[ewpostek]

Hi Hugo,

I still stay with the vtkexporter.
I took such an example. I guess I should
obtain the “dragon.obj” in vtk. However, I am getting nothing.
The file tstx.vtu is not opened as well.
Just ensure, I have the dragon.obj in the mesh dir.
It looks well with the paraview.

<Node name=”root” dt=”0.01″ gravity=”0 -9.81 0″>
    <Mesh name=”mesh” filename=”mesh/dragon.obj” />
    <MeshObjLoader name=”loader” filename=”mesh/dragon.obj” />
    <MechanicalObject src=”@loader” template=”Vec3f” name=”mecha” />
    <TetrahedronSetTopologyContainer src=”@loader” name=”topo” />
    <VTKExporter filename=”tstx.vtu” listening=”true” edges=”0″ triangles=”1″ quads=”0″ tetras=”0″ pointsDataFields=”MechanicalObject.position” />
</Node>

I have used the pointsDataFields=”mecha.position”, as well.

The command
../bin/runSofa -g batch x.scn

I was not successful with the #5858. However, the case above can
be quicker to explain.

For this case, I use ubuntu stable version.

Could you help with it ?

best regards, Elek

[ewpostek]

Hi Hugo,
I will switch off the Modeler.
I write the scenes with xml directly,
cheers,
Elek

[ewpostek]

Dear Colleagues,

Sorry,
I used gcc 5.4, however,
when I use gcc 4.9 the problem has dissapeared.
Therefore, I think we can close
the thread for now,

best regards,
Elek

[ewpostek]

Hi Hugo,
Yes, it was very useful information.
Further questions, more specific, may arise
in the course of further work,
best regards,
Elek

[ewpostek]

Hi Hugo,
I will do attempt to
correct it as well,
cheers,
Elek

[ewpostek]

Hi,
just a word more,
the fpermissive is included into flags.make

# CMAKE generated file: DO NOT EDIT!
# Generated by “Unix Makefiles” Generator, CMake Version 3.2

# compile CXX with /apl/tryton/gcc/5.4.0/bin/c++
CXX_FLAGS = -fpermissive -Wall -W -O3 -DNDEBUG -fstack-protector –param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -fPIC -I/users/kdm/ewpostek/sofa_last/sofa/v16.08/src/SofaGeneral/../modules -I/users/kdm/ewpostek/sofa_last/sofa/v16.08/build/include
…
…
etc…

that is in the dir
/users/kdm/ewpostek/sofa_last/sofa/v16.08/build/SofaGeneral/SofaOpenglVisual/CMakeFiles/SofaOpenglVisual.dir

best,
Elek

[ewpostek]

Hi Hugo,
Yes, I did.
I used the switch -DCMAKE_CXX_FLAGS:STRING=’-fpermissive’ and
it reflects in the CMakeCache.txt
//No help, variable specified on the command line.
CMAKE_CXX_FLAGS:STRING=-fpermissive

Might be, I should look deeper into the dependencies,

Besr regards,
Elek

[ewpostek]

Hi,
Thank you, yes, it’s good advice !
I was porting the program to a cluster in which I had no
admin permissions.
However, actually, the remaining libs (OpenGL, glu, glew)
are installed. Therefore, I can go with all libs.

Another problem appeared, the echo (it is for gcc-4.9 to 5>):

Could anyone to help with it ?
best regards, Elek

Another problem appeared, the echo (it is for gcc-4.9 to 5>):

In file included from /users/kdm/ewpostek/sofa_last/sofa/v16.08/src/modules/SofaOpenglVisual/OglAttribute.cpp:22:0:
/users/kdm/ewpostek/sofa_last/sofa/v16.08/src/SofaGeneral/../modules/SofaOpenglVisual/OglAttribute.inl: In member function ‘void sofa::component::visualmodel::OglAttribute<size, type, DataTypes>::enable()’:
/users/kdm/ewpostek/sofa_last/sofa/v16.08/src/SofaGeneral/../modules/SofaOpenglVisual/OglAttribute.inl:192:70: error: there are no arguments to ‘glVertexAttribLPointer’ that depend on a template parameter, so a declaration of ‘glVertexAttribLPointer’ must be available [-fpermissive]
         glVertexAttribLPointer(_index, size, type, 0, (char*)NULL + 0);
                                                                      ^
/users/kdm/ewpostek/sofa_last/sofa/v16.08/src/SofaGeneral/../modules/SofaOpenglVisual/OglAttribute.inl:192:70: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/users/kdm/ewpostek/sofa_last/sofa/v16.08/src/SofaGeneral/../modules/SofaOpenglVisual/OglAttribute.inl: In instantiation of ‘void sofa::component::visualmodel::OglAttribute<size, type, DataTypes>::enable() [with int size = 4; unsigned int type = 5125u; DataTypes = sofa::defaulttype::Vec<4, unsigned int>]’:

[ewpostek]

Dear Colleaugues,
I am very sorry.
The errors, I have shown before, were because of an error
in linking cc with the correctversion of the gcc compiler
on the cluster.

