Installing Neper on Ubuntu 22
Important
Read first: Introduction, especially Installing Neper and Testing Neper.
This tutotial describes how to install Neper step by step on a fresh Ubuntu 22 distribution. It may apply to other Ubuntu distributions too, and may be adapted to other distributions quite easily. General installation instructions are provided in Introduction (Installing Neper), and this tutorial does not aim to substitute to it. However, we adopt here a different approach by managing (dependency) issues as they occur during the installation on a fresh Ubuntu 22 distribution (which misses packages that would typically already be present on older installations).
Downloading Neper
We first download the last official version from the website (https://neper.info), neper-4.6.1.tar.gz at the time of writing.
It is then a good idea to move the archive to a dedicated directory, for example ~/Progs, and work from there.
We create directory ~/Progs and move the archive into it:
$ mkdir ~/Progs
$ mv neper-4.6.1.tar.gz ~/Progs
We change directory to Progs and unarchive the code:
$ cd ~/Progs
$ tar -zxf neper-4.6.1.tar.gz
Compiling Neper
We first compile Neper using the commands provided in Installing Neper (namely, we should follow the cmake, make, make install sequence):
$ cd neper-4.6.1
$ cd src
$ mkdir build
$ cd build
$ cmake ..
Command 'cmake' not found, but can be installed with:
sudo snap install cmake # version 3.26.4, or
sudo apt install cmake # version 3.22.1-1ubuntu1.22.04.1
See 'snap info cmake' for additional versions.
We follow the terminal output and install cmake:
$ sudo apt install cmake
We re-run Cmake:
$ cmake ..
-- The C compiler identification is GNU 11.3.0
-- The CXX compiler identification is unknown
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
CMake Error at CMakeLists.txt:11 (project):
No CMAKE_CXX_COMPILER could be found.
Tell CMake where to find the compiler by setting either the environment
variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
to the compiler, or to the compiler name if it is in the PATH.
-- Configuring incomplete, errors occurred!
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeOutput.log".
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeError.log".
A CXX (C++) compiler is missing. The GNU C++ compiler is g++; so, we install it:
$ sudo apt install g++
We re-run Cmake:
$ cmake ..
-- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig
-- WARNING: PKGCONFIG() indicates that the tool pkg-config has not been found on your system. You should install it.
FindGSL.cmake: gsl-config/pkg-config gsl not found. Please set
it manually. GSL_CONFIG=GSL_CONFIG-NOTFOUND
CMake Error at CMakeLists.txt:46 (_message):
GSL required, please specify it's location.
Call Stack (most recent call first):
cmake/FindGSL.cmake:178 (MESSAGE)
CMakeLists.txt:103 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeOutput.log".
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeError.log".
We follow the terminal output and install pkg-config:
$ sudo apt install pkg-config
We re-run Cmake:
$ cmake ..
-- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig
-- PKGCONFIG() indicates that gsl is not installed (install the package which contains gsl.pc if you want to support this feature)
FindGSL.cmake: gsl-config/pkg-config gsl not found. Please set
it manually. GSL_CONFIG=GSL_CONFIG-NOTFOUND
CMake Error at CMakeLists.txt:46 (_message):
GSL required, please specify it's location.
Call Stack (most recent call first):
cmake/FindGSL.cmake:178 (MESSAGE)
CMakeLists.txt:103 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeOutput.log".
See also "/home/rquey/Progs/neper-4.6.1/src/build/CMakeFiles/CMakeError.log".
We have to install gsl. We search for it as follows (it is a library, so, we prefix it with lib in the search):
$ sudo apt search libgsl
Sorting... Done
Full Text Search... Done
libgsl-dbg/jammy 2.7.1+dfsg-3 amd64
GNU Scientific Library (GSL) -- debug symbols package
libgsl-dev/jammy 2.7.1+dfsg-3 amd64
GNU Scientific Library (GSL) -- development package
libgsl27/jammy 2.7.1+dfsg-3 amd64
GNU Scientific Library (GSL) -- library package
libgslcblas0/jammy 2.7.1+dfsg-3 amd64
GNU Scientific Library (GSL) -- blas library package
libocamlgsl-ocaml/jammy 1.24.3-1build3 amd64
GNU scientific library for OCaml
libocamlgsl-ocaml-dev/jammy 1.24.3-1build3 amd64
GNU scientific library for OCaml
libgsl-dev is the one we need; so, we install it:
$ sudo apt install libgsl-dev
We re-run Cmake:
$ cmake ..
