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|
ALBERTA is an Adaptive multi-Level finite element toolbox using
Bisectioning refinement and Error control by Residual
Techniques for scientific Applications.
-------------------------------------------------------------------------------
Contents
========
I. Introduction
II. External Packages (all optional)
OpenGL
BLAS
GPSKCA
gltools
GRAPE
Silo
OpenDX
Paraview
alternate compilers
III. Configure Options
1.) ALBERTA's installation paths
2.) Options affecting which versions of ALBERTA are built
3.) Options controlling specific features
4.) Options controlling the search-path for external libraries
IV. Compiler flags (with examples)
V. Some platform dependent notes and examples
-------------------------------------------------------------------------------
I) Introduction
===============
This is ALBERTA Version 3.1. ALBERTA has a web-page at
http://www.alberta-fem.de/
and a mailing list
alberta-fem@math.tu-dortmund.de
The v3 release have a git repository at the following location:
https://gitlab.com/alberta-fem/alberta3
ALBERTA can be compiled on recent versions of common Linux distributions
and macOS. Other Unices are no longer support. Windows is not directly
supported but WSL2 (Windows subsystem for Linux) should work, MinGW
might work - both are not tested.
Generic installation instructions can be found in the file `./INSTALL'
in this directory. Quick instructions:
./configure --prefix=PREFIX
make
make install
This will configure and compile the package and install the entire
beast in a directory hierarchy below the path-prefix PREFIX, where
PREFIX defaults to `/usr/local/' if the `--prefix' switch is omitted.
You don't need to install ALBERTA, especially if you want to
develop its code. Just use it next to its code.
0) Build system basics
~~~~~~~~~~~~~~~~~~~~~~
ALBERTA uses Autotools as the build system. Autotools consists of
Automake, Autoconf, libtool and uses Make, M4 and various other
pieces of software. It servers ALBERTA as a cross-plattform tool
to detect and configure dependencies, setting system-dependent
variables, to offer a way to set options by the user, and to
generate Makefiles.
Everything defined with the help of Automake, Autoconf, et al. is
put into a huge shell script 'configure'. This script needs to be
executed by the user as the first step. Then the Makefiles can
take over.
ALBERTA's source code is distributed in two ways:
1. As a tar ball including all source code files with pre-computed
configure script. Using this, Automake and Autoconf are not
needed, just run the configure script. The tar balls are part
of every release. Additionally, the build pipeline generates
the tarball for every commit (and branch respectively) and
stores it as a build artefact.
2. As a Git clone without any pre-computed file. You have to
generate Automakefiles and the configure script. To do this,
Automake and Autoconf and their dependencies are required.
Run the following two command
./generate-alberta-automakefiles.sh
autoreconf --force --install
and proceed with running the freshly generated configure script.
1) Dependencies
~~~~~~~~~~~~~~~
To compile ALBERTA from a tarball you need:
- Make
- GCC or Clang
- glibc headers
- tirpc headers (not for macOS)
- pkg-config
- libtool
- gnu-getopt (only macOS)
To generate the configure script, additional dependencies are:
- Automake
- Autoconf
Optional dependencies are needed to provide some features like a
Fortran compiler, BLAS, X11 headers, OpenGL, ParaView, or GRAPE.
2) Tests
~~~~~~~~
Executable are only build as tests and run as tests. 'make check'
builds and executes the tests.
3) The directory layout
~~~~~~~~~~~~~~~~~~~~~~~
Contained in the package-tree are the following sub-directories
(omitting 3rd-level sub-directories below add_ons/):
___ 0d/
____________ alberta/ ___ src/ ______|___ 1d/
/ \ |___ 2d/
/ \__ doc/ |___ 3d/
/ ___ 1d/ |___ Common/
/ |___ 2d/ |___ alberta*/
/_ demo/ __ src/ _______|___ 3d/
/ |___ 4d/
/ |___ 5d/
/ |___ Common/
/
/
/
alberta-3.0 /
\___ alberta_util/ ___ src/
\
\ ____ bamg2alberta/
\__ add_ons/___/
\ \____ block_solve/
\ \
\ \___ geomview/
\ \
\ \___ gmv/
\ \
\ \___ grape/
\ \
\ \___ libalbas/
\ \
\ \
\ \___ meshtv/
\ \
\ \___ paraview/
\ \
\ \___ static_condensation/
\ \
\ \___ triangle2alberta/
\ \
\ \___ write_mesh_fig/
\
\_ configure and other distribution
files
Short description of the sub-directories:
* alberta
The main package.
