Online board games

Java game library and hosting

• http://www.gamegardens.com

Javascript engines

• https://github.com/bebraw/jswiki/wiki/Game-Engines
• http://ntt.cc/2011/01/31/66-open-source-javascript-game-engine-for-serious-developers.html
  

Getting hurd up & running

It seems (?) to be easier using qemu than virtualbox. 

• Install cds are here:
  http://people.debian.org/~sthibault/hurd-i386/installer/cdimage/
• Here are the instructions for a pre-installed image, suitable for use with qemu
  http://people.debian.org/~sthibault/hurd-i386/README
• This yields an error message:
  failed to initialize KVM: Device or resource busy
  No accelerator found!
• 
  
  

More linux/free games

http://freegamer.blogspot.com/
http://www.playdeb.net

Re-installing Gelato (take 2)

Well, it seems that, in addition to extra hoops for installing onto RAID, the nouveau kernel module crashes when trying to boot.  Since (unlike Ubuntu or Mint), the debian installer works with RAID, I downgraded to debian stable ("squeeze").

1. Install debian without the desktop.  Reboot.
2. Read up on nvidia drivers.  Decide to try the "debian way".  (http://wiki.debian.org/NvidiaGraphicsDrivers)
3. Nvidia proprietary drivers are updated in backports repository.  Add it to /etc/apt/sources.list
   deb http://backports.debian.org/debian-backports squeeze-backports main
4. Install desktop after the fact (http://wiki.debian.org/Gnome)
   apt-get install aptitude tasksel
   tasksel install gnome-desktop --new-install
5. Remove nouveau (http://forums.debian.net/viewtopic.php?f=6&t=69888 | http://forums.debian.net/viewtopic.php?f=30&t=54330)
   echo "blacklist nouveau" >> /etc/modprobe.d/blacklist.conf
   apt-get purge --remove xserver-xorg-video-nouveau
6. Use aptitude, and remove every package with the word "nouveau" in it.  However, nouveau.ko is in the linux kernel package, so I can't actually remove it.
7. Continue, re-install nvidia drivers
   apt-get install --reinstall nvidia-glx
8. This is a key step (see http://linux.koolsolutions.com/2009/10/11/howto-blacklisting-kernel-module-from-auto-loading-in-debian/)
   depmod -a
   update-initramfs -u -k `uname -r` -v
9. Reboot.  Success!

Re-installing gelato

1. Backup home directory.  Backup etc.  Unplug scratch drives
2. Boot live cd
3. Install mdadm and lvm2
4. Re-assemble the raid partitions
   mdadm --assemble --scan
5. Run linux mint installer.  The /dev/mdXX partitions are recognised and usable for install.  Re-format existing partitions (except /home). Choose /dev/md1 (/boot partition) as the partition for the boot loader.
6. I got an error in the install.  Maybe benign?  It says:
   An error occurred while migrating data.  More details may be found in /var/log/syslog.  The installation will continue, but some or all of the documents and settings you requested may not have been transferred to the installed system.
   The error is that it couldn't mount /dev/sdb5 (which belongs to /dev/md5), because it doesn't know the file system "linux raid member".  Click OK to continue.
7. Choose "continue testing" at the end of the install.
8. Now we have to set up the newly installed system to recognise the raid.  This is exactly as described in part 5 of this document:
   http://www.howtoforge.com/install-ubuntu-with-software-raid-10
   With the modificaiton of additional required partitions (/usr, /var, etc.), and installing lvm2 as well as mdadm.
9. Reboot.
10. Well, the reboot didn't work, because I neglected to update grub.  Here is the error that I got:
    GRUB Loading stage1.5
    GRUB loading, please wait...
    Error 15
11. Boot off of the live CD again, re-install mdadm & lvm2, re-scan raid, re-mount volumes, enter chroot.
    apt-get install mdadm lvm2
    mdadm --assemble --scan
    mkdir /myraid
    mount /dev/md5 /myraid
    mount /dev/md1 /myraid/boot
    mount /dev/md6 /myraid/usr
    mount /dev/md7 /myraid/var
    mount /dev/md8 /myraid/tmp
    mount --bind /dev /myraid/dev
    mount -t devpts devpts /myraid/dev/pts
    mount -t proc proc /myraid/proc
    mount -t sysfs sysfs /myraid/sys
    chroot /myraid
12. Follow instructions on this page:
    http://iiordanov.blogspot.com/2011/07/how-to-install-linux-ubuntu-debian-etc.html
    Start at step (10). It goes smoothly.  However, I notice that my swap is not RAID.  I wonder if this is on purpose?  So I left as two swap partitions in the fstab, to be resolved later.
13. Do step (11), note that I did not have to modify /etc/mdadm/mdadm.conf, since it already had the correct entries.
14. Do step (12).  This failed.  Note 1: the file /boot/grub/grub.cfg did not exist.  Note 2: grub-install was done to the raw disk, not the raid disk, such as:
    grub-install --recheck --modules="raid" /dev/sda
15. Reboot.
16. Now I got a grub menu, which listed a few options including "/dev/md1", "/dev/sda1", and "/dev/sdb1".  Choosting the first option causes a black screen of death.  Choosing "/dev/sda1" yields similar results.  It turns out that something is happening, but nothing is displayed.  Hitting e.g. arrow keys or ESC causes the messages to display.  The boot seems to hang on the following message:
    ** Starting CUPS printer/spooler server **    [ OK ]
17. Boot off of the live CD again, re-install mdadm & lvm2, re-scan raid, re-mount volumes, enter chroot.
18. Nothing interesting to see.  Here is boot.log:
    fsck from util-linux 2.19.1^M
    fsck from util-linux 2.19.1^M
    fsck from util-linux 2.19.1^M
    fsck from util-linux 2.19.1^M
    fsck from util-linux 2.19.1^M
    fsck from util-linux 2.19.1^M
    /dev/md5: clean, 9326/305824 files, 123307/1222912 blocks^M
    /dev/md8: clean, 12/305824 files, 54365/1222912 blocks^M
    /dev/md7: clean, 8815/305824 files, 130828/1222912 blocks^M
    /dev/md6: clean, 163285/1221600 files, 772988/4885744 blocks^M
    Reiserfs super block in block 16 on 0x90a of format 3.6 with standard journal^M
    Blocks (total/free): 110268128/33138842 by 4096 bytes^M
    Filesystem is clean^M
    /dev/md1: clean, 246/124928 files, 56798/497856 blocks^M
     * Starting mDNS/DNS-SD daemon^[[154G[ OK ]^M
     * Starting network connection manager^[[154G[ OK ]^M
     * Starting CUPS printing spooler/server^[[154G[ OK ]^M
     * Starting emergency keypress handling^[[154G[ OK ]^M
     * Stopping emergency keypress handling^[[154G[ OK ]^M
     * Starting System V runlevel compatibility^[[154G[ OK ]^M
     * Starting save system clock to hardware clock^[[154G[ OK ]^M
     * Starting save sound card(s') mixer state(s)^[[154G[ OK ]^M
     * Starting eCryptfs^[[154G[ OK ]^M
    Here is the end of kern.log:
    Apr  2 20:28:54 gelato kernel: [   18.535691] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: Rx/Tx
    Apr  2 20:28:54 gelato kernel: [   18.536853] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready
    Apr  2 20:29:04 gelato kernel: [   28.840999] eth0: no IPv6 routers present
    Apr  2 20:31:14 gelato kernel: Kernel logging (proc) stopped.
    Here is the end of syslog:
    Apr  2 20:29:04 gelato avahi: contact your administrator and convince him to use a different DNS domain,
    Apr  2 20:29:04 gelato avahi: since .local should be used exclusively for Zeroconf technology.
    Apr  2 20:29:04 gelato avahi: For more information, see http://avahi.org/wiki/AvahiAndUnicastDotLocal
    Apr  2 20:29:04 gelato kernel: [   28.840999] eth0: no IPv6 routers present
    Apr  2 20:29:12 gelato ntpdate[1303]: adjust time server 91.189.94.4 offset 0.213605 sec
    Apr  2 20:31:14 gelato kernel: Kernel logging (proc) stopped.
    Apr  2 20:31:14 gelato rsyslogd: [origin software="rsyslogd" swVersion="5.8.1" x-pid="1172" x-info="http://www.rsyslog.com"] exiting on signal 15.

