diff --git a/docs/amg4psblas_1.0-guide.pdf b/docs/amg4psblas_1.0-guide.pdf index 8f080f2d..5d03290e 100644 Binary files a/docs/amg4psblas_1.0-guide.pdf and b/docs/amg4psblas_1.0-guide.pdf differ diff --git a/docs/html/index.html b/docs/html/index.html index a3759721..df4ed87f 100644 --- a/docs/html/index.html +++ b/docs/html/index.html @@ -10,7 +10,7 @@ -

MLD2P4
User’s and Reference Guide
Configuration options
 3.4 Bug reporting
 3.5 Example and test programs
4 Getting Started
 4.1 Examples
5 User Interface
 5.1 Method init
 5.2 Method set
 5.3 Method hierarchy_build
 5.4 Method smoothers_build
 5.5 Method build
 5.6 Method apply
 5.7 Method free
 5.8 Method descr
 5.9 Auxiliary Methods
6 Adding new smoother and solver objects to AMG4PSBLAS
7 Error Handling
A License
References
References diff --git a/docs/html/userhtml.css b/docs/html/userhtml.css index fdf3d5da..3d2eaa23 100644 --- a/docs/html/userhtml.css +++ b/docs/html/userhtml.css @@ -158,6 +158,10 @@ div.abstract {width:100%;} .shadowbox { padding-left:3pt; padding-right:3pt; border:solid thin; border-right:solid thick; border-bottom:solid thick; } .doublebox { padding-left:3pt; padding-right:3pt; border-style:double; border:solid thick; } .figure img.graphics {margin-left:10%;} +.lstlisting .label{margin-right:0.5em; } +div.lstlisting{font-family: monospace; white-space: nowrap; margin-top:0.5em; margin-bottom:0.5em; } +div.lstinputlisting{ font-family: monospace; white-space: nowrap; } +.lstinputlisting .label{margin-right:0.5em;} #TBL-1 colgroup{border-left: 1px solid black;border-right:1px solid black;} #TBL-1{border-collapse:collapse;} #TBL-1 colgroup{border-left: 1px solid black;border-right:1px solid black;} diff --git a/docs/html/userhtml.html b/docs/html/userhtml.html index a3759721..df4ed87f 100644 --- a/docs/html/userhtml.html +++ b/docs/html/userhtml.html @@ -10,7 +10,7 @@ -

MLD2P4
User’s and Reference Guide
Configuration options
 3.4 Bug reporting
 3.5 Example and test programs
4 Getting Started
 4.1 Examples
5 User Interface
 5.1 Method init
 5.2 Method set
 5.3 Method hierarchy_build
 5.4 Method smoothers_build
 5.5 Method build
 5.6 Method apply
 5.7 Method free
 5.8 Method descr
 5.9 Auxiliary Methods
6 Adding new smoother and solver objects to AMG4PSBLAS
7 Error Handling
A License
References
References diff --git a/docs/html/userhtmlli1.html b/docs/html/userhtmlli1.html index 496115dd..b44e69b5 100644 --- a/docs/html/userhtmlli1.html +++ b/docs/html/userhtmlli1.html @@ -147,7 +147,7 @@ class="cmr-12">of AMG4PSBLAS. -

[next] [up]

-

diff --git a/docs/html/userhtmlli2.html b/docs/html/userhtmlli2.html index b1aeb7fc..93ef6c4a 100644 --- a/docs/html/userhtmlli2.html +++ b/docs/html/userhtmlli2.html @@ -10,7 +10,7 @@ -

[nextAuxiliary Methods class="cmr-12">  5.9.1 Method: dump
  5.9.2 Method: clone
  5.9.3 Method: sizeof
  5.9.4 Method: allocate_wrk
  5.9.5 Method: free_wrk
A License
References

diff --git a/docs/html/userhtmlli4.html b/docs/html/userhtmlli4.html index 6bf52822..d7cdab6a 100644 --- a/docs/html/userhtmlli4.html +++ b/docs/html/userhtmlli4.html @@ -29,7 +29,7 @@ class="cmr-12">]

class="cmr-12">References

+ id="Q1-28-47">

Transactions on Mathematical Software, 44, (2018) 39:1–39:2 -

[prev] [up]

-

diff --git a/docs/html/userhtmlse6.html b/docs/html/userhtmlse6.html index 8c7895e9..a88178d2 100644 --- a/docs/html/userhtmlse6.html +++ b/docs/html/userhtmlse6.html @@ -181,7 +181,7 @@ class="cmr-12">pass it as follows: -

+
 
  ! sparse matrix and preconditioner  
  type(psb_dspmat_type) :: a  
  type(amg_dprec_type)  :: prec diff --git a/docs/html/userhtmlse7.html b/docs/html/userhtmlse7.html index 77eed75f..491f49f0 100644 --- a/docs/html/userhtmlse7.html +++ b/docs/html/userhtmlse7.html @@ -61,10 +61,6 @@ class="cmr-12">. -

- - - diff --git a/docs/html/userhtmlse8.html b/docs/html/userhtmlse8.html index 5c7dcbe7..b7756c21 100644 --- a/docs/html/userhtmlse8.html +++ b/docs/html/userhtmlse8.html @@ -36,7 +36,7 @@ class="cmr-12">AMG4PSBLAS is freely distributable under the following copyright -

+
 
                           AMG4PSBLAS  version 1.0  
              Algebraic MultiGrid Preconditioners Package  
             based on PSBLAS (Parallel Sparse BLAS version 3.7) @@ -83,7 +83,7 @@ class="cmr-12">abide by its terms: -
+
 
 
                           MLD2P4  version 2.2  
  MultiLevel Domain Decomposition Parallel Preconditioners Package @@ -128,7 +128,7 @@ class="cmr-12">abide by its terms: -

