diff --git a/CHANGELOG.md b/CHANGELOG.md index 00836c01..3486d5c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,29 @@ # PetIBM Change Log + +--- + +## 0.2.1 + +--- + +### Added + +### Changed + +* Update version of AmgXWrapper (from `1.0-beta2` to `1.4`). +* Update calls to AmgXWrapper routines (due to changes in API). +* AmgXWrapper-1.4 requires to use PETSc-3.8+. Therefore, when configuring with AmgX, use PETSc-3.8+. + +### Fixed + +* When checking for AmgX, find and keep only the first occurrence of `libamgxsh.so`. + +### Removed + +* When configuring with AmgX, do not check the version of OpenMPI anymore. +* Do not check for Doxygen. + --- ## 0.2.0 diff --git a/Makefile.in b/Makefile.in index 73e30a95..cb2f8b9a 100644 --- a/Makefile.in +++ b/Makefile.in @@ -87,10 +87,8 @@ PRE_UNINSTALL = : POST_UNINSTALL = : subdir = . ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -am__aclocal_m4_deps = $(top_srcdir)/m4/check_version_openmpi.m4 \ - $(top_srcdir)/m4/configure_amgx.m4 \ +am__aclocal_m4_deps = $(top_srcdir)/m4/configure_amgx.m4 \ $(top_srcdir)/m4/configure_cuda.m4 \ - $(top_srcdir)/m4/configure_doxygen.m4 \ $(top_srcdir)/m4/configure_petsc.m4 \ $(top_srcdir)/m4/package_utilities.m4 \ $(top_srcdir)/configure.ac @@ -229,15 +227,12 @@ CXXFLAGS = @CXXFLAGS@ CYGPATH_W = @CYGPATH_W@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ -DOXYGEN = @DOXYGEN@ -DOXYGEN_DIR = @DOXYGEN_DIR@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ EGREP = @EGREP@ EXEEXT = @EXEEXT@ GREP = @GREP@ -HAVE_DOXYGEN = @HAVE_DOXYGEN@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ diff --git a/README.md b/README.md index 33578445..35752ea4 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ PetIBM solves the incompressible Navier-Stokes equations in two and three dimens ## Dependencies (last tested) * g++-4.9.2, g++-5.4.0 -* [PETSc](https://www.mcs.anl.gov/petsc/) 3.7.4 +* [PETSc](https://www.mcs.anl.gov/petsc/) 3.8.1 * Python 2.7 (optional, for pre- and post-processing) Note: Python and libraries have been installed using [`conda`](http://conda.pydata.org/docs/get-started.html) (4.3.1). diff --git a/aclocal.m4 b/aclocal.m4 index 637f11a8..0cbd59fe 100644 --- a/aclocal.m4 +++ b/aclocal.m4 @@ -1246,9 +1246,7 @@ AC_SUBST([am__tar]) AC_SUBST([am__untar]) ]) # _AM_PROG_TAR -m4_include([m4/check_version_openmpi.m4]) m4_include([m4/configure_amgx.m4]) m4_include([m4/configure_cuda.m4]) -m4_include([m4/configure_doxygen.m4]) m4_include([m4/configure_petsc.m4]) m4_include([m4/package_utilities.m4]) diff --git a/configure b/configure index bdb017ee..5e653fff 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for PetIBM 0.2.0. +# Generated by GNU Autoconf 2.69 for PetIBM 0.2.1. # # Report bugs to . # @@ -580,8 +580,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='PetIBM' PACKAGE_TARNAME='petibm' -PACKAGE_VERSION='0.2.0' -PACKAGE_STRING='PetIBM 0.2.0' +PACKAGE_VERSION='0.2.1' +PACKAGE_STRING='PetIBM 0.2.1' PACKAGE_BUGREPORT='mesnardo@gwu.edu, pychuang@email.gwu.edu' PACKAGE_URL='' @@ -639,9 +639,6 @@ PETSC_DIR LIBOBJS EGREP GREP -DOXYGEN_DIR -HAVE_DOXYGEN -DOXYGEN ac_ct_AR AR RANLIB @@ -745,7 +742,6 @@ enable_option_checking enable_silent_rules enable_maintainer_mode enable_dependency_tracking -with_doxygen with_petsc_dir with_petsc_arch with_amgx @@ -1314,7 +1310,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures PetIBM 0.2.0 to adapt to many kinds of systems. +\`configure' configures PetIBM 0.2.1 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1381,7 +1377,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of PetIBM 0.2.0:";; + short | recursive ) echo "Configuration of PetIBM 0.2.1:";; esac cat <<\_ACEOF @@ -1402,8 +1398,6 @@ Optional Features: Optional Packages: --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) - --with-doxygen=PATH manually set directory where the doxygen executable - resides to PATH --with-petsc-dir=PATH set PETSc directory --with-petsc-arch=PATH set PETSc arch folder @@ -1489,7 +1483,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -PetIBM configure 0.2.0 +PetIBM configure 0.2.1 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -2109,7 +2103,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by PetIBM $as_me 0.2.0, which was +It was created by PetIBM $as_me 0.2.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2976,7 +2970,7 @@ fi # Define the identity of the package. PACKAGE='petibm' - VERSION='0.2.0' + VERSION='0.2.1' cat >>confdefs.h <<_ACEOF @@ -5256,73 +5250,6 @@ $as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h fi -DOXYGEN_PATH=$PATH - -# Check whether --with-doxygen was given. -if test "${with_doxygen+set}" = set; then : - withval=$with_doxygen; if test ! -d "$withval" ; then - as_fn_error $? "it is necessary to specify an existing directory when using --with-doxygen=PATH" "$LINENO" 5 - fi - DOXYGEN_DIR=$withval - DOXYGEN_PATH=$DOXYGEN_DIR$PATH_SEPARATOR$DOXYGEN_PATH -fi - -# Extract the first word of "doxygen", so it can be a program name with args. -set dummy doxygen; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 -$as_echo_n "checking for $ac_word... " >&6; } -if ${ac_cv_path_DOXYGEN+:} false; then : - $as_echo_n "(cached) " >&6 -else - case $DOXYGEN in - [\\/]* | ?:[\\/]*) - ac_cv_path_DOXYGEN="$DOXYGEN" # Let the user override the test with a path. - ;; - *) - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -for as_dir in $DOXYGEN_PATH -do - IFS=$as_save_IFS - test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do - if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then - ac_cv_path_DOXYGEN="$as_dir/$ac_word$ac_exec_ext" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 - break 2 - fi -done - done -IFS=$as_save_IFS - - ;; -esac -fi -DOXYGEN=$ac_cv_path_DOXYGEN -if test -n "$DOXYGEN"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DOXYGEN" >&5 -$as_echo "$DOXYGEN" >&6; } -else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } -fi - - -if test x$DOXYGEN != x ; then - HAVE_DOXYGEN=yes -else - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: doxygen not found" >&5 -$as_echo "$as_me: WARNING: doxygen not found" >&2;} - HAVE_DOXYGEN=no - echo "if doxygen is install, specify its location via --with-doxygen=PATH" -fi -HAVE_DOXYGEN=$HAVE_DOXYGEN - -DOXYGEN=$DOXYGEN - -DOXYGEN_DIR=$DOXYGEN_DIR - - - # check for typedefs, structures, and compiler characteristics @@ -6500,7 +6427,7 @@ int main () { -#if ((PETSC_VERSION_GE(3, 7, 0) && PETSC_VERSION_LT(3, 7, 5)) || !PETSC_VERSION_RELEASE) +#if ((PETSC_VERSION_GE(3, 7, 0) && PETSC_VERSION_LT(3, 9, 0)) || !PETSC_VERSION_RELEASE) #else asdf #endif @@ -6548,121 +6475,6 @@ echo if test "${with_amgx+set}" = set; then : withval=$with_amgx; -echo -echo "========================" -echo "Check version of OpenMPI" -echo "========================" - - -PACKAGE_save_CFLAGS=$CFLAGS -PACKAGE_save_CPPFLAGS=$CPPFLAGS -PACKAGE_save_CXXFLAGS=$CXXFLAGS -PACKAGE_save_FCFLAGS=$FCFLAGS -PACKAGE_save_LDFLAGS=$LDFLAGS -PACKAGE_save_FCLIBS=$FCLIBS -PACKAGE_save_CONTRIB_LIBS=$CONTRIB_LIBS -CFLAGS="$PACKAGE_CFLAGS $CFLAGS" -CPPFLAGS="$PACKAGE_CPPFLAGS $CPPFLAGS" -CXXFLAGS="$PACKAGE_CXXFLAGS $CXXFLAGS" -FCFLAGS="$PACKAGE_FCFLAGS $FCFLAGS" -LDFLAGS="$PACKAGE_LDFLAGS $LDFLAGS" -LIBS="$PACKAGE_LIBS $LIBS" -FCLIBS="$PACKAGE_FCLIBS $FCLIBS" -CONTRIB_LIBS="$PACKAGE_CONTRIB_LIBS $CONTRIB_LIBS" - - -ac_fn_cxx_check_header_mongrel "$LINENO" "mpi.h" "ac_cv_header_mpi_h" "$ac_includes_default" -if test "x$ac_cv_header_mpi_h" = xyes; then : - -else - as_fn_error $? "could not find header file mpi.h" "$LINENO" 5 -fi - - - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for OpenMPI" >&5 -$as_echo_n "checking for OpenMPI... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ - -#include - -int -main () -{ - -#ifdef OMPI_MPI_H -#else -asdf -#endif - - - ; - return 0; -} -_ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - IS_OMPI=yes -else - IS_OMPI=no -fi -rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${IS_OMPI}" >&5 -$as_echo "${IS_OMPI}" >&6; } -if test "$IS_OMPI" = no; then - as_fn_error $? "must use OpenMPI (AmgX works with OpenMPI)" "$LINENO" 5 -fi - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for version of OpenMPI" >&5 -$as_echo_n "checking for version of OpenMPI... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ - -#include -# define CHECK (OMPI_MAJOR_VERSION >= 1 && OMPI_MINOR_VERSION >= 8) - -int -main () -{ - -#if (CHECK) -#else -asdf -#endif - - - ; - return 0; -} -_ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - OMPI_VERSION_VALID=yes -else - OMPI_VERSION_VALID=no -fi -rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${OMPI_VERSION_VALID}" >&5 -$as_echo "${OMPI_VERSION_VALID}" >&6; } -if test "$OMPI_VERSION_VALID" = no; then - as_fn_error $? "OpenMPI should not be older than version 1.8 (AmgX currently only accept OpenMPI 1.8)" "$LINENO" 5 -fi - - -CFLAGS=$PACKAGE_save_CFLAGS -CPPFLAGS=$PACKAGE_save_CPPFLAGS -CXXFLAGS=$PACKAGE_save_CXXFLAGS -FCFLAGS=$PACKAGE_save_FCFLAGS -LDFLAGS=$PACKAGE_save_LDFLAGS -LIBS=$PACKAGE_save_LIBS -FCLIBS=$PACKAGE_save_FCLIBS -CONTRIB_LIBS=$PACKAGE_save_CONTRIB_LIBS - - -echo - - - - echo echo "=================================" echo "Configuring optional package CUDA" @@ -6721,40 +6533,6 @@ fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA version" >&5 -$as_echo_n "checking for CUDA version... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ - -#include -#define CUDART_VERSION_EQ65 (CUDART_VERSION==6050) - -int -main () -{ - -#if (CUDART_VERSION_EQ65) -#else -asdf -#endif - - - ; - return 0; -} -_ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - CUDART_VERSION_VALID=yes -else - CUDART_VERSION_VALID=no -fi -rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: ${CUDART_VERSION_VALID}" >&5 -$as_echo "${CUDART_VERSION_VALID}" >&6; } -if test "$CUDART_VERSION_VALID" = no; then - as_fn_error $? "invalid CUDA version detected; please use CUDA 6.5" "$LINENO" 5 -fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cudaRuntimeGetVersion in -lcudart" >&5 $as_echo_n "checking for cudaRuntimeGetVersion in -lcudart... " >&6; } if ${ac_cv_lib_cudart_cudaRuntimeGetVersion+:} false; then : @@ -6965,7 +6743,7 @@ fi $as_echo "$as_me: using AMGX_DIR: $AMGX_DIR" >&6;} AMGX_INC_PATH=-I`find $AMGX_DIR -name amgx_c.h | sed -e 's/\/amgx_c.h//g'` -AMGX_LIB_PATH=-L`find $AMGX_DIR -name libamgxsh.so | sed -e 's/\/libamgxsh.so//g'` +AMGX_LIB_PATH=-L`find $AMGX_DIR -name libamgxsh.so | head -1 | sed -e 's/\/libamgxsh.so//g'` AMGX_LIBRARY=-lamgxsh CPPFLAGS="$AMGX_INC_PATH $CPPFLAGS" @@ -7086,7 +6864,7 @@ CONTRIB_LIBS="$PACKAGE_CONTRIB_LIBS $CONTRIB_LIBS" # list of Makefiles to generate -ac_config_files="$ac_config_files Makefile src/Makefile src/utilities/Makefile src/solvers/Makefile external/Makefile external/yaml-cpp-0.5.1/Makefile external/gtest-1.7.0/Makefile external/AmgXWrapper-1.0-beta2/Makefile tests/Makefile tests/CartesianMesh/Makefile tests/NavierStokes/Makefile tests/TairaColonius/Makefile tests/convectiveTerm/Makefile tests/diffusiveTerm/Makefile examples/Makefile" +ac_config_files="$ac_config_files Makefile src/Makefile src/utilities/Makefile src/solvers/Makefile external/Makefile external/yaml-cpp-0.5.1/Makefile external/gtest-1.7.0/Makefile external/AmgXWrapper-1.4/Makefile tests/Makefile tests/CartesianMesh/Makefile tests/NavierStokes/Makefile tests/TairaColonius/Makefile tests/convectiveTerm/Makefile tests/diffusiveTerm/Makefile examples/Makefile" # output message @@ -7632,7 +7410,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by PetIBM $as_me 0.2.0, which was +This file was extended by PetIBM $as_me 0.2.1, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -7698,7 +7476,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -PetIBM config.status 0.2.0 +PetIBM config.status 0.2.1 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" @@ -7836,7 +7614,7 @@ do "external/Makefile") CONFIG_FILES="$CONFIG_FILES external/Makefile" ;; "external/yaml-cpp-0.5.1/Makefile") CONFIG_FILES="$CONFIG_FILES external/yaml-cpp-0.5.1/Makefile" ;; "external/gtest-1.7.0/Makefile") CONFIG_FILES="$CONFIG_FILES external/gtest-1.7.0/Makefile" ;; - "external/AmgXWrapper-1.0-beta2/Makefile") CONFIG_FILES="$CONFIG_FILES external/AmgXWrapper-1.0-beta2/Makefile" ;; + "external/AmgXWrapper-1.4/Makefile") CONFIG_FILES="$CONFIG_FILES external/AmgXWrapper-1.4/Makefile" ;; "tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;; "tests/CartesianMesh/Makefile") CONFIG_FILES="$CONFIG_FILES tests/CartesianMesh/Makefile" ;; "tests/NavierStokes/Makefile") CONFIG_FILES="$CONFIG_FILES tests/NavierStokes/Makefile" ;; diff --git a/configure.ac b/configure.ac index bd6fba3a..7d652011 100644 --- a/configure.ac +++ b/configure.ac @@ -4,7 +4,7 @@ # set-up AC_PREREQ([2.69]) -AC_INIT([PetIBM], [0.2.0], [mesnardo@gwu.edu, pychuang@email.gwu.edu]) +AC_INIT([PetIBM], [0.2.1], [mesnardo@gwu.edu, pychuang@email.gwu.edu]) AC_CONFIG_AUX_DIR([config]) AC_CONFIG_MACRO_DIR([m4]) AM_INIT_AUTOMAKE([-Wall -Werror foreign subdir-objects]) @@ -25,7 +25,6 @@ AC_PROG_RANLIB AM_PROG_AR AC_PROG_MKDIR_P AC_PROG_CC_C_O -CONFIGURE_DOXYGEN # check for typedefs, structures, and compiler characteristics AC_CHECK_HEADER_STDBOOL @@ -47,8 +46,7 @@ AC_CHECK_FUNCS([dup2 fchdir getcwd getpagesize gettimeofday memset mkdir munmap # check for optional and required third-party libraries PACKAGE_INITIALIZE_ENVIRONMENT CONFIGURE_PETSC -AC_ARG_WITH([amgx],, [CHECK_VERSION_OPENMPI - CONFIGURE_CUDA +AC_ARG_WITH([amgx],, [CONFIGURE_CUDA CONFIGURE_AMGX]) AM_CONDITIONAL([WITH_AMGXWRAPPER], [test "x$WITH_AMGX" = xyes]) PACKAGE_SETUP_ENVIRONMENT @@ -61,7 +59,7 @@ AC_CONFIG_FILES([Makefile external/Makefile external/yaml-cpp-0.5.1/Makefile external/gtest-1.7.0/Makefile - external/AmgXWrapper-1.0-beta2/Makefile + external/AmgXWrapper-1.4/Makefile tests/Makefile tests/CartesianMesh/Makefile tests/NavierStokes/Makefile diff --git a/examples/Makefile.in b/examples/Makefile.in index d11fc945..07e9f629 100644 --- a/examples/Makefile.in +++ b/examples/Makefile.in @@ -87,10 +87,8 @@ PRE_UNINSTALL = : POST_UNINSTALL = : subdir = examples ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -am__aclocal_m4_deps = $(top_srcdir)/m4/check_version_openmpi.m4 \ - $(top_srcdir)/m4/configure_amgx.m4 \ +am__aclocal_m4_deps = $(top_srcdir)/m4/configure_amgx.m4 \ $(top_srcdir)/m4/configure_cuda.m4 \ - $(top_srcdir)/m4/configure_doxygen.m4 \ $(top_srcdir)/m4/configure_petsc.m4 \ $(top_srcdir)/m4/package_utilities.m4 \ $(top_srcdir)/configure.ac @@ -145,15 +143,12 @@ CXXFLAGS = @CXXFLAGS@ CYGPATH_W = @CYGPATH_W@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ -DOXYGEN = @DOXYGEN@ -DOXYGEN_DIR = @DOXYGEN_DIR@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ EGREP = @EGREP@ EXEEXT = @EXEEXT@ GREP = @GREP@ -HAVE_DOXYGEN = @HAVE_DOXYGEN@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ diff --git a/external/AmgXWrapper-1.0-beta2/Makefile.am b/external/AmgXWrapper-1.0-beta2/Makefile.am deleted file mode 100644 index 4427e103..00000000 --- a/external/AmgXWrapper-1.0-beta2/Makefile.am +++ /dev/null @@ -1,9 +0,0 @@ -if WITH_AMGXWRAPPER -noinst_LIBRARIES = libamgxwrapper.a -endif - -libamgxwrapper_a_SOURCES = src/AmgXSolver.cpp - -libamgxwrapper_a_CPPFLAGS = -I$(srcdir)/src \ - -I$(AMGX_DIR)/examples \ - -I$(CUDA_DIR)/include diff --git a/external/AmgXWrapper-1.0-beta2/README.md b/external/AmgXWrapper-1.0-beta2/README.md deleted file mode 100644 index 105f0e73..00000000 --- a/external/AmgXWrapper-1.0-beta2/README.md +++ /dev/null @@ -1,61 +0,0 @@ -# AmgXWrapper - -This wrapper simplifies the usage of AmgX, especially when using AmgX together with other libraries, like PETSc. Currently we only support its use with PETSc, but in the future we may extend it to work with other libraries. - -The usage is simple. Just follow the procedure: ***initialize -> set matrix A -> solve -> finalize***. - -For example, - -```c++ -int main(int argc, char **argv) -{ - // initialize matrix A, RHS, etc using PETSc - ... - - // create an instance of the solver wrapper - AmgXSolver solver; - // initialize the instance - solver.initialize(...); - // set matrix A. Currently it only accept PETSc AIJ matrix - solver.setA(A); - // solve. x and rhs are PETSc vectors. unkns will be the final result in the end - solver.solve(unks, rhs); - // get number of iterations - int iters = solver. getIters(); - // get residual at specific iteration - double res = solver.getResidual(iters); - // finalization - solver.finalize(); - - // other codes - .... - - return 0; -} -``` - - -Note, this wrapper is specifically designed for our CFD solver -- **[PetIBM](https://github.com/barbagroup/PetIBM)**, so it may lack some features. We are trying to make it more general. - -## Update: - -### 01/08/2016 - -Now the wrapper has better performance on the cases that MPI ranks are more than GPUs. - -It has poor performance when we have multiple MPI ranks calling AmgX solvers on one GPU. -So, in order to keep only one MPI rank on each one GPU, this wrapper will now only call AmgX solvers on part of MPI ranks when there are more MPI ranks than GPUs. Data on other ranks will be transferred to those launching AmgX solvers. - -For example, -if there are totally 18 MPI ranks and 6 GPUs (while 12 MPI ranks and 2 GPUs on node 1, and 6 MPI ranks and 4 GPUs on node 2), -only the rank 0, 6, 12, 14, 16, 17 will call AmgX solvers. -Data on rank 1-5 will be transfer to rank 0; data on rank 7-11 will go to rank 6; 13 to 12; and 15 to 14. -This causes some penalties on computing time because of data transfer between MPI ranks. -However, the overall performance is much better than calling AmgX solvers on ALL ranks directly. - -The criterion to redistribute data is based on an assumption that original data are equally distributed on each rank, i.e., each rank holds similar number of rows of a parallel matrix. It's not necessary to have row indices continuous on successive ranks. - -## Future work: -* Add support of updating entries of a matrix A which is already on CUDA device -* Support other matrix structures other than AIJ -* Add mechanisms for debugging and error handling. diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/CMakeLists.txt b/external/AmgXWrapper-1.0-beta2/example/Poisson/CMakeLists.txt deleted file mode 100644 index 6bc20116..