Category Archives: Linux

Linux and Open Source

PGI ARM OpenCL compiler gone, first victim of nVidia purchase?

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Last August PGI announced an update to its “PGI OpenCL Compiler for ARM” (PGCL 12.7), but if you go looking for that on the PGI news page you won’t find it. In fact if you go to their products page and go to the link for the “PGI OpenCL Compiler for ARM” you’ll find it’s gone too..

For the record that part of the products page currently looks like:

PGI Compilers and Tools for Mobile and Embedded Platforms

PGI OpenCL Compiler for ARM
PGCLâ„¢ is an OpenCLâ„¢ framework for compiling and running OpenCL 1.1 embedded profile
applications on the ST-Ericsson NovaThorâ„¢ U8500 and follow-on platforms using a single
ARM core as the OpenCL host and multiple ARM cores as an OpenCL computing device

The interesting thing is that this has happened recently, Google’s cache of the news page (dated July 25th 2013) still has the announcement listed:

 The Portland Group Updates its OpenCL Compiler for Multi-core ARM

Portland, Oregon
August 21, 2012
Latest PGCL includes automatic generation of NEON/SIMD instructions

The Portland Group® (PGI), a wholly-owned subsidiary of STMicroelectronics and the leading
independent supplier of compilers and tools for high-performance computing, today announced
the release of PGCL 12.7. PGCLâ„¢ is the PGI OpenCL framework for multi-core ARM-based
Systems-on-Chips (SoCs), currently available on ST-Ericsson NovaThorâ„¢ platforms. PGCL includes
a PGI OpenCL compiler for multi-core ARM CPUs as a compute device and complements OpenCL
for GPUs.

So something changed in the last week, oddly around the same time that nVidia announced it was buying PGI..

Speeding up Digikam’s face recognition (with risks)

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It’d been a while since I’d last told Digikam to scan my collection for faces, and having just upgraded to 3.2.0 I thought it was about time to have another shot at it. However, I’d noticed it was taking an awful long time and seemed to only be using one of the eight cores on this system (Ivy Bridge i7-3770K running Kubuntu 13.04) so I thought I’d see if simply taking advantage of OpenMP could improve things with multithreading.

To do that I just started a new konsole and (as a first step) told OpenMP to use all the cores with:

export OMP_NUM_THREADS=8

Running digikam from that session and starting a face scan showed that yes, it was using all 8 cores, but not really to a great amount. Running iotop showed it doing about 5MB/s in reads and latencytop showed that it was spending most of its time in fsync(). Now that’s good, because it’s making sure that the data has really hit the rust to ensure everything is consistent.

However, in this case I can rebuild the entire face database should I need to, and I have about 66GB of photos to scan, plus I wanted to see just how fast this could go. 😉 So now it’s time to get a little dangerous and try Stewart Smith’s wonderfully named “libeatmydata” library which gives you a library (surprise surprise) and helper program that lets you preload an fsync() function that really only does return(0); (which, you may be interested to know, is still POSIX compliant).

So to test that out I just needed to do:

eatmydata digikam

and suddenly I had 8 cores running flat out. iotop showed that Digikam was now doing about 25-30MB/s reads and latencytop showed most of its time waiting for things was now for user space lock contention, i.e. locks protecting shared data structures to stop threads from stomping on each other and going off into the weeds. Interestingly the disks are a lot quieter than before too. Oh, and it’s screaming through the photos now. 🙂

WARNING: Do not use eatmydata for anything you care about, it will do just what it says in the name should your power die, system hang, universe end, etc..

HPC sysadmin job in Melbourne, Australia

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No, not where I work for once, but a friend of mine is looking for an HPC sysadmin in his group in the Victoria State Government:

This role requires advanced skills in system and network administration and scripting, clustered computer systems, security, virtualisation and Petabyte-scale storage. It is highly desirable that you have acquired these skills in a Life sciences environment. The heterogeneous environment requires both Linux and Windows skills. You should have the ability to design and implement solutions for automated transfer of data within and between systems and to ensure the security of both internal and Internet-facing systems. In this complex environment, working closely in teams of multi-disciplinary scientists to deliver computing solutions, including advanced troubleshooting and diagnostic skills, will be required. Supervision of other members of the team will also be necessary.

They’ve got a 1500+ core Linux cluster.. 😉

August 1993 “Preliminary Hardware Configuration for a Main Service Linux Machine”

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From 1992 through to 1994 I was working at the Computer Unit at the University of Wales (well, wrangled an “Employment Training” position there on my own initiative) as a sysadmin and was running Linux on an IBM XT (from very dodgy memory). A friend of mine, Piercarlo Grandi, suggested to me (semi-seriously I suspect) that you could now build a large enough PC to support quite a number of users, and that the Computer Unit could use it as a central server (they were running DEC 5830s with Utrix), so I knocked up a text file and discussed it with my colleagues. They didn’t take it very seriously – little did any of suspect how much that would change.