+

diff --git a/docs/html/userhtmlsu1.html b/docs/html/userhtmlsu1.html index fc240f7b..945fed8d 100644 --- a/docs/html/userhtmlsu1.html +++ b/docs/html/userhtmlsu1.html @@ -52,7 +52,7 @@ class="cmr-12">vendor version is available for a given platform, the AT (math-atlas.sourceforge.netmath-atlas.sourceforge .net) may be employed. The reference BLAS from Netlib (] Parallel Sparse BLAS (PSBLAS) is available from psctoolkit.github.io/products/psblas/psctoolkit.github.io/ products/psblas/; version 3.7.0 (or later) is required. Indeed, all the prerequisites listed so far are also prerequisites of PSBLAS. diff --git a/docs/html/userhtmlsu3.html b/docs/html/userhtmlsu3.html index ce2d0f5c..bce51a14 100644 --- a/docs/html/userhtmlsu3.html +++ b/docs/html/userhtmlsu3.html @@ -61,213 +61,4207 @@ class="cmtt-12">./configure --help, which produces: - - - -

-‘configure’ configures MLD2P4 2.1.1 to adapt to many kinds of systems. - 
- 
Usage: ./configure [OPTION]... [VAR=VALUE]... - 
- 
To assign environment variables (e.g., CC, CFLAGS...), specify them as - 
VAR=VALUE.  See below for descriptions of some of the useful variables. - 
- 
Defaults for the options are specified in brackets. - 
- 
Configuration: - 
  -h, --help              display this help and exit - 
      --help=short        display options specific to this package - 
      --help=recursive    display the short help of all the included packages - 
  -V, --version           display version information and exit - 
  -q, --quiet, --silent   do not print ‘checking ...’ messages - 
      --cache-file=FILE   cache test results in FILE [disabled] - 
  -C, --config-cache      alias for ‘--cache-file=config.cache’ - 
  -n, --no-create         do not create output files - 
      --srcdir=DIR        find the sources in DIR [configure dir or ‘..’] - 
- 
Installation directories: - 
  --prefix=PREFIX         install architecture-independent files in PREFIX - 
                          [/usr/local] - 
  --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX - 
                          [PREFIX] - 
- 
By default, ‘make install’ will install all the files in - 
‘/usr/local/bin’, ‘/usr/local/lib’ etc.  You can specify - 
an installation prefix other than ‘/usr/local’ using ‘--prefix’, - 
for instance ‘--prefix=$HOME’. - 
- 
For better control, use the options below. - 
- 
Fine tuning of the installation directories: - 
  --bindir=DIR            user executables [EPREFIX/bin] - 
  --sbindir=DIR           system admin executables [EPREFIX/sbin] - 
  --libexecdir=DIR        program executables [EPREFIX/libexec] - 
  --sysconfdir=DIR        read-only single-machine data [PREFIX/etc] - 
  --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com] - - - - 
  --localstatedir=DIR     modifiable single-machine data [PREFIX/var] - 
  --libdir=DIR            object code libraries [EPREFIX/lib] - 
  --includedir=DIR        C header files [PREFIX/include] - 
  --oldincludedir=DIR     C header files for non-gcc [/usr/include] - 
  --datarootdir=DIR       read-only arch.-independent data root [PREFIX/share] - 
  --datadir=DIR           read-only architecture-independent data [DATAROOTDIR] - 
  --infodir=DIR           info documentation [DATAROOTDIR/info] - 
  --localedir=DIR         locale-dependent data [DATAROOTDIR/locale] - 
  --mandir=DIR            man documentation [DATAROOTDIR/man] - 
  --docdir=DIR            documentation root [DATAROOTDIR/doc/mld2p4] - 
  --htmldir=DIR           html documentation [DOCDIR] - 
  --dvidir=DIR            dvi documentation [DOCDIR] - 
  --pdfdir=DIR            pdf documentation [DOCDIR] - 
  --psdir=DIR             ps documentation [DOCDIR] - 
- 
Program names: - 
  --program-prefix=PREFIX            prepend PREFIX to installed program names - 
  --program-suffix=SUFFIX            append SUFFIX to installed program names - 
  --program-transform-name=PROGRAM   run sed PROGRAM on installed program names - 
- 
Optional Features: - 
  --disable-option-checking  ignore unrecognized --enable/--with options - 
  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no) - 
  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes] - 
  --enable-silent-rules   less verbose build output (undo: "make V=1") - 
  --disable-silent-rules  verbose build output (undo: "make V=0") - 
  --enable-dependency-tracking - 
                          do not reject slow dependency extractors - 
  --disable-dependency-tracking - 
                          speeds up one-time build - 
  --enable-serial         Specify whether to enable a fake mpi library to run - 
                          in serial mode. - 
  --enable-long-integers  Specify usage of 64 bits integers. - 
- 
Optional Packages: - 
  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes] - 
  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no) - 
  --with-psblas=DIR       The install directory for PSBLAS, for example, - 
                          --with-psblas=/opt/packages/psblas-3.5 - 
  --with-psblas-incdir=DIR - 
                          Specify the directory for PSBLAS C includes. - 
  --with-psblas-moddir=DIR - - - - 
                          Specify the directory for PSBLAS Fortran modules. - 
  --with-psblas-libdir=DIR - 
                          Specify the directory for PSBLAS library. - 
  --with-ccopt            additional [CCOPT] flags to be added: will prepend - 
                          to [CCOPT] - 
  --with-fcopt            additional [FCOPT] flags to be added: will prepend - 
                          to [FCOPT] - 
  --with-libs             List additional link flags here. For example, - 
                          --with-libs=-lspecial_system_lib or - 
                          --with-libs=-L/path/to/libs - 
  --with-clibs            additional [CLIBS] flags to be added: will prepend - 
                          to [CLIBS] - 
  --with-flibs            additional [FLIBS] flags to be added: will prepend - 
                          to [FLIBS] - 
  --with-library-path     additional [LIBRARYPATH] flags to be added: will - 
                          prepend to [LIBRARYPATH] - 
  --with-include-path     additional [INCLUDEPATH] flags to be added: will - 
                          prepend to [INCLUDEPATH] - 
  --with-module-path      additional [MODULE_PATH] flags to be added: will - 
                          prepend to [MODULE_PATH] - 
  --with-extra-libs       List additional link flags here. For example, - 
                          --with-extra-libs=-lspecial_system_lib or - 
                          --with-extra-libs=-L/path/to/libs - 
  --with-blas=<lib>       use BLAS library <lib> - 
  --with-blasdir=<dir>    search for BLAS library in <dir> - 
  --with-lapack=<lib>     use LAPACK library <lib> - 
  --with-mumps=LIBNAME    Specify the libname for MUMPS. Default: autodetect - 
                          with minimum "-lmumps_common -lpord" - 
  --with-mumpsdir=DIR     Specify the directory for MUMPS library and - 
                          includes. Note: you will need to add auxiliary - 
                          libraries with --extra-libs; this depends on how - 
                          MUMPS was configured and installed, at a minimum you - 
                          will need SCALAPACK and BLAS - 
  --with-mumpsincdir=DIR  Specify the directory for MUMPS includes. - 
  --with-mumpsmoddir=DIR  Specify the directory for MUMPS Fortran modules. - 
  --with-mumpslibdir=DIR  Specify the directory for MUMPS library. - 
  --with-umfpack=LIBNAME  Specify the library name for UMFPACK and its support - 
                          libraries. Default: "-lumfpack -lamd" - 
  --with-umfpackdir=DIR   Specify the directory for UMFPACK library and - 
                          includes. - 
  --with-umfpackincdir=DIR - 
                          Specify the directory for UMFPACK includes. - - - - 
  --with-umfpacklibdir=DIR - 
                          Specify the directory for UMFPACK library. - 
  --with-superlu=LIBNAME  Specify the library name for SUPERLU library. - 
                          Default: "-lsuperlu" - 
  --with-superludir=DIR   Specify the directory for SUPERLU library and - 
                          includes. - 
  --with-superluincdir=DIR - 
                          Specify the directory for SUPERLU includes. - 
  --with-superlulibdir=DIR - 
                          Specify the directory for SUPERLU library. - 
  --with-superludist=LIBNAME - 
                          Specify the libname for SUPERLUDIST library. - 
                          Requires you also specify SuperLU. Default: - 
                          "-lsuperlu_dist" - 
  --with-superludistdir=DIR - 
                          Specify the directory for SUPERLUDIST library and - 
                          includes. - 
  --with-superludistincdir=DIR - 
                          Specify the directory for SUPERLUDIST includes. - 
  --with-superludistlibdir=DIR - 
                          Specify the directory for SUPERLUDIST library. - 
- 
Some influential environment variables: - 
  FC          Fortran compiler command - 
  FCFLAGS     Fortran compiler flags - 
  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a - 
              nonstandard directory <lib dir> - 
  LIBS        libraries to pass to the linker, e.g. -l<library> - 
  CC          C compiler command - 
  CFLAGS      C compiler flags - 
  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if - 
              you have headers in a nonstandard directory <include dir> - 
  MPICC       MPI C compiler command - 
  MPIFC       MPI Fortran compiler command - 
  CPP         C preprocessor - 
- 
Use these variables to override the choices made by ‘configure’ or to help - 
it to find libraries and programs with nonstandard names/locations. - 
- 
Report bugs to <https://github.com/sfilippone/mld2p4-2/issues>. -
-

