few days ago I started working with Fedora 14. So far, so good, at least as far as the desktop machine goes (a laptop is another story and Kubuntu runs fine on another desktop). Something has just happened in Fedora which never happened to me before. Kate (an editor) got stuck and its memory (RAM) consumption went up through the roof to over 1.5 GB, so obviously it froze the system for a while. The process needed to be forcibly killed.

Now, it’s not entirely clear what happened there (maybe a program bug), but this is unusual and it looks bad for Fedora or for KDE (or the combination in Fedora 14 KDE spin). What did happen is that SELinux came up with an error implying that it stood in Kate’s way and maybe it’s partly responsible for this type of behaviour. It yielded the following error, implying that it was trying to help when in fact it seemed like it only stood in the way.

Summary:

SELinux is preventing /usr/bin/kate (deleted) “mmap_zero” access on <Unknown>.

Detailed Description:

SELinux denied access requested by kate. The current boolean settings do not
allow this access. If you have not setup kate to require this access this may
signal an intrusion attempt. If you do intend this access you need to change the
booleans on this system to allow the access.

Allowing Access:

Confined processes can be configured to run requiring different access, SELinux
provides booleans to allow you to turn on/off access as needed. The boolean
mmap_low_allowed is set incorrectly.
Boolean Description:
Control the ability to mmap a low area of the address space, as configured by
/proc/sys/kernel/mmap_min_addr.

Fix Command:

# setsebool -P mmap_low_allowed 1

Additional Information:

Source Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Context unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1
023
Target Objects None [ memprotect ]
Source kate
Source Path /usr/bin/kate (deleted)
Port &ltUnknown>
Host blueberry
Source RPM Packages
Target RPM Packages
Policy RPM selinux-policy-3.9.7-3.fc14
Selinux Enabled True
Policy Type targeted
Enforcing Mode Enforcing
Plugin Name catchall_boolean
Host Name blueberry
Platform Linux blueberry 2.6.35.6-45.fc14.i686 #1 SMP Mon
Oct 18 23:56:17 UTC 2010 i686 i686
Alert Count 112
First Seen Sun 14 Nov 2010 09:35:01 AM GMT
Last Seen Sun 14 Nov 2010 09:35:17 AM GMT
Local ID 4d9759c9-e672-475d-bf61-151d1688909a
Line Numbers

Raw Audit Messages

node=blueberry type=AVC msg=audit(1289727317.378:856): avc: denied { mmap_zero } for pid=1880 comm=”kate” scontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tcontext=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 tclass=memprotect

node=blueberry type=SYSCALL msg=audit(1289727317.378:856): arch=40000003 syscall=192 success=no exit=-13 a0=0 a1=100000 a2=0 a3=4022 items=0 ppid=1629 pid=1880 auid=500 uid=500 gid=500 euid=500 suid=500 fsuid=500 egid=500 sgid=500 fsgid=500 tty=(none) ses=1 comm=”kate” exe=2F7573722F62696E2F6B617465202864656C6574656429 subj=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023 key=(null)

For years I’ve been working with no data loss, but this time I had to revert back to a previously-saved version of a document I worked on and then rewrite bits of it. Perhaps I had enough confidence in the system to only hit save (CTRL+S) once in a very long time. This experience has taught me to save my work more often but more importantly it showed that Fedora can act rather bizarrely where Kubuntu never did. As a result of this behaviour I was unable to save my work. SELinux implies there was an “attack” on the system, but obviously there was not.

T HAS been a while since I last did a comprehensive survey of DICOM-related software and since I am ditching MATLAB (in the quest for Free software-only research) I decided to review or at least check out what’s available at the end of 2010. Other people may find this handy.

DICOM is notorious for being the standard that’s not quite the standard and is actually somewhat proprietary and controlled by one entity. As someone pointed out the other day, DICOM is considered “extensible”, which implies that the usual type of format ‘bastardisation’ will always occur. It’s just an inconsistent data format as someone warned, so some software would cough at it and sometimes manage to salvage some data. According to Wikipedia, some tagging of the image/s is accompanied by data fields like:

Let us say that we are more interested in the raw image data and not so much in the metadata. If that’s the case, batch conversion to a more manageable format is worthwhile. Here is the command-line converter that I use (some are for Windows only and they are proprietary) and some other options can be found on the Web through directories. There are also good software resources on scientific data formats and there is radiology CEU information regarding PACS and DICOM viewers. There is actually far more choice out there than there was a few years ago. For GNU/Linux and Free software proponents there is no lack or deficiency, either.

