Just to remind myself, set policy CMP0012 to avoid scary ITK include warning
Saturday, February 18, 2012
Wednesday, January 18, 2012
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
- 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)
- 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
Saturday, December 24, 2011
GoDaddy & SOPA
GoDaddy is foolish for supporting SOPA. Gotta change to a new provider, e.g. http://www.hostgator.com/
Tuesday, November 29, 2011
Insert Credit
Wow. Great blog.
http://insertcredit.com/
Especially:
http://insertcredit.com/2011/09/22/who-killed-videogames-a-ghost-story/
http://insertcredit.com/
Especially:
http://insertcredit.com/2011/09/22/who-killed-videogames-a-ghost-story/
Monday, November 21, 2011
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))
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))
Thursday, November 10, 2011
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.
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.
Tuesday, October 11, 2011
Saturday, October 08, 2011
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.
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.
Sunday, October 02, 2011
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/
http://www.otonomai.net
http://mlbeto1169.blogspot.com/
http://www.dimazdizon.com/category/japan/
Sunday, September 11, 2011
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
http://forums.virtualbox.org/viewtopic.php?t=9918
Saturday, September 10, 2011
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
The fix is to edit common.py as described by brianbrian
http://ubuntuforums.org/archive/index.php/t-1063483.html
Monday, September 05, 2011
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/
http://royal.pingdom.com/2008/09/26/10-amazingly-alternative-operating-systems-and-what-they-could-mean-for-the-future/
Sunday, August 21, 2011
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
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
Sunday, August 14, 2011
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
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
Tuesday, August 09, 2011
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.
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.
Saturday, August 06, 2011
Sunday, July 17, 2011
Polygon algorithms
Found this interesting web site for algorithms such as computing winding number.
http://softsurfer.com/Archive/algorithm_0103/algorithm_0103.htm
http://softsurfer.com/Archive/algorithm_0103/algorithm_0103.htm
Friday, July 08, 2011
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
<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
Wednesday, July 06, 2011
Wednesday, June 29, 2011
Tuesday, June 28, 2011
*** VTE ***: Failed to load terminal capabilities from '/etc/termcap'
Solution:
sudo ln -s /usr/share/
Saturday, June 18, 2011
Monday, June 13, 2011
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
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
Sunday, June 12, 2011
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
http://www.cs.rtu.lv/jekabsons/regression.html
Monday, June 06, 2011
Finding extra files in your svn directory
Always I forget to do this before running "make package_source".
$ svn status
$ svn status
Sunday, June 05, 2011
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:
When everything is correct, you should be able to do this:
- cd plastimatch/trunk
- uscan --force-download
- svn-buildpackage -rfakeroot -uc -us
- cd source-dir
- debuild -j4 -i -us -uc -b
- debuild -j4 -i -us -uc -S
- cd source-dir
- cp -r ../trunk/debian .
- lintian -b ./plastimatch_1.5.0-1_amd64.deb
- lintian ./plastimatch_1.5.0-1_source.changes
- make new upstream tarball (don't forget to use pristine source directory -- cmake will include everythign)
- link upstream tarball to debian upstream tarball
- run get-orig-source
- cd build/plastimatch-pristine
- make package_source
- cp plastimatch-1.5.0-beta.2493-Source.tar.bz2 ~/debian-med/packages/plastimatch
- cd ~/debian-med/packages/plastimatch
- ln -s plastimatch-1.5.0-beta.2493-Source.tar.bz2 plastimatch-1.5.0.orig.tar.bz2
- cd trunk
- debian/get-orig-source
- sudo pbuilder create
- sudo pbuilder --update
- sudo pbuilder --build
foo_version.dsc
Monday, May 30, 2011
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
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
Monday, May 23, 2011
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
http://freshmeat.net/projects/0-ad
Freelords - TBS game
http://freshmeat.net/projects/freelords
DIN - audio synthesizer
http://freshmeat.net/projects/din
Saturday, May 14, 2011
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
http://freshmeat.net/projects/qtiplot
Conquests - 4X strategy game
http://freshmeat.net/projects/conquests
HOPSPACK - parallel optimizer
http://freshmeat.net/projects/hopspack
Friday, May 06, 2011
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
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
Wednesday, April 27, 2011
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
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
Monday, April 25, 2011
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/
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/
Thursday, April 21, 2011
Tuesday, April 12, 2011
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.medphys.ca/content.php?doc=58
http://www.nrc.gov/reading-rm/doc-collections/cfr/
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.medphys.ca/content.php?doc=58
http://www.nrc.gov/reading-rm/doc-collections/cfr/
Sunday, March 20, 2011
Chromaprint
This looks very cool. A new audio fingerprinting app.