-

produces:

+ +  
‘configure’ configures AMG4PSBLAS 1.0.0 to adapt to many kinds of systems. 
 
Usage: ./configure [OPTION]... [VAR=VALUE]... 
 
To assign environment variables (e.g., CC, CFLAGS...), specify them as 
VAR=VALUE.  See below for descriptions of some of the useful variables. 
 
Defaults for the options are specified in brackets. 
 
Configuration: 
  -h, --help              display this help and exit 
      --help=short        display options specific to this package 
      --help=recursive    display the short help of all the included packages 
  -V, --version           display version information and exit 
  -q, --quiet, --silent   do not print ‘checking ...’ messages 
      --cache-file=FILE   cache test results in FILE [disabled] 
  -C, --config-cache      alias for ‘--cache-file=config.cache’ 
  -n, --no-create         do not create output files 
      --srcdir=DIR        find the sources in DIR [configure dir or ‘..’] 
 
Installation directories: 
  --prefix=PREFIX         install architecture-independent files in PREFIX 
                          [/usr/local] 
  --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX 
                          [PREFIX] 
 
By default, ‘make install’ will install all the files in 
‘/usr/local/bin’, ‘/usr/local/lib’ etc.  You can specify 
an installation prefix other than ‘/usr/local’ using ‘--prefix’, 
for instance ‘--prefix=$HOME’. 
 
For better control, use the options below. 
 
