GNU Parallel Bug Reports GNU Parallel 20120622 ('Chiang Mai') released

[Ole Tange]

GNU Parallel 20120622 ('Chiang Mai') has been released. It is
available for download at: http://ftp.gnu.org/gnu/parallel/

New in this release:

* '-L n --pipe' will use records of n lines. This is useful when
processing data that have fixed records with a fixed number of lines
(e.g. fastq).

* --filter-hosts will 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.

* --pipe now uses fork() instead of busy wait. The performance should
be better on computers with >10 cores while remaining the same on
computers with few cores.

* GNU Parallel will be represented at Chiang Mai Bar Camp.
http://barcampchiangmai.org/

* Indexing Big Data on Amazon AWS: The Screencast (Check out his
T-shirt at 18:40-21:00).
http://www.opensourceconnections.com/2012/06/06/indexing-big-data-on-amazon-aws-screencast/

* biotoolbox uses GNU Parallel.
https://code.google.com/p/biotoolbox/wiki/Pod_novo_wrapper

* Spiceweasel uses GNU Parallel. https://github.com/mattray/spiceweasel

* GNU Parallel part of The Administrators Challenge.
http://challenge.twistedrack.com/questions/qs3.php

* Finding Oldest Firefox Code using GNU Parallel.
http://gregoryszorc.com/blog/2012/06/18/finding-oldest-firefox-code/

* Bug fixes (quite a few for remote job running) and man page updates.


= About GNU Parallel =

GNU Parallel is a shell tool for executing jobs in parallel using one
or more computers. A job is 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 and pipe it into
commands 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 can even replace nested loops.

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.

You can find more about GNU Parallel at: http://www.gnu.org/s/parallel/

Watch the intro video on
http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1 or at
http://tinyogg.com/watch/TORaR/ and http://tinyogg.com/watch/hfxKj/

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.


= About GNU SQL =

GNU sql aims to give a simple, unified interface for accessing
databases through all the different databases' command line clients.
So far the focus has been on giving a common way to specify login
information (protocol, username, password, hostname, and port number),
size (database and table size), and running queries.

The database is addressed using a DBURL. If commands are left out you
will get that database's interactive shell.

When using GNU SQL for a publication please cite:

O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different
Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.


= About GNU Niceload =

GNU niceload slows down a program when the computer load average (or
other system activity) is above a certain limit. When the limit is
reached the program will be suspended for some time. If the limit is a
soft limit the program will be allowed to run for short amounts of
time before being suspended again. If the limit is a hard limit the
program will only be allowed to run when the system is below the
limit.