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Could NOT find system Scotch - using built-in
-- Could NOT find system NLopt - using built-in
-- Neper is set to be installed in: /usr/local/bin and /usr/share
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rquey/Progs/neper-4.6.1/src/build
It now seems good to go. We can compile:
$ make
[ 0%] Building C object contrib/nlopt/CMakeFiles/nlopt.dir/src/algs/direct/DIRect.c.o
...
[100%] Built target neper
We can already install Neper (with root permissions):
$ sudo make install
which copies the neper binary to a system location and makes the neper command available system-wide.
Note
It is also possible to simply copy the neper binary to a user location, e.g. ~/bin/, and make it visible to the system by including ~/bin to your $PATH, by adding PATH=$PATH:~/bin to your ~/.bashrc file (assuming you are using the Bash shell (echo $SHELL)).
We can now test the installation:
$ ctest
Test project /home/rquey/Progs/neper/neper/src/build
Start 1: T/dim
1/461 Test #1: T/dim ................................... Passed 0.02 sec
[...]
90% tests passed, 44 tests failed out of 461
Total Test time (real) = 48.33 sec
The following tests FAILED:
129 - M/cl (Failed)
130 - M/cl_expr (Failed)
133 - M/clmin (Failed)
134 - M/clratio (Failed)
135 - M/cut (Failed)
136 - M/dim (Failed)
137 - M/dim2 (Failed)
138 - M/dim_expr (Failed)
139 - M/faset (Failed)
142 - M/interface (Failed)
143 - M/interface2 (Failed)
144 - M/interface3 (Failed)
145 - M/mesh2dalgo_dela (Failed)
146 - M/mesh2dalgo_fron (Failed)
147 - M/mesh2dalgo_mead (Failed)
148 - M/mesh2dalgo_netg (Failed)
149 - M/mesh3dalgo_netggmne (Failed)
150 - M/mesh3dalgo_netggmsh (Failed)
151 - M/mesh3dalgo_netgnetg (Failed)
152 - M/meshing (Failed)
154 - M/meshqualdisexpr (Failed)
155 - M/meshqualexpr (Failed)
156 - M/meshqualmin (Failed)
157 - M/morpho_cube (Failed)
158 - M/nset1 (Failed)
159 - M/nset2 (Failed)
160 - M/nset3 (Failed)
161 - M/order (Failed)
162 - M/order_dim2 (Failed)
166 - M/part2 (Failed)
167 - M/part_dim2 (Failed)
168 - M/pl (Failed)
169 - M/rcl (Failed)
170 - M/rcl_expr (Failed)
173 - M/remesh1 (Failed)
174 - M/remesh2 (Failed)
175 - M/remesh3 (Failed)
176 - M/remesh4 (Failed)
182 - M/statelsetco (Failed)
188 - M/stateltco (Failed)
190 - M/tesr_dim2 (Failed)
193 - M/tess2ddim3 (Failed)
211 - V/asymptote (Failed)
326 - V/povray (Failed)
Some tests failed because we have not install the run-time dependencies: Gmsh, Asymptote and POV-Ray (see Installing Neper).
Installing Gmsh
Gmsh is available from the package manager (meaning that we could run sudo apt install gmsh to install it); however, it is worth installing it from source since it will run much faster.
We download the source code from the website (https://gmsh.info), latest version. It is then a good idea to move it to ~/Progs, where Neper already is:
$ mv gmsh-4.11.1-source.tgz ~/Progs/
$ tar -zxf gmsh-4.11.1-source.tgz
$ cd ~/Progs/gmsh-4.11.1-source
We can then compile it. As Gmsh is also managed with CMake, installation is no much different from that of Neper itself:
$ mkdir build
$ cd build
$ cmake ..