Fine tuning of the installation directories: 
  --bindir=DIR            user executables [EPREFIX/bin] 
  --sbindir=DIR           system admin executables [EPREFIX/sbin] 
  --libexecdir=DIR        program executables [EPREFIX/libexec] 
  --sysconfdir=DIR        read-only single-machine data [PREFIX/etc] 
  --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com] 
  --localstatedir=DIR     modifiable single-machine data [PREFIX/var] 
  --libdir=DIR            object code libraries [EPREFIX/lib] 
  --includedir=DIR        C header files [PREFIX/include] 
  --oldincludedir=DIR     C header files for non-gcc [/usr/include] 
  --datarootdir=DIR       read-only arch.-independent data root [PREFIX/share] 
  --datadir=DIR           read-only architecture-independent data [DATAROOTDIR] 
  --infodir=DIR           info documentation [DATAROOTDIR/info] 
  --localedir=DIR         locale-dependent data [DATAROOTDIR/locale] 
  --mandir=DIR            man documentation [DATAROOTDIR/man] 
  --docdir=DIR            documentation root [DATAROOTDIR/doc/amg4psblas] 
  --htmldir=DIR           html documentation [DOCDIR] 
  --dvidir=DIR            dvi documentation [DOCDIR] 
  --pdfdir=DIR            pdf documentation [DOCDIR] 
  --psdir=DIR             ps documentation [DOCDIR] 
 
Program names: 
  --program-prefix=PREFIX            prepend PREFIX to installed program names 
  --program-suffix=SUFFIX            append SUFFIX to installed program names 
  --program-transform-name=PROGRAM   run sed PROGRAM on installed program names 
 
Optional Features: 
  --disable-option-checking  ignore unrecognized --enable/--with options 
  --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no) 
  --enable-FEATURE[=ARG]  include FEATURE [ARG=yes] 
  --enable-silent-rules   less verbose build output (undo: "make V=1") 
  --disable-silent-rules  verbose build output (undo: "make V=0") 
  --enable-dependency-tracking 
                          do not reject slow dependency extractors 
  --disable-dependency-tracking 
                          speeds up one-time build 
  --enable-serial         Specify whether to enable a fake mpi library to run 
                          in serial mode. 
 
Optional Packages: 
  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes] 
  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no) 
  --with-psblas=DIR       The install directory for PSBLAS, for example, 
                          --with-psblas=/opt/packages/psblas-3.5 
  --with-psblas-incdir=DIR 
                          Specify the directory for PSBLAS C includes. 
  --with-psblas-moddir=DIR 
                          Specify the directory for PSBLAS Fortran modules. 
  --with-psblas-libdir=DIR 
                          Specify the directory for PSBLAS library. 
  --with-ccopt            additional [CCOPT] flags to be added: will prepend 
                          to [CCOPT] 
  --with-fcopt            additional [FCOPT] flags to be added: will prepend 
                          to [FCOPT] 
  --with-libs             List additional link flags here. For example, 
                          --with-libs=-lspecial_system_lib or 
                          --with-libs=-L/path/to/libs 
  --with-clibs            additional [CLIBS] flags to be added: will prepend 
                          to [CLIBS] 
  --with-flibs            additional [FLIBS] flags to be added: will prepend 
                          to [FLIBS] 
  --with-library-path     additional [LIBRARYPATH] flags to be added: will 
                          prepend to [LIBRARYPATH] 
  --with-include-path     additional [INCLUDEPATH] flags to be added: will 
                          prepend to [INCLUDEPATH] 
  --with-module-path      additional [MODULE_PATH] flags to be added: will 
                          prepend to [MODULE_PATH] 
  --with-extra-libs       List additional link flags here. For example, 
                          --with-extra-libs=-lspecial_system_lib or 
                          --with-extra-libs=-L/path/to/libs 
  --with-blas=<lib>       use BLAS library <lib> 
  --with-blasdir=<dir>    search for BLAS library in <dir> 
  --with-lapack=<lib>     use LAPACK library <lib> 
  --with-mumps=LIBNAME    Specify the libname for MUMPS. Default: autodetect 
                          with minimum "-lmumps_common -lpord" 
  --with-mumpsdir=DIR     Specify the directory for MUMPS library and 
                          includes. Note: you will need to add auxiliary 
                          libraries with --extra-libs; this depends on how 
                          MUMPS was configured and installed, at a minimum you 
                          will need SCALAPACK and BLAS 
  --with-mumpsincdir=DIR  Specify the directory for MUMPS includes. 
  --with-mumpsmoddir=DIR  Specify the directory for MUMPS Fortran modules. 
  --with-mumpslibdir=DIR  Specify the directory for MUMPS library. 
  --with-umfpack=LIBNAME  Specify the library name for UMFPACK and its support 
                          libraries. Default: "-lumfpack -lamd" 
  --with-umfpackdir=DIR   Specify the directory for UMFPACK library and 
                          includes. 
  --with-umfpackincdir=DIR 
                          Specify the directory for UMFPACK includes. 
  --with-umfpacklibdir=DIR 
                          Specify the directory for UMFPACK library. 
  --with-superlu=LIBNAME  Specify the library name for SUPERLU library. 
                          Default: "-lsuperlu" 
  --with-superludir=DIR   Specify the directory for SUPERLU library and 
                          includes. 
  --with-superluincdir=DIR 
                          Specify the directory for SUPERLU includes. 
  --with-superlulibdir=DIR 
                          Specify the directory for SUPERLU library. 
  --with-superludist=LIBNAME 
                          Specify the libname for SUPERLUDIST library. 
                          Requires you also specify SuperLU. Default: 
                          "-lsuperlu_dist" 
  --with-superludistdir=DIR 
                          Specify the directory for SUPERLUDIST library and 
                          includes. 
  --with-superludistincdir=DIR 
                          Specify the directory for SUPERLUDIST includes. 
  --with-superludistlibdir=DIR 
                          Specify the directory for SUPERLUDIST library. 
 
Some influential environment variables: 
  FC          Fortran compiler command 
  FCFLAGS     Fortran compiler flags 
  LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a 
              nonstandard directory <lib dir> 
  LIBS        libraries to pass to the linker, e.g. -l<library> 
  CC          C compiler command 
  CFLAGS      C compiler flags 
  CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if 
              you have headers in a nonstandard directory <include dir> 
  MPICC       MPI C compiler command 
  MPIFC       MPI Fortran compiler command 
  CPP         C preprocessor 
 
Use these variables to override the choices made by ‘configure’ or to help 
it to find libraries and programs with nonstandard names/locations. 
 
