Package Details: dolfin-git 20151005-1

Git Clone URL: https://aur.archlinux.org/dolfin-git.git (read-only)
Package Base: dolfin-git
Description: the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
Upstream URL: https://bitbucket.org/fenics-project/dolfin
Licenses: LGPL
Groups: fenics-git
Conflicts: dolfin
Submitter: myles
Maintainer: myles
Last Packager: myles
Votes: 7
Popularity: 0.001315
First Submitted: 2013-03-22 22:40
Last Updated: 2015-11-19 23:30

Latest Comments

heitzmann commented on 2016-11-18 13:52

For anyone interested, I've just submitted updated versions of all fenics packages (dolfin, mshr, ffc, ufl, fiat, instant, dijitso) for python 3 under the names python-*-git.

I could not get dolfin to compile with VTK support, so that is missing in the current PKGBUILD.

heitzmann commented on 2015-11-19 19:21

videan42 is right, python2-sympy is the correct dependency.
There's also a new one missing: gl2ps from extra.

videan42 commented on 2015-11-11 23:01

I just ran into the same problem as Calucinho and it looks like the script needs `python2-sympy` to be installed to generate the form files. I think this should be the dependency and not `python-sympy`? Once I fixed that, everything built fine.

ftschindler commented on 2015-11-05 11:22

Recently, I get the following error:
```
make[2]: *** No rule to make target '/usr/lib64/libgl2ps.so', needed by 'dolfin/libdolfin.so.1.7.0dev'. Stop.
```
which I could resolve by installing `gl2ps`. This should perhaps become an additional (make) dependency...

Calucinho commented on 2015-11-03 14:37

Hi Myles, I still cannot build dolfin-git from your AUR package. Could you have a look at the log files from my previous comment?

Calucinho commented on 2015-10-20 00:37

Thanks Myles for your support! I tried to run the script you mentioned and it runs fine without any output. In case if it's handy I posted the output of CMakeError.log here:

https://dl.dropboxusercontent.com/u/29638164/CMakeError.log

and the output of CMakeOutput.log here:

https://dl.dropboxusercontent.com/u/29638164/CMakeOutput.log

myles commented on 2015-10-19 19:55

Hi Calucinho, Do those logs say anything useful, (e.g. disk space)? You could try running that command manually to find out what the problem is, if you look in CMakeLists.txt it is trying to run:

python2 cmake/scripts/generate-form-files

Calucinho commented on 2015-10-18 19:34

Hi Myles, thanks for your packages. I am almost on my way to use FEniCS. Unfortunately, your dolfin-git package is not compiling for me :( I am getting the following error:

-- Generating SWIG interface.
-- --------------------------
--
-- Generating form files in demo, test, bench and dolfin directories. May take some time...
-- ----------------------------------------------------------------------------------------
CMake Error at CMakeLists.txt:883 (message):
Generation of form files failed:



-- Configuring incomplete, errors occurred!
See also "/tmp/yaourt-tmp-carlos/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeOutput.log".
See also "/tmp/yaourt-tmp-carlos/aur-dolfin-git/src/dolfin/build/CMakeFiles/CMakeError.log".

Thanks in advance!

ftschindler commented on 2015-09-29 07:12

This package would profit from the following lines in `build()`:
```
source /etc/profile.d/petsc.sh
source /etc/profile.d/slepc.sh
```

rklinux commented on 2015-07-16 03:03

(Also posted under fenics-git)

Please help - I am unable to install fenics-git becuase the dolfin-git dependency does not install due to following error message:

cmake: error while loading shared libraries: libjsoncpp.so.1: cannot open shared object file: No such file or directory
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Makepkg was unable to build dolfin-git.