* demo
The sub-directory `demo/' contains a few demonstration
programs. After running "make install" (see file `./INSTALL') a
tar-ball containing all demo programs will be installed in
`PREFIX/share/alberta/'. The tar-ball can be extracted elsewhere;
the make-files contained in the tar-ball have appropriate defaults
for the location of the (installed) ALBERTA libraries and header
files.
* alberta_util
This package contains the old ALBERTA util.c file, now split into
several smaller source files. As of version 2.0 it also contains the
former SOLVER library. It is compiled to form a separate utility
library (message macros, ALBERTA memory allocation routines, BLAS
routines and wrappers, etc.) and should linked to any program using
the ALBERTA package. It can also be used as a stand-alone utility
library.
* bamg2alberta
A converter from the FreeFem++ grid-generatar `bamd' to ALBERTA
macro file format.
* block_solve
Block-matrix support.
* geomview
Simple ALBERTA-OOGL converter.
* gmv
Stand-alone converter ALBERTA-gmv.
* grape
GRAPE interface for ALBERTA. Only for non-parametric FE of dimension
2 and 3. The GRAPE-interface consists of "make" will create
"alberta_grapeXX" and alberta_moviXX" where XX is in {22, 33}.
"make install" will install those programs below `PREFIX/bin/'.
The GRAPE interface is only installed when the GRAPE library and
header file are available on your system (determined at configure
time, use "configure --help" for appropriate command line switches
for "configure").
* libalbas
Implementation of some more fancy basis functions (bubbles, direct
sums).
* meshtv
MeshTV interface for ALBERTA. Only for non-parametric FE. The MeshTV
interface consists of the programs "alberta_meshtvX" with X in
{1,2,3}. These are installed in `PREFIX/bin/' as well.
The interface is only installed if the Silo library and header files
are available on your system. See "configure --help" for details.
* paraview
Stand-alone converte ALBERTA-Paraview
* static_condensation
Condensation of element bubbles, resulting in a drastical reduction
of the dimension.
* triangle2alberta
Converter from the Triangle grid generator to the ALBERTA macro-file format.
* write_mesh_fig
Dump a mesh to disk in a format suitable for xfig(1).
II) External packages
=====================
OpenGL -- you need some implementation of SGI's 3D-API. If your system
does not have OpenGL you can fetch the free OpenGL
implementation "MesaGL" from
http://www.mesa3d.org/
If you don't have a clue what this is all about then ask your
system-administrator. In former version OpenGL was required to
compile ALBERTA, starting with this release graphical output
is an optional feature.
BLAS -- "Basic Linear Algebra Subprograms"
You definitely need some version of the BLAS. Often the BLAS
can be found at "/usr/lib/libblas.a", but this need not be the
case.
You should have a look at
http://www.netlib.org/blas/faq.html
which lists some URLs to optimized BLAS-implementations for
some architectures. For an optimized version for AMD's Athlon
and Opteron CPUs you should have a look at AMD's web-site
(www.amd.com) and search for "acml".
Compiler dependence
-------------------
In general, you need a version of the BLAS which was compiled
by the Fortran compiler you are using to compile (parts of)
the ALBERTA package. Sometimes it is possible to get around
this restriction by linking in additional libraries, as shown
in some of the platform dependent examples listed below.
ALBERTA can be compiled without BLAS, in which case
C-replacements are used instead of the BLAS-functions.
GPSKCA -- "Gibbs-Pool-Stockmeyer" or "Gibbs-King" algorithm for either
bandwidth or profile reduction. Note that GPSKCA is a Fortran
package which also needs BLAS.
gltools -- OpenGL toolkit
We strongly recommend that you install the gltools package;
you can fetch it from
http://www.wias-berlin.de/software/gltools/
gltools provides a more flexible graphical output than would
be otherwise available with ALBERTA.
NOTE: you need at least gltools-2-4. Version 2-3 will _not_
work. "configure" does not check for right version, it's up to
yourself.
dxtools -- OpenDX toolkit
The dxtools are an interface to the OpenDX visualization software.