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/CMakeLists.txt +++ /dev/null @@ -1,204 +0,0 @@ -# ===================================================================== -# @file CMakeLists.txt -# @brief for cmake -# @author Pi-Yueh Chuang (pychuang@gwu.edu) -# @version alpha -# @date 2015-09-01 -# ===================================================================== - - -CMAKE_MINIMUM_REQUIRED(VERSION 2.8) - - -MESSAGE("===================================================================") -MESSAGE("Specifying CXX compiler and flags...\n") -MESSAGE("NOTE: clang++ is default C++ compiler. To use other compiler, ") -MESSAGE("please define the environment variable CXX\n") - -IF (NOT DEFINED ENV{CXX}) - SET(CMAKE_CXX_COMPILER "clang++") - MESSAGE("CXX compiler: clang++") -ELSE() - SET(CMAKE_CXX_COMPILER $ENV{CXX}) - MESSAGE("CXX compiler: " ${CMAKE_CXX_COMPILER}) -ENDIF() - - -SET(CMAKE_CXX_FLAGS "-std=c++11" CACHE STRING "") -SET(CMAKE_CXX_FLAGS_DEBUG "-g" CACHE STRING "") -SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "") - - - -MESSAGE("\n===================================================================") -MESSAGE("Specifying C compiler and flags...\n") -MESSAGE("NOTE: clang is default C compiler. To use other compiler, ") -MESSAGE("please define the environment variable CXX\n") - -IF (NOT DEFINED ENV{CC}) - SET(CMAKE_C_COMPILER "clang") - MESSAGE("C compiler: clang") -ELSE() - SET(CMAKE_C_COMPILER $ENV{CC}) - MESSAGE("C compiler: " ${CMAKE_C_COMPILER}) -ENDIF() - -SET(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "") -SET(CMAKE_C_FLAGS_DEBUG "-g" CACHE STRING "") - - - -MESSAGE("\n===================================================================") -MESSAGE("Specifying other variables...") -SET(CMAKE_VERBOSE_MAKEFILE ON) -SET(EXECUTABLE_OUTPUT_PATH ./bin) - -IF(NOT DEFINED CMAKE_BUILD_TYPE) - SET(CMAKE_BUILD_TYPE RELEASE CACHE STRING "") -ENDIF() - -MESSAGE("-- Build type: " ${CMAKE_BUILD_TYPE}) - -SET(CMAKE_SHARED_LINKER_FLAGS "-Wl,--no-undefined") - -MESSAGE("\n===================================================================") -MESSAGE("Starting generator...") -PROJECT(Poisson) - - -MESSAGE("\n===================================================================") -MESSAGE("Trying to find PETSc...") -MESSAGE("\nNOTE: If it fails to find PETSc, please set the environment variable") -MESSAGE("PETSC_DIR in order to notify CMake the location of PETSc\n") - -LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules") - -FIND_PACKAGE(PETSc REQUIRED) - -IF(${PETSc_FOUND}) - MESSAGE("\tPETSC_DIR: " ${PETSC_DIR}) - MESSAGE("\tPETSC_INCLUDES: " ${PETSC_INCLUDES}) - MESSAGE("\tPETSC_LIBRARIES: " ${PETSC_LIBRARIES}) -ENDIF() - - - -MESSAGE("\n===================================================================") -MESSAGE("Trying to find AmgX...") -MESSAGE("\nNOTE: If it fails to find AmgX, please set the environment variable") -MESSAGE("AMGX_DIR in order to notify CMake the location of AmgX\n") - - -MESSAGE("-- Finding amgx_c.h") -FIND_PATH(AMGX_INCLUDE_DIRS - NAMES amgx_c.h - PATHS ${AMGX_DIR} $ENV{AMGX_DIR} - PATH_SUFFIXES "include") - -IF(${AMGX_INCLUDE_DIRS} STREQUAL "AMGX_INCLUDE_DIRS-NOTFOUND") - MESSAGE(FATAL_ERROR "Could not find amgx_c.h!!!") -ELSE() - MESSAGE("-- Finding amgx_c.h - found in " ${AMGX_INCLUDE_DIRS}) -ENDIF() - - -MESSAGE("-- Finding amgx_capi.h") -FIND_FILE(AMGX_CAPI_FOUND - NAMES amgx_capi.h - PATHS ${AMGX_INCLUDE_DIRS} - NO_DEFAULT_PATH) - -IF(${AMGX_CAPI_FOUND} STREQUAL "AMGX_CAPI_FOUND-NOTFOUND") - MESSAGE(FATAL_ERROR "amgx_capi.h was not found in: " ${AMGX_INCLUDE_DIRS}) -ELSE() - MESSAGE("-- Finding amgx_capi.h - found") -ENDIF() - - -MESSAGE("-- Finding amgx_config.h") -FIND_FILE(AMGX_CONFIG_FOUND - NAMES amgx_config.h - PATHS ${AMGX_INCLUDE_DIRS} - NO_DEFAULT_PATH) - -IF(${AMGX_CONFIG_FOUND} STREQUAL "AMGX_CONFIG_FOUND-NOTFOUND") - MESSAGE(FATAL_ERROR "amgx_config.h was not found in: " ${AMGX_INCLUDE_DIRS}) -ELSE() - MESSAGE("-- Finding amgx_config.h - found") -ENDIF() - - -MESSAGE("-- Finding libamgxsh.so") -FIND_LIBRARY(AMGX_LIBRARIES - NAMES amgxsh - PATHS ${AMGX_DIR} $ENV{AMGX_DIR} - PATH_SUFFIXES "lib") - -IF(${AMGX_LIBRARIES} STREQUAL "AMGX_LIBRARIES-NOTFOUND") - MESSAGE(FATAL_ERROR "libamgxsh.so was not found") -ELSE() - MESSAGE("-- Finding libamgxsh.so - found: " ${AMGX_LIBRARIES}) -ENDIF() - - - -MESSAGE("\n===================================================================") -MESSAGE("Trying to find CUDA 6.5...") -MESSAGE("\nNOTE: If you have several different versions of CUDA, and if CMake ") -MESSAGE("can not find CUDA 6.5, please define CUDA_TOOLKIT_ROOT_DIR manually ") -MESSAGE("when calling CMake. For example:") -MESSAGE("\n\t$ cmake . -DCUDA_TOOLKIT_ROOT_DIR=/opt/cuda65\n") - -FIND_PACKAGE(CUDA 6.5 EXACT REQUIRED) - -IF(${CUDA_FOUND}) - SET(CUDA_LIBRARY_DIRS ${CUDA_TOOLKIT_ROOT_DIR}/lib64) - MESSAGE("\tCUDA_TOOLKIT_ROOT_DIR: " ${CUDA_TOOLKIT_ROOT_DIR}) - MESSAGE("\tCUDA_VERSION: " ${CUDA_VERSION_STRING}) - MESSAGE("\tCUDA_INCLUDE_DIRS: " ${CUDA_INCLUDE_DIRS}) - MESSAGE("\tCUDA_LIBRARY_DIRS: " ${CUDA_LIBRARY_DIRS}) - MESSAGE("\tCUDA_LIBRARIES: " ${CUDA_LIBRARIES}) -ENDIF() - - -MESSAGE("\n===================================================================") -MESSAGE("Setting the information for target and source files...") - - -SET(SRC ${CMAKE_SOURCE_DIR}/src) -SET(AmgXWrapperSRC ${CMAKE_SOURCE_DIR}/../../src) - -SET(SOURCE - ${SRC}/Poisson.cpp - ${SRC}/generateA.cpp - ${SRC}/generateGrid.cpp - ${SRC}/generateRHS.cpp - ${SRC}/generateExt.cpp - ${SRC}/createKSP.cpp - ${SRC}/solve.cpp - ${SRC}/applyNeumannBC.cpp - ${AmgXWrapperSRC}/AmgXSolver.cpp) - -INCLUDE_DIRECTORIES( - ${PETSC_INCLUDES} - ${AMGX_INCLUDE_DIRS} - ${CUDA_INCLUDE_DIRS} - ${AmgXWrapperSRC}) - -LINK_DIRECTORIES( - ${CUDA_LIBRARY_DIRS} - ${AMGX_LIBRARY_DIRS} - ${PETSC_LIBRARY_DIRS}) - -ADD_EXECUTABLE(Poisson ${SOURCE}) - -TARGET_LINK_LIBRARIES(Poisson - ${PETSC_LIBRARIES} - ${AMGX_LIBRARIES} - ${CUDA_LIBRARIES}) - -ADD_CUSTOM_COMMAND( - TARGET Poisson - POST_BUILD - COMMAND ${CMAKE_COMMAND} -E make_directory configs - COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/configs configs/) diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/README.md b/external/AmgXWrapper-1.0-beta2/example/Poisson/README.md deleted file mode 100644 index 9396ee32..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/README.md +++ /dev/null @@ -1,25 +0,0 @@ -To build: - -``` -$ cmake . -DCUDA_TOOLKIT_ROOT_DIR= -DAMGX_DIR= -DPETSC_DIR= - -$ make -``` - -Exectuable file will be located in the folder `bin`. To run, for example, a 100x100x100 3D Poisson benchmark using AmgX solver and two GPUs on one node: - -``` -$ mpiexec -map-by ppr:2:node -n 2 bin/Poisson -caseName test -mode GPU -Nx 100 -Ny 100 -Nz 100 -cfgFileName configs/AmgX_SolverOptions_classical.info -``` - -Or if PETSc KSP solver and 16 CPUs are preferred: - -``` -$ mpiexec -map-by ppr:16:node -n 16 bin/Poisson -caseName test -mode PETSc -Nx 100 -Ny 100 -Nz 100 -cfgFileName configs/PETSc_SolverOptions_hypre.info -optFileName performance.txt -``` - -For 2D Poisson benchmarks, do not specify `Nz` or set `Nz` as zero. For example: - -``` -$ mpiexec -map-by ppr:2:node -n 2 bin/Poisson -caseName test -mode GPU -Nx 100 -Ny 100 -cfgFileName configs/AmgX_SolverOptions_classical.info -``` diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/Poisson.cpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/Poisson.cpp deleted file mode 100644 index 1aeddce0..