feel as though I must apologise for hasty remarks that I made in yesterday’s audiocast when we discussed GNU Octave (so I posted an update). I was basing my assessment on a very old experience and my understanding, as I found it out today, is that more and more MALTAB users consider moving to Octave due to the increasing cost of MATLAB. Another person whose background is in Mathematica taught me some more about the state of Octave. To quote from IRC:

*Quadrescence (~Quad@unaffiliated/quadrescence) has joined #boycottnovell-social		Nov 01 22:25
FurnaceBoy	Quadrescence: wb // schestowitz look who’s here	Nov 01 22:26
Quadrescence	hi	Nov 01 22:26
schestowitz	Hey	Nov 01 22:28
schestowitz	I was contacted by octave dev	Nov 01 22:28
schestowitz	Did you use it?	Nov 01 22:28
schestowitz	I just need to be able to deal with DICOM in it	Nov 01 22:28
schestowitz	Problem is, octave might not have good 3d visualisation tools	Nov 01 22:28
Quadrescence	I am pretty sure Octave just uses gnuplot	Nov 01 22:29
schestowitz	sjvn: “@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.”	Nov 01 22:29
schestowitz	Quadrescence: yeah	Nov 01 22:29
schestowitz	which is rather primitive compared to binary junk	Nov 01 22:30
schestowitz	So I need to use the junk	Nov 01 22:30
Quadrescence	schestowitz: What do you mean?	Nov 01 22:30
schestowitz	“@sjvn it’s the pet peeve of mine I told you about before. Some colleagues like Gralla and pro-Windows showing up and reducing signal for me.”	Nov 01 22:30
schestowitz	I think it’s not true. He still boosts Windows (gralla)	Nov 01 22:31
schestowitz	“@schestowitz thanks anyway. I already knew about octave-bioinfo, but it’s functionality is quite limited…”	Nov 01 22:31
schestowitz	Quadrescence: re mathematica	Nov 01 22:31
schestowitz	You though of leaving it?	Nov 01 22:31
schestowitz	maple and matlab are similar	Nov 01 22:31
Quadrescence	schestowitz: Sorry, I don’t know what you mean	Nov 01 22:33
Quadrescence	schestowitz: Are you saying gnuplot is primitive compared to mathematica/maple/matlab?	Nov 01 22:34
schestowitz	for plotting I think it’s lacking in comparison	Nov 01 22:35
schestowitz	The octave guy admitted it	Nov 01 22:35
schestowitz	I work with images a lot	Nov 01 22:35
schestowitz	for just plain stats I could use octave	Nov 01 22:35
Quadrescence	Actually I’d say gnuplot is rather phenomenal.	Nov 01 22:35
FurnaceBoy	pics or gtfo	Nov 01 22:36
Quadrescence	An alternative to gnuplot would be to use Sage: http://i.imgur.com/71Hr3.png	Nov 01 22:36
TechrightsBot-sc	Title: Not a web page! Aborting image/png type .::. Size~: 0 KB	Nov 01 22:36
Quadrescence	P and Q are plots. To plot them together, just do P+Q	Nov 01 22:36
Quadrescence		Nov 01 22:36
schestowitz	Nice	Nov 01 22:36
schestowitz	Maybe it has improved	Nov 01 22:36
Quadrescence	I don’t think that is gnuplot tho	Nov 01 22:36
Quadrescence	In fact, I know it isn’t	Nov 01 22:36
MinceR	gnupowder plot	Nov 01 22:37
schestowitz	gnuspamassassin plot	Nov 01 22:37
Quadrescence	gnuplot is still great: http://gnuplot.sourceforge.net/demo_svg/singulr.html	Nov 01 22:38
TechrightsBot-sc	Title: gnuplot demo script: singulr.dem  .::. Size~: 8.92 KB	Nov 01 22:38
Quadrescence	http://gnuplot.sourceforge.net/demo_svg/contours.html	Nov 01 22:39
TechrightsBot-sc	Title: gnuplot demo script: contours.dem  .::. Size~: 10.67 KB	Nov 01 22:39
Quadrescence	stuff in general: http://gnuplot.sourceforge.net/demo_svg/	Nov 01 22:39
TechrightsBot-sc	Title: Demo scripts for SVG terminal in gnuplot version 4.4 .::. Size~: 5.63 KB	Nov 01 22:39
Quadrescence	opacity: http://gnuplot.sourceforge.net/demo/transparent_solids.2.png	Nov 01 22:40
TechrightsBot-sc	Title: Not a web page! Aborting image/png type .::. Size~: 0 KB	Nov 01 22:40
Quadrescence	Anyway, the best thing about gnuplot is that it’s incredibly fast/lightweight.	Nov 01 22:41
Quadrescence	Mathematica has a tendency of blowing 2GB of RAM just to get a decent surface plot	Nov 01 22:41
Quadrescence	MathGL is an incredible open source library for making absolutely spectacular plots: http://mathgl.sourceforge.net/pictures.html	Nov 01 22:42
TechrightsBot-sc	Title: MathGL – pictures .::. Size~: 4.34 KB	Nov 01 22:42
Quadrescence	*and* you can use it with Octave	Nov 01 22:43
FurnaceBoy	Quadrescence: that is impressive (the svg stuff)	Nov 01 22:53
*FurnaceBoy lieks svg		Nov 01 22:53
schestowitz	abeNd-org: syntax compatible?	Nov 01 22:56
schestowitz	Quadrescence ^^	Nov 01 22:56
schestowitz	Could I attempt to run old matlab programs with gnuplot and octave?	Nov 01 22:57
schestowitz	FurnaceBoy: <SFT have VML	Nov 01 22:57
schestowitz	SVG scares them cause it ain’t THEIRS.	Nov 01 22:57
schestowitz	*MSFT I meant	Nov 01 22:57
FurnaceBoy	schestowitz: fine , let it scare them	Nov 01 22:58
Quadrescence	schestowitz: it is mostly compatible	Nov 01 22:59
*Ender2070 (~Ender2070@CPE00222d6e3608-CM00222d6e3605.cpe.net.cable.rogers.com) has joined #boycottnovell-social		Nov 01 23:04
schestowitz	FurnaceBoy: they ‘joined’ this year	Nov 01 23:04
schestowitz	Only to keep pushing VML	Nov 01 23:04
schestowitz	They need to intervene in the competition too	Nov 01 23:04
schestowitz	To bend it	Nov 01 23:05
schestowitz	See MSODF for example	Nov 01 23:05
FurnaceBoy	bend -> break.	Nov 01 23:05
schestowitz	Microsoft fragmented ODF	Nov 01 23:05
FurnaceBoy	hehe	Nov 01 23:05
FurnaceBoy	tried w/ java	Nov 01 23:05
FurnaceBoy	+ html	Nov 01 23:05
schestowitz	got sued	Nov 01 23:05
schestowitz	They try again now	Nov 01 23:05
schestowitz	AZune [sic] cloud	Nov 01 23:05
FurnaceBoy	yes, they only have one trick	Nov 01 23:05
schestowitz	Inviting Java dvs	Nov 01 23:05
schestowitz	*devs	Nov 01 23:05

