[ewpostek]

Excuse me, Hugo, if it is useful
I can send the details of the
previous compilation,
Best, Elek

[ewpostek]

Hi Hugo,
Yes, I have just upgraded gcc.
Best, Elek

[ewpostek]

Hi Hugo,
I applied gcc 8.3.0.
Even with older boost (to upgrade of course)
it works,
Cheers

cmake \
 -DBoost_INCLUDE_DIR:PATH=/net/software/local/boost/1.58.0-gcc6.4.0/include \
 -DPYTHON_EXECUTABLE:FILEPATH=/net/software/local/python/3.6.5/bin/python3 \
 -DCMAKE_CXX_COMPILER:FILEPATH=/net/software/local/gcc/8.3.0/bin/c++ \
 -DCMAKE_CXX_COMPILER_AR:FILEPATH=/net/software/local/gcc/8.3.0/bin/gcc-ar \
 -DCMAKE_CXX_COMPILER_RANLIB:FILEPATH=/net/software/local/gcc/8.3.0/bin/gcc-ranlib \
 -DCMAKE_C_COMPILER:FILEPATH=/net/software/local/gcc/8.3.0/bin/gcc \
 -DCMAKE_C_COMPILER_AR:FILEPATH=/net/software/local/gcc/8.3.0/bin/gcc-ar \
 -DCMAKE_C_COMPILER_RANLIB:FILEPATH=/net/software/local/gcc/8.3.0/bin/gcc-ranlib \
 -DGLEW_INCLUDE_DIR:PATH=/net/software/local/glew/2.1.0/include \
 -DGLEW_LIBRARY:FILEPATH=/net/software/local/glew/2.1.0/lib64/libGLEW.so \
 /net/people/plgewpostek/sofa0/src

[ewpostek]

Hi Hugo,
Thank you for the hint. I will be looking into.
In the meantime, I prepared the geometry of the single composite object, that consists of the nucleus, cytoplasm, outer membrane, membrane that surrounds the nucleus and tendons.

I made it using the gmsh. Since the nonlinear models are not available to the public yet
(you mentioned about presenting the ideas during your meeting), I would like to calculate the collisions of high number of such objects, but assuming the physically linear material. After reaching the success (hoping) I would start the implementation
of the non-linear models.

I am sending you the gmsh files (*geo, *msh and two pictures).
Obviously, it is necessary to scale down the model (diameter=1).

Best regards,

Elek

[ewpostek]

Hi Hugo,
just ensure, of course,
I can share evth.
Best regards, Elek

[ewpostek]

Hi Hugo,
Sounds great.
I have the procedures in the programs that are written by myself.
These are f77/f90 procedures.

Now, I still work on the model creation of
several composite cells that are colliding.
My latest thread is “compiling_AdvancedTimer” in the subject.
In fact, these are some problems with ogl.

Cheers,
Elek

[ewpostek]

Hi,
I think the switches should be for example:

-DGLEW_INCLUDE_DIR:PATH=/usr/include -DGLEW_LIBRARY:FILEPATH=/usr/lib64/libGLEW.so

However, while building without OGL the glew should not be
linked (I believe)

I think there is a kind of conflict.

best, Elek

[ewpostek]

Hi, thank you, just one remark,
there is no problem with the stable versions,
best, Elek

[ewpostek]

Hi,
it would be great to have viscous models,
viscous-elastic (standard solid) and creep (similar to metals,
time hardening, strain hardening).
Perfect, would be to have tendons (with prestressing).

Best regards,
Elek

[ewpostek]

Hi Maxime,
I repeated the installation of GLEW as you shown, on ubuntu.
Morover, I do compilation on a cluster where the glew is installed
108731:372 usr/lib64/libGLEW.so.1.5.5
108968:0 usr/lib64/libGLEW.so.1.5
However, I still arrive at the same error.

