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Re: GNU Parallel 20191022 ('Driving IT') released [stable]


From: Saint Michael
Subject: Re: GNU Parallel 20191022 ('Driving IT') released [stable]
Date: Wed, 20 Nov 2019 22:18:39 -0500

I have a Debian Buster with 512 GB of RAM and 88 cores, 44 physical and 88 with hyperthreading.
I run a job with parallel and I get this

** THREAD_CREATE: Nsort could not create a thread: Resource temporarily unavailable
Nsort pid 7825: Aborted errno 0 code -6 addr 0x1e91
awk: cmd. line:5: fatal: xalloc: malloc failed: Cannot allocate memory
Please compress "/tmp/nsortdiag.7825"
and send it to address@hidden to speed diagnosis of this problem.
ETA: 22s Left: 560 AVG: 0.03s  local:1/36/100%/0.0s /home/sipnav/2018-02-06.zip 37
ETA: 19s Left: 560 AVG: 0.03s  local:11/36/100%/0.0s libgcc_s.so.1 must be installed for pthread_cancel to work
ETA: 18s Left: 560 AVG: 0.03s  local:12/36/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 38.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 17s Left: 558 AVG: 0.03s  local:14/38/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 37.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 16s Left: 556 AVG: 0.03s  local:12/40/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 36.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 16s Left: 555 AVG: 0.02s  local:11/41/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 35.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 16s Left: 555 AVG: 0.02s  local:11/41/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 34.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 15s Left: 555 AVG: 0.02s  local:11/41/100%/0.0s parallel: Warning: No more processes: Decreasing number of running jobs to 33.
parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help.
ETA: 15s Left: 555 AVG: 0.05s  local:11/41/100%/0.0s ^Clibgcc_s.so.1 must be installed for pthread_cancel to work
libgcc_s.so.1 must be installed for pthread_cancel to work
libgcc_s.so.1 must be installed for pthread_cancel to work
libgcc_s.so.1 must be installed for pthread_cancel to work

but my ulimit is fine, and I am root
ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1048576
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1048576
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) unlimited
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

I only 7 GB of virtual memory, and 512 GB of RAM, is too low?



On Tue, Oct 22, 2019 at 1:44 PM Ole Tange <address@hidden> wrote:
GNU Parallel 20191022 ('Driving IT') [stable] has been released. It is
available for download at: http://ftpmirror.gnu.org/parallel/

No new functionality was introduced so this is a good candidate for a
stable release.

GNU Parallel is 10 years old next year on 2020-04-22. You are here by
invited to a reception on Friday 2020-04-17.

See https://www.gnu.org/software/parallel/10-years-anniversary.html

Quote of the month:

  I've said it before: The command line program GNU Parallel is a godsend.
    -- Jo Chr. Oterhals @oterhals@twitter

New in this release:

* --tee will use --output-error=warn-nopipe if supported by tee.

* GNU Parallel will be presented at Driving IT 2019:
https://ida.dk/arrangementer-og-kurser/konferencer/driving-it/tools

* UMN Duluth: Job parallelization with task arrays and GNU parallel
https://www.msi.umn.edu/tutorials/umn-duluth-job-parallelization-task-arrays-and-gnu-parallel

* Genome updater uses GNU Parallel https://github.com/pirovc/genome_updater

* Using GNU-Parallel for bioinformatics
https://www.danielecook.com/using-gnu-parallel-for-bioinformatics/

* Speeding up PostgreSQL ETL pipeline with the help of GODS
https://cfengine.com/company/blog-detail/speeding-up-postgresql-etl-pipeline-with-the-help-of-gods/

* Runing linux commands in parallel
https://dev.to/voyeg3r/runing-linux-commands-in-parallel-4ff8

* Research Computing University of Colorado Boulder contains an intro
to GNU Parallel
https://readthedocs.org/projects/curc/downloads/pdf/latest/

* 如何使用Parallel在Shell中并行执行命令https://www.myfreax.com/gnu-parallel/

* 如何测试 Amazon Elastic File System
https://aws.amazon.com/cn/blogs/china/how-to-test-drive-amazon-elastic-file-system/

* Bug fixes and man page updates.

Get the book: GNU Parallel 2018
http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html

GNU Parallel - For people who live life in the parallel lane.


= About GNU Parallel =

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 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.

For example you can run this to convert all jpeg files into png and
gif files and have a progress bar:

  parallel --bar convert {1} {1.}.{2} ::: *.jpg ::: png gif

Or you can generate big, medium, and small thumbnails of all jpeg
files in sub dirs:

  find . -name '*.jpg' |
    parallel convert -geometry {2} {1} {1//}/thumb{2}_{1/} :::: - ::: 50 100 200


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

You can install GNU Parallel in just 10 seconds with:

    $ (wget -O - pi.dk/3 || lynx -source pi.dk/3 || curl pi.dk/3/ || \
       fetch -o - http://pi.dk/3 ) > install.sh
    $ sha1sum install.sh | grep 3374ec53bacb199b245af2dda86df6c9
    12345678 3374ec53 bacb199b 245af2dd a86df6c9
    $ md5sum install.sh | grep 029a9ac06e8b5bc6052eac57b2c3c9ca
    029a9ac0 6e8b5bc6 052eac57 b2c3c9ca
    $ sha512sum install.sh | grep f517006d9897747bed8a4694b1acba1b
    40f53af6 9e20dae5 713ba06c f517006d 9897747b ed8a4694 b1acba1b 1464beb4
    60055629 3f2356f3 3e9c4e3c 76e3f3af a9db4b32 bd33322b 975696fc e6b23cfb
    $ bash install.sh

Watch the intro video on http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

Walk through the tutorial (man parallel_tutorial). Your command line
will love you for it.

When using programs that use GNU Parallel to process data for
publication please cite:

O. Tange (2018): GNU Parallel 2018, March 2018,
https://doi.org/10.5281/zenodo.1146014.

If you like GNU Parallel:

* Give a demo at your local user group/team/colleagues
* Post the intro videos on Reddit/Diaspora*/forums/blogs/
Identi.ca/Google+/Twitter/Facebook/Linkedin/mailing lists
* Get the merchandise https://gnuparallel.threadless.com/designs/gnu-parallel
* Request or write a review for your favourite blog or magazine
* Request or build a package for your favourite distribution (if it is
not already there)
* Invite me for your next conference

If you use programs that use GNU Parallel for research:

* Please cite GNU Parallel in you publications (use --citation)

If GNU Parallel saves you money:

* (Have your company) donate to FSF https://my.fsf.org/donate/


= 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.


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