Embedding a Python script

[Oded Yaakobi]

Dear group,

 

I apologize if my question below has already been addressed in the one of deal.ii’s documentation resources, but I didn't understand how to answer it using the pieces of documentation that I have read such as

“How to use CMake to configure your projects with deal.II” https://www.dealii.org/developer/users/cmakelists.html#cmakeauto

 

and

“deal.II in Spack” https://github.com/dealii/dealii/wiki/deal.II-in-Spack

 

I am trying to embed a short Python script in my code, but get an error message after running “make release”.  Attached are an example code with a minor addition to the “main” of Step-1 and the “CMakeLists.txt” file that I tried to adapt to support Python.

 

I am running my code on a MAC OS Yosemite 10.10.5 with the special version of deal.ii that Luca prepared for me https://groups.google.com/forum/#!searchin/dealii/%22Make$20test%22$20failure$20following$20Trilinos$20installation$20with$20Mesquite%7Csort:relevance/dealii/Y7MH_BE0yko/1zvnHGR7AQAJ

 

Here are the error messages that I get:

 

[ yaakobioy L02029080  ~/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod ]$ make release

CMake Error at /Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake:57 (ADD_EXECUTABLE):

  add_executable cannot create target "step-1" because another target with

  the same name already exists.  The existing target is an executable created

  in source directory

  "/Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod".

  See documentation for policy CMP0002 for more details.

Call Stack (most recent call first):

  CMakeLists.txt:49 (DEAL_II_INVOKE_AUTOPILOT)

 

 

-- Configuring incomplete, errors occurred!

See also "/Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod/CMakeFiles/CMakeOutput.log".

make: *** [cmake_check_build_system] Error 1

 

 

 

I would appreciate if someone could explain what should I do to overcome this problem.

 

Thanks in advance,

Oded    

[Denis Davydov]

Hi Ode,

First, Spack is a tool to compile and install packages, which I don't think you are using as you said that

you play around with Luca's build. So the link to this wiki should not be relevant here.

Second, you CMake input is wrong. you need to drop

DEAL_II_INVOKE_AUTOPILOT()

see the very first example here https://www.dealii.org/developer/users/cmakelists.html#cmakesimple

My understanding is that DEAL_II_INVOKE_AUTOPILOT is for very simple cases like examples/ which don't

need to link against other than deal.II libraries and where one needs a single executable.

If you are working on something like you PhD code, then it's most likely better to keps things are

you library + unit tests + executable which calls you main class with parameter file.

Regards,

Denis.

[Oded Yaakobi]

Hi Denis,

I tried your suggestion to drop DEAL_II_INVOKE_AUTOPILOT(), and it worked.

However, if I want to keep the functionality of switching the build types between "Debug" and "Release" versions, how can I do it now?

Thanks,

Oded

[Denis Davydov]

Hi Oded,

On Tuesday, August 9, 2016 at 10:36:39 AM UTC+2, Oded Yaakobi wrote:

However, if I want to keep the functionality of switching the build types between "Debug" and "Release" versions, how can I do it now?

I just do -DCMAKE_BUILD_TYPE=Debug or Release

you can also probably try to define the same make targets as done in autopilot, but i can't help you here.

Regards,

Denis.

[Daniel Arndt]

Oded,

If you include

ADD_CUSTOM_TARGET(debug
  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR}
  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
  COMMENT "Switch CMAKE_BUILD_TYPE to Debug"
  )

ADD_CUSTOM_TARGET(release
  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR}
  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
  COMMENT "Switch CMAKE_BUILD_TYPE to Release"
  )

into your CMakeLists.txt, you can switch between debug and release mode using
$make debug
and
$make release

Best,
Daniel

[Oded Yaakobi]

HI Daniel,

I tried your suggestion but it didn't work for me. See the attached "CMakeLists.txt" file. I get the following error messages:

[ yaakobioy L02029080  ~/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod ]$ make debug

make: *** No rule to make target `debug'.  Stop.

[ yaakobioy L02029080  ~/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod ]$ make release

make: *** No rule to make target `release'.  Stop.

Thanks,

Oded

[Daniel Arndt]

Oded,

Your CMakeLists.txt file works for me. Maybe you just didn't run cmake again?
Can you try on a clean directory just containing CMakeLists.txt and step-1.cc?

Best,
Daniel

[Oded Yaakobi]

Hi Daniel,

I tried it again on a clean directory, and now it worked fine.

Thank you!

Oded

On Tuesday, August 9, 2016 at 2:35:26 PM UTC+3, Daniel Arndt wrote:

Oded,