http://forums.musicbrainz.org/viewtopic.php?id=2432
http://forums.musicbrainz.org/viewtopic.php?id=2432
Thursday, March 10, 2011
Recording playback
I can't seem to record playback in either Win 7 or Linux
Win 7
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)
Thursday, February 24, 2011
Friday, December 31, 2010
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
http://www.goodbyemicrosoft.net/news.php?item.615.2
Thursday, December 30, 2010
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.
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.
Thursday, November 25, 2010
Sunday, November 14, 2010
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/
MIght be possible using a "post-receive hook"
http://help.github.com/post-receive-hooks/
Monday, August 30, 2010
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
lame -a -m s -b 16 test.wav test.mp3
See also
http://www.hydrogenaudio.org/forums/index.php?showtopic=3270
Wednesday, August 18, 2010
Tuesday, August 17, 2010
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.
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.
Sunday, August 08, 2010
Zerogsound
Wow, excellent work by Zero G Sound to preserve our folk music heritage.
http://zerogsound.blogspot.com/
http://zerogsound.blogspot.com/
Tuesday, August 03, 2010
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
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
Tuesday, July 27, 2010
Saturday, July 24, 2010
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 foundApparently 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
grub rescue>
- 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
Sunday, July 11, 2010
Wednesday, June 16, 2010
Perl30Ex.dll + IIS
POST isn't working with Perl30Ex.dll. Here is what I've checked:
- Check install, permissions, etc (everything seems configured correctly)
http://blogs.iis.net/wadeh/archive/2009/04/13/running-perl-on-iis-7.aspx - Look through CGI doc, try different options (no apparent effect)
http://perldoc.perl.org/CGI.html - Enable failed request tracking (no failures logged)
http://mvolo.com/blogs/serverside/archive/2007/07/26/Troubleshoot-IIS7-errors-like-a-pro.aspx - Compare source pages between working (apache) and non-working (iis) systems
They are the same - Disable windows authentication in IIS
Saturday, June 12, 2010
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:
Here are the pertinent bits from /var/log/Xorg.0.log
Older kernel (working):
Originally, I had these three packages installed:
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:
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.Newer kernel (not working):
(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)
(II) Primary Device is: PCI 01@00:00:0The new (not working) kernel goes on and loads module "vgahw" as well, which the older (working) kernel doesn't.
(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 ...
...
Originally, I had these three packages installed:
xserver-xorg-video-atiSo I removed the radeon one (presumably not needed for my card?):
xserver-xorg-video-radeon
xserver-xorg-video-radeonhd
apt-get remove xserver-xorg-video-radeonThis 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"So, I manually add radeonhd to the /etc/X11/xorg.conf
(WW) Warning, couldn't open module ati
(II) UnloadModule: "ati"
(EE) Failed to load module "ati" (module does not exist, 0)
Section "Device"However, this causes X not to start with the following error:
Identifier "Device0"
Driver "radeonhd"
EndSection
(II) [DRM] Kernel mode setting enabledApparently 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
(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.
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.
- 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?26,90217,90217References:
http://wiki.debian.org/AtiHowTo
http://www.x.org/wiki/radeonhd
Friday, June 11, 2010
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
http://pooteeweet.org/blog/0/909#m909
Wednesday, June 09, 2010
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, 0.39Not sure the problem, but I will like to try upgrading the kernel. It seems there are 3 different kernel revisions in the 4 machines.
