
sem --id read cat file | compute | sem --id write cat > file
If the jobs are of the form read-compute-read-compute, it may be faster
to run more jobs in parallel than the system has CPUs, as some of the
jobs will be stuck waiting for disk access.
--nice limits command length
The current implementation of --nice is too pessimistic in the max
allowed command length. It only uses a little more than half of what it
could. This affects -X and -m. If this becomes a real problem for you
file a bug-report.
Aliases and functions do not work
If you get:
Can't exec "command": No such file or directory
or:
open3: exec of by command failed
it may be because command is not known, but it could also be because
command is an alias or a function. If it is a function you need to
export -f the function first. An alias will, however, not work (see why
http://www.perlmonks.org/index.pl?node_id=484296), so change your alias
to a script.
REPORTING BUGS
Report bugs to <bug-parallel@gnu.org> or
https://savannah.gnu.org/bugs/?func=additem&group=parallel
Your bug report should always include:
· The error message you get (if any).
· The complete output of parallel --version. If you are not running the
latest released version you should specify why you believe the
problem is not fixed in that version.
· A complete example that others can run that shows the problem. This
should preferably be small and simple. A combination of yes, seq,
cat, echo, and sleep can reproduce most errors. If your example
requires large files, see if you can make them by something like seq
1000000 > file or yes | head -n 10000000 > file. If your example
requires remote execution, see if you can use localhost - maybe using
another login.
· The output of your example. If your problem is not easily reproduced
by others, the output might help them figure out the problem.
· Whether you have watched the intro videos
(http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1), walked
through the tutorial (man parallel_tutorial), and read the EXAMPLE
section in the man page (man parallel - search for EXAMPLE:).
If you suspect the error is dependent on your environment or
distribution, please see if you can reproduce the error on one of these
VirtualBox images:
http://sourceforge.net/projects/virtualboximage/files/
Specifying the name of your distribution is not enough as you may have
installed software that is not in the VirtualBox images.
If you cannot reproduce the error on any of the VirtualBox images
above, you should assume the debugging will be done through you. That
will put more burden on you and it is extra important you give any
information that help. In general the problem will be fixed faster and
with less work for you if you can reproduce the error on a VirtualBox.
AUTHOR
When using 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.
Alternatively you can get GNU Parallel without this requirement by
paying 10000 EUR.
Copyright (C) 2007-10-18 Ole Tange, http://ole.tange.dk
Copyright (C) 2008,2009,2010 Ole Tange, http://ole.tange.dk
Copyright (C) 2010,2011,2012,2013,2014 Ole Tange, http://ole.tange.dk
and Free Software Foundation, Inc.
Parts of the manual concerning xargs compatibility is inspired by the
manual of xargs from GNU findutils 4.4.2.
LICENSE
Copyright (C) 2007,2008,2009,2010,2011,2012,2013 Free Software
Foundation, Inc.
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 3 of the License, or at your
option any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program. If not, see <http://www.gnu.org/licenses/>.
Documentation license I
Permission is granted to copy, distribute and/or modify this
documentation under the terms of the GNU Free Documentation License,
Version 1.3 or any later version published by the Free Software
Foundation; with no Invariant Sections, with no Front-Cover Texts, and
with no Back-Cover Texts. A copy of the license is included in the
file fdl.txt.
Documentation license II
You are free:
to Share to copy, distribute and transmit the work
to Remix to adapt the work
Under the following conditions:
Attribution
You must attribute the work in the manner specified by the
author or licensor (but not in any way that suggests that they
endorse you or your use of the work).
Share Alike
If you alter, transform, or build upon this work, you may
distribute the resulting work only under the same, similar or
a compatible license.
With the understanding that:
Waiver Any of the above conditions can be waived if you get
permission from the copyright holder.
Public Domain
Where the work or any of its elements is in the public domain
under applicable law, that status is in no way affected by the
license.
Other Rights
In no way are any of the following rights affected by the
license:
· Your fair dealing or fair use rights, or other applicable
copyright exceptions and limitations;
· The author's moral rights;
· Rights other persons may have either in the work itself or
in how the work is used, such as publicity or privacy
rights.
Notice For any reuse or distribution, you must make clear to others
the license terms of this work.
A copy of the full license is included in the file as cc-by-sa.txt.
DEPENDENCIES
GNU parallel uses Perl, and the Perl modules Getopt::Long, IPC::Open3,
Symbol, IO::File, POSIX, and File::Temp. For remote usage it also uses
rsync with ssh.
SEE ALSO
ssh(1), rsync(1), find(1), xargs(1), dirname(1), make(1), pexec(1),
ppss(1), xjobs(1), prll(1), dxargs(1), mdm(1)