Errors happen when run ninja #3743

jianchu00 · 2023-03-23T02:53:54Z

jianchu00
Mar 23, 2023

Hi,

I am trying to set up SOFA and sofapython3 in Ubuntu18.04. I have followed the instruction and video tutorial many times but still could not figure this out. Any help would be appreciated!

Here is what CMake-gui shows:

(base) dell@dell:~/sofa/build$ ninja
[0/1] Re-running CMake...
-- Precompiled headers: enabled (SOFA_BUILD_WITH_PCH_ENABLED is ON).
-- Install prefix: /home/dell/sofa/build/install
Using legacy headers is enabled.
Headers from v21.06 are usable, but it is advised to change your code to use the new headers introduced in v21.12.
Adding precompiled header for SofaCore
Adding module Sofa.GL
Adding plugin SofaSimpleFem
Adding plugin SofaRigid
Adding plugin SofaDeformable
Adding plugin SofaObjectInteraction
Adding plugin SofaMeshCollision
Adding plugin SofaEngine
Adding plugin SofaExplicitOdeSolver
Adding plugin SofaImplicitOdeSolver
Adding plugin SofaLoader
Adding plugin SofaGeneralVisual
Adding plugin SofaGraphComponent
Adding plugin SofaGeneralMeshCollision
Adding plugin SofaBoundaryCondition
Adding plugin SofaGeneralAnimationLoop
Adding plugin SofaGeneralDeformable
Adding plugin SofaGeneralEngine
Adding plugin SofaGeneralExplicitOdeSolver
Adding plugin SofaGeneralImplicitOdeSolver
Adding plugin SofaGeneralLinearSolver
Adding plugin SofaGeneralRigid
Adding plugin SofaGeneralObjectInteraction
Adding plugin SofaGeneralSimpleFem
Adding plugin SofaGeneralTopology
Adding plugin SofaTopologyMapping
Adding plugin SofaUserInteraction
Adding plugin SofaConstraint
Adding plugin SofaGeneralLoader
Adding plugin SofaExporter
Adding plugin SofaSparseSolver
-- SofaSparseSolver: using built-in metis library
Adding plugin SofaPreconditioner
Adding plugin SofaHaptics
Adding plugin SofaValidation
Adding plugin SofaDenseSolver
Adding plugin SofaNonUniformFem
Adding plugin SofaOpenglVisual
Adding plugin SofaMiscTopology
Adding plugin SofaMiscExtra
Adding plugin SofaMiscForceField
Adding plugin SofaMiscEngine
Adding plugin SofaMiscSolver
Adding plugin SofaMiscFem
Adding plugin SofaMiscMapping
Adding plugin SofaMiscCollision
-- SofaMiscModule: build all maintained sofa components.
-- cxxopts version 2.2.0
-- SofaGuiCommon: Sofa.GL dependent features enabled.
SofaGuiQt: will use Qt5
CMake Warning at /home/dell/sofa/build/lib/cmake/SofaEigen2SolverConfig.cmake:36 (message):
  SofaEigen2Solver has been removed.  The package still exists for
  compatibility but is empty.  Eigen classes were moved to Sofa.LinearAlgebra
  and SVDLinearSolver to SofaDenseSolver.
Call Stack (most recent call first):
  /home/dell/sofa/build/lib/cmake/SofaBaseConfig.cmake:35 (find_package)
  /home/dell/sofa/build/lib/cmake/SofaGeneralTopologyConfig.cmake:34 (find_package)
  /home/dell/sofa/build/lib/cmake/SofaMiscForceFieldConfig.cmake:36 (find_package)
  modules/SofaGuiQt/CMakeLists.txt:320 (find_package)


