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    ZFS is the FS for Containers in Ubuntu 16.04 and how it compares to btrfs

    20th February 2016

    Recently in hacker news the following was posted: ZFS is the FS for Containers in Ubuntu 16.04.

    I must admit the 16.04 demo does look very pleasant to work with.

    However, bringing in ZFS into Linux reminded me of a fairly recent comparison of ZFS and btrfs that I had to do when building my home NAS.
    At that time, few months ago, I’ve arrived (among others) at the following conclusions:

    • ZFS on FreeBSD is reliable, though a memory hog;
    • on Debian, OpenVault seems to be a good NAS web-management interface;
    • on FreeBSD, FreeNAS is good (there is also Nas4Free fork of an older version, but I haven’t looked into it deep enough);
    • running ZFS on linux (even as a kernel module) is the least efficient solution, at least partially because kernel’s file caching and ZFS’s ARC cache are two separate entities;
    • although btrfs offers features very similar to ZFS, as of few months ago OpenVault did not offer btrfs volumes support from the web-interface.

    In the end, I’ve decided to go with FreeNAS, and it seems to work well so far.

    But had anything changed in the btrfs vs ZFS on Linux field?
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    Posted in *nix, Software | No Comments »

    PGF vs PNG vs JPEG 2000 for long-term photo storage/archive

    26th May 2015

    I am using an excellent photo-management suite digiKam, which offers 3 lossless compressed formats for photos versioning and storage: PNG, JPEG 2000, and PGF. I wanted to know which one should I use, which urged me to perform this comparison.

    This post is not intended to be an in-depth comparison, but should be sufficient to choose one of the three file formats for your purposes. For more format details and history simply follow the links provided. File formats are reviewed roughly in “historical” order.

    PNG (Portable Network Graphics) was designed as GIF replacement.

    • It is lossless.
    • It is suitable for photos.
    • PNG is more space-efficient in the case of images with many pixels of the same color, such as diagrams/plots (as compared to PGF and JPEG2000). However, PNG photos are almost always larger than lossless PGF/JPEG2000 photos (real photo example: 9.9 MB in PNG, 7.0 MB in JPEG 2000).
    • PNG is fairly fast at (en|de)coding.
    • PNG is widely supported by web-browsers, image editors, and other software.
    • PNG uses CRCs internally for each data block, so if damage occurs only the damaged block(s) should be lost – theoretically. However, in practice, according to the Just One Bit paper (local copy), PNG is actually much less damage-resilient than JPEG 2000.

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    Compressors galore: pbzip2, lbzip2, plzip, xz, and lrzip tested on a FASTQ file

    28th March 2015

    About 2 years ago I had already reviewed some parallel (and not) compressing utilities, settling at that time on pbzip2 – it scales quasi-linearly with the number of CPUs/cores, stores compressed data in relatively small 900k blocks, is fast, and has good compression ratio. pbzip2 was (and still is) a very good choice.

    Yesterday I got somewhat distracted, and thus found lbzip2 -

    an independent, multi-threaded implementation of bzip2. It is commonly the fastest SMP (and uniprocessor) bzip2 compressor and decompressor

    - as it says in the Debian package description. Is it really “commonly the fastest” one? How does it compare to pbzip2? Should I use lbzip2 instead of pbzip2?

    This minor distraction had grown into a full-scale web-search and comparison, adding to the mix plzip (a parallel version of lzip), xz, and lrzip. After reading thousands of characters, all of these were put to a simple test: compressing an about 2 gigabyte FASTQ file with default options.

    All the external links and benchmarks, as well as my own mini-benchmark results, are provided below.

    The conclusion is that out of all the tested compressors lbzip2 is indeed the best one (for my practical use). It is only slightly better than the trusty pbzip2, which takes the second place. All the other compressors performed so poorly, that they do not get any place in my practical rating…

    So, let us first ask internet wisdom/foolishness, if lbzip2 or pbzip2 is faster/better?
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    Posted in *nix, Comparison, Links, Misc, Software | 6 Comments »

    Looking for a perfect Android app for TSW/GTD use

    13th March 2015

    I have recently realized that my planning habits are quite similar to what The Secret Weapon promotes. However, my planning is not as elaborate and detailed/structured as TSW, and I am using several tools:

    • Google Keep, an awesome note-taking and to-do lists application with a really good web-interface, and free;
    • Trello, convenient lists/projects/tasks management platform (especially for group work), and free;
    • Google Calendar, the de facto calendar standard for Android phones, and free;
    • my A5 format weekly paper planner, and… the only not free component.