Reproducing Kernel Hilbert Spaces

From Zero to Reproducing Kernel Hilbert Spaces in Twelve Pages or Less" by Hal Daumé III (Unpublished, 2004)
http://hal3.name/docs/daume04rkhs.pdf
Not directly related, but also I'm interested in Wolfe Dual:
http://www.cs.rochester.edu/~gildea/2008_Springwolfe.pdf
http://homepages.rpi.edu/~bennek/class/mmld/

Github on wormwood

OK, two things to know.

1. Need to set up ssh for multiple keys.  See e.g.
   http://www.karan.org/blog/index.php/2009/08/25/multiple-ssh-private-keys
2. Need to do this:
   

   $ ssh-add ~/.ssh/id_rsa_github

3. On gelato, I need something like this:

   $ exec ssh_agent bash<br />$ ssh-add ~/.ssh/id_rsa_github

Bye.

Using slicer on SPL computers

When you try to run slicer remotely on the SPL computer, you get something like this:

$ ./Slicer-build/Slicer
Number of registered modules: 94
ERROR: In /home/gcs6/build/slicer-rt/SlicerRt-build/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 404
vtkXOpenGLRenderWindow (0x333a200): Could not find a decent visual

ERROR: In /home/gcs6/build/slicer-rt/SlicerRt-build/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 404
vtkXOpenGLRenderWindow (0x333a200): Could not find a decent visual

X Error: BadValue (integer parameter out of range for operation) 2
  Extension:    135 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x21
ERROR: In /home/gcs6/build/slicer-rt/SlicerRt-build/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 629
vtkXOpenGLRenderWindow (0x333a200): Cannot create GLX context.  Aborting.

error: [/workspace/gcs6/build/slicer-rt/SlicerRt-build/Slicer-build/bin/./SlicerQT-real] exit abnormally - Report the problem.

It seems you can workaround by doing this:

$ setenv LIBGL_ALWAYS_INDIRECT y

Policy for ITK

Just to remind myself, set policy CMP0012 to avoid scary ITK include warning

Alternative platform testing

Excellent resource for testing software on different platforms

• http://gcc.gnu.org/wiki/CompileFarm
• http://www.gnu.org/software/hurd/public_hurd_boxen.html
  

Online course links

X-ray, CT

• www.imt.liu.se/edu/courses/TBMT02/ct/CT_introduction.pdf
• Kak & Slaley
• http://www.impactscan.org/ (good slides)
• http://www.sprawls.org/ppmi2/
  
• http://e-radiography.net/ (check out sword-swallowing images)
• http://www.crcpd.org/2011AnnualMeeting/Training/agenda_AAPM.aspx (slides)
• http://ric.uthscsa.edu/personalpages/lancaster/DI-II_Chapters/CT_chap.pdf
• (course page is http://ric.uthscsa.edu/personalpages/lancaster/DI_II.html)
• http://www.imt.liu.se/edu/courses/TBMT02/ct/CT_introduction.pdf
• http://en.wikibooks.org/wiki/Basic_Physics_of_Nuclear_Medicine/X-Ray_CT_in_Nuclear_Medicine
• http://en.wikibooks.org/wiki/Basic_Physics_of_Digital_Radiography/The_Applications
  
• http://eeweb.poly.edu/~yao/EL5823/CT_ch6_part1.pdf (includes some project ideas)
  

MRI

• http://www.simplyphysics.com/MAIN.HTM (Chapter 2, on right side of page)
• http://www.cis.rit.edu/class/schp730/
• MIT
• http://www.imaios.com/en/e-Courses/e-MRI
• http://www.ismrm.org/resources/mr-sites

Multi-modal

• AAPM/RSNA Resident education series
• https://www.imt.liu.se/edu/courses/TBMT02/Medical_Imaging.html
• https://www.imt.liu.se/edu/courses/TBMT02/Litteratur.html
• http://physics.rsna.org/default.asp (Great material, wish it didn't require a login)

Anatomy guides (well, not for the course...)

• http://www.neurosurvival.ca/ComputerAssistedLearning/readingCTs/Anatomy_guide/alpha.htm
• http://www.med-ed.virginia.edu/courses/rad/headct
• http://www.med-ed.virginia.edu/courses/rad/abdtrauma
• http://www.chestradiology.net/anatomy.cgi
• http://bidmc.org/MedicalEducation/Departments/Radiology/MedicalStudents/LivingAnatomy.aspx
  

Everything

• http://www.radiologyeducation.com/
  

 

GoDaddy & SOPA

GoDaddy is foolish for supporting SOPA.  Gotta change to a new provider, e.g. http://www.hostgator.com/

Insert Credit

Wow.  Great blog.

http://insertcredit.com/

Especially:

http://insertcredit.com/2011/09/22/who-killed-videogames-a-ghost-story/

LDAP on debian

Well, here is the starting point
http://research.partners.org/wiki/index.php/Active_Directory_on_Unix

But that doesn't quite work.  What is the difference between using ldap:// and ldaps://?  My opensuse box uses ldaps://, which seems to work ok.  But the debian instructions say use ldap://.

Debian has a very useful resource here.

http://www.debian-administration.org/articles/585

If I do "ldapsearch -x", this works using ldap://, but I get an error message "...a successful bind must be completed on the connection."  Possibly this is answered here:

http://forums.techarena.in/active-directory/662084-2.htm

See also this:

http://www.openldap.org/doc/admin24/appendix-common-errors.html

Eventually I learned the reason I get the error about "...a successful bind must be completed on the connection." is that I forgot to use a user name.  For example, the following works:

ldapsearch -v -D 'cn=myuser,cn=users,dc=example,dc=org' -H ldap://ldap.example.org -b dc=example,dc=org -W -x

This even works without "-x" option, which is good news.  But I still get the following error:

$ id myuser
id: myuser: No such user

Aha!  I got it.  I had mistakenly installed "nslcd, libnss-ldap, libpam-ldapd" instead of "nslcd, libnss-ldapd, libpam-ldapd"

How to restrict access to which LDAP users can log in?  See, for example:

http://linux.web.cern.ch/linux/docs/account-mgmt.shtml

The secret was to change the user names into the "filter shadow" line, like this:

filter shadow (!(cn=usr1)(cn=usr2))

Another possible problem is incorrect TLS certificate.  The web page which describes this cannot be found by web search.  Use inside knowledge to find the hidden URL on intranet.