Thank you for possible solutions
RK

TSPMP commented on 2015-03-23 13:44

@hme Can confirm. I needed to install python2-sympy to build the package, too.

hme commented on 2015-02-03 19:16

Install wont complete unless you have
python2-sympy
Should it be listed as a dependency?

simul commented on 2014-07-26 10:16

After installing dolfin-git without errors, I now get the following error when I try to run the demos:

In instant.recompile: The module did not compile with command 'make VERBOSE=1'

Any clues?

myles commented on 2014-07-08 20:06

@gasagna: quite right, I have corrected it (back to what it used to be)

gasagna commented on 2014-07-07 16:11

Apparently installing dolfin-git fails on my computer with

==> Building and installing package
==> Install or build missing dependencies for dolfin-git:
error: target not found: instant
error: target not found: ffc
==> Restart building dolfin-git ? [y/N]

However, installing instant-git and ffc-git solves this issue. Can it be automated somehow?

Thanks for the package.

ben_hutchings commented on 2014-06-09 18:34

Trying to run makepkg, failure occurs in build()

CMake Error at CMakeLists.txt:291
Could not find a configuration file for package UFC that is compatible with he requested version 1.4.0

myles commented on 2014-04-24 21:14

@sparkinson ufc has been merged into ffc so I need to update this package (and ffc-git), in the meantime I'll flag it out of date

sparkinson commented on 2014-04-20 14:20

I just tried to install this. I can't find ufc-git? I found a message saying that it had been incorporated into dolfin-git. If that is the case, can it be removed from the dependencies?

davidovitch commented on 2014-02-05 22:08

I think cppunit from [extra] should be a (build) dependency since it the build failed for me without it.

aradan_d commented on 2014-01-27 21:17

Is PETSC necessary? I could install dolfin, but when building it I got:

-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) TRILINOS
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) PETSC
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TAO
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH
-- (**) SPHINX
-- (**) HDF5

Even tough I have PETSC, SPHINX, SLEPC installed.

Raptorista commented on 2013-10-07 20:17

Please add missing depedencies
[*] eigen3
[*] ffc-git
[*] instant-git

myles commented on 2013-09-16 09:09

bshankar: This is not the place to ask for help. Did you see this: https://answers.launchpad.net/dolfin/+question/224136

Anonymous comment on 2013-09-14 04:57

Getting build errors which compiling this PKGBUILD (see the pastebin below)
http://pastebin.com/YpBvnBJs

Armadillo is not being detected.
I have armadillo installed in /usr . After seeing some forums, I modified the cmake line of PKGBUILD to:

cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/g++ \
-DCMAKE_INSTALL_PREFIX="${pkg}"/usr \
-DPYTHON_EXECUTABLE:PATH="${py2_interp}" \
-DPYTHON_INCLUDE_DIR:PATH="${py2_inc}" \
-DPYTHON_LIBRARY:FILEPATH="${py2_lib}" \
-DDOLFIN_ENABLE_VTK=ON \
-DCMAKE_SKIP_BUILD_RPATH=TRUE \
-DCMAKE_SKIP_RPATH=TRUE \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DARMADILLO_DIR=/usr \
-DARMADILLO_INCLUDE_DIRS=${ARMADILLO_DIR}/include \
-DARMADILLO_LIBRARIES=${ARMADILLO_DIR}/lib/libarmadillo.so \
-DCMAKE_BUILD_TYPE="Debug"

It made no difference.
Please help!

myles commented on 2013-08-07 21:26

Thanks megavolts I have made some changes.

Anonymous comment on 2013-07-11 19:23

This morning I installed dolfin-git from AUR on a new clean archlinux and ran in several errors, which come from missing dependencies. But I finally went through it.

