Dear group,
I apologize if my question below has already been addressed in the one of
deal.ii’s documentation resources, but I didn't understand how to answer it
using the pieces of documentation that I have read such as
“How to use CMake to configure your projects with deal.II”
https://www.dealii.org/developer/users/cmakelists.html#cmakeauto
and
“deal.II in Spack” https://github.com/dealii/dealii/wiki/deal.II-in-Spack
I am trying to embed a short Python script in my code, but get an error
message after running “make release”. Attached are an example code with a
minor addition to the “main” of Step-1 and the “CMakeLists.txt” file that I
tried to adapt to support Python.
I am running my code on a MAC OS Yosemite 10.10.5 with the special version
of deal.ii that Luca prepared for me
https://groups.google.com/forum/#!searchin/dealii/%22Make$20test%22$20failure$20following$20Trilinos$20installation$20with$20Mesquite%7Csort:relevance/dealii/Y7MH_BE0yko/1zvnHGR7AQAJ
<https://groups.google.com/forum/%23!searchin/dealii/%22Make$20test%22$20failure$20following$20Trilinos$20installation$20with$20Mesquite%7Csort:relevance/dealii/Y7MH_BE0yko/1zvnHGR7AQAJ>
Here are the error messages that I get:
[ yaakobioy L02029080
~/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod
]$ make release
CMake Error at
/Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake:57
(ADD_EXECUTABLE):
add_executable cannot create target "step-1" because another target with
the same name already exists. The existing target is an executable
created
in source directory
"/Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod".
See documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
CMakeLists.txt:49 (DEAL_II_INVOKE_AUTOPILOT)
-- Configuring incomplete, errors occurred!
See also
"/Users/yaakobioy/dealii/dealii-8-5-0pre-v2/dealii-8-5-0pre-v2-Install/examples/step-1-mod/CMakeFiles/CMakeOutput.log".
make: *** [cmake_check_build_system] Error 1
I would appreciate if someone could explain what should I do to overcome
this problem.
Thanks in advance,
Oded
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/* ---------------------------------------------------------------------
*
* Copyright (C) 1999 - 2015 by the deal.II authors
*
* This file is part of the deal.II library.
*
* The deal.II library is free software; you can use it, redistribute
* it, and/or modify it under the terms of the GNU Lesser General
* Public License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
* The full text of the license can be found in the file LICENSE at
* the top level of the deal.II distribution.
*
* ---------------------------------------------------------------------
*/
#include <Python/Python.h>
#include <deal.II/grid/tria.h>
#include <deal.II/grid/tria_accessor.h>
#include <deal.II/grid/tria_iterator.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/manifold_lib.h>
#include <deal.II/grid/grid_out.h>
#include <iostream>
#include <fstream>
#include <cmath>
using namespace dealii;
void first_grid ()
{
Triangulation<2> triangulation;
GridGenerator::hyper_cube (triangulation);
triangulation.refine_global (4);
std::ofstream out ("grid-1.eps");
GridOut grid_out;
grid_out.write_eps (triangulation, out);
std::cout << "Grid written to grid-1.eps" << std::endl;
}
void second_grid ()
{
Triangulation<2> triangulation;
const Point<2> center (1,0);
const double inner_radius = 0.5,
outer_radius = 1.0;
GridGenerator::hyper_shell (triangulation,
center, inner_radius, outer_radius,
10);
triangulation.set_all_manifold_ids(0);
const SphericalManifold<2> manifold_description(center);
triangulation.set_manifold (0, manifold_description);
for (unsigned int step=0; step<5; ++step)
{
Triangulation<2>::active_cell_iterator
cell = triangulation.begin_active(),
endc = triangulation.end();
for (; cell!=endc; ++cell)
{
for (unsigned int v=0;
v < GeometryInfo<2>::vertices_per_cell;
++v)
{
const double distance_from_center
= center.distance (cell->vertex(v));
if (std::fabs(distance_from_center - inner_radius) < 1e-10)
{
cell->set_refine_flag ();
break;
}
}
}
triangulation.execute_coarsening_and_refinement ();
}
std::ofstream out ("grid-2.eps");
GridOut grid_out;
grid_out.write_eps (triangulation, out);
std::cout << "Grid written to grid-2.eps" << std::endl;
triangulation.set_manifold (0);
}
int main ()
{
Py_Initialize();
PyRun_SimpleString("from time import time,ctime\n"
"print('Today is', ctime(time()))\n");
Py_Finalize();
first_grid ();
second_grid ();
}
##
# CMake script for the step-1 tutorial program:
##
# Set the name of the project and target:
SET(TARGET "step-1")
# Declare all source files the target consists of. Here, this is only
# the one step-X.cc file, but as you expand your project you may wish
# to add other source files as well. If your project becomes much larger,
# you may want to either replace the following statement by something like
# FILE(GLOB_RECURSE TARGET_SRC "source/*.cc")
# FILE(GLOB_RECURSE TARGET_INC "include/*.h")
# SET(TARGET_SRC ${TARGET_SRC} ${TARGET_INC})
# or switch altogether to the large project CMakeLists.txt file discussed
# in the "CMake in user projects" page accessible from the "User info"
# page of the documentation.
SET(TARGET_SRC
${TARGET}.cc
)
# Usually, you will not need to modify anything beyond this point...
CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)
FIND_PACKAGE(deal.II 8.5.0 QUIET
HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
)
IF(NOT ${deal.II_FOUND})
MESSAGE(FATAL_ERROR "\n"
"*** Could not locate a (sufficiently recent) version of deal.II. ***\n\n"
"You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to
cmake\n"
"or set an environment variable \"DEAL_II_DIR\" that contains this path."
)
ENDIF()
DEAL_II_INITIALIZE_CACHED_VARIABLES()
PROJECT(${TARGET})
find_package(PythonLibs REQUIRED)
INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS})
ADD_EXECUTABLE(${TARGET} ${TARGET}.cc)
DEAL_II_SETUP_TARGET(${TARGET})
TARGET_LINK_LIBRARIES(${TARGET} ${PYTHON_LIBRARIES})
DEAL_II_INVOKE_AUTOPILOT()
