Error in mofem installation through docker

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zahur.ullah1

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Sep 9, 2017, 8:20:41 AM9/9/17
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I was trying to install mofem through docker by following the following 


and got the following error after this command 

docker build -t mofem_build --force-rm=true --file=$HOME/mofem-cephas/Dockerfile-build $HOME/mofem-cephas


 
[ 31%] Built target ftensor_and_adolc_test
[ 31%] Built target Includes.hpp.pch_copy
Scanning dependencies of target mofem_finite_elements
[ 32%] Building CXX object src/finite_elements/CMakeFiles/mofem_finite_elements.dir/impl/All.cpp.o
Scanning dependencies of target mofem_approx
[ 32%] Building CXX object src/approximation/CMakeFiles/mofem_approx.dir/impl/All.cpp.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[2]: *** [include/CMakeFiles/MoFEM.hpp.pch.dir/MoFEM.hpp.o] Error 4
make[2]: *** Deleting file `include/CMakeFiles/MoFEM.hpp.pch.dir/MoFEM.hpp.o'
make[1]: *** [include/CMakeFiles/MoFEM.hpp.pch.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 33%] Building C object src/approximation/CMakeFiles/mofem_approx.dir/c_impl/base_functions.c.o
[ 33%] Building C object src/approximation/CMakeFiles/mofem_approx.dir/c_impl/fem_tools.c.o
[ 34%] Building C object src/approximation/CMakeFiles/mofem_approx.dir/c_impl/h1.c.o
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp: In function 'PetscErrorCode MoFEM::Hdiv_Ainsworth_EdgeBasedVolumeShapeFunctions_MBTET(int, double*, double*, double**, double**, int, PetscErrorCode (*)(int, double, double*, double*, double*, int))':
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: '*((void*)& t_diff_beta_e +16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:313:30: note: '*((void*)& t_diff_beta_e +16)' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_e;
                              ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: '*((void*)& t_diff_beta_e +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:313:30: note: '*((void*)& t_diff_beta_e +8)' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_e;
                              ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: 't_diff_beta_e' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:313:30: note: 't_diff_beta_e' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_e;
                              ^
[ 35%] Building C object src/approximation/CMakeFiles/mofem_approx.dir/c_impl/l2.c.o
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp: In function 'PetscErrorCode MoFEM::Hdiv_Ainsworth_FaceBubbleShapeFunctions_ON_FACE(int*, int, double*, double*, double*, double*, int, int, PetscErrorCode (*)(int, double, double*, double*, double*, int))':
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: '*((void*)& t_diff_beta_0ij +16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:196:30: note: '*((void*)& t_diff_beta_0ij +16)' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_0ij;
                              ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: '*((void*)& t_diff_beta_0ij +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:196:30: note: '*((void*)& t_diff_beta_0ij +8)' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_0ij;
                              ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor1.hpp:7,
                 from /mofem/src/ftensor/src/FTensor.hpp:114,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor1/Tensor1_times_generic.hpp:16:21: warning: 't_diff_beta_0ij' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N)*d;
                     ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:196:30: note: 't_diff_beta_0ij' was declared here
   FTensor::Tensor1<double,3> t_diff_beta_0ij;
                              ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp: In function 'PetscErrorCode MoFEM::Hdiv_Demkowicz_Face_MBTET_ON_FACE(int*, int, double*, double*, double*, double*, int, int)':
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +64)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +64)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +56)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +56)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +48)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +48)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +40)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +40)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +32)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +32)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +24)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_cross +24)' was declared here
   FTensor::Tensor2<double,3,3> t_diff_cross;
                                ^
In file included from /mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_Expr.hpp:13:0,
                 from /mofem/src/ftensor/src/FTensor/Tensor2.hpp:10,
                 from /mofem/src/ftensor/src/FTensor.hpp:115,
                 from /mofem/src/approximation/impl/EntPolynomialBaseCtx.cpp:32,
                 from /mofem/src/approximation/impl/All.cpp:6:
/mofem/src/ftensor/src/FTensor/Tensor2/Tensor2_times_generic.hpp:11:25: warning: '*((void*)& t_diff_cross +16)' may be used uninitialized in this function [-Wmaybe-uninitialized]
     return iterA(N1,N2)*d;
                         ^
In file included from /mofem/src/approximation/impl/All.cpp:12:0:
/mofem/src/approximation/impl/Hdiv.cpp:635:32: note: '*((void*)& t_diff_c...

Any suggestion?

Zahur 


Lukasz Kaczmraczyk

unread,
Sep 9, 2017, 11:39:47 AM9/9/17
to mofem...@googlegroups.com
Hello Zahur,

The error is at very beginning, see 

[ 32%] Building CXX object src/approximation/CMakeFiles/mofem_approx.dir/impl/All.cpp.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
make[2]: *** [include/CMakeFiles/MoFEM.hpp.pch.dir/MoFEM.hpp.o] Error 4
make[2]: *** Deleting file `include/CMakeFiles/MoFEM.hpp.pch.dir/MoFEM.hpp.o'
make[1]: *** [include/CMakeFiles/MoFEM.hpp.pch.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

This is when g++ uses more memory than you have in docker. To solve the problem go to docker preferences, advanced option and increase the size of memory available for docker application. More memory is better, the rule of thumb, set half of your physical memory. If you have old computer you will need to allow docker to use all physical memory.



Regards,
Lukasz
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