Hi Michel,
we have dedicated CMake code to add the Boost libraries required by SOFA, when
you switch it on. Atomic and date_time are no hard SOFA dependencies, though.
Maybe there is a SOFA plugin you have in mind, that is not built by the MITK
superbuild, that requires Atomic or date_time? Anyways, glad you made it. :-)
There is one thing you may stumble across when making the first steps with MITK
Simulation: Many of the well-known SOFA example scenes like liver.scn will
produce errors when loading them with MITK, because they have "magic paths" to
external files in them, which are supposed to get resolved by a SOFA class
looking in various fixed known SOFA paths. This is a bit ugly and obviously
won't work with an external program using SOFA like MITK. In these cases you
have to specify the full or relative paths in the scene files and it will work
like a charm again.
We also implemented SOFA components to easily work with MITK data manager
objects (MITK <-> SOFA bridge), so you can simulate directly on MITK surfaces
for example. Also the opposite direction is featured (but a bit hidden): You
can right-click on Visual nodes in the SOFA tree view (simulation plugin), and
click on "Render to surface". Instead of rendering with OpenGL, this visual is
then stuffed into an MITK surface (basically wraps a VTK poly data) in the data
manager, and then rendered by the usual MITK rendering pipeline. Great for
inter-op and saving simulation results together with the MITK scene.
Best,
Stefan
From: Audette, Michel A. [mailto:maude...@odu.edu]
Sent: Donnerstag, 27. Oktober 2016 15:44
To: Kislinskiy, Stefan; Sascha Zelzer; mitk-users@lists.sourceforge.net
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Dear Stefan and Sascha, and fellow MITK enthusiasts,
I managed after all to compile cleanly on Windows with MSVC 2013, however I
also specified to use the Boost libraries system;thread;chrono;date_time;atomic
. I found with my previous builds (based on 2012) that in the regular
configuration, Boost failed to produce date_time and atomic, and the build
would complain about these missing libraries. Lo and behold I noticed on CMake
that you had only set system;thread;chrono; by default, which is exactly what
the build spit out. I don't know if date_time and atomic are requirements of
SOFA versus the usual build, but all five should be specified in
MITK_Use_Boost_LIBRARIES . I could probably go back to 2012 with the full
Boost instruction and try again, but at this point, why mess with it?
I will doubtless have questions for you on the use of SOFA objects imbedded in
the code.
Thanks for your support.
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Kislinskiy, Stefan
<s.kislins...@dkfz-heidelberg.de<mailto:s.kislins...@dkfz-heidelberg.de>>
Sent: Wednesday, October 26, 2016 8:07:44 AM
To: Audette, Michel A.; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: RE: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi Michel,
There's a CMake warning when the path chosen for the build is too long. We also
mention it quite explicitly in some tutorials like [1], but you're totally
right, we need to place a hint more prominently in our documentation. BTW, it's
a Windows-related problem, so you don't have that limitations on Linux and OS X.
However, everything works perfectly for me on Windows 8.1 with MSVC 2013 Update
5. Here is what I did:
I cloned MITK 2015.05.2:
D:\>git clone --branch v2015.05.2
https://phabricator.mitk.org/diffusion/MITK/mitk.git
MITK-2015.05.2<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fphabricator.mitk.org%2Fdiffusion%2FMITK%2Fmitk.git%2520MITK-2015.05.2&data=01%7C01%7Cmaudette%40odu.edu%7Cceab87aa57434c4f3ee608d3fd98bfde%7C48bf86e811a24b8a8cb368d8be2227f3%7C0&sdata=xPuCmOPIYlKy1ZWSl6JB87M9y9LLNjlpLtRWKQDooqU%3D&reserved=0>
I opened CMake 3.6.2 GUI, set the build directory to
D:\MITK-2015.05.2-superbuild and set the following variables:
I added the variable CMAKE_PREFIX_PATH and set it to my Qt installation
"C:\Qt\5.4\msvc2013_64_opengl", enabled MITK_USE_SOFA, clicked on "Configure"
and then added "date_time" as well as "atomic" to MITK_USE_Boost_LIBRARIES, so
it reads "system;thread;chrono;date_time;atomic". To speed things up I also
switched off "MITK_BUILD_TESTING". I configured/generated the superbuild
solution again.