It may be downloaded from
http://www.opendx.org/
The visualization features are far more advanced than gltools,
however OpenDX is a huge project that takes time getting used to.
The dxtools interface was designed to keep things simple and
intuitive.
GRAPE -- Graphics Programming Environment
If GRAPE is present, the four programs alberta_grape22,
alberta_grape33, alberta_movi22 and alberta_movi33 are
compiled and installed in PREFIX/bin/. They can be used to
display data-files created by ALBERTA during your numerical
simulations.
GRAPE is available from
http://www.mathematik.uni-freiburg.de/IAM/Research/grape/GENERAL/
Silo -- Silo is a library developed at the Lawrence Livermore National
Laboratory to handle portable storage of mesh and function data. It
serves as an interface to MeshTV, an open source visualization
project also based at the LLNL.
If the Silo library is present, the programs alberta_meshtv? are
compiled and installed. They can be used to convert ALBERTA meshes
and DOF_REAL[_D]_VECS to Silo data files, which can then be
visualized using the MeshTV binary.
MeshTV and Silo are available from
http://www.llnl.gov/bdiv/meshtv/
GMV -- "General Mesh Viewer" is available from
http://www-xdiv.lanl.gov/XCM/gmv/GMVHome.html
ALBERTA provides a routine "write_mesh_gmv()", which converts
the mesh and the finite element functions to a format
understood by "gmv". This is just a separate program, no
external library needs to be linked in.
Geomview -- An ancient program, originally from the Geometry Center,
available from
http://sourceforge.net/projects/geomview/
`./demo/src/Common/geomview-graphics.c' contains an interface
from ALBERTA to Geomview. The demo-programs for parametric
meshes, especially those for higher co-dimension, can make use
of Geomview. `geomview-graphics.c' does not require any
external libraries for linking. You need Geomview version
>1.9.0, and -- for the visualization of higher dimensional
meshes -- the `gvemod-ndview' add-on. Both are available from
SourceForge.
Paraview -- For viewing the output from the alberta2paraviewXd converters.
http://www.paraview.org
III) Configure Options
======================
"configure --help" will give you a summary of available options. The file
"INSTALL" contains generic configuration instructions and a description of
generic command line options for configure.
The remaining (i.e. ALBERTA specific) options are explained here:
1.) ALBERTA's installation paths
--------------------------------
The default installation prefix of the ALBERTA-package is the default
GNU installation prefix, i.e. `/usr/local/' Of course, you can change
the default behavior by using the "--prefix=PREFIX" switch when
running configure (see `./INSTALL'). However, the default layout is
like follows:
The libraries will go to
/usr/local/lib/
the header-files and Makefile.alberta will end up in
/usr/local/include/alberta/
The configured libtool-script and the Makefile-fragment for the
demo-suite will reside in
/usr/local/libexec/alberta-VERSION/
and finally the demo package (under the name alberta-VERSION.demo.tar.gz,
where VERSION denotes the actual version of the alberta package) will
be copied to
/usr/local/share/alberta/
This will be the layout after running "make install".
2.) Options affecting which versions of ALBERTA are built
---------------------------------------------------------
Compiling all flavours of the ALBERTA libraries takes a long time. The
ALBERTA libraries are all named
libalberta_[fem_,gfx_]<DIM_OF_WORLD>d[_debug]
The options below control which of them are actually created.
--disable-alberta-1 disable building of an ALBERTA library for Finite
Elements of dimension 1. (default: enabled)
--disable-alberta-2 disable building of an ALBERTA library for Finite
Elements of dimension 2. (default: enabled)
--disable-alberta-3 disable building of an ALBERTA library for Finite
Elements of dimension 3. (default: enabled)
--enable-dim-of-world="DIM1 ... DIMk"
Compile ALBERTA libraries for DIM_OF_WORLD=DIM1,
..., DIM_OF_WORLD=DIMk. Supported dimensions range
from 4 to 9. Dimensions are separated by spaces.
Note that this does not change the maximal mesh
dimension which remains at 3. The default is NOT to
compile for any dimension > 3.
--disable-debug disable building of ALBERTA libraries with debugging
information. (default: enabled)
--disable-graphics disable support for visualization, including all
add-ons which need graphics. (default: enabled)
--disable-fem-toolbox disable building of the actual FEM-toolbox. Primarily
meant for making the Fremen a little bit
happier. This will speed up compilation
drastically. Implies "--disable-graphics". Only the
core libraries libalberta_Nd[_debug] are built.