Report bugs to <https://github.com/sfilippone/amg4psblas/issues>. + +
+

For instance, if a user has built and installed PSBLAS 3.7 under the /opt directory - - - +class="cmr-12">directory and is and is using the SuiteSparse package (which includes UMFPACK), then MLD2P4 +class="cmr-12">using the SuiteSparse package (which includes UMFPACK), then AMG4PSBLAS might be configured with: -

- ./configure --with-psblas=/opt/psblas-3.5/ \ - 
 --with-umfpackincdir=/usr/include/suitesparse/ +
+./configure --with-psblas=/opt/psblas-3.5/ \ + 
--with-umfpackincdir=/usr/include/suitesparse/
-

Once the configure script has completed execution, it will have generated the file Make.inc which will then be used by all Makefiles in the directory tree; this file will be copied in the install directory under the name Make.inc.MLD2P4Make.inc.AMG4PSBLAS. -

To use the MUMPS solver package, the user has to add the appropriate options to the configure script; by default we are looking for the libraries --with-extra-libs configure option. -

To build the library the user will now enter -

+
make
-

followed (optionally) by -

+
make install
-

+

-

[next] [up]

-

diff --git a/docs/html/userhtmlsu4.html b/docs/html/userhtmlsu4.html index c0f4b70c..b34a7972 100644 --- a/docs/html/userhtmlsu4.html +++ b/docs/html/userhtmlsu4.html @@ -10,7 +10,7 @@ -

[next]

class="cmr-12">3.4 Bug reporting -

If you find any bugs in our codes, please report them through our issues page on
https://github.com/psctoolkit/amg4psblas/issues
-

To enable us to track the bug, please provide a log from the failing application, the test conditions, and ideally a self-contained test program reproducing the @@ -48,7 +48,7 @@ class="cmr-12">issue. -

[next] [up]

-

diff --git a/docs/html/userhtmlsu5.html b/docs/html/userhtmlsu5.html index 22d1d8fe..9b5368d4 100644 --- a/docs/html/userhtmlsu5.html +++ b/docs/html/userhtmlsu5.html @@ -10,7 +10,7 @@ -

[prev]

class="cmr-12">3.5 Example and test programs -

The package contains the examples and runs subdirectories, to experiment with the full range of preconditioners implemented in the package. -

The fileread directories contain sample programs that read sparse matrices from files, diff --git a/docs/html/userhtmlsu6.html b/docs/html/userhtmlsu6.html index 0a40a378..d5983a0c 100644 --- a/docs/html/userhtmlsu6.html +++ b/docs/html/userhtmlsu6.html @@ -124,7 +124,7 @@ class="cmr-12">. -

+
  use psb_base_mod  
  use amg_prec_mod  
  use psb_krylov_mod @@ -279,7 +279,7 @@ class="cmr-12">.

-

+
... ...  
! build a V-cycle preconditioner with 1 block-Jacobi sweep (with  
! ILU(0) on the blocks) as pre- and post-smoother, and 8  block-Jacobi @@ -314,7 +314,7 @@ class="content">setup of a multilevel preconditioner based on the default decoup

-

+
... ...  
! build a W-cycle preconditioner with 2 hybrid Gauss-Seidel sweeps  
! as pre- and post-smoother, a distributed coarsest @@ -353,7 +353,7 @@ on weighted matching

