table of contents
- NAME
- SYNOPSIS
- DESCRIPTION
- OPTIONS
- EXAMPLE: Working as xargs -n1. Argument appending
- EXAMPLE: Reading arguments from command line
- EXAMPLE: Inserting multiple arguments
- EXAMPLE: Context replace
- EXAMPLE: Compute intensive jobs and substitution
- EXAMPLE: Substitution and redirection
- EXAMPLE: Composed commands
- EXAMPLE: Removing file extension when processing files
- EXAMPLE: Removing two file extensions when processing files and calling GNU Parallel from itself
- EXAMPLE: Download 10 images for each of the past 30 days
- EXAMPLE: Breadth first parallel web crawler/mirrorer
- EXAMPLE: Process files from a tar file while unpacking
- EXAMPLE: Rewriting a for-loop and a while-read-loop
- EXAMPLE: Rewriting nested for-loops
- EXAMPLE: for-loops with column names
- EXAMPLE: Using shell variables
- EXAMPLE: Group output lines
- EXAMPLE: Tag output lines
- EXAMPLE: Keep order of output same as order of input
- EXAMPLE: Parallel grep
- EXAMPLE: Using remote computers
- EXAMPLE: Transferring of files
- EXAMPLE: Distributing work to local and remote computers
- EXAMPLE: Running the same command on remote computers
- EXAMPLE: Parallelizing rsync
- EXAMPLE: Use multiple inputs in one command
- EXAMPLE: Use a table as input
- EXAMPLE: Run the same command 10 times
- EXAMPLE: Working as cat | sh. Resource inexpensive jobs and evaluation
- EXAMPLE: Processing a big file using more cores
- EXAMPLE: Working as mutex and counting semaphore
- EXAMPLE: Start editor with filenames from stdin (standard input)
- EXAMPLE: Running sudo
- EXAMPLE: GNU Parallel as queue system/batch manager
- EXAMPLE: GNU Parallel as dir processor
- QUOTING
- LIST RUNNING JOBS
- COMPLETE RUNNING JOBS BUT DO NOT START NEW JOBS
- ENVIRONMENT VARIABLES
- DEFAULT PROFILE (CONFIG FILE)
- PROFILE FILES
- EXIT STATUS
- DIFFERENCES BETWEEN GNU Parallel AND ALTERNATIVES
- BUGS
- REPORTING BUGS
- AUTHOR
- LICENSE
- DEPENDENCIES
- SEE ALSO
PARALLEL(1) | parallel | PARALLEL(1) |
NAME¶
parallel - build and execute shell command lines from standard input in parallelSYNOPSIS¶
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¶
Before looking at the options you may want to check out the EXAMPLEs after the list of options. That will give you an idea of what GNU parallel is capable of. You can also watch the intro video for a quick introduction: http://tinyogg.com/watch/TORaR/ http://tinyogg.com/watch/hfxKj/ and http://tinyogg.com/watch/YQuXd/ or http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1OPTIONS¶
- command
- Command to execute. If command or the following
arguments contain replacement strings (such as {}) every instance
will be substituted with the input.
- {}
- 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
::::.
- {.}
- 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.
- {/}
- Basename of input line. This replacement string will be
replaced by the input with the directory part removed.
- {//}
- Dirname of input line. This replacement string will be
replaced by the dir of the input line. See dirname(1).
- {/.}
- 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 {.}.
- {#}
- 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.
- {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).
- {n.}
- Argument from input source n or the n'th
argument without extension. It is a combination of
{n} and {.}.
- {n/}
- Basename of argument from input source n or the
n'th argument. It is a combination of {n} and
{/}.
- {n//}
- Dirname of argument from input source n or the
n'th argument. It is a combination of {n} and
{//}.
- {n/.}
- Basename of argument from input source n or the
n'th argument without extension. It is a combination of
{n }, {/}, and {.}.
- ::: 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.
(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"
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 ...
- --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.
- --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.
- --arg-sep sep-str
- Use sep-str instead of ::: as separator
string. Useful if ::: is used for something else by the command.
- --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.
- --bibtex
- Print the BibTeX entry for GNU parallel.
- --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.
- --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"
- --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.
- --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.
- --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.
- --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.
- --gnu
- Behave like GNU parallel. If --tollef and --gnu are both set, --gnu takes precedence.
- --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.
- --help
- -h
- Print a summary of the options to GNU parallel and exit.
- --halt-on-error <0|1|2>
- --halt <0|1|2>
- 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.
- --header regexp
- Use upto 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.
- -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 transfered, bytes in files returned, exit status, and command run.
- --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.
- --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. If the evaluated number is less than 1 then 1 will be used. 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
- -L max-lines
- 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.
- --max-lines[=max-lines]
- -l[max-lines]
- 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.
- --load max-load
- Do not start new jobs on a given computer unless the load
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 (experimental)
- -M (experimental)
- 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.
- -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.
- --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.
- --nonall
- --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.