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
Sunday, June 06, 2010
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.
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.
Monday, May 24, 2010
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/
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/
Wednesday, May 05, 2010
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/
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/
Thursday, April 01, 2010
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
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
Saturday, March 13, 2010
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
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
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:
As far as it goes, Matthew Wilson's code looks interesting too:
As far as it goes, Matthew Wilson's code looks interesting too:
Monday, March 08, 2010
Monte Carlo codes
Monte Carlo codes: MCNPX, DPM, PENELOPE, etc
GEANT4
Here is the site for MCNPX
Not sure where I can download DPM. Here is an old version
Penelope. It is hard to find as well. But eventually I found it.
GEANT4
Here is the site for MCNPX
Not sure where I can download DPM. Here is an old version
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
Sunday, March 07, 2010
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:
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
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?)
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
Saturday, March 06, 2010
New crop of blogging sites
Here is what scribefire 3.5 supports. These are APIs, not sites.
From the w.blogger site, here are a slightly dated list of blog sites.
- Wordpress
- Movable Type
- Drupal
- Textpattern
- Roller
- MetaWeblog API
- Blogger
- Tumblr
From the w.blogger site, here are a slightly dated list of blog sites.
Sunday, February 14, 2010
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.
I try to delete xserver-xorg-video-radeon (it is presumably unneeded). But when I do that, X fails to start.
Friday, February 12, 2010
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
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
Thursday, February 11, 2010
Saturday, January 23, 2010
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/2009/10/12/255In more detail, go to directory
/usr/src/fglrx-8.681Edit the file kcl_io.c, and add the following line
#includeThen run the following:.
sudo dkms build -m fglrx -v 8.681
Friday, January 22, 2010
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.
http://www.linuxquestions.org/questions/susenovell-60/xsession-login-for-someuser-is-disabled.-369654/
Xsession: Login for (user) is disabledThis 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/
Saturday, January 16, 2010
Monday, December 28, 2009
LDAP + Kerberos
I get an error like this:
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/
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/
Sunday, December 27, 2009
Wednesday, December 23, 2009
Setting up a new subversion repository
- 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 - 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?) - Create the archive:
cd /home/subversion/repos/
sudo svnadmin create name-of-project
sudo chown -R apache.apache name-of-project - Restart apache
(If you don't do this, you get the dreaded "200 OK" error)
In Centos, do this: sudo /sbin/service httpd restart
Tuesday, December 22, 2009
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
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
Saturday, December 19, 2009
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.cfmRegularization based on strain is described here:
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
ftp://ftp.math.ucla.edu/pub/camreport/cam08-27.pdf
Sunday, December 13, 2009
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.htmlStill need to find a real fix for this.
Saturday, December 05, 2009
_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
http://msdn.microsoft.com/en-us/library/e5ewb1h3(VS.80).aspx
Sunday, November 29, 2009
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=5634This is not virtualbox related, but looks interesting:
http://simh.trailing-edge.com/
Friday, November 27, 2009
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:
- System -> Preferences -> Removable drives and media
- Applications -> System tools -> Configuration editor -> Apps -> Nautilus -> Preferences
- Desktop -> Gnome -> volume_manager
http://www.fedoraforum.org/forum/showthread.php?p=1266047
Thursday, November 26, 2009
Wednesday, November 18, 2009
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
http://www.suseblog.com/quick-usb-stick-mounting-tip-for-suse-linux
Sunday, November 15, 2009
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
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
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
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
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
Horrible default colors for ls
Solution (debian):
1) dircolors --print-database > ~/.dircolors
2) Add the following line to .bashrc
eval `dircolors $HOME/dircolors`
Also, note the problem with ls hanging on orphan references:
http://blog.wompom.org/index.php/2008/01/26/ls-color-considered-harmful/
1) dircolors --print-database > ~/.dircolors
2) Add the following line to .bashrc
eval `dircolors $HOME/dircolors`
Also, note the problem with ls hanging on orphan references:
http://blog.wompom.org/index.php/2008/01/26/ls-color-considered-harmful/
Friday, November 13, 2009
Boot configuration data store could not be opened
Tried to set up dual boot on my brand new Windows 7 partition. The new way to do this is to use a utility called bcdedit. For example:
http://www.iceflatline.com/2009/09/how-to-dual-boot-windows-7-and-linux-using-bcdedit/
However, I got the error "boot configuration data store could not be opened". This is solved using the following method:
http://social.answers.microsoft.com/Forums/en-US/w7install/thread/a9ce0d39-e13c-4b77-982f-66aff94e5d17
http://www.iceflatline.com/2009/09/how-to-dual-boot-windows-7-and-linux-using-bcdedit/
However, I got the error "boot configuration data store could not be opened". This is solved using the following method:
http://social.answers.microsoft.com/Forums/en-US/w7install/thread/a9ce0d39-e13c-4b77-982f-66aff94e5d17
Sunday, November 01, 2009
Searching for mp3
Got this from slashdot. Best meta-torrent sites.