-

+
... ...  
! set RAS with overlap 2 and ILU(0) on the local blocks  
  call P%init(’AS’,info) diff --git a/docs/src/Makefile b/docs/src/Makefile index e8c6c51d..c6d3ca19 100644 --- a/docs/src/Makefile +++ b/docs/src/Makefile @@ -112,10 +112,10 @@ DATE = $(shell date +%Y-%m-%d) ## ## Programs # -LATEX = latex -LTX2HTML = latex2html -local_icons -LTX2HTML = htlatex -PDFLATEX = pdflatex +LATEX = latex -shell-escape +LTX2HTML = latex2html -local_icons +LTX2HTML = htlatex +PDFLATEX = pdflatex -shell-escape ACRO = evince XPDF = xpdf WC = wc @@ -213,10 +213,10 @@ ps: $(PS) clean: rm -f $(PDF) $(PS) - cd tmp ; rm -f * + cd tmp ; rm -r -f * clean-tmp: - cd tmp ; rm -f * + cd tmp ; rm -r -f * #---------------------------------------------------------------------------- diff --git a/docs/src/building.tex b/docs/src/building.tex index c770cadc..cb87cbe7 100644 --- a/docs/src/building.tex +++ b/docs/src/building.tex @@ -32,7 +32,7 @@ The following base libraries are needed: \item[BLAS] \cite{blas3,blas2,blas1} Many vendors provide optimized versions of BLAS; if no vendor version is available for a given platform, the ATLAS software - (\href{http://math-atlas.sourceforge.net}{math-atlas.sourceforge.net}) + (\href{http://math-atlas.sourceforge.net}{math-atlas.sourceforge .net}) may be employed. The reference BLAS from Netlib (\href{http://www.netlib.org/blas}{www.netlib.org/blas}) are meant to define the standard behaviour of the BLAS interface, so they are not optimized for any @@ -49,7 +49,7 @@ in the make.inc file of the LAPACK library. \item[MPI] \cite{MPI2,MPI1} A version of MPI is available on most high-performance computing systems. \item[PSBLAS] \cite{PSBLASGUIDE,psblas_00} Parallel Sparse BLAS (PSBLAS) is - available from \href{https://psctoolkit.github.io/products/psblas/}{psctoolkit.github.io/products/psblas/}; version + available from \href{https://psctoolkit.github.io/products/psblas/}{psctoolkit.github.io/ products/psblas/}; version 3.7.0 (or later) is required. Indeed, all the prerequisites listed so far are also prerequisites of PSBLAS. \end{description} @@ -114,184 +114,29 @@ only the PSBLAS install directory (note that the latter directory must be specified with an {\em absolute} path). The full set of options may be looked at by issuing the command \verb|./configure --help|, which produces: -\begin{verbatim} -`configure' configures MLD2P4 2.1.1 to adapt to many kinds of systems. - -Usage: ./configure [OPTION]... [VAR=VALUE]... - -To assign environment variables (e.g., CC, CFLAGS...), specify them as -VAR=VALUE. See below for descriptions of some of the useful variables. - -Defaults for the options are specified in brackets. - -Configuration: - -h, --help display this help and exit - --help=short display options specific to this package - --help=recursive display the short help of all the included packages - -V, --version display version information and exit - -q, --quiet, --silent do not print `checking ...' messages - --cache-file=FILE cache test results in FILE [disabled] - -C, --config-cache alias for `--cache-file=config.cache' - -n, --no-create do not create output files - --srcdir=DIR find the sources in DIR [configure dir or `..'] - -Installation directories: - --prefix=PREFIX install architecture-independent files in PREFIX - [/usr/local] - --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX - [PREFIX] - -By default, `make install' will install all the files in -`/usr/local/bin', `/usr/local/lib' etc. You can specify -an installation prefix other than `/usr/local' using `--prefix', -for instance `--prefix=$HOME'. - -For better control, use the options below. - -Fine tuning of the installation directories: - --bindir=DIR user executables [EPREFIX/bin] - --sbindir=DIR system admin executables [EPREFIX/sbin] - --libexecdir=DIR program executables [EPREFIX/libexec] - --sysconfdir=DIR read-only single-machine data [PREFIX/etc] - --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] - --localstatedir=DIR modifiable single-machine data [PREFIX/var] - --libdir=DIR object code libraries [EPREFIX/lib] - --includedir=DIR C header files [PREFIX/include] - --oldincludedir=DIR C header files for non-gcc [/usr/include] - --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] - --datadir=DIR read-only architecture-independent data [DATAROOTDIR] - --infodir=DIR info documentation [DATAROOTDIR/info] - --localedir=DIR locale-dependent data [DATAROOTDIR/locale] - --mandir=DIR man documentation [DATAROOTDIR/man] - --docdir=DIR documentation root [DATAROOTDIR/doc/mld2p4] - --htmldir=DIR html documentation [DOCDIR] - --dvidir=DIR dvi documentation [DOCDIR] - --pdfdir=DIR pdf documentation [DOCDIR] - --psdir=DIR ps documentation [DOCDIR] - -Program names: - --program-prefix=PREFIX prepend PREFIX to installed program names - --program-suffix=SUFFIX append SUFFIX to installed program names - --program-transform-name=PROGRAM run sed PROGRAM on installed program names - -Optional Features: - --disable-option-checking ignore unrecognized --enable/--with options - --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) - --enable-FEATURE[=ARG] include FEATURE [ARG=yes] - --enable-silent-rules less verbose build output (undo: "make V=1") - --disable-silent-rules verbose build output (undo: "make V=0") - --enable-dependency-tracking - do not reject slow dependency extractors - --disable-dependency-tracking - speeds up one-time build - --enable-serial Specify whether to enable a fake mpi library to run - in serial mode. - --enable-long-integers Specify usage of 64 bits integers. - -Optional Packages: - --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] - --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) - --with-psblas=DIR The install directory for PSBLAS, for example, - --with-psblas=/opt/packages/psblas-3.5 - --with-psblas-incdir=DIR - Specify the directory for PSBLAS C includes. - --with-psblas-moddir=DIR - Specify the directory for PSBLAS Fortran modules. - --with-psblas-libdir=DIR - Specify the directory for PSBLAS library. - --with-ccopt additional [CCOPT] flags to be added: will prepend - to [CCOPT] - --with-fcopt additional [FCOPT] flags to be added: will prepend - to [FCOPT] - --with-libs List additional link flags here. For example, - --with-libs=-lspecial_system_lib or - --with-libs=-L/path/to/libs - --with-clibs