3.) Options controlling specific features
-----------------------------------------
--enable-efence use the malloc debugger "Electric Fence" for all
allocations for the DEBUG libraries, the optimized
libraries will still use the default allocators.
(default: disabled)
--enable-fortran-blas Use BLAS routines for some basic linear algebra
stuff. (default: disabled)
--disable-vector-basis-functions
Disable support for vector-valued basis functions.
If you leave this enabled ALBERTA supports
DIM_OF_WORLD-valued basis functions and scalar basis
functions. If you disable this feature ALBERTA only
supports scalar valued basis functions.
DIM_OF_WORLD-valued basis functions play an
important role, e.g. for the discretisation of
problems involving H(div) (Maxwell equations ...)
and, e.g., for stable mixed discretisations for the
Stokes-problem. Building ALBERTA with support for
vector valued basis functions increases the
compile-time, otherwise it should not have any
measureable performance impact, therefore this
feature is normally ENABLED. Disable it to reduce
the compile time if you do not need this feature.
(default: enabled)
--disable-chained-basis-functions
Disable support for chains of basis-functions.
ALBERTA has support for forming direct sums of
FE-spaces. This is useful, e.g., to implement
certain stable mixed discretisations for the
Stokes-problem (P1+Bubble = Mini, P1+FaceBubble =
Bernardi-Raugel, weak slip b.c.). Keeping this
feature enabled will have a slight performance
impact, you may disable it if you do not need this
feature. (default: enabled)
4.) Options controlling the search-path for external libraries
--------------------------------------------------------------
See also "External Packages" above.
For each external package PKG the configure script provides the
following options:
--without-PKG
Prohibit the use of this package, even if it is installed on
your system.
--with-PKG-name=NAME
Alter the default name of the package,
e.g. "--with-opengl-name=MesaGL" or "--with-blas-name=cxml".
NOTE: it is possible to specify more than one library. For
example on (some versions of?) Solaris the BLAS-library is
called "libsunperf.so". If you want to link with this library
using gcc and g77, then you need to specify
"--with-blas-name=sunperf -lfui -lfsu -lsunmath"
Note the "-l" in front of the additional libraries.
(of course, in addition to --with-blas-name you also need
--with-blas-lib=WHATEVER)
--with-PKG-dir=DIR
Search for header-files and for the library itself below DIR,
e.g. "--with-gltools-dir=/foo/bar/gltools-2.4".
--with-PKG-lib=DIR
Search for the library below DIR,
e.g. "--with-blas-lib=/usr/people/claus/software/lib/".
--with-PKG-headers=DIR
Use DIR as search-path for the include-files for PKG,
e.g. "--with-opengl-include=/usr/people/claus/software/include/".
The following quotes the relevant fragment of the online-help obtained
by running "configure --help". Please see the file ./INSTALL for the
notation (e.g. PREFIX, EPREFIX etc.).
--with-blas-name=NAME use NAME as the name of the blas library (without
leading "lib" prefix and trailing suffix). Default:
"blas"
--with-blas-lib=DIR use blas library below directory DIR (default:
EPREFIX/lib/)
--without-OpenGL disable use of package OpenGL (default: auto-detect)
--with-OpenGL-name=NAME use NAME as the name of the OpenGL library (without
leading "lib" prefix and trailing suffix). Default:
"GL"
--with-OpenGL-dir=DIR use OpenGL library (and headers) below directory DIR
(no default)
--with-OpenGL-lib=DIR use OpenGL library below directory DIR (default:
${x_libraries})
--with-OpenGL-headers=DIR
use OpenGL include files below directory DIR
(default: ${x_includes}/GL -I/usr/include/GL/)
--without-gltools disable use of package gltools (default: auto-detect)
--with-gltools-name=NAME
use NAME as the name of the gltools library (without
leading "lib" prefix and trailing suffix). Default:
"gltools"
--with-gltools-dir=DIR use gltools library (and headers) below directory
DIR (no default)
--with-gltools-lib=DIR use gltools library below directory DIR (default:
EPREFIX/lib/)
--with-gltools-headers=DIR