"Error message" [SOLUTION] :
1) "Could not find a configuration file for package UFC that is compatible with requested version 2.2.0." [install ufc-git]
2)"ARMADILLO_LIBRARIES ARMADILLO_INCLUDE_DIRS ARMADILLO_TEST_RUNSARMADILLO_VERSION ARMADILLO_VERSION_OK) (Required is at least version"2.4.2"" [install armadillo packages]
3) "sh: ffc: command not found" [install ffc-git fiat-git packages ; fiat-git, ufl-git and ufc-git have to be installed manually as they are required by ffc-git. ffc-git calls package name ufl and ufc package name which do not exit in aur.]
4) "ImportError: No module named instant" [install instant-git]


Therefor I will suggest to update the dependencies, adding the following packages:
- ufc-git
- armadillo
- ffc-git (sub dependencies > fiat-git, ufl-git, ufc-git)
- instant-git

Anonymous comment on 2013-06-11 06:32

Without ffc-git the cmake/scripts/generate* won't work which might result in a compile error due to missing forms (it did here).

myles commented on 2013-02-19 20:23

This pkgbuild is for the bzr trunk, not version 1.1.

Anonymous comment on 2013-02-19 17:58

pkgbuild fails with dolfin 1.1.

Changing _bzrtrunk=lp:dolfin/1.0.x works. The 1.0.x branch is maintained for the time being.

Anonymous comment on 2012-12-15 15:41

Installing dolfin leads to 2 errors:

1) Armadillo issue https://answers.launchpad.net/fenics/+question/206520; I resolved it, probably in a bad hacking style, by copying /usr/lib64/libarmadillo* in /usr/lib/ .

2) cmake error, which I hasn't overcome yet! I report below the CMakeError.log:

Performing C++ SOURCE FILE Test CHOLMOD_TEST_RUNS failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec2286648684/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec2286648684.dir/build.make CMakeFiles/cmTryCompileExec2286648684.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec2286648684.dir/src.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DCHOLMOD_TEST_RUNS -fopenmp -o CMakeFiles/cmTryCompileExec2286648684.dir/src.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTryCompileExec2286648684
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2286648684.dir/link.txt --verbose=1
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DCHOLMOD_TEST_RUNS -fopenmp -Wl,--hash-style=gnu -Wl,--as-needed CMakeFiles/cmTryCompileExec2286648684.dir/src.cxx.o -o cmTryCompileExec2286648684 -rdynamic /lib64/libcholmod.a /lib64/libamd.a /lib64/libcamd.a /lib64/libcolamd.a /lib64/libccolamd.a /lib64/libsuitesparseconfig.a /lib64/libparmetis.so /lib64/libmetis.so /lib64/liblapack.so /lib64/libcblas.so /lib64/libf77blas.so /lib64/libatlas.so /lib64/libcblas.so /lib64/libf77blas.so /lib64/libatlas.so /usr/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../lib/libgfortran.so -Wl,-rpath,/lib64:/usr/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../lib
/lib64/libsuitesparseconfig.a(SuiteSparse_config.o): In function `SuiteSparse_tic':
(.text+0x131): undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status
make[1]: *** [cmTryCompileExec2286648684] Error 1
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec2286648684/fast] Error 2

Return value: 1
Source file was:

#include <stdio.h>
#include <cholmod.h>

int main()
{
cholmod_dense *D;
cholmod_sparse *S;
cholmod_dense *x, *b, *r;
cholmod_factor *L;
double one[2] = {1,0}, m1[2] = {-1,0};
double *dx;
cholmod_common c;
int n = 5;
double K[5][5] = {{1.0, 0.0, 0.0, 0.0, 0.0},
{0.0, 2.0,-1.0, 0.0, 0.0},
{0.0,-1.0, 2.0,-1.0, 0.0},
{0.0, 0.0,-1.0, 2.0, 0.0},
{0.0, 0.0, 0.0, 0.0, 1.0}};
cholmod_start (&c);
D = cholmod_allocate_dense(n, n, n, CHOLMOD_REAL, &c);
dx = (double*)D->x;
for (int i=0; i < n; i++)
for (int j=0; j < n; j++)
dx[i+j*n] = K[i][j];
S = cholmod_dense_to_sparse(D, 1, &c);
S->stype = 1;
cholmod_reallocate_sparse(cholmod_nnz(S, &c), S, &c);
b = cholmod_ones(S->nrow, 1, S->xtype, &c);
L = cholmod_analyze(S, &c);
cholmod_factorize(S, L, &c);
x = cholmod_solve(CHOLMOD_A, L, b, &c);
r = cholmod_copy_dense(b, &c);
cholmod_sdmult(S, 0, m1, one, x, r, &c);
cholmod_free_factor(&L, &c);
cholmod_free_dense(&D, &c);
cholmod_free_sparse(&S, &c);
cholmod_free_dense(&r, &c);
cholmod_free_dense(&x, &c);
cholmod_free_dense(&b, &c);
cholmod_finish(&c);
return 0;
}

