[Insight-users] ITK-ready Virtual Appliance my first impression
Oleksandr Dzyubak
adzyubak at gmail.com
Mon Oct 25 11:50:50 EDT 2010
Hi Luis,
Q:
Question: It is reasonable to expect that users
of the Virtual Appliance already know how to
configure its parameters (RAM, video... etc) ?
A: I hope so. In addition, VirtualBox has nice and quite intuitive GUI.
Q:
6) Clean the system.
itkuser at ITK-VirtualBox:~$ sudo apt-get clean
I'm curious about this step.
Did it reduced the size of the appliance ?
I confess that I have never done "sudo apt-get clean"
so, it was interesting reading about it.
A:
APT install/upgrade works using caching packages
on the local harddrive. If you do not intend to maintain
a large client network and keeping all downloaded packages
on some shared file server, you might want to get rid of those
download since after a while it could eat up all your available space.
That's why I always make system cleaning.
Just to demonstrate the idea, lets see what it does for your system.
******************
itkuser at ITK-VirtualBox:~$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 19G 2.9G 15G 17% /
none 953M 204K 953M 1% /dev
none 958M 168K 958M 1% /dev/shm
none 958M 96K 958M 1% /var/run
none 958M 0 958M 0% /var/lock
/dev/sr0 32M 32M 0 100%
/media/VBOXADDITIONS_3.2.10_66523
itkuser at ITK-VirtualBox:~$ sudo apt-get clean
[sudo] password for itkuser:
itkuser at ITK-VirtualBox:~$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 19G 2.8G 16G 16% /
none 953M 204K 953M 1% /dev
none 958M 168K 958M 1% /dev/shm
none 958M 96K 958M 1% /var/run
none 958M 0 958M 0% /var/lock
/dev/sr0 32M 32M 0 100%
/media/VBOXADDITIONS_3.2.10_66523
***************************
Regards,
Alex
Luis Ibanez wrote:
> Hi Alex,
>
> Thanks a lot for trying the virtual appliance
> and for you very detailed report.
>
> Please see comments below.
>
>
> -----------------------------------------------------------
> On Wed, Oct 20, 2010 at 5:26 PM, Oleksandr Dzyubak <adzyubak at gmail.com
> <mailto:adzyubak at gmail.com>> wrote:
>
>
> Dear ITK users,
>
>
> Since I was very exited by Lius' "ITK-ready Virtual Appliance"
> I could not wait any longer to give it a try.
>
> My "Experimental Setup".
> Five year old laptop Fujitsu LifeBook S7020.
> 32 bit Intel(R) Pentium(R) M processor 1.73GHz.
> Memory: 2 GB.
> Host Linux: Debian Lenny.
> Virtualization: Sun (now Oracle) VirtualBox VM version 3.2.10.
>
> First, I grabbed the "ITK-ready Virtual Appliance" files
> ITK-VM.mf ITK-VM.vmdk ITK-VM.ovf
> from the link provided by Luis.
> http://midas.kitware.com/item/view/450
>
> Second, I imported this appliance using
> VirtualBox menu: File --> Import Appliance...
> Afterwards everything was ready to boot into "ITK-ready Ubuntu".
>
> From now and on "My impression" comes.
>
> 1) VM configuration.
> VM configurator on my laptop annoyingly sends complaints
> about "requested memory exceeds the limit..."
> so I changed parameters from Luis' 2 GB down to 768 MB and
> I also increased Video Memory up to 64 MB.
>
>
>
> Good point, I hesitated a lot with how much
> RAM to allocate for the appliance. I guess
> that starting with a small RAM makes more
> sense (and maybe adding a prominent notice
> letting users know where they can increase
> the RAM in the Virtual Box setup).
>
> Question: It is reasonable to expect that users
> of the Virtual Appliance already know how to
> configure its parameters (RAM, video... etc) ?
>
>
>
> 2) Host-Guest integration.
> Since I am a quite lazy man, I prefer Host-Guest
> full/partial integration that makes my life easier.
>
> Because Luis has installed dkms anyway, it's very easy
> to make one step further and install "Guest Additions".
>
> Make sure, however, you do not have any vbox* drivers
> already installed.
>
> itkuser at ITK-VirtualBox:~$ sudo rm /etc/init.d/vboxadd*
> itkuser at ITK-VirtualBox:~$ sudo rm
> /lib/modules/2.6.35-22-generic/updates/vbox*
>
> And now you can mount "Guest Additions" iso and install them.
>
> itkuser at ITK-VirtualBox:~$ cd /media/VBOXADDITIONS_3.2.10_66523/
> itkuser at ITK-VirtualBox:/media/VBOXADDITIONS_3.2.10_66523$ sudo sh
> VBoxLinuxAdditions-x86.run
>
>
>
> Nice
>
>
>
>
> 4) "Security First".
> It immediately boots into Ubuntu session which I do not like at all.
> Thus, I disabled "Autologin".
>
>
>
> I thought on leaving auto login as a matter of convenience,
> but I see your point here.
>
>
>
> 5) ITK Manual and README.
> It's nice to see the ITK handy info which sits right in front of you.
>
> itkuser at ITK-VirtualBox:~$ more README.txt
>
>
> 6) Clean the system.
> itkuser at ITK-VirtualBox:~$ sudo apt-get clean
>
>
>
> I'm curious about this step.
> Did it reduced the size of the appliance ?
>
> I confess that I have never done "sudo apt-get clean"
> so, it was interesting reading about it.