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/Poisson.cpp +++ /dev/null @@ -1,312 +0,0 @@ -/** - * @file Poisson.cpp - * @brief An example and benchmark of AmgX and PETSc - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version beta - * @date 2015-02-01 - */ -# include "headers.hpp" - -static std::string help = "Test PETSc and AmgX solvers."; - -int main(int argc, char **argv) -{ - StructArgs args; // a structure containing CMD arguments - - PetscScalar Lx = 1.0, // Lx - Ly = 1.0, // Ly - Lz = 1.0; // Lz - - PetscScalar dx, // dx, calculated using Lx=1.0 - dy, // dy, calculated using Ly=1.0 - dz; // dy, calculated using Ly=1.0 - - DM grid; // DM object - - Vec x, // x-coordinates - y, // y-coordinates - z; // z-coordinates - - Vec u, // unknowns - rhs, // RHS - bc, // boundary conditions - u_exact,// exact solution - err; // errors - - Mat A; // coefficient matrix - - KSP ksp; // PETSc KSP solver instance - - AmgXSolver amgx; // AmgX wrapper instance - - PetscErrorCode ierr; // error codes returned by PETSc routines - - PetscMPIInt size, // MPI size - myRank; // rank of current process - - PetscClassId solvingID, - warmUpID; - - PetscLogEvent solvingEvent, - warmUpEvent; - - - - - - // initialize PETSc and MPI - ierr = PetscInitialize(&argc, &argv, nullptr, help.c_str()); CHK; - ierr = PetscLogDefaultBegin(); CHK; - - - // obtain the rank and size of MPI - ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHK; - ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &myRank); CHK; - - - // get parameters from command-line arguments - ierr = args.getArgs(); CHK; - - - // pring case information - { - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "="); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "-"); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - - if (myRank == 0) args.print(); - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "-"); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "="); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - - } - - // create DMDA object - if (args.Nz > 0) - { - ierr = DMDACreate3d(PETSC_COMM_WORLD, - DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, - DMDA_STENCIL_STAR, - args.Nx, args.Ny, args.Nz, - PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, - 1, 1, nullptr, nullptr, nullptr, &grid); CHK; - - ierr = DMDASetUniformCoordinates(grid, 0., 1., 0., 1., 0., 1.); CHK; - } - else if (args.Nz == 0) - { - ierr = DMDACreate2d(PETSC_COMM_WORLD, - DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, - DMDA_STENCIL_STAR, - args.Nx, args.Ny, - PETSC_DECIDE, PETSC_DECIDE, - 1, 1, nullptr, nullptr, &grid); CHK; - - ierr = DMDASetUniformCoordinates(grid, 0., 1., 0., 1., 0., 0.); CHK; - } - - ierr = PetscObjectSetName((PetscObject) grid, "DMDA grid"); CHK; - ierr = DMSetMatType(grid, MATAIJ); CHK; - - - - // create vectors (x, y, p, b, u) and matrix A - { - ierr = DMCreateGlobalVector(grid, &x); CHK; - ierr = DMCreateGlobalVector(grid, &y); CHK; - ierr = DMCreateGlobalVector(grid, &u); CHK; - ierr = DMCreateGlobalVector(grid, &rhs); CHK; - ierr = DMCreateGlobalVector(grid, &bc); CHK; - ierr = DMCreateGlobalVector(grid, &u_exact); CHK; - ierr = DMCreateGlobalVector(grid, &err); CHK; - ierr = DMCreateMatrix(grid, &A); CHK; - - ierr = PetscObjectSetName((PetscObject) x, "x coordinates"); CHK; - ierr = PetscObjectSetName((PetscObject) y, "y coordinates"); CHK; - ierr = PetscObjectSetName((PetscObject) u, "vec for unknowns"); CHK; - ierr = PetscObjectSetName((PetscObject) rhs, "RHS"); CHK; - ierr = PetscObjectSetName((PetscObject) bc, "boundary conditions"); CHK; - ierr = PetscObjectSetName((PetscObject) u_exact, "exact solution"); CHK; - ierr = PetscObjectSetName((PetscObject) err, "errors"); CHK; - ierr = PetscObjectSetName((PetscObject) A, "matrix A"); CHK; - - ierr = MatSetOption(A, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE); CHK; - ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE); CHK; - } - - - - - if (args.Nz == 0) - { - // set values of dx, dy, dx, x, y, and z - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateGrid(grid, args.Nx, args.Ny, - Lx, Ly, dx, dy, x, y); CHK; - - // set values of RHS -- the vector rhs - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateRHS(grid, x, y, rhs); CHK; - - // generate exact solution - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateExt(grid, x, y, u_exact); CHK; - - // initialize and set up the coefficient matrix A - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateA(grid, dx, dy, A); CHK; - } - else if (args.Nz > 0) - { - - ierr = DMCreateGlobalVector(grid, &z); CHK; - ierr = PetscObjectSetName((PetscObject) z, "z coordinates"); CHK; - - // set values of dx, dy, dx, x, y, and z - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateGrid(grid, args.Nx, args.Ny, args.Nz, - Lx, Ly, Lz, dx, dy, dz, x, y, z); CHK; - - // set values of RHS -- the vector rhs - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateRHS(grid, x, y, z, rhs); CHK; - - // generate exact solution - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateExt(grid, x, y, z, u_exact); CHK; - - // initialize and set up the coefficient matrix A - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = generateA(grid, dx, dy, dz, A); CHK; - } - - - // handle the issue for all-Neumann BC matrix - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = applyNeumannBC(A, rhs, u_exact); CHK; - - - // register a PETSc event for warm-up and solving - ierr = PetscClassIdRegister("SolvingClass", &solvingID); CHK; - ierr = PetscClassIdRegister("WarmUpClass", &warmUpID); CHK; - ierr = PetscLogEventRegister("Solving", solvingID, &solvingEvent); CHK; - ierr = PetscLogEventRegister("WarmUp", warmUpID, &warmUpEvent); CHK; - - // create a solver and solve based whether it is AmgX or PETSc - if (std::strcmp(args.mode, "PETSc") == 0) // PETSc mode - { - ierr = createKSP(ksp, A, grid, args.cfgFileName); CHK; - - ierr = solve(ksp, A, u, rhs, u_exact, err, - args, warmUpEvent, solvingEvent); CHK; - - // destroy KSP - ierr = KSPDestroy(&ksp); CHK; - - } - else // AmgX mode - { - if (std::strcmp(args.mode, "AmgX") == 0) // AmgX GPU mode - amgx.initialize(PETSC_COMM_WORLD, "dDDI", args.cfgFileName); - else // AmgX CPU mode (not yet implemented in the wrapper) and other mode - { - std::cerr << "Invalid mode." << std::endl; - exit(EXIT_FAILURE); - } - - - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - amgx.setA(A); - - ierr = solve(amgx, A, u, rhs, u_exact, err, - args, warmUpEvent, solvingEvent); CHK; - - // destroy solver - ierr = amgx.finalize(); CHK; - - } - - - // output a file for petsc performance - if (args.optFileBool == PETSC_TRUE) - { - PetscViewer viewer; // PETSc viewer - - std::strcat(args.optFileName ,".log"); - - ierr = PetscViewerASCIIOpen( - PETSC_COMM_WORLD, args.optFileName, &viewer); CHK; - ierr = PetscLogView(viewer); CHK; - ierr = PetscViewerDestroy(&viewer); CHK; - } - - // output VTK file for post-processing - if (args.VTKFileBool == PETSC_TRUE) - { - PetscViewer viewerVTK; - - std::strcat(args.VTKFileName ,".vts"); - - ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewerVTK); CHK; - ierr = PetscViewerSetType(viewerVTK, PETSCVIEWERVTK); CHK; - ierr = PetscViewerSetFormat(viewerVTK, PETSC_VIEWER_VTK_VTS); CHK; - ierr = PetscViewerFileSetMode(viewerVTK, FILE_MODE_WRITE); CHK; - ierr = PetscViewerFileSetName(viewerVTK, args.VTKFileName); CHK; - - ierr = VecView(u_exact, viewerVTK); CHK; - - ierr = PetscViewerFileSetMode(viewerVTK, FILE_MODE_APPEND); CHK; - - ierr = VecView(u, viewerVTK); CHK; - ierr = VecView(err, viewerVTK); CHK; - - ierr = PetscViewerDestroy(&viewerVTK); CHK; - } - - - // destroy vectors, matrix, dmda - { - ierr = VecDestroy(&x); CHK; - ierr = VecDestroy(&y); CHK; - ierr = VecDestroy(&u); CHK; - ierr = VecDestroy(&rhs); CHK; - ierr = VecDestroy(&bc); CHK; - ierr = VecDestroy(&u_exact); CHK; - ierr = VecDestroy(&err); CHK; - - ierr = MatDestroy(&A); CHK; - - if (args.Nz > 0) - { - ierr = VecDestroy(&z); CHK; - } - - ierr = DMDestroy(&grid); CHK; - } - - - { - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "="); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "-"); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "End of %s\n", args.caseName); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "-"); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - for(int i=0; i<72; ++i) ierr = PetscPrintf(PETSC_COMM_WORLD, "="); - ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHK; - } - - // finalize PETSc - ierr = PetscFinalize(); CHK; - - return 0; -} - diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/StructArgs.hpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/StructArgs.hpp deleted file mode 100644 index c1eaaac7..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/StructArgs.hpp +++ /dev/null @@ -1,100 +0,0 @@ -/** - * @file structArgs.cpp - * @brief Definition of the structure StructArgs - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2015-11-06 - */ -# include -# include - -# define MAX_LEN PETSC_MAX_PATH_LEN - -# define CHKMSG(flag, message) \ - if (!flag) \ - { \ - PetscPrintf(PETSC_COMM_WORLD, message); \ - PetscPrintf(PETSC_COMM_WORLD, "\n"); \ - exit(EXIT_FAILURE); \ - } - - -class StructArgs -{ - public: - PetscInt Nx, // number of elements in x-direction - Ny, // number of elements in y-direction - Nz = 0; // number of elements in z-direction - - PetscInt Nruns = 10; // number of runs of solving - - PetscBool optFileBool, - VTKFileBool; - - char mode[MAX_LEN], // either AmgX, or PETSc - cfgFileName[MAX_LEN], // config file - optFileName[MAX_LEN], // output file - caseName[MAX_LEN], // case name - VTKFileName[MAX_LEN]; // VTK output file name - - void print() - { - std::cout << "Case Name: " << caseName << std::endl; - std::cout << "Nx: " << Nx << std::endl; - std::cout << "Ny: " << Ny << std::endl; - std::cout << "Nz: " << Nz << std::endl; - std::cout << "Mode: " << mode << std::endl; - std::cout << "Config File: " << cfgFileName << std::endl; - std::cout << "Number of Solves: " << Nruns << std::endl; - - std::cout << "Output PETSc Log File ? " << optFileBool << std::endl; - if (optFileBool == PETSC_TRUE) - std::cout << "Output PETSc Log File Name: " - << optFileName << std::endl; - - std::cout << "Output VTK file ? " << VTKFileBool << std::endl; - if (VTKFileBool == PETSC_TRUE) - std::cout << "Output VTK File Name: " - << VTKFileName << std::endl; - } - - PetscErrorCode getArgs() - { - PetscErrorCode ierr; // error codes returned by PETSc routines - PetscBool set; // temporary booling variable - - ierr = PetscOptionsGetString(nullptr, nullptr, "-caseName", - caseName, MAX_LEN, &set); CHKERRQ(ierr); - CHKMSG(set, "caseName not yet set!"); - - ierr = PetscOptionsGetString(nullptr, nullptr, "-mode", - mode, MAX_LEN, &set); CHKERRQ(ierr); - CHKMSG(set, "mode not yet set!"); - - ierr = PetscOptionsGetString(nullptr, nullptr, "-cfgFileName", - cfgFileName, MAX_LEN, &set); CHKERRQ(ierr); - CHKMSG(set, "cfgFileName (configuration file) not yet set!"); - - ierr = PetscOptionsGetString(nullptr, nullptr, "-optFileName", - optFileName, MAX_LEN, &(optFileBool)); CHKERRQ(ierr); - - ierr = PetscOptionsGetString(nullptr, nullptr, "-VTKFileName", - VTKFileName, MAX_LEN, &(VTKFileBool)); CHKERRQ(ierr); - - ierr = PetscOptionsGetInt(nullptr, nullptr, - "-Nx", &Nx, &set); CHKERRQ(ierr); - CHKMSG(set, "Nx not yet set!"); - - ierr = PetscOptionsGetInt(nullptr, nullptr, - "-Ny", &Ny, &set); CHKERRQ(ierr); - CHKMSG(set, "Ny not yet set!"); - - ierr = PetscOptionsGetInt(nullptr, nullptr, - "-Nz", &Nz, &set); CHKERRQ(ierr); - - ierr = PetscOptionsGetInt(nullptr, nullptr, - "-Nruns", &Nruns, &set); CHKERRQ(ierr); - - return 0; - } -}; diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/applyNeumannBC.cpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/applyNeumannBC.cpp deleted file mode 100644 index adcf316c..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/applyNeumannBC.cpp +++ /dev/null @@ -1,34 +0,0 @@ -/** - * @file applyNeumannBC.cpp - * @brief Definition of function applyNeumannBC(...) - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version beta - * @date 2016-02-13 - */ -# include "headers.hpp" - -/** - * @brief Modify matrix A and RHS vector for all-Neumann BCs - * - * All Neumann BCs causes issues like indefinite matrix or infinite number of - * solutions. We hence assume the exact solution at the node i = j = 0 is known. - * (The same way we deal with the pressure in CFD applications.) The entry - * A[0, 0] is modified to 1, and A[0, *] = A[*, 0] = 0; also all corresponding - * entries in RHS vector is modified respectively. - * - * @param A Matrix A generated from the function generateA(...) - * @param RHS The right-hand-side vector generated from generateRHS(...) - * @param exact The exact solution vector generated from generateExt(...) - * - * @return - */ -PetscErrorCode applyNeumannBC(Mat &A, Vec &RHS, const Vec &exact) -{ - PetscErrorCode ierr; - - PetscInt row[1] = {0}; - - ierr = MatZeroRowsColumns(A, 1, row, 1.0, exact, RHS); CHKERRQ(ierr); - - return 0; -} diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/createKSP.cpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/createKSP.cpp deleted file mode 100644 index e8c0bb9d..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/createKSP.cpp +++ /dev/null @@ -1,23 +0,0 @@ -# include "headers.hpp" - - -PetscErrorCode createKSP(KSP &ksp, Mat &A, DM &grid, char *FN) -{ - PetscErrorCode ierr; - - // create ksp solver - ierr = PetscOptionsInsertFile( - PETSC_COMM_WORLD, nullptr, FN, PETSC_FALSE); CHKERRQ(ierr); - - // create KSP for intermaediate fluxes system - ierr = KSPCreate(PETSC_COMM_WORLD, &ksp); CHKERRQ(ierr); - ierr = KSPSetDM(ksp, grid); CHKERRQ(ierr); - ierr = KSPSetDMActive(ksp, PETSC_FALSE); CHKERRQ(ierr); - ierr = KSPSetOperators(ksp, A, A); CHKERRQ(ierr); - ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE); CHKERRQ(ierr); - ierr = KSPSetType(ksp, KSPCG); CHKERRQ(ierr); - ierr = KSPSetReusePreconditioner(ksp, PETSC_TRUE); CHKERRQ(ierr); - ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr); - - return 0; -} diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/generateExt.cpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/generateExt.cpp deleted file mode 100644 index 16f010c2..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/generateExt.cpp +++ /dev/null @@ -1,104 +0,0 @@ -# include "headers.hpp" - - -/** - * @brief Generte exact solution for the 3D Poisson equation - * - * @param grid - * @param x - * @param y - * @param z - * @param exact - * - * @return - */ -PetscErrorCode generateExt(const DM &grid, - const Vec &x, const Vec &y, const Vec &z, Vec &exact) -{ - PetscErrorCode ierr; // error codes returned by PETSc routines - - PetscInt xbg, xed, - ybg, yed, - zbg, zed; - - PetscScalar ***x_arry, - ***y_arry, - ***z_arry, - ***exact_arry; - - - // get indices for left-bottom and right-top corner - ierr = DMDAGetCorners(grid, &xbg, &ybg, &zbg, &xed, &yed, &zed); CHKERRQ(ierr); - - xed += xbg; - yed += ybg; - zed += zbg; - - // generate rhs - ierr = DMDAVecGetArray(grid, x, &x_arry); CHKERRQ(ierr); - ierr = DMDAVecGetArray(grid, y, &y_arry); CHKERRQ(ierr); - ierr = DMDAVecGetArray(grid, z, &z_arry); CHKERRQ(ierr); - ierr = DMDAVecGetArray(grid, exact, &exact_arry); CHKERRQ(ierr); - for(int k=zbg; k -# include -# include -# include -# include -# include - -# include -# include -# include -# include - -# include "StructArgs.hpp" -# include "AmgXSolver.hpp" - - -# define CHK CHKERRQ(ierr) - -# define c1 2.0*1.0*M_PI - - -PetscErrorCode generateGrid(const DM &grid, - const PetscInt &Nx, const PetscInt &Ny, const PetscInt &Nz, - const PetscScalar &Lx, const PetscScalar &Ly, const PetscScalar &Lz, - PetscScalar &dx, PetscScalar &dy, PetscScalar &dz, - Vec &x, Vec &y, Vec &z); - -PetscErrorCode generateGrid(const DM &grid, - const PetscInt &Nx, const PetscInt &Ny, - const PetscScalar &Lx, const PetscScalar &Ly, - PetscScalar &dx, PetscScalar &dy, - Vec &x, Vec &y); - -PetscErrorCode generateRHS(const DM &grid, - const Vec &x, const Vec &y, const Vec &z, Vec &rhs); - -PetscErrorCode generateRHS(const DM &grid, - const Vec &x, const Vec &y, Vec &rhs); - -PetscErrorCode generateExt(const DM &grid, - const Vec &x, const Vec &y, const Vec &z, Vec &exact); - -PetscErrorCode generateExt(const DM &grid, - const Vec &x, const Vec &y, Vec &exact); - -PetscErrorCode generateA(const DM &grid, - const PetscScalar &dx, const PetscScalar &dy, const PetscScalar &dz, Mat &A); - -PetscErrorCode generateA(const DM &grid, - const PetscScalar &dx, const PetscScalar &dy, Mat &A); - -PetscErrorCode createKSP(KSP &ksp, Mat &A, DM &grid, char *FN); - -PetscErrorCode solve(KSP &ksp, Mat &A, Vec &u, Vec &rhs, Vec &u_exact, Vec &err, - StructArgs &args, PetscLogEvent &warmUpEvent, PetscLogEvent &solvingEvent); - -PetscErrorCode solve(AmgXSolver &amgx, Mat &A, Vec &u, Vec &rhs, Vec &u_exact, Vec &err, - StructArgs &args, PetscLogEvent &warmUpEvent, PetscLogEvent &solvingEvent); - -PetscErrorCode applyNeumannBC(Mat &A, Vec &RHS, const Vec &exact); diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/solve.cpp b/external/AmgXWrapper-1.0-beta2/example/Poisson/src/solve.cpp deleted file mode 100644 index 4334047c..00000000 --- a/external/AmgXWrapper-1.0-beta2/example/Poisson/src/solve.cpp +++ /dev/null @@ -1,216 +0,0 @@ -/** - * @file solve.cpp - * @brief functions of solving behavior - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2016-02-04 - */ -# include "headers.hpp" - - -PetscErrorCode solve(KSP &ksp, Mat &A, Vec &u, Vec &rhs, Vec &u_exact, Vec &err, - StructArgs &args, PetscLogEvent &warmUpEvent, PetscLogEvent &solvingEvent) -{ - - PetscErrorCode ierr; - - - PetscLogDouble totalTime = 0., - avgTime; - - - auto postSolving = - [&ierr, &ksp, &u, &u_exact, &err] (PetscLogDouble time) -> PetscErrorCode - { - KSPConvergedReason reason; // to store the KSP convergence reason - - PetscInt Niters; // iterations used to converge - - PetscScalar norm2, // L2 norm of solution errors - normM; // infinity norm of solution errors - - ierr = KSPGetConvergedReason(ksp, &reason); CHK; - - if (reason < 0) - { - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\nDiverged: %d\n", reason); CHK; - exit(EXIT_FAILURE); - } - - ierr = KSPGetIterationNumber(ksp, &Niters); CHK; - - // calculate norms of errors - ierr = VecCopy(u, err); CHK; - ierr = VecAXPY(err, -1.0, u_exact); CHK; - ierr = VecNorm(err, NORM_2, &norm2); CHK; - ierr = VecNorm(err, NORM_INFINITY, &normM); CHK; - - // print infromation - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tSolve Time: %f\n", time); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tL2-Norm: %g\n", (double)norm2); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tMax-Norm: %g\n", (double)normM); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tIterations %D\n", Niters); CHK; - - return 0; - }; - - - auto solving = - [&ierr, &A, &u, &rhs, &ksp, &postSolving] (PetscLogEvent &event) -> PetscLogDouble - { - PetscLogDouble