Basic Installation
The installation procedure outlined below will work on commodity linux/unix systems without modification. However, users are still encouraged to carefully read this entire section before attempting to install the SUNDIALS suite, in case non-default choices are desired for compilers, compilation options, or the like. In lieu of reading the option list below, the user may invoke the configuration script with the help flag to view a complete listing of available options, which may be done by issuing
% ./configure —help
from within the top-level SUNDIALS source directory.
In the remainder of this section, we make the following distinctions:
- srcdir
- is the directory 'solver'-x.y.z created above; i.e., the directory containing the SUNDIALS sources.
- builddir
- is the directory under which SUNDIALS is built; i.e., the directory from within which the configure command is issued. Usually, this is the same as srcdir.
- instdir
- is the directory under which the SUNDIALS exported header files and libraries will be installed. Typically, header files are exported under a directory instdir/include while libraries are installed under instdir/lib, with instdir specified with the —prefix flag to configure. See below for more details on the installation directories, including the special cases of the SUNDIALS examples and the sundialsTB toolbox.
Note: The installation directory instdir should NOT be the same as the source directory srcdir.
The installation steps for SUNDIALS can be as simple as
% tar xzf solver-x.y.z.tgz
% cd solver-x.y.z
% ./configure
% make
% make install
in which case the SUNDIALS header files and libraries are installed under /usr/local/include and /usr/local/lib, respectively. Note that, by default, neither the example programs nor the sundialsTB toolbox are built and installed.
If disk space is a priority, then to delete all temporary files created by building SUNDIALS, issue
% make clean
To prepare the SUNDIALS distribution for a new install (using, for example, different options and/or installation destinations), issue
% make distclean
Installation Names
By default, 'make install' will install the SUNDIALS libraries under libdir and the public header files under includedir. The default values for these directories are instdir/lib and instdir/include, respectively, but can be changed using the configure script options —prefix, —exec-prefix, —includedir, and —libdir (see below). For example, a global installation of SUNDIALS on a *NIX system could be accomplished using
% ./configure —prefix=/opt/sundials-2.3.0
Although all installed libraries reside under libdir, the public header files are further organized into subdirectories under includedir.
A typical user program need not explicitly include any of the shared SUNDIALS header files from under the includedir/sundials directory since they are explicitly included by the appropriate solver header files (e.g., cvode_dense.h includes sundials_dense.h). However, it is both legal and safe to do so (e.g., the functions declared in sundials_smalldense.h could be used in building a preconditioner.
The SUNDIALS libraries and header files are summarized below (names are relative to libdir for libraries and to includedir for header files)
| SHARED module | |
|---|---|
| header files | sundials/sundials_types.h sundials/sundials_math.h sundials/sundials_config.h sundias/sundials_nvector.h sundials/sunials_smalldense.h sundials/sundials_dense.h sundials/sundials_iterative.h sundials/sundials_band.h sundials/sundials_spbcgs.h sundials/sundials_sptfqmr.h sundials/sundials_spgmr.h |
| NVECTOR_SERIAL module | |
| libraries | libsundials_nvecserial.{a,so} libsundials_fnvecserial.a |
| header files | nvector/nvector_serial.h |
| NVECTOR_PARALLEL module | |
| libraries | libsundials_nvecparallel.{a,so} libsundials_fnvecparallel.a |
| header files | nvector/nvector_parallel.h |
| CVODE module | |
| libraries | libsundials_cvode.{a,so} libsundials_fcvode.a |
| header files | cvode/cvode.h cvode/cvode_dense.h cvode/cvode_band.h cvode/cvode_diag.h cvode/cvode_spils.h cvode/cvode_bandpre.h cvode/cvode_bbdpre.h cvode/cvode_spgmr.h cvode/cvode_spbcgs.h cvode/cvode_sptfqmr.h cvode/cvode_impl.h |
| CVODES module | |
| library | libsundials_cvodes.{a,so} |
| header files | cvodes/cvodes.h cvodes/cvodes_dense.h cvodes/cvodes_band.h cvodes/cvodes_diag.h cvodes/cvodes_spils.h cvodes/cvodes_bandpre.h cvodes/cvodes_bbdpre.h cvodes/cvodes_spgmr.h cvodes/cvodes_spbcgs.h cvodes/cvodes_sptfqmr.h cvodes/cvodes_impl.h cvodes/cvodea_impl.h |
| IDA module | |
| library | libsundials_ida.{a,so} libsundials_fida.a |
| header files | ida/ida.h ida/ida_dense.h ida/ida_band.h ida/ida_spils.h ida/ida_spgmr.h ida/ida_spbcgs.h ida/ida_sptfqmr.h ida/ida_bbdpre.h ida/ida_impl.h |
| KINSOL module | |
| libraries | libsundials_kinsol.{a,so} libsundials_fkinsol.a |
| header files | kinsol/kinsol.h kinsol/kinsol_dense.h kinsol/kinsol_band.h kinsol/kinsol_spils.h kinsol/kinsol_spgmr.h kinsol/kinsol_spbcgs.h kinsol/kinsol_sptfqmr.h kinsol/kinsol_bbdpre.h kinsol/kinsol_impl.h |
Compilers and Options
Some systems require unusual options for compilation or linking that the ‘configure’ script does not know about. Run ‘./configure —help’ for details on some of the pertinent environment variables.