Pulse audio glitches again

Maybe it's not pulse, but usually it is.  Time to debug the problem

• Amarok skips.  It seems to use phonon, pulse, and xine
• mpg321 works fine.  I suppose it uses alsa.
• Mplayer works fine.  It uses ffmpeg and alsa.
• I tried amarok with phonon-backend-vlc.  But amarok skips with that one too
• I tried to disable time-based scheduling as recommended here:
• http://fedoraunity.org/Members/fenris02/pulseaudio-fixes-and-workarounds
• https://fedoraproject.org/wiki/How_to_debug_PulseAudio_problems
• I did the tsched=0 thing.  It helped, but not enough
• Then, I edited /etc/pulse/daemon.conf, and changed realtime scheduling.  But this doesn't seem to make a difference.

$ cat /proc/asound/cards
  0 [SB             ]: HDA-Intel - HDA ATI SB
                      HDA ATI SB at 0xfe8f4000 irq 16
 1 [HDMI           ]: HDA-Intel - HDA ATI HDMI
                      HDA ATI HDMI at 0xfe9ec000 irq 44

Not sure what it really means.  Phonon can be configured to use either of them, but they both skip.  My device is some kind of "on motherboard" thing.

$ lspci -v

00:14.2 Audio device: ATI Technologies Inc SBx00 Azalia (Intel HDA)
        Subsystem: Dell Device 02e2
        Flags: bus master, slow devsel, latency 64, IRQ 16
        Memory at fe8f4000 (64-bit, non-prefetchable) [size=16K]
        Capabilities:
        Kernel driver in use: snd_hda_intel

01:00.1 Audio device: ATI Technologies Inc RV710/730
        Subsystem: PC Partner Limited R700 Audio Device [Radeon HD 4000 Series]
        Flags: bus master, fast devsel, latency 0, IRQ 44
        Memory at fe9ec000 (64-bit, non-prefetchable) [size=16K]
        Capabilities:
        Kernel driver in use: snd_hda_intel

Then, I read a web page that suggests deleting the ~/.pulse directory, and so I did.  And it fixed it!  But only until the next reboot.

SBRT references

These came in the medphys listserv

http://www.astro.org/PublicPolicy/WhitePapersAndOtherDocuments/documents/SVReqsUpdate6211.pdf

http://www.astro.org/PublicPolicy/WhitePapersAndOtherDocuments/documents/SVFAQs0210.pdf

http://www.astro.org/PublicPolicy/WhitePapersAndOtherDocuments/documents/SBRTMP.pdf

Haiku stuff

Virtual box settings

http://www.haiku-os.org/documents/user/haiku_under_emulation

https://www.haiku-os.org/guides/virtualizing/virtualbox

Gnome-terminal problems (again)

Sigh...looks like gnome-terminal bug came back:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=631116

1) The problem is probably related to an incompatibility with SCIM.  Disabling SCIM (using im-config) solves the problem.  See also:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=632094

2) Probably the answer is to switch from SCIM to IBus.

http://en.wikipedia.org/wiki/Intelligent_Input_Bus

3) Gnome-terminal has its own special way of setting an input method: using a right-click menu (wtf??)

http://superuser.com/questions/109554/removing-scim-input-method-as-default-from-gnome-terminal

Maybe you can set it to XIM and then use SCIM.

JPOP resources

A big thanks to these web sites for preserving our cultural heritage.

http://www.otonomai.net
http://mlbeto1169.blogspot.com/
http://www.dimazdizon.com/category/japan/

Virtualbox + windows 98

This turned out to be trickier than I thought.  Virutalbox is not well optimized for windows 98.  Here are some tricks:

http://forums.virtualbox.org/viewtopic.php?t=9918

glib.GError: Unrecognized image file format

Deluge crashes with this error.  How boring.

The fix is to edit common.py as described by brianbrian

http://ubuntuforums.org/archive/index.php/t-1063483.html

Alternative OS

Be sure to check the comments for additional ideas.

http://royal.pingdom.com/2008/09/26/10-amazingly-alternative-operating-systems-and-what-they-could-mean-for-the-future/

Freshmeat review 2011-08-21 to 2011-07-24

Eliot - scrabble game
http://freshmeat.net/projects/eliot

Potrace - bitmap tracing code
http://freshmeat.net/projects/potrace

Cinelerra - audio/video production system
http://freshmeat.net/projects/cinelerra

OpenMP Template Library - parallel STL implementation
http://freshmeat.net/projects/omptl

Freshmeat review *RANDOM*

Assassin of the Underdark - 2D RPG
http://freshmeat.net/projects/assassin-of-the-underdark

Kobold's Quest 2 - RPG
http://freshmeat.net/projects/kobolds-quest-2

Evermeet - 2D RPG
http://freshmeat.net/projects/everme

Liquid War 6 - RTS
http://freshmeat.net/projects/liquid-war-6

Digibuild - Minecraft clone
http://freshmeat.net/projects/digbuild

Beastlands - Song of the Were - 2D RPG
http://freshmeat.net/projects/beon-astlands-ehlonnas-boon

Cdrcat - (MP3) catalog program
http://freshmeat.net/projects/cdcat

The Golden Hasweg: A Dwarven Tale - Dwarf fortress clone
http://freshmeat.net/projects/the-golden-hasweg-a-dwarven-tale

D* Lite - Advanced (?) A* search algorithm
http://freshmeat.net/projects/d-star-lite

Econtycoon - Economy tycoon game
http://freshmeat.net/projects/econtycoon

Construder - Minecraft clone
http://freshmeat.net/projects/construder

Penultimate Generation - Trek clone
http://freshmeat.net/projects/penultimate-generation

District Builder - Anti-gerrymandering software (!)
http://freshmeat.net/projects/district-builder

WarTactical - War game
http://freshmeat.net/projects/wartactical

Remove old kernels in debian

http://tuxtweaks.com/2009/12/remove-old-kernels-in-ubuntu/

Starview KVM sticky key problem

After moving my office, I started having trouble with my Starview KVM.  It is a problem I vaguely remember having some years ago after it first arrived, and then I worked around the problem.  But now, after putting my computer together again, it came back.

The problem is that sometimes, a letter will stick, and get repeated.  Like thisssssssssssss. 

It seems to be a firmware bug.  According to Mike, you can fix it by installing new firmware.

http://www.newegg.com/Product/Product.aspx?Item=N82E16817707139

Now, after reading his posts, I understand how I solved it before.  There are dedicated keyboard mouse ports on the starview, but you can also plug your keyboard & mouse to the general purpose ports.  The general purpose ports don't have this problem.

