make for CSXCAD failed

[felipebm]

Hi Thorsten,

thanks again for all your help. I'll try to answer your questions:

Do you use the system vtk version??

Yes, I use vtk from the standard Debian Jessie's repository.
Right now I'm playing with both versions (5 and 6) to see which one may help me to solve this installation problem. Can you tell me which version of vtk I shall use in order to install the "master" branch?

Where is it installed??

Do you mean libvtkCommon.so?

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$ find /usr/lib* ! -path "*paraview*"  -name 'libvtkCommon.so'
/usr/lib/libvtkCommon.so

For completeness, I've attached the output of all the different vtk versions installed in my machine (see findVTK.txt).

This time, with the new cmake build, it seems the problem has to do with the SOURCE_DIR variable. Seems there is some info missing about where to download the packages. I'd attached the shell output (see output.log) and the CMake log file. Here I'm copying the error messages that seem more relevant to me:

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CMake Error at /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message):
  error: no download info for 'fparser' -- please specify existing/non-empty
  SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY,
  GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND
Call Stack (most recent call first):
  /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command)
  CMakeLists.txt:15 (ExternalProject_Add)


CMake Error at /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message):
  error: no download info for 'CSXCAD' -- please specify existing/non-empty
  SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY,
  GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND
Call Stack (most recent call first):
  /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command)
  CMakeLists.txt:21 (ExternalProject_Add)


CMake Error at /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message):
  error: no download info for 'openEMS' -- please specify existing/non-empty
  SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY,
  GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND
Call Stack (most recent call first):
  /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command)
  CMakeLists.txt:28 (ExternalProject_Add)


CMake Error at /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message):
  error: no download info for 'QCSXCAD' -- please specify existing/non-empty
  SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY,
  GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND
Call Stack (most recent call first):
  /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command)
  CMakeLists.txt:35 (ExternalProject_Add)


CMake Error at /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1467 (message):
  error: no download info for 'AppCSXCAD' -- please specify
  existing/non-empty SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE,
  SVN_REPOSITORY, GIT_REPOSITORY, HG_REPOSITORY or DOWNLOAD_COMMAND
Call Stack (most recent call first):
  /usr/share/cmake-3.0/Modules/ExternalProject.cmake:1847 (_ep_add_download_command)
  CMakeLists.txt:42 (ExternalProject_Add)

Thank you very much,
Felipe.

[felipebm]

Could it be a problem with the hdf5 installation directory?

This is the first error message I get when trying to compile with vtk5 and the stable branch:

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compiling CSXCAD ... please wait
src/CSPropDiscMaterial.cpp:19:18: fatal error: hdf5.h: No such file or directory
 #include <hdf5.h>
                  ^
compilation terminated.

Thanks a lot!

[thorsten]

Hi,

sorry for the late answer.

You have lots of wired errors that I really have not seen and hardly can explain.
The path to your vtk 5.8 looks fine and I do not understand why the script cannot find the correct path.
I guess the vtk 6.1 interferes somehow... cmake should be the solution here for the future..

Have you made sure your submodules are up to date?

git submodule init
git submodue update

Check if e.g. in sub-dir fparser a cmake is present...
Maybe try a clean checkout...

git clone https://github.com/thliebig/openEMS-Project.git
cd openEMS-Project
git submodule init
git submodule update
mkdir build; cd build
cmake -DCMAKE_INSTALL_PREFIX=~/opt ..
make

regards
Thorsten

[felipebm]

Dear Thorsten,

When you ask:

Check if e.g. in sub-dir fparser a cmake is
present...

Do you mean to check if there is a CMakeLists.txt inside the fparser
sub-dir?

If that so, then...

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~/opt/openEMS-Project$ ls fparser/
CMakeLists.txt	extrasrc/	   fparser.hh	    fpconfig.hh
docs/		fparser.cc	   fparser_mpfr.hh  fpoptimizer.cc
examples/	fparser_gmpint.hh  fparser.pro	    mpfr/

I have uninstalled every single package that has 'vtk6' on its name. I
also deleted the folder openEMS-Project and created a new one, using the
instructions you kindly sent to me:

Code: Select all

git clone https://github.com/thliebig/openEMS-Project.git
cd openEMS-Project
git submodule init
git submodule update
mkdir build; cd build
cmake -DCMAKE_INSTALL_PREFIX=~/opt ..
make

The output can be seen in the attached file (output.log). For me, those
error messages remain the same.

From the first warning:

-- The imported target "vtkWrapTcl" references the file
"/usr/bin/vtkWrapTcl"

it seems the problem in the vtk has not been solved by uninstalling
vtk6.