- --onall
- 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.
- --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.
- --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.
- --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.
- --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.
- --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).
- --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.
- --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.
- --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.
- --recstart startstring
- --recend endstring
- If --recstart is given startstring will be
used to split at record start.
- --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.
- --resume
- Resumes from the last unfinished job. By reading
--joblog 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.
- --retries n
- If a job fails, retry it on another computer. Do this n times. If there are fewer than n computers in --sshlogin GNU parallel will re-use 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
echo /tmp/foo/bar.txt | parallel \ --sshlogin server.example.com --return {.}.out touch {.}.out
echo /tmp/foo/bar.txt | \ parallel --sshlogin server.example.com \ --return {.}.out --return {.}.out2 touch {.}.out {.}.out2
- --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.
- --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.
- --semaphorename name
- --id name
- Use name as the name of the semaphore. Default is
the name of the controlling tty (output from tty).
- --semaphoretimeout secs (not implemented)
- If the semaphore is not released within secs seconds, take
it anyway.
- --seqreplace replace-str
- Use the replacement string replace-str instead of {#} for job sequence number.
- --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).
- -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.
[sshcommand [options]][username@]hostname
- --sshloginfile filename
- --slf filename
- 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/:
- --noswap
- Do not start new jobs on a given computer if there is both
swap-in and swap-out activity.
- --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.
- --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.
- --timeout sec
- Time out for command. If the command runs for longer than sec seconds it will get killed with SIGTERM, followed by SIGTERM 200 ms later, followed by SIGKILL 200 ms later.
- --tollef
- Make GNU parallel behave like Tollef's parallel command. To override use --gnu.
- --verbose
- -t
- Print the job to be run on stderr (standard error).
- --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 login dir. E.g.
echo foo/bar.txt | parallel \ --sshlogin server.example.com --transfer wc
echo /tmp/foo/bar.txt | parallel \ --sshlogin server.example.com --transfer wc
- --trc filename
- Transfer, Return, Cleanup. Short hand for:
- --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. This may cause output from different commands to be mixed. GNU parallel runs faster with -u. Can be reversed with --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.
- --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.
- --wait
- Wait for all commands to complete.
- -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.
- --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.
parallel echo {1} {2} ::: 1 2 3 ::: a b c parallel --xapply echo {1} {2} ::: 1 2 3 ::: a b c
- --shebang
- --hashbang
- GNU Parallel can be called as a shebang (#!) command
as the first line of a script. Like this:
#!/usr/bin/parallel --shebang -r traceroute foss.org.my debian.org freenetproject.org
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 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 ::: *.html To convert *.wav to *.mp3 using LAME running one process per CPU core run: parallel lame {} -o {.}.mp3 ::: *.wavEXAMPLE: 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 {} destdirEXAMPLE: 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.jpgEXAMPLE: 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 charaters (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 no exist. cat file_list | parallel 'if [ ! -e {} ] ; then echo {}; fi'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/{/.}.mp3EXAMPLE: Removing two file extensions when processing files and calling GNU Parallel from itself¶
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: ls *.tar.gz| parallel --er {tar} 'echo {tar}|parallel "mkdir -p {.} ; 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_##.jpgwhere 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: 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_outputand while-read-loops like this:
cat list | (while read x ; do do_something $x done) | process_outputcan be written like this: cat list | parallel do_something | process_output If the processing requires more steps the for-loop like this:
(for x in `cat list` ; do no_extension=${x%.*}; do_something $x scale $no_extension.jpg do_step2 <$x $no_extension done) | process_outputand while-loops like this:
cat list | (while read x ; do no_extension=${x%.*}; do_something $x scale $no_extension.jpg do_step2 <$x $no_extension done) | process_outputcan 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_outputcan 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) | sortcan be written like this: parallel echo {1} {2} ::: M F ::: S M L XL XXL | sort
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 XXLThis also works if the input file is a file with columns:
cat addressbook.tsv | parallel --colsep '\t' --header : echo {Name} {E-mail address}
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 ::: ${V[@]} # This is probably not what you wantand:
V=("My brother's 12\" records are worth <\$\$\$>"'!' Foo Bar) parallel echo ::: "${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 the output to be printed while the job is running you can use -u. Compare the output of: parallel traceroute ::: foss.org.my debian.org freenetproject.org to the output of: parallel -u traceroute ::: foss.org.my debian.org freenetproject.orgEXAMPLE: 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 Check the uptime of the servers in ~/.parallel/sshloginfile: parallel --tag -S .. --nonall uptimeEXAMPLE: 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. To grep a big file in parallel use --pipe: cat bigfile | parallel --pipe grep foo Depending on your disks and CPUs it may be faster to read larger blocks: cat bigfile | parallel --pipe --block 10M grep fooEXAMPLE: 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). To run echo on server.example.com:seq 10 | parallel --sshlogin server.example.com echoTo run commands on more than one remote computer run:
seq 10 | parallel --sshlogin server.example.com,server2.example.net echoOr:
seq 10 | parallel --sshlogin server.example.com \ --sshlogin server2.example.net echoIf the login username is foo on server2.example.net use:
seq 10 | parallel --sshlogin server.example.com \ --sshlogin foo@server2.example.net echoTo 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.comThen run:
seq 10 | parallel --sshloginfile mycomputers echoTo 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: find src-dir -type f -size +100000 | parallel -v ssh fooserver mkdir -p /dest-dir/{//}\;rsync -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/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 {} {#}.pngEXAMPLE: Use a table as input¶
Content of table_file.tsv:foo<TAB>bar baz <TAB> quuxTo run:
cmd -o bar -i foo cmd -o quux -i bazyou 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_argsEXAMPLE: 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=10.0.0.255To 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.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 `ls *.log` ; do echo $i sem -j10 gzip $i ";" echo done done sem --waitA 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{}' myfileAs 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 ideais 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 ideaor:
sudo parallel echo ::: This is a good ideaThis 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: echo >jobqueue; tail -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: echo >jobqueue; tail -f jobqueue | parallel -S .. There are a two small issues when using GNU parallel as queue system/batch manager:- •
- You will get a warning if you do not submit JobSlots jobs within the first second. E.g. if you have 8 cores and use -j+2 you have to submit 10 jobs. These can be dummy jobs (e.g. echo foo). You can also simply ignore the warning.