Virutal functions, but non-virtual destructor

Something to read when I have some free cycles:

http://www.gotw.ca/publications/mill18.htm

Polygon algorithms

Found this interesting web site for algorithms such as computing winding number.
http://softsurfer.com/Archive/algorithm_0103/algorithm_0103.htm

Tree data structures

How boring.  No tree in STL.  Too lazy to write my own...

http://stlplus.sourceforge.net/

http://stlab.adobe.com/group__forest__related.html

http://code.google.com/p/treetree/

http://www.codeproject.com/KB/architecture/treedata_class.aspx

http://www.scalingweb.com/bplus_tree.php

Installing W7 SP1

I'm trying to install W7 SP1 on Snowball.  The error message is:

<put error message here>

The problem is apparently that w7 requires access to boot manager (formerly boot.ini) to install SP1.

http://forums.opensuse.org/english/get-technical-help-here/how-faq-forums/unreviewed-how-faq/454535-opensuse-dual-booting-windows-7-loading-service-pack-1-windows-7-a.html

GUI testing

Sikuli - GUI testing tool
http://sikuli.org/

GMER

A rootkit detection program for windows

http://www.gmer.net/

*** VTE ***: Failed to load terminal capabilities from '/etc/termcap'

Solution:

sudo ln -s /usr/share/vte/termcap-0.0/xterm /usr/share/vte/termcap/xterm

https://bugs.launchpad.net/ubuntu/+source/vte/+bug/140011

Freshmeat review 2011-06-18 to 2011-06-13

None

Freshmeat review 2011-06-13 to 2011-05-22

World War vi - Side-scrolling game
http://freshmeat.net/projects/wordwarvi

JShot - One-step screen capture, annotate and upload
http://freshmeat.net/projects/jshot

Freeberb3 - Sound processing library
http://freshmeat.net/projects/freeverb3

Turious - TBS game
http://freshmeat.net/projects/turious

Morituri - CD ripper
http://freshmeat.net/projects/morituri

Naev - Space trading game
http://freshmeat.net/projects/naev

OCE - 3D computer aided design (CAD)
http://freshmeat.net/projects/oce

Cottage - graphics and sound engine for HTML5 games
http://freshmeat.net/projects/cottage

TPS in octave

I was crying.  Needed some plots of TPS in 1D.  Gints Jekabson comes to the rescue!

http://www.cs.rtu.lv/jekabsons/regression.html

Finding extra files in your svn directory

Always I forget to do this before running "make package_source".

$ svn status

Build debian package: take 2

This is my interpretation of http://debian-med.alioth.debian.org/docs/policy.html

When everything is correct, you should be able to do this:

1. cd plastimatch/trunk
2. uscan --force-download
   
3. svn-buildpackage -rfakeroot -uc -us

However, while you are debugging, the above workflow is perhaps cumbersome if you are maintaining the source package.  It would require you to update e.g. the source tarball.  Instead, you can do this:

1. cd source-dir
   
2. debuild -j4 -i -us -uc -b
3. debuild -j4 -i -us -uc -S

Note that the last one doesn't work if the debian subdirectory in the source directory is a symlink.  You need to actually make a copy.

1. cd source-dir
2. cp -r ../trunk/debian .

If you just want to run lintian, you can do this:

1. lintian -b ./plastimatch_1.5.0-1_amd64.deb
2. lintian ./plastimatch_1.5.0-1_source.changes
   

When you are messing around with cmake settings and get-orig-source, you can use the following workflow:

1. make new upstream tarball (don't forget to use pristine source directory -- cmake will include everythign)
2. link upstream tarball to debian upstream tarball
3. run get-orig-source
   

For me, the following commands implement the above idea

1. cd build/plastimatch-pristine
2. make package_source
3. cp plastimatch-1.5.0-beta.2493-Source.tar.bz2 ~/debian-med/packages/plastimatch
4. cd ~/debian-med/packages/plastimatch
5. ln -s plastimatch-1.5.0-beta.2493-Source.tar.bz2 plastimatch-1.5.0.orig.tar.bz2
6. cd trunk
7. debian/get-orig-source
   

To test the package dependencies, you need a "clean pbuilder environment".  Do this:

1. sudo pbuilder create
2. sudo pbuilder --update
3. sudo pbuilder --build foo_version.dsc

The first time you do it, you need to do a few more steps.  See the debian policy document for details (http://www.debian.org/doc/manuals/maint-guide/build.en.html  See specifically section 6.4).

Partial update of packages

Here is how to track testing, but update some packages from unstable

http://www.debian.org/doc/manuals/reference/ch02.en.html#_tracking_literal_testing_literal_with_some_packages_from_literal_unstable_literal

Building a debian package

Wow, lots to learn.

• Create the launchpad account
  https://launchpad.net/~gregsharp-geo
  
• Here is some background reading
  https://wiki.ubuntu.com/PackagingGuide/HandsOn
  https://wiki.ubuntu.com/PbuilderHowto
• http://willnichols.me.uk/progs/debpack/ar01s02s02.html
  
• Read section 3 of HandsOn, "Packaging From Scratch"
• Think about the CUDA dependency.  There are some packages available here:
  wheezy (devel): 3.2.16-2 [non-free]
  sid (devel): 3.2.16-2 [non-free]
  experimental (devel): 4.0.17-1 [non-free] 
• See also this:
  http://groups.google.com/group/theano-users/browse_thread/thread/543033f4fc06548a/58e4221f43b59bee?#58e4221f43b59bee
  https://launchpad.net/~aaron-haviland/+archive/cuda-4.0
• lib32cublas4, lib32cudart4, lib32cufft4, lib32curand4, lib32cusparse4, lib32npp4, libcublas4, libcudart4, libcufft4, libcurand4, libcusparse4, libnpp4, nvidia-compute-profiler, nvidia-cuda-dev, nvidia-cuda-doc, nvidia-cuda-gdb, nvidia-cuda-toolkit, nvidia-opencl-dev

Freshmeat review 2011-05-15 to 2011-05-22

0 A.D. - RTS game
http://freshmeat.net/projects/0-ad

Freelords - TBS game
http://freshmeat.net/projects/freelords

DIN - audio synthesizer
http://freshmeat.net/projects/din

Freshmeat review 2011-05-04 to 2011-05-14

QtiPlot - clone for origin
http://freshmeat.net/projects/qtiplot

Conquests - 4X strategy game
http://freshmeat.net/projects/conquests

HOPSPACK - parallel optimizer
http://freshmeat.net/projects/hopspack

IHE-RO

The IHE-RO documentation is somewhat elusive. 