It turns out that my employer may also allow me to move from MALTAB to Octave, thus using only Free software in my research. In fact, I’m installing Octave at this very moment.

“No episode number, this isn’t a soap opera”

Direct download as Ogg (1:09:43, 38 MB) | Direct download as MP3

Summary: TechBytes audiocast opens with a pre-launch episode where we mostly explore the terrain

HIS IS OUR test episode, a pilot so to speak. We did it all in one go (over an hour) without any notes or scripts and it is not edited. We hope that it’ll be acceptable and in our next episode (probably in November) we’ll use experience from this first run and also refine by doing some planning, then editing. Please treat it as a beta episode if it helps and we thank you for listening.

As embedded (HTML5):

Download:

Cross-posted in Techrights

Summary: Techrights is in the December 2010 issue of Linux Format Magazine

OR THOSE who want to know more about the history of Techrights, there is a new article in the December 2010 issue of Linux Format. The content is available only to subscribers. We thank Linux Format for generally being quite supportive over the years. There are some circles that are hostile towards us and upon closer inspection it usually turns out that they also oppose GNU/Linux and/or Free software, in which case this hostility may actually be indicative of the idea that we are effective. Techrights is still a group effort and achievements that are being made are communal, not personal. Thanks to all those who recommend the site to friends and colleagues, thus ensuring the continued growth of readership and input that accompanies it (recently we have been getting translations too).