>
>
>
> 7) Ready for the very first test?
>
> itkuser at ITK-VirtualBox:~$ mkdir ITK_test && cd ITK_test
> itkuser at ITK-VirtualBox:~/ITK_test$ mkdir BUILD && mkdir Src
> itkuser at ITK-VirtualBox:~/ITK_test$ cd Src && touch CMakeLists.txt
> itkuser at ITK-VirtualBox:~/ITK_test/Src$ locate
> ImageReadRegionOfInterestWrite
>
> /home/itkuser/src/ITK/Examples/IO/ImageReadRegionOfInterestWrite.cxx
>
> itkuser at ITK-VirtualBox:~/ITK_test/Src$ cp
> /home/itkuser/src/ITK/Examples/IO/ImageReadRegionOfInterestWrite.cxx
> ./
>
> itkuser at ITK-VirtualBox:~/ITK_test/Src$ ls
> CMakeLists.txt ImageReadRegionOfInterestWrite.cxx
>
> Almost ready! Lets create a simple CMakeLists.txt file.
>
> ######################
> #
> # Example on the use of ImageReadRegionOfInterestWrite
> #
>
> cmake_minimum_required(VERSION 2.8)
>
> PROJECT(Region)
>
> # Find ITK.
> FIND_PACKAGE(ITK REQUIRED)
> INCLUDE(${ITK_USE_FILE})
>
> ADD_EXECUTABLE(
> ImageReadRegionOfInterestWrite
> ImageReadRegionOfInterestWrite.cxx )
>
> TARGET_LINK_LIBRARIES(
> ImageReadRegionOfInterestWrite
> ITKIO
> ITKBasicFilters
> )
> #########################
>
>
>
> Excellent,
> this is a nice first test.
>
>
>
>
> Nice! Lets try compiling...
>
> 8) First example compilation.
>
> itkuser at ITK-VirtualBox:~/ITK_test/Src$ cd ~/ITK_test/BUILD
> itkuser at ITK-VirtualBox:~/ITK_test/BUILD$ ccmake ../Src/
>
> Ooops!!!
>
> ****************
> CMake Warning at /usr/lib/InsightToolkit/UseITK.cmake:98
> (FIND_PACKAGE):
> Could not find module FindGDCM.cmake or a configuration file for
> package
> GDCM.
>
>
> mm,
> I'm surprised about this one.
> I haven't seen this error before,
>
> The appliance had the Gaussian example in
>
> /home/itkuser/src/Example/
>
> and it was build in
>
> /home/itkuser/bin/Example
>
> Note that this one is built against the
> ITKv4 (alpha) that is compiled in
>
> /home/itkuser/bin/ITK/Release
>
> Did you build your example against
> the ITK 3.18 that is installed ?
>
>
> ---------------------------------------
>
> Adjust CMAKE_MODULE_PATH to find FindGDCM.cmake or set GDCM_DIR
> to the
> directory containing a CMake configuration file for GDCM. The
> file will
> have one of the following names:
>
> GDCMConfig.cmake
> gdcm-config.cmake
>
> Call Stack (most recent call first):
> CMakeLists.txt:11 (INCLUDE)
>
> Errors occurred during the last pass
>
> CMake Version 2.8.2
> Press [e] to exit help
> *************
>
>
>
>
>
>
> 9) Which version has been installed?
> Is that from Ubuntu repository or compiled by Luis?
>
> Lets clean the system and make sure that the version
> compiled by Luis gets installed.
>
> itkuser at ITK-VirtualBox:~$ apt-cache search insighttoolkit
> itkuser at ITK-VirtualBox:~$ sudo apt-get purge insighttoolkit*
> itkuser at ITK-VirtualBox:~$ cd ~/bin/ITK/Release/
> itkuser at ITK-VirtualBox:~/bin/ITK/Release$ sudo make install
>
>
> mm,
> I intentionally didn't installed this one,
> so we could have both...
>
> We have now prepared a modification,
> to make possible to have two versions
> of ITK installed without conflict. We
> will have to update the virtual appliance
> to reflect this.
>
>
>
>
> 10) Now lets try compiling again.
>
> itkuser at ITK-VirtualBox:~$ cd ~/ITK_test/BUILD
> itkuser at ITK-VirtualBox:~/ITK_test/BUILD$ ccmake ../Src/
> itkuser at ITK-VirtualBox:~/ITK_test/BUILD$ make
> Scanning dependencies of target ImageReadRegionOfInterestWrite
> [100%] Building CXX object
> CMakeFiles/ImageReadRegionOfInterestWrite.dir/ImageReadRegionOfInterestWrite.cxx.o
> Linking CXX executable ImageReadRegionOfInterestWrite
> [100%] Built target ImageReadRegionOfInterestWrite
>
> Full success!!!
>
>
> I guess that answers the question,...
> (I'm still unclear of why the build against
> the pre-installed ITK 3.18 failed. It should
> have worked. I'll have to try again in the
> original appliance).
>
>
>
> Kudos Luis Ibanez,
> the creator of a Virtual Appliance with a pre-installed ITK!
>
> The system is fully operational and very easy to use.
>
> Thanks for this Virtual Appliance,
>
> Alex
>
>
>
> Thanks a lot to you for suggesting the idea,
> and for giving it a try.
>
> It looks like we can improve a couple of
> things on the installation side of ITK.
>
>
> Regards,
>
>
> Luis
>
>
>
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