As a desperate shoot, since the problem seems related with something
related with Tcl and Vtk, I have installed tcl-vtk .
The output message after running make and cmake is:

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$ make
[ 20%] Built target fparser
[ 22%] Performing build step for 'CSXCAD'
Linking CXX shared library libCSXCAD.so
/usr/bin/ld: cannot find -lhdf5
/usr/bin/ld: cannot find -lhdf5_hl
collect2: error: ld returned 1 exit status
src/CMakeFiles/CSXCAD.dir/build.make:1040: recipe for target
'src/libCSXCAD.so' failed
...

It seems to me there is a problem with hdf5, all the previous attempts
show errors message related to the hdf5 library. For that reason I'd made the following symbolic links in order to cmake find the hdf5 libraries:

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libhdf5_cpp.a -> /usr/lib/x86_64-linux-gnu/libhdf5_cpp.a
libhdf5_cpp.so -> /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.8.0.2
libhdf5_hl.so -> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so
libhdf5_serial_hl.so.8 -> libhdf5_hl.so
libhdf5_serial.so.8 -> libhdf5.so
libhdf5.so -> /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so

After making the previous modifications I'd followed (again) the
instructions on your previous message. Some warning messages appeared
relating python, vtk and java; therefore I'd installed python-vtk and libvtk-java and miraculously seems to have resolved the problem.

Now I have a working openEMS installation!!!.... or that looks like
Please find attached the output log. After the make command, the same warnings (related to CGAL) from my first post appeared.

Although there are some problems when trying the First Steps tutorial

Invoke the openEMS solver

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./openEMS

the file does not exists, although I'd managed to found it at bin/openEMS. I did a symbolic link pointing to that file: ln -s bin/openEMS .

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>> InitCSX

ans = 

    Properties: []
     ATTRIBUTE: [1x1 struct]

>> InitFDTD

ans = 

    ATTRIBUTE: [1x1 struct]

>> RunOpenEMS( '.', 'nonexistant.xml', '' )
??? Error using ==> searchBinary at 46
openEMS.sh binary not found!

Error in ==> invoke_openEMS at 30
    openEMS_bin = searchBinary('openEMS.sh', ...

Error in ==> RunOpenEMS at 181
        invoke_openEMS(args);

I can't find any openEMS.sh file.

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>> CSXGeomPlot('nonexistant.xml')
invoking AppCSXCAD, exit to continue script...
/bin/bash: /home/felipe/opt/openEMS/share/CSXCAD/matlab/../../../bin/AppCSXCAD.sh: Permission denied

I did a:

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chmod a+x AppCSXCAD.sh

and solved the problem.

So is this a useful installation? Can you tell?

Thanks again!
Felipe.

[thorsten]

Hi,

I'm glad you got it finally to compile. I have really no idea what is wrong with your system and why it gave you so much trouble.
Maybe someone should try a fresh Debian Jessie in a VM to find the proper dependencies and test it.
I do not see why tcl, python or java should be required. The only reason I can think of that it helped is, that it pulled in other required dependencies ...

I can't find any openEMS.sh file.

Yes that is a bug in the cmake build. I have to fix it.

chmod a+x AppCSXCAD.sh

That too

So is this a useful installation? Can you tell?

Just add the CSXCAD and openEMS matlab path to Octave and run a Tutorial. But I would think so...

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addpath('/home/felipe/opt/openEMS/share/CSXCAD/matlab');
addpath('/home/felipe/opt/openEMS/share/openEMS/matlab');

Have fun
Thorsten

[felipebm]

Hi Thorsten, me again,

in the tutorials: Parallel plate waveguide + Rectangular waveguide

everything seems to work fine until I reach the command RunOpenEMS. The error message was:

??? Error using ==> searchBinary at 46
openEMS.sh binary not found!

Error in ==> invoke_openEMS at 30
openEMS_bin = searchBinary('openEMS.sh', ...

Error in ==> RunOpenEMS at 181
invoke_openEMS(args);

Therefore it seems my installation useless without the openEMS.sh file.
Can you please fix the cmake build so I can get a running installation?

Thanks!
Felipe.
PS. I'm downloading the images to make a test using two VM with Debian stable and Debian testing. I'll give you a feedback as soon as I have a result.

[thorsten]

Hi,

I have fixed it yesterday already. Please update and let me know if now everything works fine.
But you could also just grab the missing openEMS.sh and put it in the bin folder...


regards
Thorsten

[felipebm]

Hi Thorsten,

after executing $ git submodule update
I get:

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fatal: reference is not a tree: dd51199ffbe7de5af155c3bfd2109e5f5dae721e
Unable to checkout 'dd51199ffbe7de5af155c3bfd2109e5f5dae721e' in submodule path 'AppCSXCAD'

From this forum I read:

One possible cause for such a problem is, that the one who published the new commit from the super module, did not publish the necessary commits from the submodule. He has to publish the commits from the submodule first.

Can you tell if that's the reason?

Cheers,
Felipe.

[thorsten]

Hi,

yes my mistake

Try again please. Sorry for the delay...

regards
Thorsten

[felipebm]

success!

thank you very much!