    It is easy to see that I am using too many tools.

    In an effort to use less tools, and also to try some of the features of TSW, I’ve performed a brief search for GTD/TSW-compatible Android apps.

    TSW website is built around the Evernote app. However, I am not sure if this would be a good solution for me, as I have been already using Evernote since several years for longer-term note-keeping, and thus already have a bunch of notepads, notes, and tags there. Moreover, Evernote’s website mentions something about “offline notes” in the Premium (non-free) tier for mobile apps; this hints at the requirement to have internet connectivity to be able to work with TSW+Evernote efficiently through the day.

    Oh, before I forget: all the 4 tools that I am using have their purpose, with overlap between Keep and Trello.
    My A5 format paper planner (weekview compact 2015) is not a simple weekly planner; it has a structure that stimulates goal-oriented planning.
    More specifically, it provides means to plan:
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    Posted in Comparison, Links, Misc, Notepad, Software | No Comments »

    My smartd.conf, explained

    28th February 2015

    After fixing offline uncorrectable sector warning email, I have taken a closer look at my /etc/smartd.conf, and now it looks like this:

    DEFAULT -d sat -H -f -p -t -W 0,40,45 -n standby -S on -m example@example.com
    # Attributes 1, 230, and 231 are very important (-r 1! -r 230! -R 230! -r 231! -R 231!), but likely covered by -t.
    /dev/sda -s (S/../../6/01|L/../(01|02|03|04|05|06|07)/7/00) -C 0 -I 189 -I 194
    # -a implies -f and -p (through -t)
    DEFAULT -d sat -a -I 194 -W 0,40,45 -n standby -o on -S on -m example@example.com
    /dev/sdb -s (S/../../6/02|L/../(01|02|03|04|05|06|07)/7/02)
    # This drive does not decrement Offline_Uncorrectable (198) after re-allocation,
    # so only monitoring for increase, not for non-zero value.
    /dev/sdc -s (S/../../6/03|L/../(01|02|03|04|05|06|07)/7/04) -U 198+
    # This drive has 40 “normally”.
    /dev/sdd -s (S/../../6/04|L/../(01|02|03|04|05|06|07)/7/06) -W 0,42,45

    Note: explanations below are intentionally simplified; please consult man smartd.conf for more precise, complete, and up-to-date information.

    Ok, so what do these settings mean, and how is this different from default settings?
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    Posted in *nix, how-to, Notepad, Software | No Comments »

    How to fix Offline Uncorrectable sector outside of a partition

    26th February 2015

    A few days ago my smartd daemon (from the smartmontools package) notified me about a +1 increase in Current_Pending_Sector (197) and Offline_Uncorrectable (198) SMART attributes. The 2.5″ Fujitsu laptop hard-drive these appeared on is very old, and it also has been working 24/365 since a little over a year.

    Running a short SMART self-test (sudo smartctl -t short /dev/sdc) produced a read error at sector 1289:

    Num Test_Description Status Remaining LifeTime(hours) LBA_of_first_error
    1 Short offline Completed: read failure 80% 22339 1289

    Looking at the partition table of /dev/sdc, we see that this sector is outside of the only RAID partition on the disk, which starts at sector 2048:

    Device Boot Start End Blocks Id System
    /dev/sdc1 2048 117209087 58605088 fd Lnx RAID auto

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    Posted in *nix, how-to, Software | 1 Comment »

    Mini-review: offline navigators for Android

    18th October 2014

    Sygic, Waze, Osmand, Navfree, Navigator, or (Nokia’s) Here Navigation beta: which is a better offline navigation solution for your Android?

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    Posted in Comparison, Software | No Comments »