use gltools include files below directory DIR
(default: PREFIX/include/)
--without-OpenDX disable use of package OpenDX (default: auto-detect)
--with-OpenDX-name=NAME use NAME as the name of the OpenDX library (without
leading "lib" prefix and trailing suffix). Default:
"DXL"
--with-OpenDX-dir=DIR use OpenDX library (and headers) below directory DIR
(no default)
--with-OpenDX-lib=DIR use OpenDX library below directory DIR (default:
EPREFIX/lib/)
--with-OpenDX-headers=DIR
use OpenDX include files below directory DIR
(default: PREFIX/include/)
--without-grape disable use of package grape (default: auto-detect)
--with-grape-name=NAME use NAME as the name of the grape library (without
leading "lib" prefix and trailing suffix). Default:
"gr"
--with-grape-dir=DIR use grape library (and headers) below directory DIR
(no default)
--with-grape-lib=DIR use grape library below directory DIR (default:
EPREFIX/lib/)
--with-grape-headers=DIR
use grape include files below directory DIR
(default: PREFIX/include/)
--without-silo disable use of package silo (default: auto-detect)
--with-silo-name=NAME use NAME as the name of the silo library (without
leading "lib" prefix and trailing suffix). Default:
"silo"
--with-silo-dir=DIR use silo library (and headers) below directory DIR
(no default)
--with-silo-lib=DIR use silo library below directory DIR (default:
EPREFIX/lib/)
--with-silo-headers=DIR use silo include files below directory DIR (default:
PREFIX/include/)
--with-efence enable use of package efence (default: disabled)
--with-efence-name=NAME use NAME as the name of the efence library (without
leading "lib" prefix and trailing suffix). Default:
"efence"
--with-efence-dir=DIR use efence library (and headers) below directory DIR
(no default)
--with-efence-lib=DIR use efence library below directory DIR (default:
EPREFIX/lib/)
--with-efence-headers=DIR
use efence include files below directory DIR
(default: PREFIX/include/)
IV. Compiler flags
==================
The default flags for the optimized libraries are "-O3" when using gcc
and "-O" otherwise.
The default flags for the debugging-enabled libraries are
"-O0 -ggdb -fno-inline -fno-builtin" with gcc and "-g" otherwise.
The relevant environment- respectively make-variables are listed at
the end of the online-help provided by running `configure --help'.
They include:
CFLAGS
C-compiler flags used for _both_, optimized and debug enabled libraries
ALBERTA_OPTIMISM_CFLAGS
C-compiler flags used for the optimized library. They are prepended
to the CFLAGS variable.
ALBERTA_DEBUG_CFLAGS
C-compiler flags used for the debug enabled library. They are
prepended to the CFLAGS variable.
ALBERTA_FFLAGS
Fortran-compiler flags. They are separated from the CFLAGS because
in general the Fortran compiler can come from a different vendor
than the C-compiler in which case the flags understood by the
Fortran compiler are different from the flags understood by the
C-compiler.
You have to consult the documentation for the compiler(s) you are using
to determine the appropriate switches for your setup.
There are three ways to set those flags:
a.) arguments to configure
b.) environment variables (have to be defined _before_ running configure)
c.) arguments to make
We recommend using a.).
Examples:
---------
1.) gcc with a Pentium 4
./configure [OTHER OPTIONS] \
CFLAGS="-march=pentium4 -mfpmath=sse" \
FFLAGS="-march=pentium4 -mfpmath=sse"
make
make install
or (assuming a Bourne-shell)
CFLAGS="-march=pentium4 -mfpmath=sse"
FFLAGS="-march=pentium4 -mfpmath=sse"
export CFLAGS FFLAGS
./configure [OTHER OPTIONS]
make
make install
or
./configure [OTHER OPTIONS]
make CFLAGS="-march=pentium4 -mfpmath=sse" \
FFLAGS="-march=pentium4 -mfpmath=sse"
make install
2.) Pentium 4 with icc and with Intel "math kernel library" (BLAS
implementation)
./configure [OTHER OPTIONS] \
CC=icc CFLAGS="-xW" ALBERTA_OPTIMIZE_CFLAGS="-O3" \
ALBERTA_DEBUG_CFLAGS="-O0 -g" \
F77=ifc FFLAGS="-xW -O3" \
--with-blas-name=mkl --with-blas-lib=/opt/intel/mkl61/lib/32/
make
make install
or set environment variables or use arguments to "make" as shown in
example 1.)
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