Performing C++ SOURCE FILE Test UMFPACK_TEST_RUNS failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec3575677258/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec3575677258.dir/build.make CMakeFiles/cmTryCompileExec3575677258.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec3575677258.dir/src.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DUMFPACK_TEST_RUNS -fopenmp -o CMakeFiles/cmTryCompileExec3575677258.dir/src.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTryCompileExec3575677258
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3575677258.dir/link.txt --verbose=1
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DUMFPACK_TEST_RUNS -fopenmp -Wl,--hash-style=gnu -Wl,--as-needed CMakeFiles/cmTryCompileExec3575677258.dir/src.cxx.o -o cmTryCompileExec3575677258 -rdynamic /lib64/libumfpack.a /lib64/libamd.a /lib64/libcblas.so /lib64/libf77blas.so /lib64/libatlas.so /lib64/libsuitesparseconfig.a /usr/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../lib/libgfortran.so -Wl,-rpath,/lib64:/usr/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../lib
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x9e): undefined reference to `cholmod_start'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x1cd): undefined reference to `cholmod_analyze'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x1e4): undefined reference to `cholmod_free_sparse'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x298): undefined reference to `cholmod_free_factor'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x2b1): undefined reference to `cholmod_print_common'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x2be): undefined reference to `cholmod_finish'
/lib64/libumfpack.a(umf_i_cholmod.o): In function `umf_i_cholmod':
(.text+0x440): undefined reference to `cholmod_transpose'
/lib64/libsuitesparseconfig.a(SuiteSparse_config.o): In function `SuiteSparse_tic':
(.text+0x131): undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status
make[1]: *** [cmTryCompileExec3575677258] Error 1
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec3575677258/fast] Error 2

Return value: 1
Source file was:

/* Test program umfpack-ex1.c */

#include <umfpack.h>

int main()
{
int n = 5;
double x[5];
void *Symbolic, *Numeric;
int i;

int Ap[] = { 0, 2, 5, 9, 10, 12 };
int Ai[] = { 0, 1, 0, 2, 4, 1, 2, 3, 4, 2, 1, 4 };
double Ax[] = { 2, 3, 3, -1, 4, 4, -3, 1, 2, 2, 6, 1 };
double b[] = { 8, 45, -3, 3, 19 };

umfpack_di_symbolic(n, n, Ap, Ai, Ax, &Symbolic, NULL, NULL);
umfpack_di_numeric(Ap, Ai, Ax, Symbolic, &Numeric, NULL, NULL);
umfpack_di_free_symbolic(&Symbolic);

umfpack_di_solve(UMFPACK_A, Ap, Ai, Ax, x, b, Numeric, NULL, NULL);
umfpack_di_free_numeric(&Numeric);

return 0;
}

Performing C++ SOURCE FILE Test PETSC_CUSP_FOUND failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec3933088938/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec3933088938.dir/build.make CMakeFiles/cmTryCompileExec3933088938.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec3933088938.dir/src.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DPETSC_CUSP_FOUND -fopenmp -I/opt/petsc/arch-linux2-cxx-opt/include -o CMakeFiles/cmTryCompileExec3933088938.dir/src.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTryCompileExec3933088938
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3933088938.dir/link.txt --verbose=1
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -DPETSC_CUSP_FOUND -fopenmp -Wl,--hash-style=gnu -Wl,--as-needed CMakeFiles/cmTryCompileExec3933088938.dir/src.cxx.o -o cmTryCompileExec3933088938 -rdynamic /opt/petsc/arch-linux2-cxx-opt/lib/libpetsc.so /usr/lib/openmpi/libmpi.so -ldl -lhwloc -Wl,-rpath,/opt/petsc/arch-linux2-cxx-opt/lib:/usr/lib/openmpi
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'