It has been corrected.

Actually: the cmake looks as follows:
cd build
/users/kdm/ewpostek/soffa/cmake_tmp/cmake-3.2.2-Linux-i386/bin/cmake -DSOFA_NO_OPENGL:BOOL=ON -DSOFA_OPENMP:BOOL=OFF -DSOFA_BUILD_SCENECREATOR:BOOL=OFF ../src

with the echo

— The C compiler identification is GNU 5.4.0
— The CXX compiler identification is GNU 5.4.0
— Check for working C compiler: /apl/tryton/gcc/5.4.0/bin/cc
— Check for working C compiler: /apl/tryton/gcc/5.4.0/bin/cc — works
— Detecting C compiler ABI info
— Detecting C compiler ABI info – done
— Detecting C compile features
— Detecting C compile features – done
— Check for working CXX compiler: /apl/tryton/gcc/5.4.0/bin/c++
— Check for working CXX compiler: /apl/tryton/gcc/5.4.0/bin/c++ — works
— Detecting CXX compiler ABI info
— Detecting CXX compiler ABI info – done
— Detecting CXX compile features
— Detecting CXX compile features – done
— Install prefix: /users/kdm/ewpostek/soffa/sofa/master/build/install
— Boost version: 1.41.0
— Found PythonInterp: /apl/tryton/python/2.7.11/bin/python (found version “2.7.11”)
— Looking for include file pthread.h
— Looking for include file pthread.h – 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
— Found ZLIB: /usr/lib64/libz.so (found version “1.2.3”)
— Found PNG: /usr/lib64/libpng.so (found version “1.2.49”)
— Looking for XOpenDisplay in /usr/lib64/libX11.so
— Looking for XOpenDisplay in /usr/lib64/libX11.so – found
— Looking for gethostbyname
— Looking for gethostbyname – found
— Looking for connect
— Looking for connect – found
— Looking for remove
— Looking for remove – found
— Looking for shmat
— Looking for shmat – found
— Found X11: /usr/lib64/libX11.so
— SofaSparseSolver: metis was not found, SparseLDLSolver won’t be built
— SofaSparseSolver: csparse was found, SparseLUSolver and SparseCholeskySolver will be built
— SofaTest: optional dependency SofaPython NOT found, Python_test won’t be built
Adding Application runSofa
— Configuring done
— Generating done
— Build files have been written to: /users/kdm/ewpostek/soffa/sofa/master/build

The compilation starts to give the results:

[ 0%] Built target gtest
[ 1%] Built target gtest_main
[ 1%] Built target csparse
[ 3%] Built target newmat
[ 4%] Built target tinyxml
[ 12%] Built target SofaHelper
[ 12%] Built target SofaDefaultType
[ 22%] Built target SofaCore
[ 22%] Building CXX object SofaKernel/SofaFramework/SofaSimulationCore/CMakeFiles/SofaSimulationCore.dir/Node.cpp.o
In file included from /apl/tryton/gcc/5.4.0/include/c++/5.4.0/backward/hash_set:60:0,
from /usr/include/boost/graph/adjacency_list.hpp:25,
from /users/kdm/ewpostek/soffa/sofa/master/src/SofaKernel/framework/sofa/simulation/Node.cpp:52:
/apl/tryton/gcc/5.4.0/include/c++/5.4.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
#warning \
^
In file included from /usr/include/boost/functional/hash/hash.hpp:477:0,
from /usr/include/boost/functional/hash.hpp:6,
from /usr/include/boost/multi_index/detail/hash_index_args.hpp:17,
from /usr/include/boost/multi_index/hashed_index_fwd.hpp:16,
from /usr/include/boost/multi_index/hashed_index.hpp:33,
from /usr/include/boost/graph/named_graph.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:51,
from /users/kdm/ewpostek/soffa/sofa/master/src/SofaKernel/framework/sofa/simulation/Node.cpp:52:
/usr/include/boost/functional/hash/extensions.hpp:38:33: error: ‘template<class T, class A> std::size_t boost::hash_value’ conflicts with a previous declaration
std::size_t hash_value(std::list<T, A> const& v);
^
In file included from /usr/include/boost/functional/hash/hash.hpp:477:0,
from /usr/include/boost/functional/hash.hpp:6,
from /usr/include/boost/multi_index/detail/hash_index_args.hpp:17,
from /usr/include/boost/multi_index/hashed_index_fwd.hpp:16,
from /usr/include/boost/multi_index/hashed_index.hpp:33,
from /usr/include/boost/graph/named_graph.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:51,
from /users/kdm/ewpostek/soffa/sofa/master/src/SofaKernel/framework/sofa/simulation/Node.cpp:52:
/usr/include/boost/functional/hash/extensions.hpp:38:33: error: ‘template<class T, class A> std::size_t boost::hash_value’ conflicts with a previous declaration
std::size_t hash_value(std::list<T, A> const& v);
^
/usr/include/boost/functional/hash/extensions.hpp:36:17: note: previous declaration ‘namespace boost { }::hash_value’
std::size_t hash_value(std::vector<T, A> const&);