bgTime, - edTime; - - // set all entries as zeros in the vector of unknows - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = VecSet(u, 0.0); CHK; - - // beging logging this solving event - ierr = PetscLogEventBegin(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - // obtain the begining time - ierr = PetscTime(&bgTime); CHK; - - // solve - ierr = KSPSolve(ksp, rhs, u); CHK; - - // obtain the ending time - ierr = PetscTime(&edTime); CHK; - - // end logging this solving event - ierr = PetscLogEventEnd(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - ierr = postSolving(edTime - bgTime); CHK; - - return edTime - bgTime; - }; - - - - - // start a warm-up cycle - ierr = PetscPrintf(PETSC_COMM_WORLD, "Warm-up cycle ... \n"); CHK; - solving(warmUpEvent); - - - // start `Nruns` runs to get averaged solving time - for(int i=0; i PetscErrorCode - { - PetscInt Niters; // iterations used to converge - - PetscScalar norm2, // L2 norm of solution errors - normM; // infinity norm of solution errors - - Niters = amgx.getIters(); - - // calculate norms of errors - ierr = VecCopy(u, err); CHK; - ierr = VecAXPY(err, -1.0, u_exact); CHK; - ierr = VecNorm(err, NORM_2, &norm2); CHK; - ierr = VecNorm(err, NORM_INFINITY, &normM); CHK; - - // print infromation - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tSolve Time: %f\n", time); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tL2-Norm: %g\n", (double)norm2); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tMax-Norm: %g\n", (double)normM); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tIterations %D\n", Niters); CHK; - - return 0; - }; - - - auto solving = - [&ierr, &A, &u, &rhs, &amgx, &postSolving] (PetscLogEvent &event) -> PetscLogDouble - { - PetscLogDouble bgTime, - edTime; - - // set all entries as zeros in the vector of unknows - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = VecSet(u, 0.0); CHK; - - // beging logging this solving event - ierr = PetscLogEventBegin(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - // obtain the begining time - ierr = PetscTime(&bgTime); CHK; - - // solve - ierr = amgx.solve(u, rhs); CHK; - - // obtain the ending time - ierr = PetscTime(&edTime); CHK; - - // end logging this solving event - ierr = PetscLogEventEnd(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - ierr = postSolving(edTime - bgTime); CHK; - - return edTime - bgTime; - }; - - - // start a warm-up cycle - ierr = PetscPrintf(PETSC_COMM_WORLD, "Warm-up cycle ... \n"); CHK; - solving(warmUpEvent); - - - // start `Nruns` runs to get averaged solving time - for(int i=0; i PetscErrorCode - { - KSPConvergedReason reason; // to store the KSP convergence reason - - PetscInt Niters; // iterations used to converge - - PetscScalar norm2, // L2 norm of solution errors - normM; // infinity norm of solution errors - - ierr = KSPGetConvergedReason(ksp, &reason); CHK; - - if (reason < 0) - { - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\nDiverged: %d\n", reason); CHK; - exit(EXIT_FAILURE); - } - - ierr = KSPGetIterationNumber(ksp, &Niters); CHK; - - // calculate norms of errors - ierr = VecCopy(u, err); CHK; - ierr = VecAXPY(err, -1.0, u_exact); CHK; - ierr = VecNorm(err, NORM_2, &norm2); CHK; - ierr = VecNorm(err, NORM_INFINITY, &normM); CHK; - - // print infromation - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tSolve Time: %f\n", time); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tL2-Norm: %g\n", (double)norm2); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tMax-Norm: %g\n", (double)normM); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tIterations %D\n", Niters); CHK; - - return 0; - }; - - - auto solving = - [&ierr, &A, &u, &rhs, &ksp, &postSolving] (PetscLogEvent &event) -> PetscLogDouble - { - PetscLogDouble bgTime, - edTime; - - // set all entries as zeros in the vector of unknows - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = VecSet(u, 0.0); CHK; - - // beging logging this solving event - ierr = PetscLogEventBegin(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - // obtain the begining time - ierr = PetscTime(&bgTime); CHK; - - // solve - ierr = KSPSolve(ksp, rhs, u); CHK; - - // obtain the ending time - ierr = PetscTime(&edTime); CHK; - - // end logging this solving event - ierr = PetscLogEventEnd(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - ierr = postSolving(edTime - bgTime); CHK; - - return edTime - bgTime; - }; - - - - - // start a warm-up cycle - ierr = PetscPrintf(PETSC_COMM_WORLD, "Warm-up cycle ... \n"); CHK; - solving(warmUpEvent); - - - // start `Nruns` runs to get averaged solving time - for(int i=0; i PetscErrorCode - { - PetscInt Niters; // iterations used to converge - - PetscScalar norm2, // L2 norm of solution errors - normM; // infinity norm of solution errors - - Niters = amgx.getIters(); - - // calculate norms of errors - ierr = VecCopy(u, err); CHK; - ierr = VecAXPY(err, -1.0, u_exact); CHK; - ierr = VecNorm(err, NORM_2, &norm2); CHK; - ierr = VecNorm(err, NORM_INFINITY, &normM); CHK; - - // print infromation - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tSolve Time: %f\n", time); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tL2-Norm: %g\n", (double)norm2); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tMax-Norm: %g\n", (double)normM); CHK; - ierr = PetscPrintf(PETSC_COMM_WORLD, - "\tIterations %D\n", Niters); CHK; - - return 0; - }; - - - auto solving = - [&ierr, &A, &u, &rhs, &amgx, &postSolving] (PetscLogEvent &event) -> PetscLogDouble - { - PetscLogDouble bgTime, - edTime; - - // set all entries as zeros in the vector of unknows - ierr = MPI_Barrier(PETSC_COMM_WORLD); CHK; - ierr = VecSet(u, 0.0); CHK; - - // beging logging this solving event - ierr = PetscLogEventBegin(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - // obtain the begining time - ierr = PetscTime(&bgTime); CHK; - - // solve - ierr = amgx.solve(u, rhs); CHK; - - // obtain the ending time - ierr = PetscTime(&edTime); CHK; - - // end logging this solving event - ierr = PetscLogEventEnd(event, - (PetscObject) A, (PetscObject) rhs, (PetscObject) u, 0); CHK; - - ierr = postSolving(edTime - bgTime); CHK; - - return edTime - bgTime; - }; - - - // start a warm-up cycle - ierr = PetscPrintf(PETSC_COMM_WORLD, "Warm-up cycle ... \n"); CHK; - solving(warmUpEvent); - - - // start `Nruns` runs to get averaged solving time - for(int i=0; i -# include -# include -# include -# include -# include - -# include -# include - -# include -# include -# include - -# include "check.hpp" - -/** - * @brief A wrapper class for an interface between PETSc and AmgX - * - * This class is a wrapper of AmgX library. PETSc user only need to pass - * PETSc matrix and vectors into the AmgXSolver instance to solve their problem. - * - */ -class AmgXSolver -{ - public: - - /// default constructor - AmgXSolver() = default; - - /// initialization of instance - int initialize(MPI_Comm comm, - const std::string &_mode, const std::string &cfg_file); - - /// finalization - int finalize(); - - /// convert PETSc matrix into AmgX matrix and pass it to solver - int setA(const Mat &A); - - /// solve the problem, soultion vector will be updated in the end - int solve(Vec &p, Vec &b); - - /// Get the number of iterations of last solve phase - int getIters(); - - /// Get the residual at a specific iteration in last solve phase - double getResidual(const int &iter); - - /// get the memory usage on device - int getMemUsage(); - - - private: - - - - int nDevs, /*< # of cuda devices*/ - devID; - - int gpuProc = MPI_UNDEFINED; - - MPI_Comm globalCpuWorld, - localCpuWorld, - gpuWorld, - devWorld; - - int globalSize, - localSize, - gpuWorldSize, - devWorldSize; - - int myGlobalRank, - myLocalRank, - myGpuWorldRank, - myDevWorldRank; - - int nodeNameLen; - char nodeName[MPI_MAX_PROCESSOR_NAME]; - - - - static int count; /*!