The technical framework web page has 3 documents.

http://www.ihe.net/Technical_Framework/index.cfm

And there are several more documents on the wiki

http://wiki.ihe.net/index.php?title=Radiation_Oncology

Also there are things like that have no links to them:

http://wiki.ihe.net/index.php?title=File:IHE-RO_Dose_Compositing_Supplement_v1.0-TI.pdf&oldid=41224

Setting up CDash

Well, this is awesome.  In the last few years when I wasn't paying attention, Kitware allowed to make your own project page for CDash. 

http://iborco.blogspot.com/2008/11/cdart-cdart2-or-cdash-no-cdash-public.html

Some suggestions about how to set up nightly:

http://cmake.3232098.n2.nabble.com/MSVC-Console-Environment-in-CTest-td3830925.html
http://www.vtk.org/Wiki/ITK/Examples/Instructions/ForAdministrators
http://code.google.com/p/dynamorio/source/browse/trunk/suite/nightly.cmake?spec=svn385&r=200

Cloud Storage

S3

Dropbox
2GB free, 50GB = $120/yr

Live Mesh
5GB free (skydrive)
PC/Mac client (Web access for linux)

Ubuntu One
2GB free, 20GB = $36/yr
Linux, Windows in beta

JungleDisk

SpiderOak
2GB free, 100GB = $120/yr

Box.net

SugarSync

Cloudsafe

Reviews:
http://hardware.slashdot.org/story/11/07/27/0547218/DIY-Dropbox-Alternatives
http://yro.slashdot.org/story/11/06/16/1618206/Open-Source-Alternative-To-Dropbox
http://web.appstorm.net/roundups/data-management-roundups/dropbox-vs-spideroak-file-sync-battle/
http://web.appstorm.net/roundups/communication-roundups/10-easy-sites-for-file-sharing/

CUDA + VS2010

http://blog.cuvilib.com/2011/02/24/how-to-run-cuda-in-visual-studio-2010/

Rad Onc sites

Here are some rad onc sites for future reference

http://en.wikibooks.org/wiki/Radiation_Oncology
http://ozradonc.wikidot.com/start
http://www.isocentre.org/

Physics sites

http://www-naweb.iaea.org/nahu/dmrp/slides.shtm

http://www.medphyswiki.com/wiki/Main_Page

http://www.trad.umn.edu/divisions/radiationphysics/qualityassurance/home.html
http://www.medphys.ca/content.php?doc=58
http://www.nrc.gov/reading-rm/doc-collections/cfr/

Chromaprint

This looks very cool.  A new audio fingerprinting app.

http://forums.musicbrainz.org/viewtopic.php?id=2432

Recording playback

I can't seem to record playback in either Win 7 or Linux

Win 7

• There is no option for stereo mix in my recording device properties
• My hardware is Dell Inspiron Desktop 546MT, Via 1708S
• I have updated my driver to Dell's latest version (R237832.exe, 10/25/2009)

MR Acronyms

http://www.mr-tip.com/serv1.php?type=cam

Compiler list

An excellent resource for compilers.

http://www.math.utah.edu/faq/compilers/compilers.html

Configuring Amarok with my Sansa Fuze

Apparently Amarok can copy files to the FUZE.  The trick is the little unlabeled button on the FUZE bar of the Amarok collection list.

http://www.goodbyemicrosoft.net/news.php?item.615.2

Machine learning

After my frustration with LIBSVM, I decided to look into other methods.  Weka suggests that PLS works well for my problem.  But anyway, I need to find a good package (weka is java therefore unsuitable).

http://www.support-vector-machines.org/SVM_soft.html
http://www.linux.org/docs/ldp/howto/AI-Alife-HOWTO-2.html
http://torch5.sourceforge.net/
http://mloss.org/software/
https://spreadsheets.google.com/ccc?key=0Aunb9cCVAP6NdDVBMzY1TjdPcmx4ei1EeUZNNGtKUHc&hl=en#gid=0

Reviews.

Weka
Very good for exploring data.  I found several good algorithms (mostly linear algorithms such as PLS).  However, not a final solution because it is written in Java.

LIBSVM
Performs poorly on my data.

LIBLinear
Not yet benchmarked.

Waffles
This will be good, but currently doesn't compile due to being 64-bit clean (gcc 4.5).

dlib
Looks promising.  There is no benchmarking tool (?)

Shark
Looks promising.  Not yet benchmarked.

Shogun
I previously reviewed this, using the Octave plugin.  However, I don't remember the results.  Need to re-benchmark.

Another jpop site

Seems to have downloadable music: http://www.nautiljon.com/

Workarounds for github unreliability

Recently looking at how to handle github unreliability problems.  This will probably involve creating a mirror site.

MIght be possible using a "post-receive hook"

http://help.github.com/post-receive-hooks/

Lame settings for transcoding voice

Here is a reasonably good setting for low quality voice

lame -a -m s -b 16 test.wav test.mp3

See also

http://www.hydrogenaudio.org/forums/index.php?showtopic=3270

Another music site

http://www.daytrotter.com/al/artists/alphabetical.html

Saving gmail messages

I needed to re-compose a file which was split into 7 parts and sent to my gmail account.  Strangely, you cannot do this through the web interface -- instead you have to set up POP3 or IMAP to do this (!).  While trending on this idea, I learned that you can access Yahoo! mail through POP3 too, using the YPOPs! application.

http://ypopsemail.com/

Out of sight!

But anyway, back to gmail.  I enabled POP3 (actually it was already enabled), and set up Claws to retrieve.  There is some complicated-looking instructions in the Claws help pages:

http://www.claws-mail.org/faq/index.php/Installation_and_Configuration#Does_Claws_Mail_work_with_Gmail_accounts.3F

Well, actually that part is not so complicated, but the part about effectively using gmail tags is.  The thing is, if you don't do that correctly, all of your "archive"d emails get thrown in your inbox together with everything else.

Zerogsound

Wow, excellent work by Zero G Sound to preserve our folk music heritage. 

http://zerogsound.blogspot.com/

SSE flags with CMake

Some pointers:

http://vir.homelinux.org/blog/index.php?url=archives/140-Automatic-Optimization-for-your-CPU-with-CMake.html&serendipity[csuccess]=moderate#feedback

https://gforge.sci.utah.edu/gf/project/Manta/scmsvn/?action=browse&path=%2F*checkout*%2Ftrunk%2FCMake%2FCheckSSE.cmake

http://trac.libyuni.org/browser/trunk/src/cmake/DetectInstructionsSets.cmake?rev=799

https://code.ros.org/discuss/ros-users/messages/4179?noheader=1

http://www.cmake.org/pipermail/cmake/2010-March/036115.html

Fun with ion chambers

Oh, this is so cool!

http://www.techlib.com/science/ion.html

Grub error: symbol grub_xputs not found

Yet another bad version of Grub got pushed to Debian testing.  Those guys really are not doing QA properly.  Anyway, the error message appears before the grub screen starts, and looks like this:

Grub error: The symbol grub_xputs not found
grub rescue>

Apparently grub is confused because I have 2 hard disks (duh...).  You can read many bug reports about this, and it is still not solved after most of a year.  For example

• https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/509797
• https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/609280
• http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=588370
• http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=589737

The solution is to burn a live cd (I use USB for this), and fix.  Here is the solution details, and it works quite well:

• http://grub.enbug.org/Grub2LiveCdInstallGuide
  

American Buddha Online Library

When you have a little free time, the following is a good read.

http://www.american-buddha.com/

Perl30Ex.dll + IIS

POST isn't working with Perl30Ex.dll.  Here is what I've checked:

1. Check install, permissions, etc (everything seems configured correctly)
   http://blogs.iis.net/wadeh/archive/2009/04/13/running-perl-on-iis-7.aspx
2. Look through CGI doc, try different options (no apparent effect)
   http://perldoc.perl.org/CGI.html
3. Enable failed request tracking (no failures logged)
   http://mvolo.com/blogs/serverside/archive/2007/07/26/Troubleshoot-IIS7-errors-like-a-pro.aspx
4. Compare source pages between working (apache) and non-working (iis) systems
   They are the same
   
5. Disable windows authentication in IIS
6. 
   

Radeon+Debian (again)

This morning's update of Debian testing borked my X again.  If I try to run startx, the system hangs (black screen, unresponsive (?) keyboard).  Luckily, when booting from an older kernel, X seems to run fine.