-- The CXX compiler identification is GNU 11.3.0
-- The C compiler identification is GNU 11.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Git (missing: GIT_EXECUTABLE)
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found 64Bit
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP
-- Found Eigen[contrib]
-- Found Mesh
-- Found Solver
-- Found Post
-- Found Plugins
-- Found Parser
-- Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY OPENGL_INCLUDE_DIR)
-- Could NOT find X11 (missing: X11_X11_INCLUDE_PATH X11_X11_LIB)
-- Could NOT find FLTK (missing: FLTK_LIBRARIES FLTK_INCLUDE_DIR)
-- Found ONELAB
-- Found ONELABMetamodel
-- Found ANN[contrib]
-- Found ALGLIB[contrib]
-- Found DIntegration
-- Found Kbipack
-- GMP not found: Kbipack uses long int
-- Found MathEx[contrib]
-- Found Metis[contrib]
-- Found TetGen/BR
-- Found Voro++[contrib]
-- Found OptHom
-- Found DomHex
-- Found QuadTri
-- Found Blossom
-- Found Netgen
-- Found Bamg
-- Found Hxt
-- Found QuadMeshingTools
-- Found WinslowUntangler
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) (found version "")
-- HDF5 not found
-- Found Gmm[contrib]
-- Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS)
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Looking for sys/socket.h
-- Looking for sys/socket.h - found
-- Check size of socklen_t
-- Check size of socklen_t - done
-- Check size of intptr_t
-- Check size of intptr_t - done
-- Looking for dlfcn.h
-- Looking for dlfcn.h - found
-- Found Dlopen
-- Looking for linux/joystick.h
-- Looking for linux/joystick.h - found
-- Found LinuxJoystick
-- Performing Test WALL
-- Performing Test WALL - Success
-- Performing Test WCAST
-- Performing Test WCAST - Failed
-- Performing Test WDEPREC
-- Performing Test WDEPREC - Success
-- Performing Test WIND
-- Performing Test WIND - Success
-- Performing Test WATTR
-- Performing Test WATTR - Success
-- Performing Test NOWARN
-- Performing Test NOWARN - Success
-- Performing Test NOOPT
-- Performing Test NOOPT - Success
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/api/square.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/baffles.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/boolean.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/chamfer.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/coherence.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/compsolid.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/compsolid2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/extend_field.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/extrude.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/extrude2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fillet.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fillet2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fillet3.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fillet4.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fillet_chamfer.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fleur.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/fragment_numbering.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/hybrid_occ_builtin.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/hyperboloid.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/import.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/import2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/intersect_line_volume.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/neuron.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/number_of_tets.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/periodic.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/periodic_embedded.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/pipe.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/primitives.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/revolve.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/revolve2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/shell_sewing.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple2.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple3.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple4.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple5.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple6.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/simple7.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/slicer.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/slicer_surfaces.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/spherical_surf.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/spline.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/step_assembly.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/surface_filling.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/thicksolid.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/thrusections.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/transfinite.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/transform.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/boolean/twist.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/examples/post_processing/compute_area_volume.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t16.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t17.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t18.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t19.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t20.geo
Skipping test /home/rquey/Progs/gmsh-4.11.1-source/tutorials/t21.geo
--
-- Gmsh 4.11.1 has been configured for Linux64
--
-- * Build options: 64Bit ALGLIB[contrib] ANN[contrib] Bamg Blossom DIntegration Dlopen DomHex Eigen[contrib] Gmm[contrib] Hxt Kbipack LinuxJoystick MathEx[contrib] Mesh Metis[contrib] Netgen ONELAB ONELABMetamodel OpenMP OptHom Parser Plugins Post QuadMeshingTools QuadTri Solver TetGen/BR Voro++[contrib] WinslowUntangler
-- * Build type: RelWithDebInfo
-- * C compiler: /usr/bin/cc
-- * C++ compiler: /usr/bin/c++
-- * Install prefix: /usr/local
--
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rquey/Progs/gmsh-4.11.1-source/build
Configuration completed and is sufficient for Neper. So, we can make and install:
$ make
$ sudo make install
The second command copies the gmsh binary file to a system location, which makes the command available to Neper.
Back to Neper’s build directory, we re-run the tests:
$ cd ~/Progs/neper-4.6.1/src/build
$ ctest
99% tests passed, 2 tests failed out of 461
Total Test time (real) = 47.92 sec
The following tests FAILED:
211 - V/asymptote (Failed)
325 - V/povray (Failed)
Errors while running CTest
All “M” tests now pass.