< only one instance allowed*/ - int ring; /*< a parameter used by AmgX*/ - - AMGX_Mode mode; /*< AmgX mode*/ - AMGX_config_handle cfg = nullptr; /*< AmgX config object*/ - AMGX_matrix_handle AmgXA = nullptr; /*< AmgX coeff mat*/ - AMGX_vector_handle AmgXP = nullptr, /*< AmgX unknowns vec*/ - AmgXRHS = nullptr; /*< AmgX RHS vec*/ - AMGX_solver_handle solver = nullptr; /*< AmgX solver object*/ - static AMGX_resources_handle rsrc; /*< AmgX resource object*/ - - - - bool isInitialized = false; /*< as its name*/ - - - - /// set up the mode of AmgX solver - int setMode(const std::string &_mode); - - /// a printing function using stdout - static void print_callback(const char *msg, int length); - - /// a printing function that prints nothing, used by AmgX - static void print_none(const char *msg, int length); - - - int initMPIcomms(MPI_Comm &comm); - int initAmgX(const std::string &_mode, const std::string &_cfg); - - - VecScatter redistScatter = nullptr; - Vec redistLhs = nullptr, - redistRhs = nullptr; - - int getLocalMatRawData(Mat &localA, PetscInt &localN, - std::vector &row, std::vector &col, - std::vector &data); - - int getDevIS(const Mat &A, IS &devIS); - int getLocalA(const Mat &A, const IS &devIS, Mat &localA); - int redistMat(const Mat &A, const IS &devIS, Mat &newA); - int getPartVec( - const IS &devIS, const PetscInt &N, std::vector &partVec); - int destroyLocalA(const Mat &A, Mat &localA); - int getVecScatter(const Mat &A1, const Mat &A2, const IS &devIS); - - int solve_real(Vec &p, Vec &b); - -}; diff --git a/external/AmgXWrapper-1.0-beta2/src/check.hpp b/external/AmgXWrapper-1.0-beta2/src/check.hpp deleted file mode 100644 index 02d5979e..00000000 --- a/external/AmgXWrapper-1.0-beta2/src/check.hpp +++ /dev/null @@ -1,14 +0,0 @@ -# pragma once - -# define CHECK(call) \ -{ \ - const cudaError_t error = call; \ - if (error != cudaSuccess) \ - { \ - printf("Error: %s:%d, ", __FILE__, __LINE__); \ - printf("code:%d, reason: %s\n", error, cudaGetErrorString(error)); \ - exit(1); \ - } \ -} - -# define CHK CHKERRQ(ierr) diff --git a/external/AmgXWrapper-1.0-beta2/src/init.inl b/external/AmgXWrapper-1.0-beta2/src/init.inl deleted file mode 100644 index 3ad2f09e..00000000 --- a/external/AmgXWrapper-1.0-beta2/src/init.inl +++ /dev/null @@ -1,276 +0,0 @@ -/** - * @file init.inl - * @brief Definition of some member functions of the class AmgXSolver - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2016-01-08 - */ -# include "AmgXSolver.hpp" - - -/** - * @brief Initialization of AmgXSolver instance - * - * @param comm MPI communicator for all processes - * @param _mode The mode this solver will run in. Please refer to AmgX manual. - * @param cfg_file A file containing the configurations of this solver - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::initialize(MPI_Comm comm, - const std::string &_mode, const std::string &cfg_file) -{ - // get the number of total cuda devices - CHECK(cudaGetDeviceCount(&nDevs)); - - // Check whether there is at least one CUDA device on this node - if (nDevs == 0) - { - std::cerr << "There are no CUDA devices on the node " - << nodeName << " !!" << std::endl; - - exit(EXIT_FAILURE); - } - - // initialize other communicators - initMPIcomms(comm); - - if (gpuProc == 0) initAmgX(_mode, cfg_file); - - return 0; -} - - -/** - * @brief Initialize different MPI communicators - * - * This private initializes all communicators needed: - * - * 1. globalCpuWorld is the communicator for all cpu processors, which is - * usually the same with MPI_COMM_WORLD - * 2. localCpuWorld is the communicaotr for cpu processors located in the same - * node, which can use CUDA devices on that node - * 3. gpuWorld is the communicator for the cpu processors that involved in AmgX - * function calls, i.e., those who will call AmgX functions - * 4. devWorld is the communicator for the cpu processors that share one CUDA - * device. The first processor in this communicator will also be in gpuWorld. - * And all other processors in this communicator will transfer their data to - * that fisrt processor. - * - * XXXXXXXSize and XXXXXXXRank represent the size and rank obtained from these - * communicators. - * - * @param comm A communicator for all processes - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::initMPIcomms(MPI_Comm &comm) -{ - // Get the name of this node - MPI_Get_processor_name(nodeName, &nodeNameLen); - - // Copy communicator for all processors - globalCpuWorld = comm; - MPI_Comm_set_name(globalCpuWorld, "globalCpuWorld"); - - // get size and rank for global communicator - MPI_Comm_size(globalCpuWorld, &globalSize); - MPI_Comm_rank(globalCpuWorld, &myGlobalRank); - - // Get the communicator for processors on the same node (local world) - MPI_Comm_split_type(globalCpuWorld, - MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &localCpuWorld); - MPI_Comm_set_name(localCpuWorld, "localCpuWorld"); - - // get size and rank for local communicator - MPI_Comm_size(localCpuWorld, &localSize); - MPI_Comm_rank(localCpuWorld, &myLocalRank); - - - if (nDevs == localSize) - { - devID = myLocalRank; - gpuProc = 0; - } - else if (nDevs > localSize) - { - PetscPrintf(localCpuWorld, - "CUDA devices on the node %s ", nodeName); - PetscPrintf(localCpuWorld, - "are more than the MPI processes launched. "); - PetscPrintf(localCpuWorld, - "Only %d CUDA devices will be used.\n", localSize); - - devID = myLocalRank; - gpuProc = 0; - } - else - { - int nBasic = localSize / nDevs, - nRemain = localSize % nDevs; - - if (myLocalRank < (nBasic+1)*nRemain) - { - devID = myLocalRank / (nBasic + 1); - if (myLocalRank % (nBasic + 1) == 0) gpuProc = 0; - } - else - { - devID = (myLocalRank - (nBasic+1)*nRemain) / nBasic + nRemain; - if ((myLocalRank - (nBasic+1)*nRemain) % nBasic == 0) gpuProc = 0; - } - } - - MPI_Barrier(globalCpuWorld); - - // split the global world into a world involved in AmgX and a null world - MPI_Comm_split(globalCpuWorld, gpuProc, 0, &gpuWorld); - MPI_Comm_set_name(gpuWorld, "gpuWorld"); - - // get size and rank for the communicator corresponding to gpuWorld - if (gpuWorld != MPI_COMM_NULL) - { - MPI_Comm_size(gpuWorld, &gpuWorldSize); - MPI_Comm_rank(gpuWorld, &myGpuWorldRank); - } - else - { - gpuWorldSize = MPI_UNDEFINED; - myGpuWorldRank = MPI_UNDEFINED; - } - - - // split local world into worlds corresponding to each CUDA device - MPI_Comm_split(localCpuWorld, devID, 0, &devWorld); - MPI_Comm_set_name(devWorld, "devWorld"); - - // get size and rank for the communicator corresponding to myWorld - MPI_Comm_size(devWorld, &devWorldSize); - MPI_Comm_rank(devWorld, &myDevWorldRank); - - MPI_Barrier(globalCpuWorld); - - return 0; -} - - - -/** - * @brief Initialize the AmgX library - * - * This function initializes the current instance (solver). Based on the count, - * only the instance initialized first is in charge of initializing AmgX and the - * resource instance. - * - * @param _mode The mode this solver will run in. Please refer to AmgX manual. - * @param _cfg A file containing the configurations of this solver - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::initAmgX(const std::string &_mode, const std::string &_cfg) -{ - count += 1; - - // only the first instance (AmgX solver) is in charge of initializing AmgX - if (count == 1) - { - // initialize AmgX - AMGX_SAFE_CALL(AMGX_initialize()); - - // intialize AmgX plugings - AMGX_SAFE_CALL(AMGX_initialize_plugins()); - - // use user-defined output mechanism. only the master process can output - // something on the screen - if (myGpuWorldRank == 0) - { - AMGX_SAFE_CALL( - AMGX_register_print_callback(&(AmgXSolver::print_callback))); - } - else - { - AMGX_SAFE_CALL( - AMGX_register_print_callback(&(AmgXSolver::print_none))); - } - - // let AmgX to handle errors returned - AMGX_SAFE_CALL(AMGX_install_signal_handler()); - } - - // create an AmgX configure object - AMGX_SAFE_CALL(AMGX_config_create_from_file(&cfg, _cfg.c_str())); - - // let AmgX handle returned error codes internally - AMGX_SAFE_CALL(AMGX_config_add_parameters(&cfg, "exception_handling=1")); - - // create an AmgX resource object, only the first instance is in charge - if (count == 1) AMGX_resources_create(&rsrc, cfg, &gpuWorld, 1, &devID); - - // set mode - setMode(_mode); - - // create AmgX vector object for unknowns and RHS - AMGX_vector_create(&AmgXP, rsrc, mode); - AMGX_vector_create(&AmgXRHS, rsrc, mode); - - // create AmgX matrix object for unknowns and RHS - AMGX_matrix_create(&AmgXA, rsrc, mode); - - // create an AmgX solver object - AMGX_solver_create(&solver, rsrc, mode, cfg); - - // obtain the default number of rings based on current configuration - AMGX_config_get_default_number_of_rings(cfg, &ring); - - isInitialized = true; - - return 0; -} - - -/** - * @brief Finalizing the instance. - * - * This function destroys AmgX data. The instance last destroyed also needs to - * destroy shared resource instance and finalizing AmgX. - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::finalize() -{ - - if (gpuProc == 0) - { - // destroy solver instance - AMGX_solver_destroy(solver); - - // destroy matrix instance - AMGX_matrix_destroy(AmgXA); - - // destroy RHS and unknown vectors - AMGX_vector_destroy(AmgXP); - AMGX_vector_destroy(AmgXRHS); - - // only the last instance need to destroy resource and finalizing AmgX - if (count == 1) - { - AMGX_resources_destroy(rsrc); - AMGX_SAFE_CALL(AMGX_config_destroy(cfg)); - - AMGX_SAFE_CALL(AMGX_finalize_plugins()); - AMGX_SAFE_CALL(AMGX_finalize()); - } - else - { - AMGX_config_destroy(cfg); - } - - // change status - isInitialized = false; - - count -= 1; - } - - return 0; -} - diff --git a/external/AmgXWrapper-1.0-beta2/src/misc.inl b/external/AmgXWrapper-1.0-beta2/src/misc.inl deleted file mode 100644 index 5c6aa49a..00000000 --- a/external/AmgXWrapper-1.0-beta2/src/misc.inl +++ /dev/null @@ -1,122 +0,0 @@ -/** - * @file misc.cpp - * @brief Definition of some member functions of the class AmgXSolver - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2016-01-08 - */ -# include "AmgXSolver.hpp" - - -/** - * @brief