Here is my card:

gsharp@wormwood:~$ lspci -v |grep VGA
01:00.0 VGA compatible controller: ATI Technologies Inc RV710 [Radeon HD 4350] (prog-if 00 [VGA controller])

Here are the pertinent bits from /var/log/Xorg.0.log

Older kernel (working):

(II) [KMS] Kernel modesetting enabled.
(WW) Falling back to old probe method for vesa
(WW) Falling back to old probe method for fbdev
(II) LoadModule: "fbdevhw"
(II) Loading /usr/lib/xorg/modules/linux/libfbdevhw.so
(II) Module fbdevhw: vendor="X.Org Foundation"
        compiled for 1.7.7, module version = 0.0.2
        ABI class: X.Org Video Driver, version 6.0
(II) RADEON(0): Creating default Display subsection in Screen section
        "Default Screen" for depth/fbbpp 24/32
(==) RADEON(0): Depth 24, (--) framebuffer bpp 32
(II) RADEON(0): Pixel depth = 24 bits stored in 4 bytes (32 bpp pixmaps)

Newer kernel (not working):

(II) Primary Device is: PCI 01@00:00:0
(II) [KMS] drm report modesetting isn't supported.
(WW) Falling back to old probe method for vesa
(WW) Falling back to old probe method for fbdev
(II) Loading sub module "fbdevhw"
(II) LoadModule: "fbdevhw"
(II) Loading /usr/lib/xorg/modules/linux/libfbdevhw.so
(II) Module fbdevhw: vendor="X.Org Foundation"
        compiled for 1.7.7, module version = 0.0.2
        ABI class: X.Org Video Driver, version 6.0
(EE) open /dev/fb0: No such file or directory
(II) RADEON(0): TOTO SAYS 00000000fe9f0000
(II) RADEON(0): MMIO registers at 0x00000000fe9f0000: size 64KB
(II) RADEON(0): PCI bus 1 card 0 func 0
(II) RADEON(0): Creating default Display subsection in Screen section
        "Default Screen" for depth/fbbpp 24/32
...
(EE) RADEON(0): Timeout trying to update memory controller settings !
(EE) RADEON(0): You will probably crash now ...
(EE) RADEON(0): Timeout trying to update memory controller settings !
(EE) RADEON(0): You will probably crash now ...
...

The new (not working) kernel goes on and loads module "vgahw" as well, which the older (working) kernel doesn't.

Originally, I had these three packages installed:

xserver-xorg-video-ati
xserver-xorg-video-radeon
xserver-xorg-video-radeonhd

So I removed the radeon one (presumably not needed for my card?):

apt-get remove xserver-xorg-video-radeon

This worked (in the sense that I get video), but didn't work (in the sense that X reverted to VESA).  The Xorg.log yields:

(II) LoadModule: "ati"
(WW) Warning, couldn't open module ati
(II) UnloadModule: "ati"
(EE) Failed to load module "ati" (module does not exist, 0)

So, I manually add radeonhd to the /etc/X11/xorg.conf

Section "Device"
    Identifier     "Device0"
    Driver         "radeonhd"
EndSection

However, this causes X not to start with the following error:

(II) [DRM] Kernel mode setting enabled
(EE) FATAL: RadeonHD presently does not work with kernel modesetting (KMS).
Please disable KMS in your kernel.
(II) UnloadModule: "radeonhd"
(EE) Screen(s) found, but none have a usable configuration.

Apparently the best way to deal with this is to tell the kernel to disable kernel modesetting, by adding radeon.modeset=0 (or is it radeonhd.modeset ??).  See e.g. this link: http://lists.opensuse.org/radeonhd/2009-11/msg00175.html

To test this, I need to reboot, and specify the kernel parameters to grub.  This method is described in this link http://grumpymole.blogspot.com/2007/05/ubuntu-how-to-edit-grub-boot-parameters.html:

• Press "Esc" to intercept boot countdown
• Go to the grub menu entry
• Press 'e' to start editing.
• Scroll down to the "linux..." line. Add "radeon.modeset=0" to the end.  (Yes, radeon, not radeonhd).
  
• Press CTRL-x to boot using that kernel and those parameters.

The method for making these changes permanent are not well described, but here is how to do it:

• Edit /etc/default/grub
• Change GRUB_CMDLINE_LINUX to include "radeon.modeset=0"
• grub-mkconfig -o /boot/grub/grub.cfg
• grub-install /dev/sdb (or whichever drive has the relevant MBR)
  

http://forum.nginx.org/read.php?26,90217,90217

References:

http://wiki.debian.org/AtiHowTo
http://www.x.org/wiki/radeonhd

Cluster file synchronization

I like unison well enough, but maybe something better needed for the cluster.  For example csync2.  Look at the post by Vitek, with his recommendations:

http://pooteeweet.org/blog/0/909#m909

kondemand problem

I am getting sluggish performance out of twofish, with the following output from top.  Sometimes %si (software interrupts) goes very high, though it is not shown in the current top dump.

top - 18:21:05 up 35 days,  3:30,  1 user,  load average: 0.71, 0.48, 0.39
Tasks: 250 total,   1 running, 249 sleeping,   0 stopped,   0 zombie
Cpu(s):  0.0%us,  0.0%sy,  0.0%ni, 99.7%id,  0.0%wa,  0.0%hi,  0.3%si,  0.0%st
Mem:  20557640k total,   865564k used, 19692076k free,   159480k buffers
Swap: 23446828k total,        0k used, 23446828k free,   532112k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
13359 gcs6      20   0 51564 3560 2560 R   18  0.0   0:03.12 top
   93 root      15  -5     0    0    0 S    2  0.0 305:29.57 kondemand/5
 4168 root      20   0  8908  504  376 S    2  0.0 199:42.04 irqbalance
   95 root      15  -5     0    0    0 S    2  0.0 303:43.57 kondemand/7
   50 root      15  -5     0    0    0 S    1  0.0 217:07.99 events/15
   99 root      15  -5     0    0    0 S    1  0.0 306:53.07 kondemand/11
  101 root      15  -5     0    0    0 S    1  0.0 332:41.09 kondemand/13
   89 root      15  -5     0    0    0 S    1  0.0 308:02.11 kondemand/1
   91 root      15  -5     0    0    0 S    1  0.0 319:29.00 kondemand/3
 4750 root      20   0 14608  632  476 S    1  0.0   2:11.19 cron

Not sure the problem, but I will like to try upgrading the kernel.  It seems there are 3 different kernel revisions in the 4 machines.

id3 tools on linux

Ugh. Every time I need to debug ID3 tags, I have to sort through a bunch of buggy, obsolete id3 tools.  Well, this time I'll try to take notes.