- •
- Jobs will be run immediately, but output from jobs will only be printed when JobSlots more jobs has been started. E.g. if you have 10 jobslots then the output from the first completed job will only be printed when job 11 is started.
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 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. The -u is needed because of a small bug in GNU parallel. If that proves to be a problem, file a bug report. You can of course use -S to distribute the jobs to remote computers: inotifywait -q -m -r -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.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. 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\"' 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 filethen 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 and have GNU parallel call that script.
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 halfcompleted 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.
- $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.
- $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
\.
DEFAULT PROFILE (CONFIG FILE)¶
The file ~/.parallel/config (formerly known as .parallelrc) will be read if it exists. Lines starting with '#' will be ignored. It can be formatted like the environment variable $PARALLEL, but it is often easier to simply put each option on its own line. Options on the command line takes precedence over the environment variable $PARALLEL which takes precedence over the file ~/.parallel/config.PROFILE FILES¶
If --profile set, GNU parallel will read the profile from that file instead of ~/.parallel/config. 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 uptimeExample: 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.
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 sacrifying ease of use.SUMMARY TABLE¶
The following features are in some of the comparable tools: InputsI1. 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 MaxStartup can handle
R8. Configurable SSH command
R9. Retry if connection breaks occationally 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). ClusterSSH: TODO - Please file a bug-report if you know what features ClusterSSH supports (See REPORTING BUGS).
DIFFERENCES BETWEEN xargs AND GNU Parallel¶
xargs offer some of the same possibilites 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 rmdirYou 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 --line-buffered 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 possibilites 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 "$ITEM"' 4 parallel -a list-of-urls.txt wget -q {} 5 ./ppss config -C config.cfg -c 'encode.sh ' -d /source/dir -m 192.168.1.100 -u ppss -k ppss-key.key -S ./encode.sh -n nodes.txt -o /some/output/dir --upload --download ; ./ppss deploy -C config.cfg ; ./ppss start -C config 5 # parallel does not use configs. If you want a different username put it in nodes.txt: user@hostname 5 find source/dir -type f | parallel --sshloginfile nodes.txt --trc {.}.mp3 lame -a {} -o {.}.mp3 --preset standard --quiet 6 ./ppss stop -C config.cfg 6 killall -TERM parallel 7 ./ppss pause -C config.cfg 7 Press: CTRL-Z or killall -SIGTSTP parallel 8 ./ppss continue -C config.cfg 8 Enter: fg or killall -SIGCONT parallel 9 ./ppss.sh status -C config.cfg 9 killall -SIGUSR2 parallelDIFFERENCES BETWEEN pexec AND GNU Parallel¶
pexec is also a tool for running jobs in parallel. Here are the examples from pexec's info page with the equivalent using GNU parallel: 1 pexec -o sqrt-%s.dat -p "$(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_pipeDIFFERENCES 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 ::: *.jpgDIFFERENCES 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 MaxStartup. 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 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 barBUGS¶
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. Half of the startup time is spent finding the maximal length of a command line. Setting -s will remove this part of the startup time. Job startup Starting a job on the local machine takes around 3 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. Using --ungroup the 3 ms can be lowered to around 2 ms. 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 MaxStartup). 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 > fileIf 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 > fileIf 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 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. A combination of 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.
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. 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 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 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
- 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.
- Waiver
- Any of the above conditions can be waived if you get permission from the copyright holder.
- Public Domain
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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, make(1), pexec(1), ppss(1), xjobs(1), prll(1), dxargs(1), mdm(1),2012-04-21 | 20120422 |