Question #156058 on DOLFIN changed:
https://answers.launchpad.net/dolfin/+question/156058
Status: Answered => Open
Chunhe Lee is still having a problem:
Hi, Johannes:
I think you have help me solve this question, and I appreciate your help very
much. Now, armadillo can be found, and I can also build dolfin, but it seems
that there are another errors about UFC.
So, I reinstalled UFC package. But when installing ufc, there are some
questions. If I do not set BOOST_ROOT="/home/rhome/lihe/bin/boost", ufc can be
installed successfully. I guess that in this time ufc use the old boost lib in
the /usr/local, and it's version is 1.33. If I set
BOOST_ROOT="/home/rhome/lihe/bin/boost", ufc can not be made successfully.
The error information is showed:
cmake ..
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
SWIG_MODULE_LOCATION /home/rhome/lihe/program/install/ufc-2.0.0/build/_ufc.so
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/rhome/lihe/program/install/ufc-2.0.0/build
[lihe@node1 build]$ make
make: Warning: File `Makefile' has modification time 3.1e+02 s in the future
make[1]: Warning: File `CMakeFiles/Makefile2' has modification time 3.1e+02 s
in the future
make[2]: Warning: File `CMakeFiles/_ufc.dir/flags.make' has modification time
3.1e+02 s in the future
[ 50%] Swig source
/home/rhome/lihe/program/install/ufc-2.0.0/src/ufc/ufc.i:14: Error: Unable to
find 'boost_shared_ptr.i'
make[2]: *** [src/ufc/ufcPYTHON_wrap.cxx] Error 1
make[1]: *** [CMakeFiles/_ufc.dir/all] Error 2
make: *** [all] Error 2
I also tried first install UFC without seting
BOOST_ROOT="/home/rhome/lihe/bin/boost", and then set BOOST_ROOT to
install dolfin. But there are still question about UFC.
The following is error log when build dolfin:
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 3.1e+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_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;
}
Best regards!
Chunhe
2011-05-11
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