Here are the ones in Debian (starting with command line tools):

id3
http://code.google.com/p/id3/
Completely useless (id3v1 only).

id3tool
http://nekohako.xware.cx/id3tool/
Completely useless (id3v1 only).


id3v2
http://id3v2.sourceforge.net/
Mostly useless.  Does not, for example, show encoding information.

mp3diags
http://mp3diags.sourceforge.net/
Nice program.  Wish it would give more information about encoding.

Setting up NFS with a firewall

The below post explains how to do this for CentOS (the relevant post is the one by MensaWater).  It works great!  Thanks MensaWater.  :)

http://www.linuxquestions.org/questions/linux-networking-3/help-nfs-error-no-route-to-host-341562/page2.html

The relevant text-mode firewall configuration tool is called system-config-securitylevel.  You can use spaces to separate the "other ports" that you need to add.

For NFS4, the following post looks useful:

http://blog.laimbock.com/2009/05/21/nfsv4-on-centos-53-and-fedora-11/

Sudo + ssh

It can be done.  The first step is to do the ssh-agent and ssh-add stuff.

http://www.sudo.ws/pipermail/sudo-users/2003-April/001477.html
http://mah.everybody.org/docs/ssh

Then the second piece of the puzzle is to do ssh -t so you can answer the sudo prompt properly.  But you need to "prime" sudo, so it caches your password.  See comment by crashingdaily in the following post:

http://crashingdaily.wordpress.com/2007/06/29/rsync-and-sudo-over-ssh/

BFGS notes

In addition to the wikipedia articles, I found these nice notes:

http://www.math.mtu.edu/~msgocken/ma5630spring2003/lectures.html
http://www.math.mtu.edu/~msgocken/ma5630spring2003/lectures/

Also these:

http://www.srl.gatech.edu/education/ME6103/Quasi-Newton.ppt

This looks really hands on:

http://hal3.name/docs/daume04cg-bfgs.pdf

A nice looking implementation.  Also, check references on this one, esp. for line search code:

http://www.chokkan.org/software/liblbfgs/

Matlab implementations of several optimizers:

http://www4.ncsu.edu/~ctk/matlab_darts.html

Another lbfgs implementation:

http://www.cs.umd.edu/~oleary/LBFGS/

Another paper describing LBFGS

http://www.fs.utm.my/matematika/images/stories/matematika/200117103.pdf

A survey of truncated newton methods

http://iris.gmu.edu/~snash/nash/assets/TN_Survey/tn_survey.html

Dicom test files

From Steve Pieper:

http://www.slicer.org/slicerWiki/index.php/File:Dicom-database-examples-2010-03-09.zip

Optimizer summary

L-BFGS-B:
http://www.ece.northwestern.edu/~nocedal/lbfgsb.html
License: GPL

M2QN1:
http://www-rocq.inria.fr/~gilbert/modulopt/optimization-routines/m2qn1/m2qn1.html
License: proprietary

TNBC:
http://iris.gmu.edu/~snash/nash/software/software.html
License: unspecified

DONLP2:
http://www.mathematik.tu-darmstadt.de/fbereiche/numerik/staff/spellucci/DONLP2/
License: commercial

ALGLIB
http://www.alglib.net/
License: GPL

L-BFGS-B license

I was poking around with the L-BFGS-B optimizer, which is used by plastimatch (also ITK).  I discovered it is GPL licensed, (and/or covered by ACM license):

http://www.eecs.northwestern.edu/~nocedal/lbfgsb.html
http://www.acm.org/publications/policies/softwarecrnotice

I wonder if the license changed.  For example SciPy uses under a different license:

http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.fmin_l_bfgs_b.html

The SciPy list has a discussion of alternate optimizers of this class.

http://osdir.com/ml/python.scientific.devel/2004-04/msg00005.html

See also this regarding GSL routines.

http://www.mail-archive.com/help-gsl@gnu.org/msg00603.html

String libraries redux

Well, the string library stuff is coming up again.  For my C++ code, I'm interested in what can be done better than std::string.  E.g. is CBstring better?  There are some comparisons by the authors:

• http://www.and.org/vstr/comparison
• http://bstring.sourceforge.net/features.html

As far as it goes, Matthew Wilson's code looks interesting too:

• http://www.fastformat.org/

Monte Carlo codes

Monte Carlo codes: MCNPX, DPM, PENELOPE, etc

GEANT4

• http://geant4.web.cern.ch/geant4/

Here is the site for MCNPX

• https://mcnpx.lanl.gov/

Not sure where I can download DPM. Here is an old version

• http://www-personal.umich.edu/~bielajew/DPM/

Penelope. It is hard to find as well. But eventually I found it.

• http://www.nea.fr/abs/html/nea-1525.html
• http://www.nea.fr/html/dbprog/usacan.htm
• http://www.dosisoft.com/PDF/Presentations_seminaire_0704/Penelope-J%20Barthe-CEA.pdf

VMC++. Apparently it is proprietary

• http://www.nrc-cnrc.gc.ca/eng/projects/inms/vmc.html

Smart pointers

Plastimatch would benefit from smart pointers (or GC).  There are a couple of places in the code where logic must swap around data between containers, and do bookkeeping because the containers own the data.

Here are some implementations of smart pointers:

• ITK smart pointers (advantage - already required by project)
• Boost (disadvantage - many incompatible versions)
  
• Loki
• Yasper
• RefPtr (not thread safe?)

It would seem that smart pointers require C++.  Using C is too cumbersome (though possible, see earlier post).

I'm slightly concerned about the loss of performance in naive reference
counted smart pointers.  See for example this description:

http://c2.com/cgi/wiki?ReferenceCounting

New crop of blogging sites

Here is what scribefire 3.5 supports.  These are APIs, not sites.

• Wordpress
• Movable Type
• Drupal
• Textpattern
• Roller
• MetaWeblog API
  
• Blogger
• Tumblr

My current dissatisfaction with blogger is that you can only edit the 25 most recent posts.  This makes it difficult to update/merge older entries.

From the w.blogger site, here are a slightly dated list of blog sites.

• Blogger
• MSN Spaces
• TypePad
• BigBlogTool
• Blogalia
• TheBlog
• Blog-City
• EraBlog.NET
• Upsaid
• UBlog
• SquareSpace
• BlogWare
• DearDiary.Net

Radeon + debian 2.0

Still having problems with my ATI Radeon HD 4350 on linux.  The card has a RV710 (according to lspci), which means it should be supported by the debian radeonhd package.

I try to delete xserver-xorg-video-radeon (it is presumably unneeded).  But when I do that, X fails to start.

Star Wars

A couple of star wars links came on slashdot.  I'll check them out when I have a free minute:

http://www.gappon.com/star-wars-return-of-the-ewok-1982-583635.html

http://entertainment.slashdot.org/story/09/12/21/1637235/The-Definitive-Evisceration-of-The-Phantom-Menace-NSFW?art_pos=14

http://entertainment.slashdot.org/story/09/10/06/1647234/Fans-Come-Together-To-Complete-Star-Wars-Uncut

PDF markup and review

Here are the contenders:

• flpsed
• scribus
  
• pdfedit
• Xournal

DKMS autoload fails for fglrx (ATI proprietary driver)

This message flashes on the screen at boot time, after the latest debian kernel update.  Unfortunately it doesn't appear in the log anywhere.I suppose the solution is to patch the driver like the following link. 

http://lkml.org/lkml/2009/10/12/255

In more detail, go to directory

/usr/src/fglrx-8.681

Edit the file kcl_io.c, and add the following line

#include .