You can give ‘configure’ initial values for these variables by setting them in the environment. You can do that on the command line like this:
% ./configure CC=gcc CFLAGS=-O2 F77=g77 FFLAGS=-O
Here is a detailed description of the configure options that are pertinent to SUNDIALS. In what follows, 'build_tree' is the directory from where 'configure' was invoked.
General options
--help
-h
print a summary of the options to ‘configure’, and exit.
--quiet
--silent
-q
do not print messages saying which checks are being made. To suppress all normal output, redirect it to ‘/dev/null’ (any error messages will still be shown).
--prefix=PREFIX
Location for architecture-independent files.
Default: PREFIX=/usr/local
--exec-prefix=EPREFIX
Location for architecture-dependent files.
Default: EPREFIX=/usr/local
--includedir=DIR
Alternate location for header files.
Default: DIR=PREFIX/include
--libdir=DIR
Alternate location for libraries.
Default: DIR=EPREFIX/lib
--disable-solver
Although each existing solver module is built by default, support for a given solver can be explicitly disabled using this option. The valid values for solver are: cvode, cvodes, ida, and kinsol.
--enable-examples
Available example programs are not built by default. Use this option to enable compilation of all pertinent example programs. Upon completion of the 'make' command, the example executables will be created under solver-specific subdirectories of builddir/examples:
builddir/examples/'solver'/serial : serial C examples
builddir/examples/'solver'/parallel : parallel C examples
builddir/examples/'solver'/fcmix_serial : serial Fortran examples
builddir/examples/'solver'/fcmix_parallel : parallel Fortran examples
Note: Some of these subdirectories may not exist depending upon the
solver and/or the configuration options given.
--with-examples-instdir=EXINSTDIR
Alternate location for example executables and sample output files (valid only if examples are enabled). Note that installtion of example files can be completely disabled by issuing EXINSTDIR=no (in case building the examples is desired only as a test of the sundials libraries).
Default: DIR=EPREFIX/examples
--with-cppflags=ARG
Specify additional C preprocessor flags (e.g., ARG=-I<include_dir> if necessary header files are located in nonstandard locations).
--with-cflags=ARG
Specify additional C compilation flags.
--with-ldflags=ARG
Specify additional linker flags (e.g., ARG=-L<lib_dir> if required libraries are located in nonstandard locations).
--with-libs=ARG
Specify additional libraries to be used (e.g., ARG=-l<foo> to link with the library named libfoo.a or libfoo.so).
--with-precision=ARG
By default, sundials will define a real number (internally referred to as realtype) to be a double-precision floating-point numeric data type (double C-type); however, this option may be used to build sundials with realtype alternatively defined as a single-precision floating-point numeric data type (float C-type) if ARG=single, or as a long double C-type if ARG=extended.
Default: ARG=double
Options for Fortran support
--disable-f77
Using this option will disable all F77 support. The fcvode, fkinsol and fnvector modules will not be built regardless of availability.
--with-fflags=ARG
Specify additional F77 compilation flags.
The configuration script will attempt to automatically determine the function name mangling scheme required by the specified F77 compiler, but the following two options may be used to override the default behavior.
--with-f77underscore=ARG
This option pertains to the fkinsol, fcvode and fnvector F/C interface modules and is used to specify the number of underscores to append to function names so F77 routines can properly link with the associated sundials libraries. Valid values for ARG are: none, one, and two.
Default: ARG=one
--with-f77case=ARG
Use this option to specify whether the external names of the fkinsol, fcvode and fnvector F/C interface functions should be lowercase or uppercase so F77 routines can properly link with the associated sundials libraries. Valid values for ARG are: lower and upper.
Default: ARG=lower
Options for MPI support
The following configuration options are only applicable to the parallel sundials packages:
--disable-mpi
Using this option will completely disable MPI support.
--with-mpicc=ARG
--with-mpif77=ARG
By default, the configuration utility script will use the MPI compiler scripts named mpicc and mpif77 to compile the parallelized sundials subroutines; however, for reasons of compatibility, different executable names may be specified via the above options. Also, ARG=no can be used to disable the use of MPI compiler scripts, thus causing the serial C and F compilers to be used to compile the parallelized sundials functions and examples.
--with-mpi-root=MPIDIR
This option may be used to specify which MPI implementation should be used. The sundials configuration script will automatically check under the subdirectories MPIDIR/include and MPIDIR/lib for the necessary header files and libraries. The subdirectory MPIDIR/bin will also be searched for the C and F MPI compiler scripts, unless the user uses —with-mpicc=no or —with-mpif77=no.