http://netforbeginners.about.com/od/peersharing/f/torrentsearch.htm
On google you can do this:
"artist name" intitle:index.of mp3 -html -htm -php -asp -txt -pls
What does the . do? Match a single character?
http://netforbeginners.about.com/od/peersharing/f/torrentsearch.htm
On google you can do this:
"artist name" intitle:index.of mp3 -html -htm -php -asp -txt -pls
What does the . do? Match a single character?
Wednesday, October 21, 2009
Emacs development tools
Ran across CEDET while looking for the matlab editor settings. Looks interesting.
http://cedet.sourceforge.net/
http://cedet.sourceforge.net/
Sunday, October 04, 2009
Levenberg-Marquardt Code
Ran across this on freshmeat, might be worth a look.
http://www.ics.forth.gr/~lourakis/levmar/
The lecture notes also worth a look.
http://www.imm.dtu.dk/pubdb/views/edoc_download.php/3215/pdf/imm3215.pdf
http://www.ics.forth.gr/~lourakis/levmar/
The lecture notes also worth a look.
http://www.imm.dtu.dk/pubdb/views/edoc_download.php/3215/pdf/imm3215.pdf
Saturday, October 03, 2009
Jack in debian
Rosegarden fails with message "Failed to connect to JACK audio server". So, need to start jack. Jack fails with message "JACK is running in realtime mode, but you are not allowed to use realtime scheduling." I guess JACK ignores the fact that I unchecked "Realtime" option in the setup window. Oh well. Guess it really wants realtime (lame). Probably it's just a bug in the Qt gui rather than a Jack bug, because I see the -L flag is not actually sent on the jackd command line.
Anyway, I run sudo dpkg-reconfigure jackd, and tell it to use realtime priorities. This doesn't seem do anything at all.
Next, I do what Jack suggests, and edit /etc/security/limits.conf
Also, I get a warning from Jack that I need to set the maximum locked memory. How much is a good value? I just try the recommended value.
All is not well however. Starting Jack from qjackctl causes the program to freeze, and I have to kill it. Starting it from command line and starting rosegarden yields the following:
In addition to jack dying, rosegarden complains about the lack of an RT timer, suggesting sudo modprobe snd-rtctimer.
Anyway, I run sudo dpkg-reconfigure jackd, and tell it to use realtime priorities. This doesn't seem do anything at all.
Next, I do what Jack suggests, and edit /etc/security/limits.conf
@audio - rtprio 100<br />@audio - nice -10<br />This didn't do it for me though. Maybe I have to reboot? Yep, that solves this problem. Probably I could have restarted pam, but I had no patience for sidetrack on this issue.
Also, I get a warning from Jack that I need to set the maximum locked memory. How much is a good value? I just try the recommended value.
@audio - memlock 240144<br />Next, I get an error message:
ALSA: final selected sample format for capture: 16bit little-endian<br />ALSA: cannot set period size to 1024 frames for capture<br />ALSA: cannot configure capture channel<br />cannot load driver module alsa<br />Turns out that my card doesn't like 1024 frames per capture. Change this using qjackctl. 512 is OK? Well OK!