Adding collection SofaComponentAll
Adding plugin CImgPlugin
-- CImgPlugin: TIFF Image Format enabled
-- CImgPlugin: JPEG Image Format enabled
-- CImgPlugin: PNG Image Format enabled
-- SofaPython3 is compiled as a subproject to the external project 'Sofa'.
Adding plugin SofaPython3
-- Python:
    Version: 3.8.0
    Executable: /usr/bin/python3.8
    Headers: /usr/include/python3.8
    Libraries: /usr/lib/x86_64-linux-gnu/libpython3.8.so
    User site: /home/dell/.local/lib/python3.8/site-packages
-- pybind11:
    Version: 2.10.4
    Config: /home/dell/anaconda3/envs/sofa/share/cmake/pybind11/pybind11Config.cmake
Adding application runSofa
Write Plugin list at /home/dell/sofa/build/lib/plugin_list.conf.default
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dell/sofa/build
[32/1398] Building CXX object 'SofaKer...duct[CompressedRowSparseMatrix].cpp.o'
FAILED: SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp.o 
/usr/bin/c++ -DNDEBUG -DSOFA_BUILD_SOFA_LINEARALGEBRA -DSOFA_BUILD__LINEAR_ALGEBRA -DSofa_LinearAlgebra_EXPORTS -I/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src -Iinclude/Sofa.LinearAlgebra -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Type/src -Iinclude/Sofa.Type -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Config/src -Iinclude/Sofa.Config -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Compat/src -Iinclude/Sofa.Compat -I/home/dell/sofa/src/SofaKernel/modules/SofaHelper/src -Iinclude/Sofa.Helper -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Topology/src -Iinclude/Sofa.Topology -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Geometry/src -Iinclude/Sofa.Geometry -isystem /home/dell/sofa/src/SofaKernel/extlibs/json -isystem /usr/include/eigen3 -O3 -DNDEBUG -fPIC -Wno-attributes -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wall -W -Wno-padded -MD -MT 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp.o' -MF SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp.o.d -o 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp.o' -c '/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp'
In file included from /home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].h:25,
                 from /home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp:23:
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h: In instantiation of ‘void sofa::linearalgebra::CompressedRowSparseMatrix<TBlock, TVecBlock, TVecIndex>::mul(sofa::linearalgebra::CompressedRowSparseMatrix<RB, RVB, RVI>&, const sofa::linearalgebra::CompressedRowSparseMatrix<MB, MVB, MVI>&) const [with RB = float; RVB = sofa::type::vector<float, sofa::type::CPUMemoryManager<float> >; RVI = sofa::type::vector<unsigned int>; MB = float; MVB = sofa::type::vector<float, sofa::type::CPUMemoryManager<float> >; MVI = sofa::type::vector<unsigned int>; TBlock = float; TVecBlock = sofa::type::vector<float, sofa::type::CPUMemoryManager<float> >; TVecIndex = sofa::type::vector<unsigned int>]’:
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp:31:17:   required from here
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h:1406:27: warning: comparison between ‘enum sofa::linearalgebra::CompressedRowSparseMatrix<float>::<unnamed>’ and ‘enum sofa::linearalgebra::CompressedRowSparseMatrix<float>::<unnamed>’ [-Wenum-compare]
 1406 |         static_assert( NC == CompressedRowSparseMatrix<MB,MVB,MVI>::NL );
      |                        ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h:1433:62: warning: comparison of integer expressions of different signedness: ‘const value_type’ {aka ‘const unsigned int’} and ‘sofa::linearalgebra::BaseMatrix::Index’ {aka ‘int’} [-Wsign-compare]
 1433 |                 while( mr<m.rowIndex.size() && m.rowIndex[mr]<col ) mr++;
      |                                                ~~~~~~~~~~~~~~^~~~
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h: In instantiation of ‘void sofa::linearalgebra::CompressedRowSparseMatrix<TBlock, TVecBlock, TVecIndex>::mul(sofa::linearalgebra::CompressedRowSparseMatrix<RB, RVB, RVI>&, const sofa::linearalgebra::CompressedRowSparseMatrix<MB, MVB, MVI>&) const [with RB = double; RVB = sofa::type::vector<double, sofa::type::CPUMemoryManager<double> >; RVI = sofa::type::vector<unsigned int>; MB = double; MVB = sofa::type::vector<double, sofa::type::CPUMemoryManager<double> >; MVI = sofa::type::vector<unsigned int>; TBlock = double; TVecBlock = sofa::type::vector<double, sofa::type::CPUMemoryManager<double> >; TVecIndex = sofa::type::vector<unsigned int>]’:
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[CompressedRowSparseMatrix].cpp:37:17:   required from here
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h:1406:27: warning: comparison between ‘enum sofa::linearalgebra::CompressedRowSparseMatrix<double>::<unnamed>’ and ‘enum sofa::linearalgebra::CompressedRowSparseMatrix<double>::<unnamed>’ [-Wenum-compare]
 1406 |         static_assert( NC == CompressedRowSparseMatrix<MB,MVB,MVI>::NL );
      |                        ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/CompressedRowSparseMatrix.h:1433:62: warning: comparison of integer expressions of different signedness: ‘const value_type’ {aka ‘const unsigned int’} and ‘sofa::linearalgebra::BaseMatrix::Index’ {aka ‘int’} [-Wsign-compare]
 1433 |                 while( mr<m.rowIndex.size() && m.rowIndex[mr]<col ) mr++;
      |                                                ~~~~~~~~~~~~~~^~~~