--with-mpi-incdir=INCDIR
--with-mpi-libdir=LIBDIR
--with-mpi-libs=LIBS
These options may be used if the user would prefer not to use a preexisting MPI compiler script, but instead would rather use a serial complier and provide the flags necessary to compile the MPI-aware subroutines in sundials.
Often an MPI implementation will have unique library names and so it may be necessary to specify the appropriate libraries to use (e.g., LIBS=-lmpich).
Default: INCDIR=MPIDIR/include, LIBDIR=MPIDIR/lib and LIBS=-lmpi
--with-mpi-flags=ARG
Specify additional MPI-specific flags.
Options for library support
By default, only static libraries are built, but the following option may be used to build shared libraries on supported platforms.
--enable-shared
Using this particular option will result in both static and shared versions of the available sundials libraries being built if the systsupports shared libraries. To build only shared libraries also specify —disable-static.
Note: The fcvode and fkinsol libraries can only be built as static libraries because they contain references to externally defined symbols, namely user-supplied F77 subroutines. Although the F77 interfaces to the serial and parallel implementations of the supplied nvector module do not contain any unresolvable external symbols, the libraries are still built as static libraries for the purpose of consistency.
Options for Matlab support
The following options are relevant only for configuring and building the sundialsTB Matlab toolbox:
--enable-sundialsTB
The sundialsTB Matlab toolbox is not built by default. Use this option to enable configuration and compilation of the mex files. Upon completion of the make command, the following mex files will be created:
builddir/sundialsTB/cvodes/cvm/cvm.'mexext'
builddir/sundialsTB/idas/idm/idm.'mexext'
builddir/sundialsTB/kinsol/kim/kim.'mexext'
where 'mexext' is the platform-specific extension of mex files.
--with-sundialsTB-instdir=STBINSTDIR
Alternate location for the installed sundialsTB toolbox (valid only if sundialsTB is enabled). As for the example programs, installation of sundialsTB can be completely disabled by issuing STBINSTDIR=no (in case building the toolbox is desired but its installtion will be done manually afterwards). Otherwise, all required sundialsTB files will be installed under the directory STBINSTDIR/sundialsTB.
Default: DIR=MATLAB/toolbox (see below for the definition of MATLAB).
--with-matlab=MATLAB
This option can be used to specify the locatin of the Matlab installation. If it is defined, the environment variable MATLAB will be used. Otherwise, the configure system will attempt to infer MATLAB from the location of the matlab executable.
--with-mex=ARG
Specify the mex compiler to be used.
Default: ARG=MATLAB/bin/mex
--with-mexopts=ARG
Specify the mex options file to be used.
Default: Standard Matlab mex options file.
Environment variables
The following environment variables can be locally (re)defined for use during the configuration of sundials. See the next section for illustrations of these.
CC
F77
Since the configuration script uses the first C and F77 compilers found in the current executable search path, then each relevant shell variable (CC and F77) must be locally (re)defined in order to use a different compiler. For example, to use xcc (executable name of chosen compiler) as the C language compiler, use CC=xcc in the configure step.
CFLAGS
FFLAGS
Use these environment variables to override the default C and F77 compilation flags.
Configuration examples
The following examples are meant to help demonstrate proper usage of the configure options.
To build SUNDIALS using the default C and Fortran compilers, and default mpicc and mpif77 parallel compilers, enable compilation of examples, build the Matlab mex files for sundialsTB, and install it under /home/myname/matlab/sundialsTB, use
% ./configure --prefix=/home/myname/sundials --enable-examples --enable-sundialsTB --with-sundialsTB-instdir=/home/myname/matlab
To disable installation of the examples, use:
% ./configure --prefix=/home/myname/sundials --enable-examples --with-examples-instdir=no --enable-sundialsTB --with-sundialsTB-instdir=/home/myname/matlab
The following example builds SUNDIALS using gcc as the serial C compiler, g77 as the serial Fortran compiler, mpicc as the parallel C compiler, mpif77 as the parallel Fortran compiler, and appends the -g3 compilaton flag to the list of default flags:
% ./configure CC=gcc F77=g77 --with-cflags=-g3 --with-fflags=-g3 --with-mpicc=/usr/apps/mpich/1.2.4/bin/mpicc --with-mpif77=/usr/apps/mpich/1.2.4/bin/mpif77
The next example again builds SUNDIALS using gcc as the serial C compiler, but the —with-mpicc=no option explicitly disables the use of the corresponding MPI compiler script. In addition, since the —with-mpi-root option is given, the compilation flags-I/usr/apps/mpich/1.2.4/include and -L/usr/apps/mpich/1.2.4/lib are passed to gcc when compiling the MPI-enabled functions. The —disable-examples option explicitly disables the examples (which means a Fortran compiler is not required).The —with-mpi-libs option is required so that the configure script can check if gcc can link with the appropriate MPI library.
% ./configure CC=gcc --disable-examples --with-mpicc=no --with-mpi-root=/usr/apps/mpich/1.2.4 --with-mpi-libs=-lmpich