I then opened the generated MITK-superbuild solution and built "MITK-Configure"
in Release configuration.
Both date_time and atomic were built and installed properly besides the other
Boost libraries.
After it was done, I opened CMake again and set the build directory to
D:\MITK-2015.05.2\MITK-build this time to configure the MITK build itself:
I switched on MITK_BUILD_org.mitk.gui.qt.simulation and configured/generated.
Finally I opened the generated MITK.sln via the according batch file
"D:\MITK-2015.05.2\MITK-build\StartVS_release.bat", built MitkWorkbench in
release mode and successfully started the application afterwards (remember to
set MitkWorkbench as startup project in MSVC).
Hope that helps.
Stefan
[1]
http://mitk.org/wiki/Developer_Tutorial_(Microsoft_Windows)<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmitk.org%2Fwiki%2FDeveloper_Tutorial_(Microsoft_Windows)&data=01%7C01%7Cmaudette%40odu.edu%7Cceab87aa57434c4f3ee608d3fd98bfde%7C48bf86e811a24b8a8cb368d8be2227f3%7C0&sdata=h8Ze%2Fq8Oj%2FaNKet7OuC%2FDdL8vUu3wQUCSQGs9%2BMovHs%3D&reserved=0>
From: Audette, Michel A. [mailto:maude...@odu.edu]
Sent: Dienstag, 25. Oktober 2016 22:33
To: Kislinskiy, Stefan; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Still seeing an incomplete build of the internal Boost with MSVC 2012.
17> Boost version: 1.56.0
17>
17> Boost include path: C:/MITK/MITK15052MSVC2012/ep/include/boost-1_56
17>
17> Could not find the following Boost libraries:
17>
17> boost_date_time
17> boost_atomic
17>
17> Some (but not all) of the required Boost libraries were found. You may
17> need to install these additional Boost libraries. Alternatively, set
17> BOOST_LIBRARYDIR to the directory containing Boost libraries or
BOOST_ROOT
17> to the location of Boost.
17> Call Stack (most recent call first):
17> cmake/externals.cmake:84 (find_package)
17> CMakeLists.txt:46 (include)
17>
There must be something wrong in the internal Boost setup in MITK. It does not
make sense that the build process would successfully produce boost_thread,
boost_chrono and boost_system, while failing to produce boost_data_time and
boost_atomic. That does not jibe at all.
Anyhow, I will retry with both an external Boost with MSVC 2012 as well as with
MSVC 2013, once I get it installed.
Warm wishes,
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Audette, Michel A.
Sent: Tuesday, October 25, 2016 3:48:54 PM
To: Kislinskiy, Stefan; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi again,
please disregard the previous message. I had intended to set the external Boost
path and ended up setting the GLUT path by mistake.
I am trying again with a fresh build. I have found that the superbuild fails
due to ITK if the ITK path is longer than 50 characters, so I am trying once
more with a shorter total pathname. I don't know if it says that on your
website, but you should state that somewhere. Still building right now; will
follow up shortly.
Cheers,
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Audette, Michel A.
Sent: Tuesday, October 25, 2016 2:18:50 PM
To: Kislinskiy, Stefan; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi Stefan and Sascha,
I neglected to follow up on this due to MICCAI and some proposals that were
outgoing these past few weeks.
I'm back at it. I am using MSVE 2012, and somehow it complained about Boost,
but that went away when I gave it an external Boost. The build is still
complaining about something:
Could NOT find GLUT (missing: GLUT_glut_LIBRARY GLUT_INCLUDE_DIR).
Is this due to the build process? Can I find a workaround with an external
FreeGlut?
Cheers,
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Audette, Michel A. <maude...@odu.edu<mailto:maude...@odu.edu>>
Sent: Monday, October 3, 2016 9:34:24 AM
To: Kislinskiy, Stefan; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi Stefan,
thanks for your kind reply and support. I will give it a try with MITK
2015.05.2 and report back.
