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[Question #157005]: dolfin installation errors

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New question #157005 on DOLFIN:
https://answers.launchpad.net/dolfin/+question/157005

Hi,
When I build dolfin, it's ok, but errors come when I try to make it. 

[ 93%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/SpecialFacetFunction.cpp.o
[ 93%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/LocalAssembler.cpp.o
[ 94%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/adapt.cpp.o
[ 94%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/TimeSeries.cpp.o
[ 94%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/Extrapolation.cpp.o
[ 96%] Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/GoalFunctional.cpp.o
[ 96%] Building CXX object dolfin/CMakeFiles/dolfin.dir/plot/FunctionPlotData.cpp.o
[ 96%] Building CXX object dolfin/CMakeFiles/dolfin.dir/plot/plot.cpp.o
[ 97%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/RadauQuadrature.cpp.o
[ 97%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/GaussQuadrature.cpp.o
[ 97%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/Quadrature.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/GaussianQuadrature.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/BarycenterQuadrature.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/quadrature/LobattoQuadrature.cpp.o
Linking CXX shared library libdolfin.so
/usr/bin/ld: /home/rhome/lihe/bin/lapack/lib/libblas.a(dgemm.f.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/rhome/lihe/bin/lapack/lib/libblas.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [dolfin/libdolfin.so.0.9.10] Error 1
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [all] Error 2


The following is the contents of CmakeError.log. Can you tell me where is the problem? Thanks!

Performing C++ SOURCE FILE Test ARMADILLO_TEST_RUNS failed with the following output:
Change Dir: /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec/fast"
gmake: Warning: File `Makefile' has modification time 3.1e+02 s in the future
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build
gmake[1]: Entering directory `/home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp'
gmake[1]: Warning: File `CMakeFiles/cmTryCompileExec.dir/flags.make' has modification time 3.1e+02 s in the future
/home/cluster/cmake/2.8.2/bin/cmake -E cmake_progress_report /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec.dir/src.cxx.o
/usr/bin/c++    -DARMADILLO_TEST_RUNS -I/home/rhome/lihe/bin/armadillo/include -I/home/rhome/lihe/bin/boost/include   -o CMakeFiles/cmTryCompileExec.dir/src.cxx.o -c /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTryCompileExec
/home/cluster/cmake/2.8.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/usr/bin/c++      -DARMADILLO_TEST_RUNS   CMakeFiles/cmTryCompileExec.dir/src.cxx.o  -o cmTryCompileExec -rdynamic /home/rhome/lihe/bin/armadillo/lib64/libarmadillo.so -lgfortran -Wl,-rpath,/home/rhome/lihe/bin/armadillo/lib64 
CMakeFiles/cmTryCompileExec.dir/src.cxx.o: In function `void arma::lapack::gesv<double>(int*, int*, double*, int*, int*, double*, int*, int*)':
src.cxx:(.text._ZN4arma6lapack4gesvIdEEvPiS2_PT_S2_S2_S4_S2_S2_[void arma::lapack::gesv<double>(int*, int*, double*, int*, int*, double*, int*, int*)]+0x5c): undefined reference to `dgesv_'
CMakeFiles/cmTryCompileExec.dir/src.cxx.o: In function `void arma::lapack::gels<double>(char*, int*, int*, int*, double*, int*, double*, int*, double*, int*, int*)':
src.cxx:(.text._ZN4arma6lapack4gelsIdEEvPcPiS3_S3_PT_S3_S5_S3_S5_S3_S3_[void arma::lapack::gels<double>(char*, int*, int*, int*, double*, int*, double*, int*, double*, int*, int*)]+0x77): undefined reference to `dgels_'
/home/rhome/lihe/bin/armadillo/lib64/libarmadillo.so: undefined reference to `dgemm_'
/home/rhome/lihe/bin/armadillo/lib64/libarmadillo.so: undefined reference to `dgetrf_'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec] Error 1
gmake[1]: Leaving directory `/home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec/fast] Error 2

Return value: 1
Source file was:

#include <armadillo>

using namespace arma;

int main()
{
  int n = 20;
  double h = 1.0/(n-1);
  mat A(n, n);
  vec b(n);
  vec u(n);
  double beta = 0.2;
  double gamma = 1000;

  A.fill(0.0);
  b.fill(0.0);
  double x; int i;

  i = 0;
  A(i, i) = 1;
  b(i) = 0;
  for (i=1; i<n-1; i++) {
    x = (i-1)*h;
    A(i, i-1) = 1;  A(i, i) = -2;  A(i, i+1) = 1;
    b(i) = - h*h*gamma*exp(-beta*x);
  }
  i = n-1;  x = (i-1)*h;
  A(i, i-1) = 2;  A(i, i) = -2;

  u = solve(A, b);

  return 0;
}

Performing C++ SOURCE FILE Test ARMADILLO_LAPACK_TEST_RUNS failed with the following output:
Change Dir: /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec/fast"
gmake: Warning: File `Makefile' has modification time 3.2e+02 s in the future
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec.dir/build.make CMakeFiles/cmTryCompileExec.dir/build
gmake[1]: Entering directory `/home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp'
gmake[1]: Warning: File `CMakeFiles/cmTryCompileExec.dir/flags.make' has modification time 3.2e+02 s in the future
/home/cluster/cmake/2.8.2/bin/cmake -E cmake_progress_report /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec.dir/src.cxx.o
/usr/bin/c++    -DARMADILLO_LAPACK_TEST_RUNS -I/home/rhome/lihe/bin/armadillo/include -I/home/rhome/lihe/bin/boost/include   -o CMakeFiles/cmTryCompileExec.dir/src.cxx.o -c /home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTryCompileExec
/home/cluster/cmake/2.8.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1
/usr/bin/c++      -DARMADILLO_LAPACK_TEST_RUNS   CMakeFiles/cmTryCompileExec.dir/src.cxx.o  -o cmTryCompileExec -rdynamic /home/rhome/lihe/bin/armadillo/lib64/libarmadillo.so -lgfortran /home/rhome/lihe/bin/lapack/lib/liblapack.a -Wl,-rpath,/home/rhome/lihe/bin/armadillo/lib64 
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dgetrf.f.o): In function `dgetrf_':
dgetrf.f:(.text+0x5a1): undefined reference to `dtrsm_'
dgetrf.f:(.text+0x6ea): undefined reference to `dgemm_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dgetrs.f.o): In function `dgetrs_':
dgetrs.f:(.text+0x21a): undefined reference to `dtrsm_'
dgetrs.f:(.text+0x28d): undefined reference to `dtrsm_'
dgetrs.f:(.text+0x305): undefined reference to `dtrsm_'
dgetrs.f:(.text+0x378): undefined reference to `dtrsm_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dlarfb.f.o): In function `dlarfb_':
dlarfb.f:(.text+0x224): undefined reference to `dcopy_'
dlarfb.f:(.text+0x2ad): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x385): undefined reference to `dgemm_'
dlarfb.f:(.text+0x3f7): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x4cf): undefined reference to `dgemm_'
dlarfb.f:(.text+0x53f): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x757): undefined reference to `dcopy_'
dlarfb.f:(.text+0x7e0): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x8bd): undefined reference to `dgemm_'
dlarfb.f:(.text+0x92f): undefined reference to `dtrmm_'
dlarfb.f:(.text+0xa0c): undefined reference to `dgemm_'
dlarfb.f:(.text+0xa7c): undefined reference to `dtrmm_'
dlarfb.f:(.text+0xc9d): undefined reference to `dcopy_'
dlarfb.f:(.text+0xd4f): undefined reference to `dtrmm_'
dlarfb.f:(.text+0xde7): undefined reference to `dgemm_'
dlarfb.f:(.text+0xe59): undefined reference to `dtrmm_'
dlarfb.f:(.text+0xeeb): undefined reference to `dgemm_'
dlarfb.f:(.text+0xf84): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x11d3): undefined reference to `dcopy_'
dlarfb.f:(.text+0x1288): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1320): undefined reference to `dgemm_'
dlarfb.f:(.text+0x1392): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1424): undefined reference to `dgemm_'
