make for CSXCAD failed

Install support for openEMS

Moderators: thorsten, sebastian

felipebm
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Fri 27 Feb 2015, 15:52

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.
Attachments
findVTK.txt
$ find -iname *vtk* 1> /tmp/findVTK.txt 2> /dev/null
(233.89 KiB) Downloaded 937 times
output.log
shell output
(2.57 KiB) Downloaded 928 times
CMakeOutput.log
Cmake log
(13.55 KiB) Downloaded 956 times

felipebm
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Mon 02 Mar 2015, 19:42

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
Posts: 1430
Joined: Mon 27 Jun 2011, 12:26

Re: make for CSXCAD failed

Post by thorsten » Mon 02 Mar 2015, 21:51

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
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Wed 04 Mar 2015, 21:51

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:

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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.
Attachments
instalation_output.log
(37.76 KiB) Downloaded 972 times

thorsten
Posts: 1430
Joined: Mon 27 Jun 2011, 12:26

Re: make for CSXCAD failed

Post by thorsten » Wed 04 Mar 2015, 22:35

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
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Thu 05 Mar 2015, 20:05

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
Posts: 1430
Joined: Mon 27 Jun 2011, 12:26

Re: make for CSXCAD failed

Post by thorsten » Thu 05 Mar 2015, 21:23

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
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Fri 06 Mar 2015, 19:17

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
Posts: 1430
Joined: Mon 27 Jun 2011, 12:26

Re: make for CSXCAD failed

Post by thorsten » Fri 06 Mar 2015, 20:38

Hi,

yes my mistake :oops:

Try again please. Sorry for the delay...

regards
Thorsten

felipebm
Posts: 23
Joined: Wed 10 Dec 2014, 14:15

Re: make for CSXCAD failed

Post by felipebm » Fri 06 Mar 2015, 21:50

success!

thank you very much!

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