Cheers,
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Kislinskiy, Stefan
<s.kislins...@dkfz-heidelberg.de<mailto:s.kislins...@dkfz-heidelberg.de>>
Sent: Saturday, October 1, 2016 4:14:24 AM
To: Audette, Michel A.; Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: AW: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi Michel,
MITK and SOFA have some common third-party dependencies. We try to build these
only once and use them in both MITK and SOFA, but that doesn't work for all
libraries. In case of Eigen, our version of SOFA (which is from the beginning
of 2015 btw), uses its own, already packaged, header-only Eigen. So if I
remember correctly, it isn't a trivial task to inject your own Eigen to SOFA
through the MITK-superbuild. However, building SOFA with MITK is supposed to be
as easy as any other feature of MITK, which is why it should work out of the
box by simply switching on MITK_USE_SOFA. This is tested by our dart clients
and works for Windows (MSVC), Linux, and OS X. As Sascha said, switching on
MITK_USE_SOFA will automatically switch on common dependencies like the
necessary Boost libraries. Hence, for the beginning, I highly recommend not to
put extra work in fiddling around with external toolkits. In fact, the only
manual steps necessary should be to set the right Qt path if it wasn't detected
automatically, switch on MITK_USE_SOFA, run the superbuild, and after it's
finished, go one level down to the actual MITK build and switch on the
org.mitk.gui.qt.simulation plugin in CMake.
Please note, that MITK 2016.03 doesn't support MSVC 2012 anymore, so you should
use MITK 2015.05.2 instead, if you don't do so already.
Regarding the CMake output: If you're using CMake GUI, just copy the error
message from its output window. If you use command line CMake, you can either
copy the error from the terminal or in general just look for the files
CMakeOutput.log and CMakeError.log in the build directory.
I'm happy to help you with MITK+SOFA. Please don't hesitate to ask.
Best,
Stefan
________________________________
Von: Audette, Michel A. <maude...@odu.edu<mailto:maude...@odu.edu>>
Gesendet: Freitag, 30. September 2016 22:15
An: Sascha Zelzer;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi Sascha,
for the time being, I am trying to get around that by using a prebuilt Boost
externally, where it was building properly only 3 of the Boost libraries
(thread, system, forget the third), however I'm still up against a problem
compiling Eigen. I've seen that before trying to compile Sofa standalone on
Windows. I will try with separate Eigen build as well and report back.
For my future use, when you say CMake output, where do I look for this file? Is
it a log file of some kind?
Best wishes,
Michel
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________
From: Sascha Zelzer <sascha.zel...@gmail.com<mailto:sascha.zel...@gmail.com>>
Sent: Friday, September 30, 2016 4:00:35 PM
To: Audette, Michel A.;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] Superbuild on Windows MSVC 2012 leads to incomplete
building of Boost libraries
Hi,
normally, the MITK superbuild sets the required boost libraries depending on
the MITK_USE_* CMake variables being set to ON. E.g. if MITK_USE_SOFA is on, it
adds the system, thread and chrono library. If you send us the full cmake
output, it is easier to tell what is going on and which dependency requires
data_time and atomic.
However, you can manually append required libraries in the
MITK_USE_Boos_LIBRARIES cmake variable (e.g. using the CMake GUI). It would
look like "date_time;atomic", but I am wondering why this is needed at all.
Cheers,
Sascha
On 09/30/2016 05:25 PM, Audette, Michel A. wrote:
Hello,
I would like to build MITK with SOFA, using MS Visual Studio 2012 (with service
packs) and the superbuild does not seem to produce all of the needed Boost
libraries.
The build process complains of the following:
19> Unable to find the requested Boost libraries.
19>
19> Boost version: 1.59.0
19>
19> Boost include path:
C:/MITK/MITK16.3.0-buildMSVS2012/ep/include/boost-1_59
19>
19> Could not find the following Boost libraries:
19>
19> boost_date_time
19> boost_atomic
Is there an easy fix?
Best wishes,
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
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