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    Archive for the '*nix' Category

    drush pm-update fails: tar hangs when extracting *.tar.gz module archives from

    25th August 2014

    Drush is awesome, especially for updating multisite Drupal installations.
    I had only started using it a few days ago, and I’ve immediately hit a problem, to which I did find a workaround.


    • running drush @sites pm-update results in normal execution up to after answering ‘y[es]‘; then drush seems to hang indefinitely (haven’t waited beyond about 10 minutes, maybe it does produce an error after a long while);
    • running the same command with --debug shows that drush hangs when trying to untar the downloaded module.tar.gz archive; there are no errors/warnings, it just hangs with no CPU usage;
    • trying to untar any of the modules downloaded from manually is also unsuccessful: tar -xzvf module.tar.gz seems to do nothing, it also hangs with zero CPU usage/time and no warnings/errors;
    • interestingly, if I create some test.tar.gz locally, tar does happily extract that;
    • finally, running strace tar -xzvf module.tar.gz shows a number of unexpected lines, such as references to NSS and libnss files (I am only showing some of the lines of strace output, including the last line):

      open(“/etc/nsswitch.conf”, O_RDONLY) = 4
      read(4, “# /etc/nsswitch.conf\n#\n# Example”…, 4096) = 683
      open(“/lib/x86_64-linux-gnu/″, O_RDONLY) = 4
      open(“/lib/x86_64-linux-gnu/″, O_RDONLY) = 4
      open(“/etc/passwd”, O_RDONLY|O_CLOEXEC) = 4
      open(“/usr/lib/x86_64-linux-gnu/″, O_RDONLY) = 4
      open(“/etc/group”, O_RDONLY|O_CLOEXEC) = 4
      open(“/etc/libnss-mysql.cfg”, O_RDONLY) = -1 EACCES (Permission denied)
      open(“/etc/libnss-mysql-root.cfg”, O_RDONLY) = -1 EACCES (Permission denied)
      futex(0x7fd0816e8c48, FUTEX_WAIT_PRIVATE, 2, NULL

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    Posted in *nix, Drupal, Notepad, Software | No Comments »

    Debian command of the day: popcon-largest-unused

    2nd January 2014

    From the Debian squeeze to wheezy upgrade guide:

    Remove packages that take up too much space and are not currently needed (you can always reinstall them after the upgrade). If you have popularity-contest installed, you can use sudo popcon-largest-unused to list the packages you do not use that occupy the most space. You can find the packages that just take up the most disk space with dpigs (available in the debian-goodies package) or with wajig (running wajig size). They can also be found with aptitude. Start aptitude in “visual mode”, select Views → New Flat Package List, press l and enter ~i, then press S and enter ~installsize. This will give you a handy list to work with.


    Posted in *nix | No Comments »

    Alternatives to GNU make

    19th October 2013

    Right now, when I see that I have to often repeat/retype some sets and sequences of commands, I’m trying to wrap them up into some kind of a script, every time choosing the most appropriate language – shell when I need to start lots of existing command-line tools, Python when there’s some data handling and processing involved, and R when I’m invoking commands from R packages. So far I have been avoiding the fairly popular makefile-based approach to automating pipelines and workflows which rely heavily on existing tools. However, being curious, I’ve compiled a short list of modern make-like alternatives, to possibly explore… sometime later…

    • First comes make itself – the oldest and the most widely used software build tool. Stable and powerful. Still, even people who got used to using make, have some gripes about it. The most detailed list of gripes is probably here.
    • SCons is a build tool written in Python. I guess I like that “configuration files are Python scripts” – maybe knowing Python is enough to use SCons, which makes SCons a better choice than make for me. SCons seems to have gained some support (scroll down for comments/discussion). There were some doubts about SCons performance (1, 2, and 3); not sure where SCons is at right now in that regard.
    • waf, a Python-based framework for configuring, compiling and installing applications.
    • pyDoIt is a Python automation tool. It seems to use Python syntax. It aims at bringing the power of build-tools to execute any kind of task, where a task describes some computation to be done (actions), and contains some extra meta-data. Based on the description alone, I’m quite intrigued! I wonder if anyone had already worked with pyDoIt and can share experiences?…
    • Rake – Ruby make – is a simple build program with capabilities similar to those of make. Had seen a lot of positive feedback about this one – mostly regarding simplicity of use. Still [py]DoIt so far looks more attractive to me personally.
    • Ruffus is a lightweight python module for running computational pipelines. Sounds like some good competition to [py]DoIt!
    • Anduril is an open source component-based workflow framework for scientific data analysis. Sounds promising, though the latest downloadable version is over 400 MBs… It probably already contains a bunch of binaries and maybe even data and complete workflows for data analysis. Probably worth a look, but may turn out a little overweight for simple pipelining.
    • snakemake is a scalable bioinformatics workflow engine. I get the feeling that Python is truly dominating the pipelines/workflows world: snakemake, as even the name suggests, is in Python, too. The front-page example is so simple and clear, that snakemake immediately pushes DoIt down from the 1st place! Awesome.
    • Paver is a yet-another Python-based software project scripting tool along the lines of Make or Rake, designed to help out with repetitive tasks with the convenience of Python’s syntax. Sounds similar to DoIt. Have no idea how they actually compare to each other.