.
.
.
. goes furtherr and finishes
.
.
.

usr/include/boost/graph/detail/adjacency_list.hpp:1620:5: note: template argument deduction/substitution failed:
In file included from /usr/include/boost/graph/detail/adjacency_list.hpp:30:0,
from /usr/include/boost/graph/adjacency_list.hpp:345,
from /users/kdm/ewpostek/soffa/sofa/master/src/SofaKernel/framework/sofa/simulation/Node.cpp:52:
/usr/include/boost/graph/graph_concepts.hpp:92:17: error: using invalid field ‘boost::concepts::IncidenceGraph<G>::p’
e = *p.first;
^
make[2]: *** [SofaKernel/SofaFramework/SofaSimulationCore/CMakeFiles/SofaSimulationCore.dir/Node.cpp.o] Error 1
make[1]: *** [SofaKernel/SofaFramework/SofaSimulationCore/CMakeFiles/SofaSimulationCore.dir/all] Error 2
make: *** [all] Error 2

Could you help with it ?

Best regards,
Elek

[ewpostek]

Hello,

I do attempt to build SOFA without OpenGL on a cluster
with the compilers:
1) tryton/compiler/gcc/5.4.0 2) tryton/python3/3.5.1

with the command
/users/kdm/ewpostek/soffa/cmake_tmp/cmake-3.2.2-Linux-i386/bin/cmake -DSOFA_NO_OPENGL:BOOL=ON -DSOFA_OPENMP:BOOL=OFF ../src

I downloaded the today’s version,

However, I reach an error:

[ 4%] Building CXX object SofaKernel/SofaFramework/SofaHelper/CMakeFiles/SofaHelper.dir/AdvancedTimer.cpp.o
In file included from /users/kdm/ewpostek/soffa/sofa/master/src/SofaKernel/framework/sofa/helper/../../sofa/helper/logging/MessageDispatcher.h:37,
.
,
,
,

/helper/logging/Message.h:89: error: type ‘<type error>’ argument given to ‘delete’, expected pointer
make[2]: *** [SofaKernel/SofaFramework/SofaHelper/CMakeFiles/SofaHelper.dir/AdvancedTimer.cpp.o] Error 1
make[1]: *** [SofaKernel/SofaFramework/SofaHelper/CMakeFiles/SofaHelper.dir/all] Error 2
make: *** [all] Error 2

The system:

Linux version 2.6.32-504.el6.x86_64 (mockbuild@c6b9.bsys.dev.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) ) #1 SMP Wed Oct 15 04:27:16 UTC 2014
Command line: initrd=osgv01/diskless_initrd-2.6.32-504.el6.x86_64.img console=tty0 console=ttyS1,115200n8 root=nfs:10.26.7.209:/srv/diskless/osgv01/root rw SNAPSHOT=osgv01 consoleblank=0 nosoftlockup intel_idle.max_cstate=0 mce=ignore_ce BOOT_IMAGE=osgv01/vmlinuz-2.6.32-504.el6.x86_64
KERNEL supported cpus:
Intel GenuineIntel
AMD AuthenticAMD
Centaur CentaurHauls

Could you be so kind, and help with it ?

best regards,
Elek

[ewpostek]

Hi,
No, I did not do anything particular.
I simply made a copy/paste of the link
you gave on the download page,
Elek

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