Well tonight I indulged in a bit of computer archaeology and managed to get the data off my Amiga hard disk (from a GVP A530 expansion unit) and browsing around happpened to stumbleover that text file, dated 8:20pm on the 8th August 1993. It’s quite touchingly naive in places, and my numbers are pretty ropey.. 🙂

Preliminary Hardware Configuration for a Main Service Linux Machine

Item                            Each    Number          Total

Case                             100    1                 100
Keyboard + Mouse                 100    1                 100
Floppies                         100    1                 100
DAT Drives                       750    4                3000
EISA SCSI Controllers            300    2                 600
Memory (Mb)                       25    256              6400
Pentium EISA Motherboard        1000    1                1000
3.5Gb SCSI-II Disks             1800    5                7000
Screen+SVGA Card                1000    1                1000
EISA Ethernet Card               200    2                 400
CD-ROM Drive                     300    1                 300

                                                        20000

Projected to be able to support between 200-400 users running Linux 0.99.p12
        (Alpha release kernel with patched IP - appears stable)


Notes:

(1) I've seen reports that the ethernet driver code may suffer from a
    memory leak, but I've not seen any evidence for this yet as my
    machine hasn't been turned on for a long enough period for it to
    cause any problems.

(2) As it is so new there is very little commercial software available
    for it, but there is a quite sizeable free software base with many
    of the GNU packages already ported for it, and this is generally of
    high quality.

(3) The Linux kernel is well thought out, and includes support for shared
    libraries (which Ultrix sadly never picked up) which significantly
    reduces the amount of memory applications need.

(4) A Linux box of the size proposed for the service machine has not
    been attempted yet (as far as I know), but ones of the size of the
    proposed testbed machine are already in usage on the Internet. I
    believe that Linux can handle this scaling up with no problem.

(5) There are apparently companies within the UK who sell support services
    for Linux, I will investigate further.

(6) There is already a large amount of Linux expertise on the Internet,
    including the comp.os.linux newsgroup, the linux-activists mailing
    list and even an IRC channel dedicated to Linux users.

This post is dedicated to Rob Ash, my then boss, who took a chance taking me on after my time as a student mucking around on computers when I was meant to be doing my Physics degree, and who was a great mentor for me.

Want to help with the Linux kernel?

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Greg Kroah-Hartman, the maintainer of the stable releases of the Linux kernel (the point releases after a 3.x release, e.g. 3.6.5, etc) is looking for help for about 6 months as he’s getting overwhelmed.

I’m looking for someone to help me out with the stable Linux kernel release process. Right now I’m drowning in trees and patches, and could use some one to help me sanity-check the releases I’m doing.

Specifically, I’m looking for someone to help with:

  • test boot the -rc stable kernels to make sure I didn’t do anything foolish.
  • dig through the Linux kernel distro trees and send me the git commit ids, or the backported patches, of things they are shipping that are not in the stable and longterm kernel releases.
  • do code review of the patches going into the stable releases.

If you can help out with this, I’d really appreciate it.

You’ll need to show you’ve had kernel patches accepted, are running the latest stable release candidate kernel and can find distro patches (details at his website). You’ve got until November 7th to apply!

Paying for Freedom (Updated)

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There has been much furore over the Microsoft Windows 8 Logo requirements, and how they require UEFI Secure Boot to be enabled, requiring the user to reconfigure their UEFI firmare (on x86 platforms) to be able to boot non-Windows 8 operating systems. People are concerned about the fact that this may be a slippery slope to systems that are locked down completely (as ARM powered Windows 8 systems already will be) with Secure Boot not being allowed to be disabled in order to get the MS Windows logo tick and thus the valuable marketing dollars from Redmond.

Now to me the solution seems obvious – don’t buy systems from people who sell such systems, but instead buy from vendors who believe in making systems that are under your control, and agree that it is you who gets to decide whether or not you want to turn Secure Boot on, or not. Go to companies like ZaReason (who sell around the world and have an Asia Pacific setup in New Zealand now) and System 76 (who used to be US only, but now apparently ship internationally).

The problem seems to be though that people complain that their systems tend to be a bit more expensive than the Dell’s of the world, companies who ship millions of PCs and have huge economies of scale (and power over their OEMs). Because ZaReason and System 76 work on much smaller volumes they don’t get the same deals and so of course their hardware will be more expensive – but that extra cost is actually an investment, a small downpayment on having vendors around in the future who will care about our freedoms to do with our computers as we see fit.