Digital Control

am not always a pessimist, but I do believe that in order to make positive progress we must concentrare on the illnesses and try to cure them. This is why most of my work at present revolves around advancing collaborative platforms like GNU/Linux (no tyranny on people’s desktops and servers). Sure, companies like Google and IBM make a lot of money out of the platform, but it does not take away from anyone else’s ability to use the same code. Overall, it leads to solidarity. Just watch how many companies jointly develop Linux (kernel space), including giants like AMD, Intel, and NVIDIA, which must play nice with the free graphics stack. A decade ago it was hardly conceivable, but here we are today with some truly powerful applications for GNU/Linux (some are still proprietary, especially games). It is exciting to see desktop environments like the K Desktop Environment (KDE SC) and GNOME desktop becoming highly competitive with whatever else is out there, proprietary included. LXDE and Xfce continue to serve an important role, especially in less capable PCs that rely on light-weight distributions. New releases of GNU/Linux come at a pace of about one per day and diversity continues to exist, with popular branches like the Mandrake/Mandriva family (with several derivatives), the Red Hat family (including Fedora), and the Debian family, which notably includes Ubuntu for the desktops (it has a huge number of variants).

The devices/embedded space is an area of considerable strength for Linux and sometimes GNU too. Phones are increasingly running Linux (with the industry’s leader, Nokia, among its biggest embracers, but Google’s Android is getting a lot more attention). Then we have sub-notebooks and tablets, many of which run Linux/Android. This is a triumph that almost nobody talks about. It also helped eliminate Microsoft’s margins in this area and got Apple so nervous that it decided to pathetically sue with software patents.

Sharing, Not Hoarding

Free software/Open Source is an even broader area where companies like Mozilla and projects like the Apache Web server show that technical merit is found in licences that encourage sharing. SaaS is increasingly a threat to software freedom, but it relies heavily on this software (databases, CMSs, etc.). Businesses increasingly adopt Free software, even though they typically call it “open source” (they are just allergic to the notion of “free”, perhaps still not realising that it’s about freedom, not cost). Funding for Free software continues to come as projects prove their worth to the market (MySQL for example) and BSD continues to evolve nicely along with GNU/Linux. Establishments like FSF/FSFE/SFLC provide a centre of power that is not driven by shareholders and GNU accommodates many important projects that are used by many millions (e.g. GRUB). Governments increasingly realise the importance of Free software licensing and openness of their data, which prevents perceptions of secrecy and thus corruption. Programmers increasingly teach themselves how to use languages and frameworks that put them in control, rather than put them in the hands of some ‘masters’ of a platform and an SDK/IDE. Applications that are free make up the ‘network effect’ that’s so crucial to the success of GNU/Linux and BSD. Almost anyone can now use a Free desktop without trouble (except for re-learning). Standards are promoted and made more prevalent as a result of Free software proliferation.

Addressing the Negatives

The revolution of Free software has wide-ranging effects on many other aspects of our lives. Science is enriched by it (increased sharing speeds up development), security is improved and surveillance gets reduced, the environment benefits from increased reuse of hardware components, and the financial market becomes more honest and transparent (e.g. for scrutiny before disaster strikes). The culture of AstroTurfing/lobbying is impeded by this culture of honesty and ethics; also, censorship is reduced, privacy honoured, and civil rights held up as more important and simpler to defend (no secrecy or conspiracy like ACTA or the Digital Economy Bill). The Internet becomes a more valuable resource (Wikipedia and Google are examples of valuable services), net neutrality is easier to defend (wireless meshes come to mind), and DRM becomes a relic from the past, much to the regret of the intellectual monopolies and copyrights cartel (which should not be allowed to exist in the first place).

KDE4 does not cease to excite.

have been a user of KDE for about decade, but I did use almost every other desktop environment and window manager, especially in the earlier days of GNU/Linux on the desktop. KDE came naturally to me as a SuSE user (until
Novell’s deal with Microsoft) and its suitability for power user was a great plus. I still use GNOME in other places and I am pleased to say that it’s a pleasant environment too.

My first impression of KDE 4.3 is that it is a lot simpler for newcomers (than KDE 3) and it looks fantastic. I used earlier versions of KDE4 and they didn’t cause me trouble, but this one is almost perfect and I am unable to find noticeable wrinkles or creases. In fact, the new release incorporates so many wonderful changes that it would be irrational to ever step back to KDE3 again.

In the process of setting up this workstation I needed to use GParted, which is another invaluable distribution that does precisely what it says on the tin and does it nicely, too. I am currently on Kubuntu 9.10 (alpha 5), but I did not leave Mandriva behind. In fact, almost every distribution that I try these days leaves me satisfied. They all do, after all, share the same components; integration work is where it all counts.

I thought about doing a review, but that would be time consuming and rather boring to people who read my personal Web site.

So, thumbs up to the KDE team, the Kubuntu team, and the GParted maintainer/s. At this pace, the domination of GNU/Linux on the desktop too seems only like a matter of time.