[ 91%] Building CXX object SofaKernel/SofaFramework/framework_test/CMakeFiles/SofaFramework_test.dir/helper/gl/GLSLShader_test.cpp.o
In file included from /home/eligiusz/tmp_feb_sofa/sofa-master/SofaKernel/framework/framework_test/helper/gl/GLSLShader_test.cpp:4:0:
/home/eligiusz/tmp_feb_sofa/sofa-master/SofaKernel/framework/sofa/core/../../sofa/helper/gl/GLSLShader.h:38:2: error: #error GL Shader support requires GLEW. Please define SOFA_HAVE_GLEW to use shaders.
#error GL Shader support requires GLEW. Please define SOFA_HAVE_GLEW to use shaders.

I think I should rather not get the error with the cmake switches like this:

cd build
/home/eligiusz/cmake_tmp/cmake-3.2.2-Linux-i386/bin/cmake -DSOFA_NO_OPENGL:BOOL=ON -DSOFA_BUILD_SCENECREATOR:BOOL=OFF -DSOFA_OPENMP:BOOL=OFF -DAPPLICATION_MODELER:BOOL=OFF -DCMAKE_CXX_FLAGS:STRING=’-fpermissive’ -DCMAKE_CXX_FLAGS_DEBUG:STRING=’-fpermissive’ ../sofa-master

I use gcc 4.8 and 4.9.

best regards,
Elek

[ewpostek]

Hello,
Thank you, yes, it is. I am using 4.8 now.
However, one problem arises.
I build without opengl for batch mode.
However, it appears an error with GLEW,
as follows.

[ 91%] Building CXX object SofaKernel/SofaFramework/framework_test/CMakeFiles/SofaFramework_test.dir/helper/gl/GLSLShader_test.cpp.o
In file included from /home/eligiusz/tmp_feb_sofa/sofa-master/SofaKernel/framework/framework_test/helper/gl/GLSLShader_test.cpp:4:0:
/home/eligiusz/tmp_feb_sofa/sofa-master/SofaKernel/framework/sofa/core/../../sofa/helper/gl/GLSLShader.h:38:2: error: #error GL Shader support requires GLEW. Please define SOFA_HAVE_GLEW to use shaders.
 #error GL Shader support requires GLEW. Please define SOFA_HAVE_GLEW to use shaders.
  ^
/home/eligiusz/tmp_feb_sofa/sofa-master/SofaKernel/framework/framework_test/helper/gl/GLSLShader_test.cpp: In member function ‘virtual void GLSLShader_test_GLSLShader_SetFiles_Test::TestBody()’:

I think this problem was removed with the stable versions. I use v16.08.
I works without ogl well. The same with 16.12.

Would you mind to help with it ?

Bes regards, Elek

[ewpostek]

hi Hugo,
Thank you, I think we can close
the topic,
best, Elek

[ewpostek]

right, I will check the format,
Elek

[ewpostek]

Hi Hugo,
yes, it has helped, the triangles cover
the surface.
Just one concern.
Is it possible to identify the triangles on the surface
in the resulting *.vtu file (vtkExporter) ?
The total number of cells is
<Piece NumberOfPoints=”3009″ NumberOfCells=”65516″>
the tetrahedrals only – 15033;

cheers,
Elek

[ewpostek]

Yes, it is,
cheers, Elek

[ewpostek]

Hi Hugo,
Yes, I did. There still is quite much work
to build the framework of the system before
adding nonlinearities.
Best regards, Elek.

[ewpostek]

Thank you, I will do the test on comparison
of the stiffnesses (hetero and homogenous structure).

So far, I have checked the reading of the file
and the applicability of the drawHeterogeneousTetra=”1″ to
the TetrahedronFEMForceField
and TetrahedralCorotationalFEMForceField

Both commands read the file *pos. However, the
TetrahedralCorotationalFEMForceField gives the warning:
Unused Attribute: “drawHeterogeneousTetra” with value: “1”.

Could you tell me if the vector *pos should work with
other parameters as well? Namely, Poisson’s ratio,
and for the nonlinear materials parameters like for example neohokean.
This is because I intend to have nonlinear viscous-elastic
finite strains materials in the bodies.