dlarfb.f:(.text+0x14bd): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1730): undefined reference to `dcopy_'
dlarfb.f:(.text+0x17b9): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1896): undefined reference to `dgemm_'
dlarfb.f:(.text+0x1908): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x19e5): undefined reference to `dgemm_'
dlarfb.f:(.text+0x1a55): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1c6d): undefined reference to `dcopy_'
dlarfb.f:(.text+0x1cf6): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1dd8): undefined reference to `dgemm_'
dlarfb.f:(.text+0x1e4a): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x1f2c): undefined reference to `dgemm_'
dlarfb.f:(.text+0x1f9c): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x21bd): undefined reference to `dcopy_'
dlarfb.f:(.text+0x2274): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x230c): undefined reference to `dgemm_'
dlarfb.f:(.text+0x237e): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x2410): undefined reference to `dgemm_'
dlarfb.f:(.text+0x24ae): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x26f7): undefined reference to `dcopy_'
dlarfb.f:(.text+0x27b1): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x2849): undefined reference to `dgemm_'
dlarfb.f:(.text+0x28bb): undefined reference to `dtrmm_'
dlarfb.f:(.text+0x294d): undefined reference to `dgemm_'
dlarfb.f:(.text+0x29eb): undefined reference to `dtrmm_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dlarft.f.o): In function `dlarft_':
dlarft.f:(.text+0x3ac): undefined reference to `dgemv_'
dlarft.f:(.text+0x556): undefined reference to `dgemv_'
dlarft.f:(.text+0x5fe): undefined reference to `dtrmv_'
dlarft.f:(.text+0x9d1): undefined reference to `dgemv_'
dlarft.f:(.text+0xc85): undefined reference to `dgemv_'
dlarft.f:(.text+0xd7c): undefined reference to `dtrmv_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dtrtrs.f.o): In function `dtrtrs_':
dtrtrs.f:(.text+0x30b): undefined reference to `dtrsm_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dgetf2.f.o): In function `dgetf2_':
dgetf2.f:(.text+0x1d4): undefined reference to `idamax_'
dgetf2.f:(.text+0x281): undefined reference to `dswap_'
dgetf2.f:(.text+0x359): undefined reference to `dscal_'
dgetf2.f:(.text+0x55a): undefined reference to `dger_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dlarf.f.o): In function `dlarf_':
dlarf.f:(.text+0x190): undefined reference to `dgemv_'
dlarf.f:(.text+0x1f2): undefined reference to `dger_'
dlarf.f:(.text+0x25e): undefined reference to `dgemv_'
dlarf.f:(.text+0x2bc): undefined reference to `dger_'
/home/rhome/lihe/bin/lapack/lib/liblapack.a(dlarfg.f.o): In function `dlarfg_':
dlarfg.f:(.text+0x54): undefined reference to `dnrm2_'
dlarfg.f:(.text+0x17b): undefined reference to `dscal_'
dlarfg.f:(.text+0x1e0): undefined reference to `dnrm2_'
dlarfg.f:(.text+0x2aa): undefined reference to `dscal_'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec] Error 1
gmake[1]: Leaving directory `/home/rhome/lihe/program/install/dolfin-0.9.10/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec/fast] Error 2

Return value: 1
Source file was:

#include <armadillo>

using namespace arma;

int main()
{
  int n = 20;
  double h = 1.0/(n-1);
  mat A(n, n);
  vec b(n);
  vec u(n);
  double beta = 0.2;
  double gamma = 1000;

  A.fill(0.0);
  b.fill(0.0);
  double x; int i;

  i = 0;
  A(i, i) = 1;
  b(i) = 0;
  for (i=1; i<n-1; i++) {
    x = (i-1)*h;
    A(i, i-1) = 1;  A(i, i) = -2;  A(i, i+1) = 1;
    b(i) = - h*h*gamma*exp(-beta*x);
  }
  i = n-1;  x = (i-1)*h;
  A(i, i-1) = 2;  A(i, i) = -2;

  u = solve(A, b);

  return 0;
}



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