[34/1398] Building CXX object 'SofaKer...StorageOrder[EigenSparseMatrix].cpp.o'
FAILED: SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixStorageOrder[EigenSparseMatrix].cpp.o 
/usr/bin/c++ -DNDEBUG -DSOFA_BUILD_SOFA_LINEARALGEBRA -DSOFA_BUILD__LINEAR_ALGEBRA -DSofa_LinearAlgebra_EXPORTS -I/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src -Iinclude/Sofa.LinearAlgebra -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Type/src -Iinclude/Sofa.Type -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Config/src -Iinclude/Sofa.Config -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Compat/src -Iinclude/Sofa.Compat -I/home/dell/sofa/src/SofaKernel/modules/SofaHelper/src -Iinclude/Sofa.Helper -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Topology/src -Iinclude/Sofa.Topology -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Geometry/src -Iinclude/Sofa.Geometry -isystem /home/dell/sofa/src/SofaKernel/extlibs/json -isystem /usr/include/eigen3 -O3 -DNDEBUG -fPIC -Wno-attributes -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wall -W -Wno-padded -MD -MT 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixStorageOrder[EigenSparseMatrix].cpp.o' -MF SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixStorageOrder[EigenSparseMatrix].cpp.o.d -o 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixStorageOrder[EigenSparseMatrix].cpp.o' -c '/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixStorageOrder[EigenSparseMatrix].cpp'
[41/1398] Building CXX object 'SofaKer...atrixProduct[EigenSparseMatrix].cpp.o'
FAILED: SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[EigenSparseMatrix].cpp.o 
/usr/bin/c++ -DNDEBUG -DSOFA_BUILD_SOFA_LINEARALGEBRA -DSOFA_BUILD__LINEAR_ALGEBRA -DSofa_LinearAlgebra_EXPORTS -I/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src -Iinclude/Sofa.LinearAlgebra -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Type/src -Iinclude/Sofa.Type -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Config/src -Iinclude/Sofa.Config -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Compat/src -Iinclude/Sofa.Compat -I/home/dell/sofa/src/SofaKernel/modules/SofaHelper/src -Iinclude/Sofa.Helper -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Topology/src -Iinclude/Sofa.Topology -I/home/dell/sofa/src/SofaKernel/modules/Sofa.Geometry/src -Iinclude/Sofa.Geometry -isystem /home/dell/sofa/src/SofaKernel/extlibs/json -isystem /usr/include/eigen3 -O3 -DNDEBUG -fPIC -Wno-attributes -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wall -W -Wno-padded -MD -MT 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[EigenSparseMatrix].cpp.o' -MF SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[EigenSparseMatrix].cpp.o.d -o 'SofaKernel/SofaFramework/Sofa.LinearAlgebra/CMakeFiles/Sofa.LinearAlgebra.dir/src/sofa/linearalgebra/SparseMatrixProduct[EigenSparseMatrix].cpp.o' -c '/home/dell/sofa/src/SofaKernel/modules/Sofa.LinearAlgebra/src/sofa/linearalgebra/SparseMatrixProduct[EigenSparseMatrix].cpp'
[73/1398] Building CXX object modules/...SofaGeneralRigid.dir/cmake_pch.hxx.gch
ninja: build stopped: subcommand failed.

And following is the cmake shows:

-- Precompiled headers: enabled (SOFA_BUILD_WITH_PCH_ENABLED is ON).
Install prefix: /home/dell/sofa/build/install
Using legacy headers is enabled.
Headers from v21.06 are usable, but it is advised to change your code to use the new headers introduced in v21.12.
Adding precompiled header for SofaCore
Adding module Sofa.GL
Adding plugin SofaSimpleFem
Adding plugin SofaRigid
Adding plugin SofaDeformable
Adding plugin SofaObjectInteraction
Adding plugin SofaMeshCollision
Adding plugin SofaEngine
Adding plugin SofaExplicitOdeSolver
Adding plugin SofaImplicitOdeSolver
Adding plugin SofaLoader
Adding plugin SofaGeneralVisual
Adding plugin SofaGraphComponent
Adding plugin SofaGeneralMeshCollision
Adding plugin SofaBoundaryCondition
Adding plugin SofaGeneralAnimationLoop
Adding plugin SofaGeneralDeformable
Adding plugin SofaGeneralEngine
Adding plugin SofaGeneralExplicitOdeSolver
Adding plugin SofaGeneralImplicitOdeSolver
Adding plugin SofaGeneralLinearSolver
Adding plugin SofaGeneralRigid
Adding plugin SofaGeneralObjectInteraction
Adding plugin SofaGeneralSimpleFem
Adding plugin SofaGeneralTopology
Adding plugin SofaTopologyMapping
Adding plugin SofaUserInteraction
Adding plugin SofaConstraint
Adding plugin SofaGeneralLoader
Adding plugin SofaExporter
Adding plugin SofaSparseSolver
SofaSparseSolver: using built-in metis library
Adding plugin SofaPreconditioner
Adding plugin SofaHaptics
Adding plugin SofaValidation
Adding plugin SofaDenseSolver
Adding plugin SofaNonUniformFem
Adding plugin SofaOpenglVisual
Adding plugin SofaMiscTopology
Adding plugin SofaMiscExtra
Adding plugin SofaMiscForceField
Adding plugin SofaMiscEngine
Adding plugin SofaMiscSolver
Adding plugin SofaMiscFem
Adding plugin SofaMiscMapping
Adding plugin SofaMiscCollision
SofaMiscModule: build all maintained sofa components.
cxxopts version 2.2.0
-- SofaGuiCommon: Sofa.GL dependent features enabled.
SofaGuiQt: will use Qt5
CMake Warning at /home/dell/sofa/build/lib/cmake/SofaEigen2SolverConfig.cmake:36 (message):  SofaEigen2Solver has been removed.  The package still exists for  compatibility but is empty.  Eigen classes were moved to Sofa.LinearAlgebra  and SVDLinearSolver to SofaDenseSolver.Call Stack (most recent call first):  /home/dell/sofa/build/lib/cmake/SofaBaseConfig.cmake:35 (find_package)  /home/dell/sofa/build/lib/cmake/SofaGeneralTopologyConfig.cmake:34 (find_package)  /home/dell/sofa/build/lib/cmake/SofaMiscForceFieldConfig.cmake:36 (find_package)  modules/SofaGuiQt/CMakeLists.txt:320 (find_package)
Adding collection SofaComponentAll
Adding plugin CImgPlugin
CImgPlugin: TIFF Image Format enabled
CImgPlugin: JPEG Image Format enabled
CImgPlugin: PNG Image Format enabled
SofaPython3 is compiled as a subproject to the external project 'Sofa'.
Adding plugin SofaPython3
Python:
    Version: 3.8.0
    Executable: /usr/bin/python3.8
    Headers: /usr/include/python3.8
    Libraries: /usr/lib/x86_64-linux-gnu/libpython3.8.so
    User site: /home/dell/.local/lib/python3.8/site-packages
pybind11:
    Version: 2.10.4
    Config: /home/dell/anaconda3/envs/sofa/share/cmake/pybind11/pybind11Config.cmake
Adding application runSofa
Write Plugin list at /home/dell/sofa/build/lib/plugin_list.conf.default
Configuring done
Generating done

hugtalbot · 2023-04-04T11:32:17Z

hugtalbot
Apr 4, 2023
Maintainer

Hey @jianchu00

Welcome on the SOFA forum!
The CMake configuration step seems to end successfully:

Write Plugin list at /home/dell/sofa/build/lib/plugin_list.conf.default
-- Configuring done
-- Generating done

However your compiler seems to be strict and considering the compilation as failing as soon as a warning is detected.
What is your compiler?
Could you check your flags?

Cheers

0 replies

@jianchu00 · 2023-12-14T09:31:28Z

github-actions[bot]
bot Dec 14, 2023

⚠️ ⚠️ ⚠️
@jianchu00
We are setting a new forum management policy: topics like this one, in which the last reply is more than 4 months old, will automatically be closed. Without further news in the coming weeks, our bot will proceed to automatic closure, thus keeping this forum clean and fresh 🌱 Thank you for your understanding

0 replies

@jianchu00 · 2024-02-26T06:12:26Z

github-actions[bot]
bot Feb 26, 2024

⚠️ ⚠️ ⚠️
@jianchu00
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.

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@jianchu00 · 2024-05-06T06:13:23Z

github-actions[bot]
bot May 6, 2024

⚠️ ⚠️ ⚠️
@jianchu00
In accordance with our forum management policy, the last reply is more than 4 months old and is therefore closed. Our objective is to keep the forum up to date and offer the best support experience.

Please feel free to reopen it if the topic is still active by providing us with an update. Please feel free to open a new thread at any time - we'll be happy to help where and when we can.

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Errors happen when run ninja #3743

jianchu00 Mar 23, 2023

Replies: 4 comments

hugtalbot Apr 4, 2023 Maintainer

github-actions[bot] bot Dec 14, 2023

github-actions[bot] bot Feb 26, 2024

github-actions[bot] bot May 6, 2024

jianchu00
Mar 23, 2023

hugtalbot
Apr 4, 2023
Maintainer

github-actions[bot]
bot Dec 14, 2023

github-actions[bot]
bot Feb 26, 2024

github-actions[bot]
bot May 6, 2024