If we don’t make that investment in these companies then we will have no right to complain should we suddenly wake up one morning and find we have a choice between a beige PC that will only boot Windows 8 or later (and the ability to get your own code blessed so it will boot has gone away) and a shiny white Apple iProduct that will allow you to install any of the applications from the App store, but nothing outside of that walled garden.

So I have made my choices, when my desktop PC came a cropper and cooked itself due to the Linux leap second bug I bought a ZaReason Valta desktop and I then replaced my 9 year old laptop with a shiny new UltraLap 430 ultrabook which, I have to say, absolutely rocks with 8GB of RAM and an i5 Ivy Bridge CPU. 🙂

I believe freedom is worth investing in.

Update:

As spufidoo mentions in the comments the situation for desktops is not too bad at present whilst you can build your own, though there is always the chance that you end up with motherboards shipping with Secure Boot enabled and only Microsofts key installed (“why would you want anything else?”).

More of an issue are laptops and tablets where you can’t really build your own and you rely on companies to sell you the finished product. This was really the issue I had in mind when I wrote the article but failed to articulate it. We’ve already seen examples of the issues around tablets being locked down with the Nook Tablet from Barnes and Noble (though as the linked article reports people have worked around that now) so unless we support projects like the ZaTab where the package includes the source code we are purely relying on the munificence of companies for whom freedom is not the first thing they are thinking about.

Problems getting stack traces from a Python program (Kubuntu 12.10 development version)

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I’m trying to get to the bottom of this bug on Launchpad which completely breaks Synaptic touchpad configuration under KDE:

https://bugs.launchpad.net/ubuntu/+source/synaptiks/+bug/1039261

The tl;dr version is that the Python interpreter is somehow emitting two calls to the Xorg libXi function XIQueryVersion(), the first call sends a client XInput version number of 2.1 and then the second one sends 2.0 (seen using xtrace).

The second call causes a BadValue error, because you’re not meant to send a lower value on any later calls (as can be seen from this Xorg libXi git commit).

This causes the comical error:

The version of the XInput extension installed on your system is too old. Version 2.0 was found, but at least version 2.0 is required

The problem is that the Python code only has the second call sending the 2.0 version number, there is no other call in the package that will send anything else, let alone the 2.1 value.

So I want to generate a call trace every time the XIQueryVersion() function is called, but I’m struggling to get it to work.

The killer at the moment is that both ltrace and gdb (when told to trace children) hang when python runs dash to run ldconfig.real and that blocks – so I never get to the point where the function gets called the first time.

With GDB I’m using:

set detach-on-fork off
set follow-fork-mode child
set follow-exec-mode new
catch load /libXi/
break XIQueryVersion

…and this is what happens:

chris@chris-ultralap:~/Code/Ubuntu$ gdb /usr/bin/python
GNU gdb (GDB) 7.5-ubuntu
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
...
Reading symbols from /usr/bin/python...Reading symbols from /usr/lib/debug/usr/bin/python2.7...done.
done.
(gdb) set detach-on-fork off
(gdb) set follow-fork-mode child
(gdb) set follow-exec-mode new
(gdb) catch load /libXi/
Catchpoint 1 (load)
(gdb) break XIQueryVersion
Function "XIQueryVersion" not defined.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 2 (XIQueryVersion) pending.
(gdb) run /usr/bin/synaptiks
Starting program: /usr/bin/python /usr/bin/synaptiks
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New process 3788]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Thread 0x7ffff6ccc700 (LWP 3788) is executing new program: /bin/dash
[New process 3789]
process 3789 is executing new program: /bin/dash
process 3789 is executing new program: /sbin/ldconfig.real

…and there it hangs, forever. We never even get to the point where the Python interpreter loads libXi.so, let alone calls the function. 🙁

Any ideas?

Patch for Modules to use shell functions with BASH, not aliases

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Whilst the Modules system is awesome in making life easy to maintain multiple versions of packages and their dependencies (and is heavily used in HPC centres like VLSCI) it can have some annoyances (and seems to be fairly half-heartedly maintained looking at the bugtracker on SourceForge). One thing that’s bitten us from time to time is that you can’t really use its “set-alias” functionality as the bash shell does not expand aliases in non-interactive shells and that includes jobs that are launched from an HPC queuing system like Torque, PBSPro, etc.

It does have the compile time option “--disable-shell-alias” but annoyingly the condition is only applied when your shell is “sh“, not “bash“, so I’ve ended up having to patch Modules to make this work for bash as well. This patch is against 3.2.9c:

--- utility.c.orig      2011-11-29 08:27:13.000000000 +1100
+++ utility.c   2012-05-16 15:08:34.012038000 +1000
@@ -1422,7 +1422,7 @@
         **  Shells supporting extended bourne shell syntax ....
         **/
        if( (!strcmp( shell_name, "sh") && bourne_alias)
-               ||  !strcmp( shell_name, "bash")
+               || ( !strcmp( shell_name, "bash") && bourne_alias )
                 ||  !strcmp( shell_name, "zsh" )
                 ||  !strcmp( shell_name, "ksh")) {
            /**
@@ -1471,7 +1471,7 @@
 
            fprintf( aliasfile, "'%c", alias_separator);
 
-        } else if( !strcmp( shell_name, "sh")
+        } else if( ( !strcmp( shell_name, "sh") || !strcmp( shell_name, "bash") )
                &&   bourne_funcs) {
        /**

Hopefully this patch will be of use to people..