additional [CLIBS] flags to be added: will prepend - to [CLIBS] - --with-flibs additional [FLIBS] flags to be added: will prepend - to [FLIBS] - --with-library-path additional [LIBRARYPATH] flags to be added: will - prepend to [LIBRARYPATH] - --with-include-path additional [INCLUDEPATH] flags to be added: will - prepend to [INCLUDEPATH] - --with-module-path additional [MODULE_PATH] flags to be added: will - prepend to [MODULE_PATH] - --with-extra-libs List additional link flags here. For example, - --with-extra-libs=-lspecial_system_lib or - --with-extra-libs=-L/path/to/libs - --with-blas= use BLAS library - --with-blasdir= search for BLAS library in - --with-lapack= use LAPACK library - --with-mumps=LIBNAME Specify the libname for MUMPS. Default: autodetect - with minimum "-lmumps_common -lpord" - --with-mumpsdir=DIR Specify the directory for MUMPS library and - includes. Note: you will need to add auxiliary - libraries with --extra-libs; this depends on how - MUMPS was configured and installed, at a minimum you - will need SCALAPACK and BLAS - --with-mumpsincdir=DIR Specify the directory for MUMPS includes. - --with-mumpsmoddir=DIR Specify the directory for MUMPS Fortran modules. - --with-mumpslibdir=DIR Specify the directory for MUMPS library. - --with-umfpack=LIBNAME Specify the library name for UMFPACK and its support - libraries. Default: "-lumfpack -lamd" - --with-umfpackdir=DIR Specify the directory for UMFPACK library and - includes. - --with-umfpackincdir=DIR - Specify the directory for UMFPACK includes. - --with-umfpacklibdir=DIR - Specify the directory for UMFPACK library. - --with-superlu=LIBNAME Specify the library name for SUPERLU library. - Default: "-lsuperlu" - --with-superludir=DIR Specify the directory for SUPERLU library and - includes. - --with-superluincdir=DIR - Specify the directory for SUPERLU includes. - --with-superlulibdir=DIR - Specify the directory for SUPERLU library. - --with-superludist=LIBNAME - Specify the libname for SUPERLUDIST library. - Requires you also specify SuperLU. Default: - "-lsuperlu_dist" - --with-superludistdir=DIR - Specify the directory for SUPERLUDIST library and - includes. - --with-superludistincdir=DIR - Specify the directory for SUPERLUDIST includes. - --with-superludistlibdir=DIR - Specify the directory for SUPERLUDIST library. - -Some influential environment variables: - FC Fortran compiler command - FCFLAGS Fortran compiler flags - LDFLAGS linker flags, e.g. -L if you have libraries in a - nonstandard directory - LIBS libraries to pass to the linker, e.g. -l - CC C compiler command - CFLAGS C compiler flags - CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if - you have headers in a nonstandard directory - MPICC MPI C compiler command - MPIFC MPI Fortran compiler command - CPP C preprocessor - -Use these variables to override the choices made by `configure' or to help -it to find libraries and programs with nonstandard names/locations. - -Report bugs to . -\end{verbatim} - +\ifpdf +\inputminted[breaklines=true,bgcolor=bg,fontsize=\small]{console}{../configureout.txt} +\else +\lstinputlisting{../configureout.txt} +\fi For instance, if a user has built and installed PSBLAS 3.7 under the \verb|/opt| directory and is -using the SuiteSparse package (which includes UMFPACK), then MLD2P4 +using the SuiteSparse package (which includes UMFPACK), then AMG4PSBLAS might be configured with: +\ifpdf +\begin{minted}[breaklines=true,bgcolor=bg,fontsize=\small]{console} +./configure --with-psblas=/opt/psblas-3.5/ --with-umfpackincdir=/usr/include/suitesparse/ +\end{minted} +\else \begin{verbatim} - ./configure --with-psblas=/opt/psblas-3.5/ \ - --with-umfpackincdir=/usr/include/suitesparse/ +./configure --with-psblas=/opt/psblas-3.5/ \ +--with-umfpackincdir=/usr/include/suitesparse/ \end{verbatim} +\fi Once the configure script has completed execution, it will have generated the file \verb|Make.inc| which will then be used by all Makefiles in the directory tree; this file will be copied in the -install directory under the name \verb|Make.inc.MLD2P4|. +install directory under the name \verb|Make.inc.AMG4PSBLAS|. To use the MUMPS solver package, the user has to add the appropriate options to the configure script; @@ -302,13 +147,25 @@ SCOTCH, as well as enabling OpenMP; in such cases it is necessary to add linker options with the \verb|--with-extra-libs| configure option. To build the library the user will now enter +\ifpdf +\begin{minted}[breaklines=true,bgcolor=bg,fontsize=\small]{console} +make +\end{minted} +\else \begin{verbatim} make \end{verbatim} +\fi followed (optionally) by +\ifpdf +\begin{minted}[breaklines=true,bgcolor=bg,fontsize=\small]{console} +make install +\end{minted} +\else \begin{verbatim} make install \end{verbatim} +\fi \subsection{Bug reporting} If you find any bugs in our codes, please report them through our issues page on \\[2mm] diff --git a/docs/src/configureout.txt b/docs/src/configureout.txt new file mode 100644 index 00000000..e1ae3914 --- /dev/null +++ b/docs/src/configureout.txt @@ -0,0 +1,162 @@ +`configure' configures AMG4PSBLAS 1.0.0 to adapt to many kinds of systems. + +Usage: ./configure [OPTION]... [VAR=VALUE]... + +To assign environment variables (e.g., CC, CFLAGS...), specify them as +VAR=VALUE. See below for descriptions of some of the useful variables. + +Defaults for the options are specified in brackets. + +Configuration: + -h, --help display this help and exit + --help=short display options specific to this package + --help=recursive display the short help of all the included packages + -V, --version display version information and exit + -q, --quiet, --silent do not print `checking ...' messages + --cache-file=FILE cache test results in FILE [disabled] + -C, --config-cache alias for `--cache-file=config.cache' + -n, --no-create do not create output files + --srcdir=DIR find the sources in DIR [configure dir or `..'] + +Installation directories: + --prefix=PREFIX install architecture-independent files in PREFIX + [/usr/local] + --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX + [PREFIX] + +By default, `make install' will install all the files in +`/usr/local/bin', `/usr/local/lib' etc. You can specify +an installation prefix other than `/usr/local' using `--prefix', +for instance `--prefix=$HOME'. + +For better control, use the options below. + +Fine tuning of the installation directories: + --bindir=DIR user executables [EPREFIX/bin] + --sbindir=DIR system admin executables [EPREFIX/sbin] + --libexecdir=DIR program executables [EPREFIX/libexec] + --sysconfdir=DIR read-only single-machine data [PREFIX/etc] + --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] + --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --libdir=DIR object code libraries [EPREFIX/lib] + --includedir=DIR C header files [PREFIX/include] + --oldincludedir=DIR C header files for non-gcc [/usr/include] + --datarootdir=DIR read-only arch.