    That is it for now.

    What were your experiences with automating repetitive tasks and building simple pipelines?


    Posted in *nix, Notepad, Programming, Software | No Comments »

    Saving and restoring the list of packages installed on a Debian system using aptitude or deborphan

    18th October 2013

    The usual, or even classical way is to create the list of installed packages with sudo dpkg --get-selections > package_list, and then restore when/if necessary with cat package_list | xargs sudo apt-get -y install.

    As VihangD points out in his serverfault answer, the same can be achieved with aptitude, while also excluding dependent, automatically installed packages (which are included by the classical method). To create the list of packages, run aptitude search -F '%p' '~i!~M' > package_list. Here, -F '%p' asks aptitude to only print package names (instead of the default output, which also contains package state and description); search term ‘~i!~M’ asks for all non-automatically installed packages.

    To install packages using the created list, run xargs aptitude --schedule-only install < package_list; aptitude install. The first of these two commands instructs aptitude to mark all the packages from the list as scheduled for installation. The second command actually performs the installation.

    Hamish Downer suggests an alternative way of getting the initial package_list: using the deborphan utility, deborphan -a --no-show-section > package_list. This command asks deborphan to show a list of packages, which have no dependencies on them. Sounds very similar to what we did with aptitude above, but using deborphan will most likely result in a much shorter list of packages (on my system, deborphan printed 291 package names, aptitude printed 847, and dpkg printed 3650 package names). One more potentially important difference between aptitude- and deborphan-produced package lists is that aptitude only specifies package architecture when it is different from native (e.g. 'googleearth:i386' on a 64-bit system), while deborphan specifies architectures for all the packages (resulting in e.g. 'google-talkplugin:amd64' and 'googleearth-package:all' on a 64-bit system).


    Posted in *nix, how-to, Notepad | 2 Comments »

    GUIs for R

    17th October 2013

    I’ve tried [briefly] Cantor (which also supports Octave and KAlgebra as backends), rkward, deducer/JGR, R Commander, and RStudio.

    My personal choice was RStudio: it is good-looking, intuitive, easy-to-use, while powerful.

    Next step would be using some R-equivalent of the excellent ipython’s Mathematica-like Notebook webinterface…


    Posted in *nix, Notepad, Programming, Science, Software | No Comments »

    The favourite file compressor: gzip, bzip2, or 7z?

    17th October 2013

    Here comes a heap of assorted web-links!

    I had personally settled on using pbzip2 for these simple reasons:

    • performance scales quasi-linearly with the number of CPU cores (until one hits an I/O bottleneck);
    • when archive is damaged, you are only guaranteed to loose the damaged block(s) of size 100-900 KiB – remaining information might be salvable.

    Compared to pbzip2, neither gzip nor 7z (lzma) offer quasi-linear speedups proportional to the number of CPU cores.
    pigz, the parallel gzip, does parallelize compression, but gzip compresses not as good as bzip2, and decompression is not parallel like in pbzip2.
    7z is multi-threaded, but it tops out at using 2 CPU cores (see links below for tests).

    pbzip2 is also quite a good choice for FASTQ data files: even if a few blocks get lost due to data corruption, this should not noticeably affect the entire dataset.
    Specialized tools for FASTQ compression do exist (see e.g. this article, also Fastqz, fqzcomp, and samcomp project pages.) I think I liked fastqz quite a bit, but I still have to examine data recoverability in the case of archive damage. It is possible to use external parity tools which support file repair using pre-calculated recovery files – like the linux par2 utility, also for bzip2 archives and any other files in general – but adding parity file may negate the higher compression ratio benefits. Also, if there is no independent block structure of the archive, insufficient parity file may lead to the loss of the entire archive. In other words, this still has to be tested.

    Now the long-promised web-links!
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    Posted in *nix, Links, Notepad, Software | 1 Comment »

    Debian: how to whitelist IP addresses in tumgrey-SPF

    7th August 2013

    SPF is nice for protecting your mail server from spam, but sometimes there is a need to bypass SPF checking. For example, if you rely on 3rd party servers to do spam protection for you :)

    Current setup:

    • MX records point to the spam protection mail servers, which then
    • connect to my server and deliver (hopefully spam-free) mail.

    Problem: some senders (like do have proper, strict SPF records. Tumgreyspf on my server then rejects emails relayed through the spam-protection service.

    If these spam protection relay servers are the only which send mail to your server, then it makes sense to fully disable/uninstall tumgreyspf. Putting tumgreyspf into the permanent “learning mode” (set defaultSeedOnly = 1 in /etc/tumgreyspf/tumgreyspf.conf) may not fix the SPF problem described above, as SeedOnly seems to only affect greylisting, and not rejecting unauthorized senders.

    Solution: whitelist relay server IPs.
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    Posted in *nix, how-to, Software | No Comments »