[Insight-users] ITK-ready Virtual Appliance my first impression

[Luis Ibanez]

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>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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