Return value: 1
Source file was:

#include "petsc.h"
int main()
{
#if PETSC_HAVE_CUSP
return 0;
#else
return 1;
#endif
}

Determining if the Q_WS_WIN exist failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec138763340/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec138763340.dir/build.make CMakeFiles/cmTryCompileExec138763340.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec138763340.dir/CheckSymbolExists.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -frounding-math -o CMakeFiles/cmTryCompileExec138763340.dir/CheckSymbolExists.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘Q_WS_WIN’ was not declared in this scope
make[1]: *** [CMakeFiles/cmTryCompileExec138763340.dir/CheckSymbolExists.cxx.o] Error 1
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec138763340/fast] Error 2

File /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <QtCore/qglobal.h>

int main(int argc, char** argv)
{
(void)argv;
#ifndef Q_WS_WIN
return ((int*)(&Q_WS_WIN))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the Q_WS_QWS exist failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec2065892581/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec2065892581.dir/build.make CMakeFiles/cmTryCompileExec2065892581.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec2065892581.dir/CheckSymbolExists.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -frounding-math -o CMakeFiles/cmTryCompileExec2065892581.dir/CheckSymbolExists.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘Q_WS_QWS’ was not declared in this scope
make[1]: *** [CMakeFiles/cmTryCompileExec2065892581.dir/CheckSymbolExists.cxx.o] Error 1
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec2065892581/fast] Error 2

File /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <QtCore/qglobal.h>

int main(int argc, char** argv)
{
(void)argv;
#ifndef Q_WS_QWS
return ((int*)(&Q_WS_QWS))[argc];
#else
(void)argc;
return 0;
#endif
}

Determining if the Q_WS_MAC exist failed with the following output:
Change Dir: /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec3070239012/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec3070239012.dir/build.make CMakeFiles/cmTryCompileExec3070239012.dir/build
make[1]: Entering directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec3070239012.dir/CheckSymbolExists.cxx.o
/usr/bin/g++ -DMPICH_IGNORE_CXX_SEEK -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -frounding-math -o CMakeFiles/cmTryCompileExec3070239012.dir/CheckSymbolExists.cxx.o -c /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8:19: error: ‘Q_WS_MAC’ was not declared in this scope
make[1]: *** [CMakeFiles/cmTryCompileExec3070239012.dir/CheckSymbolExists.cxx.o] Error 1
make[1]: Leaving directory `/home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp'
make: *** [cmTryCompileExec3070239012/fast] Error 2

File /home/roberto/computer/programs_software/dolfin/dolfin-bzr/src/dolfin-build/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <QtCore/qglobal.h>

int main(int argc, char** argv)
{
(void)argv;
#ifndef Q_WS_MAC
return ((int*)(&Q_WS_MAC))[argc];
#else
(void)argc;
return 0;
#endif
}

myles commented on 2012-12-11 23:12

All the pkgbuild scripts that I maintain that are relevent for fenics are available at https://github.com/mylese/fenics-arch.git

myles commented on 2012-12-11 23:12

All the pkgbuild scripts that I maintain that are relevent for fenics are available on https://github.com/mylese/fenics-arch.git

myles commented on 2012-12-11 23:12

All the pkgbuild scripts that I maintain that are relevent for fenics are available on [https://github.com/mylese/fenics-arch.git/ github]

myles commented on 2012-12-11 23:10

All the pkgbuild scripts that I maintain and are relevent for fenics are available at [https://github.com/mylese/fenics-arch.git github].

myles commented on 2012-12-11 23:08

All the pkgbuild scripts that I maintain and are relevent for fenics are available at [git@github.com:mylese/fenics-arch.git github].