The ZaTab from @ZaReason – a fully open source Android (or whatever you want to load) tablet (UPDATED)

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ZaReason are a US company who only make Linux based computers and have recently been tweeting about building a completely open source tablet device, shipping with Android but unlocked so you can install whatever you would wish on it. They have even been working with the Software Freedom Conservancy to ensure that it passes muster as an open source device.

ZaReason ZaTab

However, other than some photos of it on Twitter details have been a little lacking, but now the ZaReason CEO (who is in New Zealand working on setting up a store there) tweeted the URL for pre-orders which includes the details about it:

  • Pure Android
  • Allwinner A10 SoC
  • 9.7″ IPS 1024×768 display
  • 5 point capacitive touchscreen
  • 16 GB internal storage + microSD for additional storage
  • 1 GB ram
  • b/g/n WiFi
  • Front and Back cameras
  • Sturdy metal back
  • High-capacity 8000 mAh battery
  • Ultra-light 630 grams

Ports:

  • Headphone
  • microSD card slot
  • mini-HDMI video out
  • 2x micro-USB ports

The device is shipping with CyanogenMod 9 (so based on Google’s Android Open Source Programme – AOSP – Ice Cream Sandwich release) and yes, it has root access available (CyanogenMod 9 doesn’t enable it by default, but it is just a configuration option). I would suspect this means it won’t ship with the Google Apps package which are not open source and so you won’t have access to the Google Play Store (formerly the Android Market), but you could still access the F-Droid open source application repository from it and should you feel the need for the proprietary Google Apps then you could reflash CyanogenMod9 with the Google Apps package available from their site. Most importantly it ships with all the source code.

The Socket on a Chip (SoC) is the Allwinner A10 which has a 1GHz ARM Coretex A8 and a MALI 400 MP1 GPU. Whilst the GPU manufacturer releases GPL driver code you apparently need a proprietary DDK to be able to produce a functional driver and so the Lima project has been born to create a fully open driver. Quite how the ZaReason people are dealing with this is unclear, if they are really shipping a fully open tablet then perhaps the Lima driver is a lot more stable than their project website claims. 🙂 (Clarified below in the update)

They’ve also promised the boot loader is unlocked so you can put whatever software you should wish to try out on it, on Twitter they said that they intend to try and get KDE going on it (presumably the KDE Plasma Active project, possibly using Mer as the supporting distribution). There’s even been a tongue-in-cheek reference to Gentoo.. 🙂

Update:

Two updates on the ZaTab:

  • firstly that the pre-orders they are taking are limited to FOSS people, they want you to contact them via email as part of the process (they have concerns about fraud).
  • Secondly on the openness and GPU driver, they have confirmed that “Initially there may be some binary blobs. Lima isn’t far enough along at this time, but we have high hopes for it”.

Xorg.conf for multihead on Dell Lattitude Z600

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I spent a little time recently creating a minimal xorg.conf file to get multi-display working on my work Dell Latitude Z600, such that it sets up an external HP monitor (via the Display Port connector DP1) to the right of the laptop display (LVDS1), with both display and monitor running at their native resolutions. Took a little fiddling to get it right, but this works for me (of course you’d want to adjust the PreferredMode to suit your equipment). Without this it defaults to cloning the main display and running both at 1280×1024, which isn’t very nice.

Section "Screen"
        Identifier "Screen0"
        Monitor "LVDS1"
EndSection

Section "Screen"
        Identifier "Screen1"
        Monitor "DP1"
EndSection

Section "Monitor"
        Identifier      "LVDS1"
        Option  "Primary"       "true"
        Option  "PreferredMode" "1600x900"
EndSection

Section "Monitor"
        Identifier      "DP1"
        Option  "Primary"       "false"
        Option  "RightOf"       "LVDS1"
        Option  "PreferredMode" "1920x1080"
EndSection

Section "Device"
        Identifier "Intel0"
        Option "Monitor-LVDS1" "LVDS1"
        Option "Monitor-DP1" "DP1"
EndSection

NB: Whilst the xorg.conf does set the primary display to the laptop screen (LVDS1) either KDE or X itself continues to use the external display (DP1) as the primary. However, I can change that in my KDE settings and that then persists across logins.