Cheers, Elek

[ewpostek]

Hi,
Sorry, may be it is redundant.
Would you mind to give a hint
how to build a composite object based
on one single mesh (gmsh 1.0 format) ?
(different kind of materials)

kindest regards, Elek

[ewpostek]

Hi,
I think, I created
TetrahedralCorotationalFEMForceField.scn #182
best,
Elek

[ewpostek]

Hi,
I am sorry, yes, it is warning only,
cheers, Elek

[ewpostek]

Hi Hugo,
Yes, it would be much better, definitely.
I simply do not see the coincidence
between ‘rphys’ variable and the
definition of the for example
<TetrahedralCorotationalFEMForceField template=”Vec3d” name=”FEM” method=”large” poissonRatio=”0.3″ youngModulus=”100″ computeGlobalMatrix=”0″ />

<TetrahedralCorotationalFEMForceField template=”Vec3d” name=”FEM” method=”large” poissonRatio=”0.3″ youngModulus=”500″ computeGlobalMatrix=”0″ />

since I should set it twice for two different physical models. This is the second tet.
rphys = 1
2 4 1 1 4 654 1708 1974 2101

and this is the 15032th tet with rphys = 2
15032 4 2 2 4 1319 1390 1320 3008

Because both kind of elements should be
in the same Mechanical Object.

best, Elek

Thank you for the hint on the (“)

[ewpostek]

Hi Hugo,
Thank you very much for the template.
I obtained the displacements and forces in the test2a(_n).vtu files.
There is only one surprising comment from the program:

eligiusz@eligiusz-laptop:~/tmp_stable_sofa/tmp_exa/stan_t1$ /home/eligiusz/tmp_stable_sofa/sofa/v16.08/build/bin/runSofa -g batch -n 3 x2_hg.scn
[WARNING] [VTKExporter] File test_2a NOT FOUND in :/home/eligiusz/tmp_stable_sofa/sofa/v16.08/src/examples:/home/eligiusz/tmp_stable_sofa/sofa/v16.08/src/share
File test_2a NOT FOUND in :/home/eligiusz/tmp_stable_sofa/sofa/v16.08/src/examples:/home/eligiusz/tmp_stable_sofa/sofa/v16.08/src/share
Could not read value for data field position: mecaDOFs.position
The model is NeoHookean
Computing 3 iterations.
3 iterations done in 3.32091 s ( 0.903368 FPS).
3 iterations done in 3.32091 s ( 0.903366 FPS).
eligiusz@eligiusz-laptop:~/tmp_stable_sofa/tmp_exa/stan_t1$

thank you,
Elek

[ewpostek]

Hi Hugo,
The problem is that when putting the
vtkExporter at the second place (correctly) I do not
obtain neither displacements (deformed structure)
nor forces.
The files from the step one or step 10 are the same.
I run the example in the interactive mode. It gives
the deformation.

There are zeros the the end

<VTKFile type=”UnstructuredGrid” version=”0.1″ byte_order=”BigEndian”>
<UnstructuredGrid>
<Piece NumberOfPoints=”510″ NumberOfCells=”10589″>
<PointData>
<DataArray type=”Float64″ Name=”force” NumberOfComponents=”3″ format=”ascii”>
0 0 0
0 0 0
0 0 0

I applied different combinations of the parameters but
it gave me the same result.

I see that the vtkExporter should not
be put on the place “one” because the mechanical
object is defined above the node <Node name=”FastTetrahedronCorotationalForceField”>
(I believe ?).

However, “experimentally”, while putting the vtkExporter at the position “one”
I have got a deformation. However, it’s true I do
not know if this is right (correct).
Morover, there is the error:

[WARNING] [VTKExporter] VTKExporter : error while fetching data field 'force' of object 'dofs', check object name

best, Elek

[ewpostek]

Hi Hugo,
Thank you, works!
regards, Elek

[ewpostek]

hi, sorry, I have found it,
just a confusion,
best regards, Elek

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