-independent data root [PREFIX/share] + --datadir=DIR read-only architecture-independent data [DATAROOTDIR] + --infodir=DIR info documentation [DATAROOTDIR/info] + --localedir=DIR locale-dependent data [DATAROOTDIR/locale] + --mandir=DIR man documentation [DATAROOTDIR/man] + --docdir=DIR documentation root [DATAROOTDIR/doc/amg4psblas] + --htmldir=DIR html documentation [DOCDIR] + --dvidir=DIR dvi documentation [DOCDIR] + --pdfdir=DIR pdf documentation [DOCDIR] + --psdir=DIR ps documentation [DOCDIR] + +Program names: + --program-prefix=PREFIX prepend PREFIX to installed program names + --program-suffix=SUFFIX append SUFFIX to installed program names + --program-transform-name=PROGRAM run sed PROGRAM on installed program names + +Optional Features: + --disable-option-checking ignore unrecognized --enable/--with options + --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no) + --enable-FEATURE[=ARG] include FEATURE [ARG=yes] + --enable-silent-rules less verbose build output (undo: "make V=1") + --disable-silent-rules verbose build output (undo: "make V=0") + --enable-dependency-tracking + do not reject slow dependency extractors + --disable-dependency-tracking + speeds up one-time build + --enable-serial Specify whether to enable a fake mpi library to run + in serial mode. + +Optional Packages: + --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] + --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) + --with-psblas=DIR The install directory for PSBLAS, for example, + --with-psblas=/opt/packages/psblas-3.5 + --with-psblas-incdir=DIR + Specify the directory for PSBLAS C includes. + --with-psblas-moddir=DIR + Specify the directory for PSBLAS Fortran modules. + --with-psblas-libdir=DIR + Specify the directory for PSBLAS library. + --with-ccopt additional [CCOPT] flags to be added: will prepend + to [CCOPT] + --with-fcopt additional [FCOPT] flags to be added: will prepend + to [FCOPT] + --with-libs List additional link flags here. For example, + --with-libs=-lspecial_system_lib or + --with-libs=-L/path/to/libs + --with-clibs additional [CLIBS] flags to be added: will prepend + to [CLIBS] + --with-flibs additional [FLIBS] flags to be added: will prepend + to [FLIBS] + --with-library-path additional [LIBRARYPATH] flags to be added: will + prepend to [LIBRARYPATH] + --with-include-path additional [INCLUDEPATH] flags to be added: will + prepend to [INCLUDEPATH] + --with-module-path additional [MODULE_PATH] flags to be added: will + prepend to [MODULE_PATH] + --with-extra-libs List additional link flags here. For example, + --with-extra-libs=-lspecial_system_lib or + --with-extra-libs=-L/path/to/libs + --with-blas= use BLAS library + --with-blasdir= search for BLAS library in + --with-lapack= use LAPACK library + --with-mumps=LIBNAME Specify the libname for MUMPS. Default: autodetect + with minimum "-lmumps_common -lpord" + --with-mumpsdir=DIR Specify the directory for MUMPS library and + includes. Note: you will need to add auxiliary + libraries with --extra-libs; this depends on how + MUMPS was configured and installed, at a minimum you + will need SCALAPACK and BLAS + --with-mumpsincdir=DIR Specify the directory for MUMPS includes. + --with-mumpsmoddir=DIR Specify the directory for MUMPS Fortran modules. + --with-mumpslibdir=DIR Specify the directory for MUMPS library. + --with-umfpack=LIBNAME Specify the library name for UMFPACK and its support + libraries. Default: "-lumfpack -lamd" + --with-umfpackdir=DIR Specify the directory for UMFPACK library and + includes. + --with-umfpackincdir=DIR + Specify the directory for UMFPACK includes. + --with-umfpacklibdir=DIR + Specify the directory for UMFPACK library. + --with-superlu=LIBNAME Specify the library name for SUPERLU library. + Default: "-lsuperlu" + --with-superludir=DIR Specify the directory for SUPERLU library and + includes. + --with-superluincdir=DIR + Specify the directory for SUPERLU includes. + --with-superlulibdir=DIR + Specify the directory for SUPERLU library. + --with-superludist=LIBNAME + Specify the libname for SUPERLUDIST library. + Requires you also specify SuperLU. Default: + "-lsuperlu_dist" + --with-superludistdir=DIR + Specify the directory for SUPERLUDIST library and + includes. + --with-superludistincdir=DIR + Specify the directory for SUPERLUDIST includes. + --with-superludistlibdir=DIR + Specify the directory for SUPERLUDIST library. + +Some influential environment variables: + FC Fortran compiler command + FCFLAGS Fortran compiler flags + LDFLAGS linker flags, e.g. -L if you have libraries in a + nonstandard directory + LIBS libraries to pass to the linker, e.g. -l + CC C compiler command + CFLAGS C compiler flags + CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if + you have headers in a nonstandard directory + MPICC MPI C compiler command + MPIFC MPI Fortran compiler command + CPP C preprocessor + +Use these variables to override the choices made by `configure' or to help +it to find libraries and programs with nonstandard names/locations. + +Report bugs to . diff --git a/docs/src/userguide.tex b/docs/src/userguide.tex index 27984125..d171b66d 100644 --- a/docs/src/userguide.tex +++ b/docs/src/userguide.tex @@ -20,6 +20,10 @@ \newtheorem{corollary}{Corollary} \usepackage{rotating} \usepackage{microtype} +\usepackage{minted} +\usemintedstyle{friendly} +\definecolor{bg}{rgb}{0.95,0.95,0.95} +\usepackage{breakurl} %\newboolean{mtc} %\setboolean{mtc}{true} diff --git a/docs/src/userhtml.tex b/docs/src/userhtml.tex index fd2235db..76f97ca0 100644 --- a/docs/src/userhtml.tex +++ b/docs/src/userhtml.tex @@ -20,6 +20,8 @@ \usepackage{rotating} %\newboolean{mtc} %\setboolean{mtc}{true} +\usepackage{microtype} +\usepackage{listings} \pdfoutput=0 \relax