myles commented on 2012-12-11 23:08

All the pkgbuild scripts that I maintain and are relevent for fenics are available at [github git@github.com:mylese/fenics-arch.git].

myles commented on 2012-12-11 23:07



All the pkgbuild scripts that I maintain and are relevent for fenics are available at [[github][git@github.com:mylese/fenics-arch.git]].

myles commented on 2012-12-11 23:06

All the pkgbuild scripts that I maintain and are relevent for fenics are available at git@github.com:mylese/fenics-arch.git

davidovitch commented on 2012-08-03 15:05

First time I installed the FEniCS project. Its a bit confusing when installing the bzr packages: when using yaourt it will pull in the non bzr packages as dependencies. As a result I installed them one at the time. Also, I would assume the dependency list of the bzr package is not as complete is the "normal" but orphaned package. Order I took in installing (mostly using yaourt): parmetis, metis, scotch, slepc, trilinos (directly with makepkg, yaourt failed with out of disc space), armadillo, cgal, ufc-bzr, ufl-bzr, fiat-bzr, ffc-bzr, dolfin-bzr (directly with makepkg just to be sure)

My optional package list looks like:

-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) TRILINOS
-- (OK) UMFPACK
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
--
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) PETSC --> installed, dolfin fails to locate it
-- (**) SLEPC --> installed, dolfin fails to locate it
-- (**) MTL4
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH --> installed, dolfin fails to locate it
-- (**) VTK

Thanks for making this package!!

Anonymous comment on 2012-07-08 05:58

I got '/usr' for TRILINOS_DIR too. Sourcing /etc/profile.d/trilinos.sh doesn't make a difference.

myles commented on 2012-07-07 00:54

What is the result of 'echo $TRILINOS_DIR'? I get '/usr'. It may be that you need to do 'source /etc/profile.d/trilinos.sh' or log in and out again before the environment variable is set. Please report back.

Anonymous comment on 2012-07-06 22:56

I'm trying to install dolfin using the provided PKGBUILD, but it fails when trying to find armadillo. I've reinstalled armadillo multiple times from AUR, but no go. Every time I try to build dolfin it fails at the ARMADILLO_TEST_RUNS. Any suggestions?

myles commented on 2012-05-09 23:31

Orphaned, please see http://aur.archlinux.org/packages.php?ID=58971

myles commented on 2012-05-09 23:28

The latest stable dolfin version is 1.0.0 released on 2011-12-19, and aimed at Ubuntu users. In Arch terms this means that several dependencies are quite 'old' (e.g. the required version of CGAL also requires an earlier Boost). So, whilst it would be possible to make the older fenics work with newer versions of dependencies, and it would be possible to work out how to install older versions of dependencies, I think that Arch Users would rather be using the latest fenics software and, if necessary, make it work on our very fresh systems.

So, I am going to maintain these packages: dolfin-bzr ffc-bzr fiat-bzr instant-bzr ufc-bzr ufl-bzr viper-bzr
and I am going to orphan these: dolfin ffc fiat instant ufc ufl viper, and if no one adopts them (and I can see no reason to do so) they will be deleted in a week.

myles commented on 2012-05-05 11:28

Just to be clear, there are still some optional packages that are not found, but then I didn't install them.

-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) SLEPC
-- (OK) TRILINOS
-- (OK) UMFPACK
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
--
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) MTL4
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SCOTCH

myles commented on 2012-05-05 02:17

...and this package: i.e. dolfin-bzr not dolfin.

kkimdev commented on 2012-05-05 02:02

@myles

Thanks for making this work! :D

myles commented on 2012-05-05 01:51

Works now for both C++ and dolfin demos, well this one at least:

$ python2 /usr/share/dolfin/demo/pde/poisson/python/demo_poisson.py

The working combination of packages is to use all the fenics
packages in the AUR (these are now up to date) and use viper-bzr
instead of viper.