Note
We could also re-run only the “M” tests, using ctest -R M.
Installing POV-Ray and Asymptote
We install povray as follows:
$ sudo apt install povray
We re-run the tests:
$ ctest
99% tests passed, 1 tests failed out of 461
Total Test time (real) = 47.92 sec
The following tests FAILED:
211 - V/asymptote (Failed)
Errors while running CTest
Note
We could also simply run ctest -R V/povray
We now install Asymptote, which itself required full Tex Live, as we know from Installing Neper:
$ sudo apt install asymptote
$ sudo apt install texlive-full
We re-run the tests:
$ ctest
[...]
100% tests passed, 0 tests failed out of 461
Note
We could also simply run ctest -R V/asymptote
Depending on your use of Neper, it may be necessary to make the following changes in your /etc/ImageMagick-6/policy.xml file:
Comment out the following lines:
<policy domain="coder" rights="none" pattern="PS" /> <policy domain="coder" rights="none" pattern="PS2" /> <policy domain="coder" rights="none" pattern="PS3" /> <policy domain="coder" rights="none" pattern="EPS" /> <policy domain="coder" rights="none" pattern="PDF" /> <policy domain="coder" rights="none" pattern="XPS" />Increase the following limits (especially
memoryanddisk):<policy domain="resource" name="memory" value="256MiB"/> <policy domain="resource" name="map" value="512MiB"/> <policy domain="resource" name="width" value="16KP"/> <policy domain="resource" name="height" value="16KP"/> <!-- <policy domain="resource" name="list-length" value="128"/> --> <policy domain="resource" name="area" value="128MP"/> <policy domain="resource" name="disk" value="1GiB"/>
The installation is now complete!
Improving Gmsh’s Installation (optional)
Back to Gmsh, the Gmsh installation may be improved so that we can actually open Gmsh’s GUI, by installing OpenGL’s development package (OpenGL itself may already be installed) and FLTK:
$ sudo apt-get install freeglut3-dev
$ sudo apt-get install libfltk1.3 libfltk1.3-dev
$ cd ~/Progs/gmsh-4.11.1-source
$ cmake ..
$ make
$ sudo make install
Installing Neper’s documentation (optional)
Neper’s documentation is available online, but we can also build our own local copy:
From the doc directory, we compile the documentation:
$ cd ~/Progs/neper-4.6.0/doc
$ make html
sphinx-build -b html -d build/doctrees . build/html
Traceback (most recent call last):
File "/home/rquey/.local/bin/sphinx-build", line 5, in <module>
from sphinx.cmd.build import main
ModuleNotFoundError: No module named 'sphinx'
make: *** [Makefile:53: html] Error 1
Sphinx is missing. We install it:
$ sudo apt-get install python3-sphinx
We re-compile the documentation:
$ make html
sphinx-build -b html -d build/doctrees . build/html
Running Sphinx v4.3.2
loading translations [en]... done
loading pickled environment... done
WARNING: sphinx_rtd_theme (< 0.3.0) found. It will not be available since Sphinx-6.0
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 11 source files that are out of date
updating environment: [config changed ('version')] 11 added, 0 changed, 0 removed
reading sources... [100%] versions
/home/rquey/Progs/fepx/doc/copying.rst:24: WARNING: duplicate citation DAWSON15, other instance in /home/rquey/Progs/fepx/doc/develhistory.rst
/home/rquey/Progs/fepx/doc/develhistory.rst:77: WARNING: duplicate citation DAWSON15, other instance in /home/rquey/Progs/fepx/doc/copying.rst
/home/rquey/Progs/fepx/doc/input.rst:1020: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] versions
/home/rquey/Progs/fepx/doc/versions.rst:7: WARNING: Pygments lexer name 'plain' is not known
generating indices... genindex done
writing additional pages... search done
copying images... [100%] images/minimalbcs.png
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 5 warnings.
The HTML pages are in build/html.
Build finished. The HTML pages are in build/html.
All done! We may now copy the html directory to somewhere more appropriate (there is no make install command for the documentation).