built hermes-tutorial devel

[Tomas Svaton]

Hello everybody,

I apologise for such a lot of questions. After the installation of hermes (devel), the problems of making hermes-tutorial occurs (CMake.vars enclosed). I see that he misses in some way the recognition of ‘MeshSharedPtr’, which in the hermes2d/test_examples/* are used also and the compilation passes well therein.

Could someone give me a hint where the problem could be?

Thank you very much.

Kind regards,

Tomas.

tomas@tomas-VirtualBox:~/workspace/hermes-tutorial$ cmake .
-- Found UMFPACK: /usr/lib/libumfpack.so;/usr/lib/libamd.so  
-- Found PTHREAD: /usr/lib/i386-linux-gnu/libpthread.so  
-- Found TCMALLOC: /usr/lib/libtcmalloc.so  
-- Found PARALUTION: /home/tomas/workspace/paralution-0.4.0/build/lib/libparalution.a  
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found HERMES_COMMON: /usr/local/lib/libhermes_common.so  
-- Found HERMES: /usr/local/lib/libhermes2d.so  

Hermes-tutorial Configuration results
---------------------

-------Features-------
Build with OpenMP: YES
Build with TCMalloc: YES
Build with BSON: NO
Build with MATIO: NO
Build with MPI: YES
Build with EXODUSII: NO

-------Solvers-------
Build with UMFPACK: YES
Build with PARALUTION: YES
Build with PETSC: !TO_DO!
Build with MUMPS: NO
Build with SUPERLU: NO
Build with TRILINOS: !TO_DO!
---------------------


-- Configuring done
-- Generating done
-- Build files have been written to: /home/tomas/workspace/hermes-tutorial

=========

tomas@tomas-VirtualBox:~/workspace/hermes-tutorial$ make
[  1%] Building CXX object A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/main.cpp.o
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp: In function ‘int main(int, char**)’:
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:33:3: error: ‘MeshSharedPtr’ was not declared in this scope
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:33:17: error: expected ‘;’ before ‘mesh’
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:40:34: error: ‘mesh’ was not declared in this scope
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:40:34: note: suggested alternatives:
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h2d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:38,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h2d_xml.h:2111:9: note:   ‘XMLMesh::mesh’
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h1d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:39,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h1d_xml.h:804:9: note:   ‘XMLMesh1D::mesh’
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:51:33: error: ‘mesh’ was not declared in this scope
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:51:33: note: suggested alternatives:
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h2d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:38,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h2d_xml.h:2111:9: note:   ‘XMLMesh::mesh’
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h1d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:39,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h1d_xml.h:804:9: note:   ‘XMLMesh1D::mesh’
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:55:3: error: ‘mesh’ was not declared in this scope
/home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:55:3: note: suggested alternatives:
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h2d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:38,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h2d_xml.h:2111:9: note:   ‘XMLMesh::mesh’
In file included from /usr/local/include/hermes2d/mesh/mesh_reader_h1d_xml.h:26:0,
                 from /usr/local/include/hermes2d/hermes2d.h:39,
                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:
/usr/local/include/hermes2d/mesh/mesh_h1d_xml.h:804:9: note:   ‘XMLMesh1D::mesh’
make[2]: *** [A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/main.cpp.o] Error 1
make[1]: *** [A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/all] Error 2
make: *** [all] Error 2

[Lukas Korous]

Hi,

all SharedPtrs (MeshSharedPtr, MeshFunctionSharedPtr, SpaceSharedPtr)
are defined in the namespace Hermes::Hermes2D, before they were in the
global namespace, I am working on the update of both tutorial &
examples.

Best,
Lukas

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--
Lukáš Korous

[Tomas Svaton]

Hi Lukas,

Thank you for your response. I looked where the problem could be. Please correct me when I am wrong.

The installation directories are in the /home/user_name/usr/lib and /home/user_name/usr/local, hence I added these lines 

set(HERMES_DIRECTORY "/home/tomas/usr/lib")

set(HERMES_INCLUDE_PATH "/home/tomas/usr/include")

set(DEP_INCLUDE_PATHS "/home/tomas/usr/include")

to CMake.vars file.

then I performed classical

$rm CMakeCache.txt

$cmake .

$make

and the following error appeared:

tomas@tomas-VirtualBox:~/workspace/hermes-tutorial$ make

Scanning dependencies of target A-01-mesh

[  1%] Building CXX object A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/main.cpp.o

In file included from /home/tomas/usr/include/hermes2d/hermes2d.h:39:0,

                 from /home/tomas/workspace/hermes-tutorial/A-linear/01-mesh/main.cpp:1:

/home/tomas/usr/include/hermes2d/mesh/mesh_reader_h2d_xml.h:26:26: fatal error: mesh_h2d_xml.h: No such file or directory

compilation terminated.

make[2]: *** [A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/main.cpp.o] Error 1

make[1]: *** [A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/all] Error 2

make: *** [all] Error 2

tomas@tomas-VirtualBox:~/workspace/hermes-tutorial$

Before I installed hermes as normal user (without sudo). Please let me know whether could be the problem. Thank you.

Kind regards,

Tomas.

[Lukas Korous]

Hi,

one question, why are you not installing with sudo to the standard
directories /usr/local/lib (/usr/lib), /usr/local/include
(/usr/include)?

Also, did your hermes (library) compilation and installation finish
successfully? Did you set CMAKE_INSTALL_PREFIX?

This looks like there is some problem going on, since there is no
reason why it would find the file mesh_reader_h2d_
xml.h, but not mesh_h2d_xml.h, they are installed together.

Also, some days ago I sent you a personal email, asking if you would
be interested to meet in person in Pilsen, where some of us reside,
maybe we could figure stuff out faster.

Lukas

[Tomas Svaton]

Hi Lukas,

I am sorry, but I did not received any personal e-mail from you. Could you resend me it, please? This is only possible meaning of communication that I can use now. I apologize about the spam on basic problems to everyone.

I did it as written in the help for install hermes: http://hpfem.org/hermes-doc/hermes/html/src/installation/linux.html
for such purpose I added to CMake.vars the line set(CMAKE_INSTALL_PREFIX "~/usr"). Then it was installed everything to /home/tomas/usr/lib and /home/tomas/usr/include

Now I removed this option from CMake.vars and it installed to /usr/local/lib/ and /usr/local/include/ correctly. I removed also the most of the optionally stuff to understand where the problem could be. Anyway the errors still appear when building hermes-tutorial

tomas@tomas-VirtualBox:~/workspace/hermes-tutorial$ make

Scanning dependencies of target A-01-mesh

[  1%] Building CXX object A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/main.cpp.o

Linking CXX executable A-01-mesh

CMakeFiles/A-01-mesh.dir/main.cpp.o: In function `main':

main.cpp:(.text+0x16d): undefined reference to `Hermes::Hermes2D::MeshReaderH2DXML::load(char const*, std::tr1::shared_ptr<Hermes::Hermes2D::Mesh>)'

main.cpp:(.text+0x34f): undefined reference to `Hermes::Hermes2D::Views::MeshView::show(std::tr1::shared_ptr<Hermes::Hermes2D::Mesh>)'

collect2: error: ld returned 1 exit status

make[2]: *** [A-linear/01-mesh/A-01-mesh] Error 1

make[1]: *** [A-linear/01-mesh/CMakeFiles/A-01-mesh.dir/all] Error 2

make: *** [all] Error 2

Thank you for your response.

Kind regards,

Tomas.