myles commented on 2012-05-05 01:47

dolfin-bzr works fine now dolfin-bzr (http://aur.archlinux.org/packages.php?ID=58971)

myles commented on 2012-05-04 01:03

PARMETIS: for it to find parmetis, both metis and parmetis need to be installed

myles commented on 2012-05-04 00:34

SLEPC: this works fine for me: it is found and the test passes. Maybe it is because the exports are in
/etc/profile.d/{slepc,petsc}.sh and they are only sourced when you login
MTL4: I haven't installed this yet, something about a secure certificate...
UMFPACK: The umfpack one works for me fine and the tests run.
PASTIX: N/A
SCOTCH: This is not found, although it is installed with petsc and from AUR.
PARMETIS: This is not found, although it is installed with petsc and from AUR. Did you have to set an environment variable?

For scotch and parmetis maybe dolfin needs to look harder.

kkimdev commented on 2012-05-03 22:22

1 python examples didn't work for me either for different reasons. For example, demo/pde/poisson/python/

File "/usr/lib/python2.7/site-packages/viper/viper_dolfin.py", line 134, in plot_genericfunction
data.compute_vertex_values(self.x, self.mesh)
TypeError: GenericFunction_compute_vertex_values expected 2 arguments, got 3

different examples give different errors, but not import error. However, it seems this runs c++ examples successfully.


2 Another optional package issue: during cmake CMakeLists.txt,

...
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) SLEPC
-- (**) MTL4
-- (**) UMFPACK
-- (**) PASTIX
-- (**) SCOTCH
...

SLEPC: We should do "export SCOTCH_DIR=/usr/petsc/arch-linux2-cxx-opt/ ", but it still says "-- SLEPc test failed".
MTL4: This is in AUR and I had it. I don't know why it couldn't find it.
UMFPACK: This is offered by either umfpack or suitesparse. I don't know why it couldn't find it.
PASTIX: This is not in AUR
SCOTCH: This is in AUR, or there is petsc downloaded version. If you wish to use the latter one, "export SCOTCH_DIR=/usr/petsc/arch-linux2-cxx-opt/" solves the problem.

kkimdev commented on 2012-05-03 22:21

python examples didn't work for me either for different reasons. For example, demo/pde/poisson/python/

File "/usr/lib/python2.7/site-packages/viper/viper_dolfin.py", line 134, in plot_genericfunction
data.compute_vertex_values(self.x, self.mesh)
TypeError: GenericFunction_compute_vertex_values expected 2 arguments, got 3

different examples give different errors, but not import error. However, it seems this runs c++ examples successfully.


Another optional package issue: during cmake CMakeLists.txt,

...
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) SLEPC
-- (**) MTL4
-- (**) UMFPACK
-- (**) PASTIX
-- (**) SCOTCH
...

SLEPC: We should do "export SCOTCH_DIR=/usr/petsc/arch-linux2-cxx-opt/ ", but it still says "-- SLEPc test failed".
MTL4: This is in AUR and I had it. I don't know why it couldn't find it.
UMFPACK: This is offered by either umfpack or suitesparse. I don't know why it couldn't find it.
PASTIX: This is not in AUR
SCOTCH: This is in AUR, or there is petsc downloaded version. If you wish to use the latter one, "export SCOTCH_DIR=/usr/petsc/arch-linux2-cxx-opt/" solves the problem.

myles commented on 2012-05-03 18:49

This builds but there are some missing python imports (common.py,la.py...) on trying to run a demo and it is not a PYTHONPATH problem. Maybe I will find the answer soon but any help appreciated.

myles commented on 2012-05-03 18:48

Sorry but I can't get this to work anymore, the build fails at 17% http://pastebin.com/sXcfNpgF . I think it is something to do with the version of CGAL, if I try to downgrade it then it wants an older version of Boost - looks like a can of worms.