ALSA: final selected sample format for capture: 16bit little-endian<br />ALSA: use 2 periods for capture<br />ALSA: cannot set hardware parameters for capture<br />ALSA: cannot configure capture channel<br />Hm, not so clear what this means. Google is utterly without comment. However, I found if I change the input channels from (default) to 2, this error message is cleared.
All is not well however. Starting Jack from qjackctl causes the program to freeze, and I have to kill it. Starting it from command line and starting rosegarden yields the following:
gsharp@stonesmith:~$ /usr/bin/jackd -dalsa -dhw:0 -r44100 -p512 -n2 -S -i2<br />no message buffer overruns<br />jackd 0.116.2<br />Copyright 2001-2005 Paul Davis and others.<br />jackd comes with ABSOLUTELY NO WARRANTY<br />This is free software, and you are welcome to redistribute it<br />under certain conditions; see the file COPYING for details<br />JACK compiled with System V SHM support.<br />loading driver ..<br />apparent rate = 44100<br />creating alsa driver ... hw:0|hw:0|512|2|44100|2|0|nomon|swmeter|-|16bit<br />control device hw:0<br />configuring for 44100Hz, period = 512 frames (11.6 ms), buffer = 2 periods<br />ALSA: final selected sample format for capture: 16bit little-endian<br />ALSA: use 2 periods for capture<br />ALSA: final selected sample format for playback: 16bit little-endian<br />ALSA: use 2 periods for playback<br />jackd watchdog: timeout - killing jackd<br />
In addition to jack dying, rosegarden complains about the lack of an RT timer, suggesting sudo modprobe snd-rtctimer.
Wednesday, September 30, 2009
Linux software raid
Most of what you need is on the Linux Raid wiki.
When I rebooted a few months later, I found that my raid was gone! Here is how I recovered:
http://linux-raid.osdl.org/index.php/Linux_RaidHowever, you also need to know that the initial mdadm command puts the raid in read-only mode. To fix this, you need to need to do something like "mdadm --readwrite /dev/md10"
http://linux.derkeiler.com/Newsgroups/comp.os.linux.misc/2007-11/msg00012.htmlHere is what I did:
/sbin/mdadm --create --verbose /dev/md20 --level=mirror --raid-devices=2 /dev/sdc /dev/sddI don't know what monitor does. In another terminal I did this:
/sbin/mdadm --monitor /dev/md20
/sbin/mdadm --readwrite /dev/md20This changes the status from paused to resync.
gcs6@gelato:> cat /proc/mdstatOK. Time to make the file system. I choose reiserfs, because that's what OpenSUSE came with on my other disks. The wiki page says I can do this while it resyncs, so that is what I did.
md20 : active (auto-read-only) raid1 sdd[1] sdc[0]
488386496 blocks [2/2] [UU]
resync=PENDING
md10 : active raid1 sda10[0] sdb10[1]
441072512 blocks [2/2] [UU]
gcs6@gelato:> /sbin/mdadm --readwrite /dev/md20
gcs6@gelato:> cat /proc/mdstat
Personalities : [raid0] [raid1] [raid6] [raid5] [raid4]
md20 : active raid1 sdd[1] sdc[0]
488386496 blocks [2/2] [UU]
[>....................] resync = 3.8% (18745664/488386496) finish=123.0min speed=63594K/sec
md10 : active raid1 sda10[0] sdb10[1]
441072512 blocks [2/2] [UU]
/sbin/mkfs.reiserfs -b 4096 /dev/md20Add entry to fstab, mount, and good to go!
When I rebooted a few months later, I found that my raid was gone! Here is how I recovered:
/sbin/mdadm -A /dev/md20 --scanLooks like it is OK. Whew! Also, I added the following line to /etc/mdadm.conf. Maybe it is necessary?
mount -t reiserfs /dev/md20 /scratch1
ARRAY /dev/md20 level=1 num-devices=2 devices=/dev/sdc,/dev/sdd
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