Then run the following:

sudo dkms build -m fglrx -v 8.681

Xsession: Login for (user) is disabled

After upgrading my kernel, I got the error message, and X would not allow me to run a session.

Xsession: Login for (user) is disabled

This is fixed by editing /etc/shells, and adding a line for the LDAP-specified shell (in my case, /bin/PHSshell).

http://www.linuxquestions.org/questions/susenovell-60/xsession-login-for-someuser-is-disabled.-369654/

More lisp game resources

http://lispgamesdev.blogspot.com/
http://common-lisp.net/cgi-bin/mailman/listinfo/lisp-game-dev

LDAP + Kerberos

I get an error like this:

gcs6@gelato:/etc> ldapwhoami
SASL/GSSAPI authentication started
ldap_sasl_interactive_bind_s: Local error (-2)

Not yet completely fixed, but looks like you need to do both of the following:

http://research.imb.uq.edu.au/~l.rathbone/ldap/gssapi.shtml
http://www.linuxquestions.org/questions/linux-networking-3/kerberos-kinit-reply-did-not-match-expectations-445698/

OLPC free sound samples

http://wiki.laptop.org/go/Sound_samples

Setting up a new subversion repository

1. Edit /etc/httpd/conf.d
   Add section where "Location" is the name of the module
   Set "SVNPath" as appropriate
   Set "AuthUserFile" to name of a new file
   
2. Create password file, such as /var/www/svnusers-name-of-project
   For each user, add password such as:
   sudo htpasswd -m svnusers-name-of-project new-user
   (Actually, maybe the -m is not desired?)
   
3. Create the archive:
   cd /home/subversion/repos/
   sudo svnadmin create name-of-project
   sudo chown -R apache.apache name-of-project
4. Restart apache
   (If you don't do this, you get the dreaded "200 OK" error)
   In Centos, do this:  sudo /sbin/service httpd restart
   
   

Some RT links

I'm looking for the definitions of machine coordinate system IEC 61217.  This doesn't seem to be available in any of the web pages.  Here is the reference for the spec:

International Electrotechnical Commission, IEC 61217: Radiotherapy Equipment—Coordinates, Movements and Scales ~International Electrotechnical Commission, Geneva, 1996.

Best reference I could find is the AAPM task group report.

http://www.aapm.org/pubs/reports/OR_01.pdf

What is IEC 60601-2-11?

Medical electrical equipment - Part 2-11: Particular requirements for
the safety and essential performance of gamma beam therapy equipment

Short but useful link.  Describes IEC 61217 patient coordinates...
http://atc.wustl.edu/home/news/2004_dicom_workshop/WRB2004%20Image%20IODs%20v3.pdf

Good tutorial for DicomRT
http://www.sgsmp.ch/dicom/germond.pdf

NA-MIC kit test-based programming hints

http://www.na-mic.org/Wiki/index.php/NA-MIC-kit-curriculum/Testing-Based_Programming

Strain

First, basic description here.  For the moment, we are interested in the term "epsion_ij", which is Cauchy's strain tensor.  There is a simplified version (see Wikipedia page), in which the cross terms are neglected.  Consider only this one.

http://www.efunda.com/formulae/solid_mechanics/mat_mechanics/strain.cfm
http://en.wikipedia.org/wiki/Infinitesimal_strain_theory
http://en.wikipedia.org/wiki/Hooke%27s_law
http://en.wikipedia.org/wiki/Lam%C3%A9_parameters

Regularization based on strain is described here:

ftp://ftp.math.ucla.edu/pub/camreport/cam08-27.pdf

libtool hangs

I got this problem when building streamripper.  I guess it is because of the old configure script in libmad.  The workaround is to add the following line to the libtool script (after it is generated), after the line ECHO="echo":

echo="echo"

Here is the original poster who found the workaround:

http://lists.opensuse.org/opensuse-bugs/2009-01/msg02935.html

Still need to find a real fix for this.

_CRTDBG_MAP_ALLOC

Looks like the microsoft compiler has a tool for debugging memory leaks.
http://msdn.microsoft.com/en-us/library/e5ewb1h3(VS.80).aspx

Virtual box and debian

Goal:  Virtualbox + solaris + X on debian.  There seem to be no "uber-newbie" tutorials out there.

http://forums.virtualbox.org/viewtopic.php?f=7&t=5634

This is not virtualbox related, but looks interesting:

http://simh.trailing-edge.com/

Turning off autoplay for Debian

When I pop in a CD on my debian box, it fires up Sound Juicer.  Yuck.  So, I removed Sound Juicer.  But now it fires up something else!  How to disable this puppy?  There are three possibilities discussed in various web pages:

1. System -> Preferences -> Removable drives and media
2. Applications -> System tools -> Configuration editor -> Apps -> Nautilus -> Preferences
3. Desktop -> Gnome -> volume_manager

It seems #2 is the correct option.  See also this site, for information how to do #2 by the command line.

http://www.fedoraforum.org/forum/showthread.php?p=1266047

Scheduling library

This may be useful for streamripper
http://freshmeat.net/projects/libscheduler

USB mounting on OpenSUSE

This is an example of how to mount the usb stick on OpenSUSE.  Why doesn't it automount?  Even debian does.
http://www.suseblog.com/quick-usb-stick-mounting-tip-for-suse-linux

OpenCL segmentation faults on linux

Apparently I'm not the only one who has this problem:
http://forums.amd.com/devforum/messageview.cfm?catid=390&threadid=120456

Here is the OpenCL page:
http://developer.amd.com/GPU/ATISTREAMSDKBETAPROGRAM/Pages/default.aspx

Ripping on linux

I've been looking around for CD ripping solution for linux.  Look no further than "The Art of the Rip":

https://thomas.apestaart.org/thomas/trac/wiki/DAD/Rip

Name lookup with WINS on linux

Go into the file nsswitch.conf located at /etc/nsswitch.conf. Find the Line "hosts: files dns". It's missing wins so make it like this "hosts: files dns wins". Then you can ping by NetBIOS name.

http://www.linuxquestions.org/questions/susenovell-60/enabling-wins-lookup-463012/

You need to install /lib/libnss_wins.so, which is in the winbind package.

What does [NOTFOUND=return] in nsswitch.conf mean? Briefly, [NOTFOUND=return] means that the name service whose entry it follows should be considered authoritative (so that if it's up and it says such a name doesn't exist, believe it and return instead of continuing to hunt for an answer).

http://www.unixguide.net/sun/faq/4.03.shtml

Apparently this change requires a reboot (!) as well:

http://docs.hp.com/en/5992-0715/ch06s01.html

ScribeFire

Welcome to the 21st century, Greg.  ScribeFire is a Firefox plugin for doing blogging, which is already much better than the web interface.

https://addons.mozilla.org/en-US/firefox/addon/1730

It even lets me edit previous posts which I made using the web interface.

By default, it adds tracking cookies to your web site.  Probably you want to turn these off:

http://blog.coldtobi.de/1_coldtobis_blog/archive/242_scribefire_inserts_zemanta_web_bug.html