So, I have submitted the package dolfin-bzr (http://aur.archlinux.org/packages.php?ID=58971), which builds fine, but there are some missing python imports.
Myles

Anonymous comment on 2012-03-16 06:18

Has a hard time finding dependencies also installed through AUR: e.g. PETSc
I had to modify src/dolfin-1.0.0/cmake/module/FindPETSc.cmake to even pick up petscconf.h
-- Checking for package 'PETSc'
-- PETSC_DIR is /usr/petsc
-- PETSC_ARCH is arch-linux2-cxx-opt
-- Found petscconf.h
-- Include directory /usr/include/include does not exist
-- PETSc test failed
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_TEST_RUNS)

TEST_RUNS is defined in /usr/petsc/arch-linux2-cxx-opt/conf/petscvariables

Anybody have luck with this going through automatically?

Anonymous comment on 2011-11-07 21:15

Package broken: the source was relocated to:
http://launchpad.net/dolfin/1.0.x/0.9.11/+download/dolfin-0.9.11.tar.gz

Changing the path to the source is sufficient, MD5 stays the same.

Anonymous comment on 2011-09-14 12:47

New version 1.0beta is out!
Anyway I must report the very same error as lecio

Anonymous comment on 2011-08-15 20:20

Just two things:

1) Installing dolfin from AUR and trying to import the relative module in python let to the following error:

Python 2.7.2 (default, Jun 29 2011, 11:10:00)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import dolfin
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/site-packages/dolfin/__init__.py", line 13, in <module>
from dolfin.cppimports import *
File "/usr/lib/python2.7/site-packages/dolfin/cppimports.py", line 4, in <module>
import dolfin.cpp as cpp
File "/usr/lib/python2.7/site-packages/dolfin/cpp.py", line 30, in <module>
_cpp = swig_import_helper()
File "/usr/lib/python2.7/site-packages/dolfin/cpp.py", line 26, in swig_import_helper
_mod = imp.load_module('_cpp', fp, pathname, description)
ImportError: /usr/lib/libdolfin.so.0: undefined symbol: _ZN3MPI14Is_initializedEv


2) 'swig', 'trilinos' and 'armadillo' seem not to be necessary as dependences any more. Instead 'cgal' and 'openmpi' should be inserted.

Anonymous comment on 2011-08-15 20:17

Just two things:

1) Installing dolfin from AUR and trying to import the relative module in python let to the following error:

Python 2.7.2 (default, Jun 29 2011, 11:10:00)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import dolfin
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/site-packages/dolfin/__init__.py", line 13, in <module>
from dolfin.cppimports import *
File "/usr/lib/python2.7/site-packages/dolfin/cppimports.py", line 4, in <module>
import dolfin.cpp as cpp
File "/usr/lib/python2.7/site-packages/dolfin/cpp.py", line 30, in <module>
_cpp = swig_import_helper()
File "/usr/lib/python2.7/site-packages/dolfin/cpp.py", line 26, in swig_import_helper
_mod = imp.load_module('_cpp', fp, pathname, description)
ImportError: /usr/lib/libdolfin.so.0: undefined symbol: _ZN3MPI14Is_initializedEv


2) 'swig', 'trilinos' and 'armadillo' seem not to be necessary as dependences any more. Instead 'cgal' and 'openmpi' should be inserted.

toffyrn commented on 2011-02-07 20:31

The file "cmake/modules/FindArmadillo.cmake" uses a deprecated method "rand". Find/replace the four occurences to the new method "randu" and it detects armadillo, and compiles.

Should armadillo be a required dependency?

jasper commented on 2011-02-07 06:17

makepkg aborts with:

CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):
Armadillo could not be found. Be sure to set ARMADILLO_DIR. (missing:
ARMADILLO_TEST_RUNS)

??

Anonymous comment on 2011-01-13 20:39

myles, could you please update the PKGBUILD to work with ver.0.9.9? The build system has switched from scons to cmake, and as Radfahrer pointed out,
the python dependencies of your packages need to be changed to refer to python2 explicitly.

Anonymous comment on 2010-10-20 11:43

new verion is out and python dependency has to be changed to python2