Setting up AmgX mode. - * - * Convert a STL string to AmgX mode and then store this mode. For the usage of - * AmgX modes, please refer to AmgX manual. - * - * @param _mode A STL string describing the mode. - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::setMode(const std::string &_mode) -{ - if (_mode == "hDDI") - mode = AMGX_mode_hDDI; - else if (_mode == "hDFI") - mode = AMGX_mode_hDFI; - else if (_mode == "hFFI") - mode = AMGX_mode_hFFI; - else if (_mode == "dDDI") - mode = AMGX_mode_dDDI; - else if (_mode == "dDFI") - mode = AMGX_mode_dDFI; - else if (_mode == "dFFI") - mode = AMGX_mode_dFFI; - else - { - std::cerr << "error: " - << _mode << " is not an available mode." << std::endl; - exit(0); - } - return 0; -} - - -/** - * @brief Get the number of iterations of last solve phase - * - * @return number of iterations - */ -int AmgXSolver::getIters() -{ - int iter = 0; - - if (gpuProc == 0) - AMGX_solver_get_iterations_number(solver, &iter); - - return iter; -} - - -/** - * @brief Get the residual at a specific iteration in last solve phase - * - * @param iter a specific iteration during the last solve phase - * - * @return residual - */ -double AmgXSolver::getResidual(const int &iter) -{ - double res = 0; - - if (gpuProc == 0) - AMGX_solver_get_iteration_residual(solver, iter, 0, &res); - - return res; -} - - -/** - * @brief A printing function, using stdout, needed by AmgX. - * - * @param msg C-style string - * @param length The length of the string - */ -void AmgXSolver::print_callback(const char *msg, int length) -{ - std::cout << msg; -} - - -/** - * @brief A printing function, print nothing, needed by AmgX. - * - * @param msg C-style string - * @param length The length of the string - */ -void AmgXSolver::print_none(const char *msg, int length) { } - - -/** - * @brief Get the memory usage on devices - * - * @return error codes in the future. - */ -int AmgXSolver::getMemUsage() -{ - size_t free_byte, - total_byte; - - if (gpuProc == 0) - { - CHECK(cudaMemGetInfo(&free_byte, &total_byte)); - - std::cout << "myGlobalRank: " << myGlobalRank << " " - << free_byte / 1024.0 / 1024.0 << " MB " - << " / " << total_byte / 1024.0 / 1024.0 << " MB " << std::endl; - } - - return 0; -} - - diff --git a/external/AmgXWrapper-1.0-beta2/src/setA.inl b/external/AmgXWrapper-1.0-beta2/src/setA.inl deleted file mode 100644 index 89c15ac6..00000000 --- a/external/AmgXWrapper-1.0-beta2/src/setA.inl +++ /dev/null @@ -1,302 +0,0 @@ -/** - * @file setA.inl - * @brief Definition of some member functions of the class AmgXSolver - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2016-01-08 - */ -# include "AmgXSolver.hpp" - - -/** - * @brief A function convert PETSc Mat into AmgX matrix and bind it to solver - * - * This function will first extract the raw data from PETSc Mat and convert the - * column index into 64bit integers. It also create a partition vector that is - * required by AmgX. Then, it upload the raw data to AmgX. Finally, it binds - * the AmgX matrix to the AmgX solver. - * - * Be cautious! It lacks mechanism to check whether the PETSc Mat is AIJ format - * and whether the PETSc Mat is using the same MPI communicator as the - * AmgXSolver instance. - * - * @param A A PETSc Mat. The coefficient matrix of a system of linear equations. - * The matrix must be AIJ format and using the same MPI communicator as AmgX. - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::setA(const Mat &A) -{ - PetscErrorCode ierr; - - - Mat localA; - - IS devIS; - - PetscInt nGlobalRows, - nLocalRows; - - std::vector row; - std::vector col; - std::vector data; - std::vector partVec; - - - // Get number of rows in global matrix - ierr = MatGetSize(A, &nGlobalRows, nullptr); CHK; - - ierr = getDevIS(A, devIS); CHK; - ierr = getLocalA(A, devIS, localA); CHK; - ierr = getLocalMatRawData(localA, nLocalRows, row, col, data); CHK; - ierr = destroyLocalA(A, localA); CHK; - - ierr = getPartVec(devIS, nGlobalRows, partVec); CHK; - - - // upload matrix A to AmgX - if (gpuWorld != MPI_COMM_NULL) - { - MPI_Barrier(gpuWorld); - AMGX_matrix_upload_all_global( - AmgXA, nGlobalRows, nLocalRows, row[nLocalRows], - 1, 1, row.data(), col.data(), data.data(), - nullptr, ring, ring, partVec.data()); - - // bind the matrix A to the solver - MPI_Barrier(gpuWorld); - AMGX_solver_setup(solver, AmgXA); - - // connect (bind) vectors to the matrix - AMGX_vector_bind(AmgXP, AmgXA); - AMGX_vector_bind(AmgXRHS, AmgXA); - } - MPI_Barrier(globalCpuWorld); - - return 0; -} - - -int AmgXSolver::getLocalA(const Mat &A, const IS &devIS, Mat &localA) -{ - PetscErrorCode ierr; - MatType type; - - Mat tempA; - - // Get the Mat type - ierr = MatGetType(A, &type); CHK; - - // Check whether the Mat type is supported - if (std::strcmp(type, MATSEQAIJ) == 0) - { - // make localA point to the same memory as A does - localA = A; - } - else if (std::strcmp(type, MATMPIAIJ) == 0) - { - redistMat(A, devIS, tempA); - - ierr = MatMPIAIJGetLocalMat( - tempA, MAT_INITIAL_MATRIX, &localA); CHK; - - if (tempA == A) - { - tempA = nullptr; - } - else - { - ierr = MatDestroy(&tempA); CHK; - } - } - else - { - std::cerr << "Mat type " << type - << " is not supported!" << std::endl; - exit(0); - } - - return 0; -} - - -int AmgXSolver::getDevIS(const Mat &A, IS &devIS) -{ - PetscErrorCode ierr; - - // get index sets of A locally owned by each process - // note that devIS is now a serial IS on each process - ierr = MatGetOwnershipIS(A, &devIS, nullptr); CHK; - - // concatenate index sets that belong to the same devWorld - // note that now devIS is a parallel IS of communicator devWorld - ierr = ISOnComm(devIS, devWorld, PETSC_USE_POINTER, &devIS); CHK; - - // all gather in order to have all indices belong to a devWorld on the - // leading rank of that devWorld. This is not efficient. - // note that now devIS is again a serial IS on each process - ierr = ISAllGather(devIS, &devIS); CHK; - - // empty devIS on ranks other than the leading ranks in each devWorld - if (myDevWorldRank != 0) - ierr = ISGeneralSetIndices(devIS, 0, nullptr, PETSC_COPY_VALUES); CHK; - - // devIS is not guaranteed to be sorted. We sort it here. - ierr = ISSort(devIS); CHK; - - return 0; -} - - -int AmgXSolver::redistMat(const Mat &A, const IS &devIS, Mat &newA) -{ - PetscErrorCode ierr; - - if (gpuWorldSize == globalSize) - { - newA = A; - } - else - { - IS is; - ierr = ISOnComm(devIS, globalCpuWorld, PETSC_USE_POINTER, &is); CHK; - ierr = MatGetSubMatrix(A, is, is, MAT_INITIAL_MATRIX, &newA); CHK; - - ierr = getVecScatter(A, newA, is); CHK; - ierr = ISDestroy(&is); CHK; - } - - return 0; -} - - -int AmgXSolver::getPartVec( - const IS &devIS, const PetscInt &N, std::vector &partVec) -{ - PetscErrorCode ierr; - - VecScatter scatter; - Vec tempMPI, - tempSEQ; - - PetscInt n; - - PetscScalar *tempPartVec; - - ierr = ISGetLocalSize(devIS, &n); CHK; - - if (gpuWorld != MPI_COMM_NULL) - { - ierr = VecCreateMPI(gpuWorld, n, N, &tempMPI); CHK; - - IS is; - ierr = ISOnComm(devIS, gpuWorld, PETSC_USE_POINTER, &is); CHK; - ierr = VecISSet(tempMPI, is, (PetscScalar) myGpuWorldRank); CHK; - ierr = ISDestroy(&is); CHK; - - ierr = VecScatterCreateToAll(tempMPI, &scatter, &tempSEQ); CHK; - ierr = VecScatterBegin(scatter, - tempMPI, tempSEQ, INSERT_VALUES, SCATTER_FORWARD); CHK; - ierr = VecScatterEnd(scatter, - tempMPI, tempSEQ, INSERT_VALUES, SCATTER_FORWARD); CHK; - - ierr = VecScatterDestroy(&scatter); CHK; - ierr = VecDestroy(&tempMPI); CHK; - - ierr = VecGetArray(tempSEQ, &tempPartVec); CHK; - - partVec.assign(tempPartVec, tempPartVec+N); - - ierr = VecRestoreArray(tempSEQ, &tempPartVec); CHK; - - ierr = VecDestroy(&tempSEQ); CHK; - } - MPI_Barrier(globalCpuWorld); - - return 0; -} - - -int AmgXSolver::destroyLocalA(const Mat &A, Mat &localA) -{ - PetscErrorCode ierr; - MatType type; - - // Get the Mat type - ierr = MatGetType(A, &type); CHK; - - // Check whether the Mat type is supported - if (std::strcmp(type, MATSEQAIJ) == 0) - { - localA = nullptr; - } - else if (std::strcmp(type, MATMPIAIJ) == 0) - { - ierr = MatDestroy(&localA); CHK; - } - - return 0; -} - - -int AmgXSolver::getLocalMatRawData(Mat &localA, PetscInt &localN, - std::vector &row, std::vector &col, - std::vector &data) -{ - PetscErrorCode ierr; - PetscInt tempN; - const PetscInt *rawCol, - *rawRow; - PetscScalar *rawData; - PetscBool done; - - ierr = MatGetRowIJ(localA, 0, PETSC_FALSE, PETSC_FALSE, - &tempN, &rawRow, &rawCol, &done); CHK; - - if (! done) - { - std::cerr << "MatGetRowIJ did not work!" << std::endl; - exit(0); - } - - ierr = MatSeqAIJGetArray(localA, &rawData); CHK; - - localN = tempN; - - col.assign(rawCol, rawCol+rawRow[localN]); - row.assign(rawRow, rawRow+localN+1); - data.assign(rawData, rawData+rawRow[localN]); - - - ierr = MatRestoreRowIJ(localA, 0, PETSC_FALSE, PETSC_FALSE, - &tempN, &rawRow, &rawCol, &done); CHK; - - // check whether MatRestoreRowIJ worked - if (! done) - { - std::cerr << "MatRestoreRowIJ did not work!" << std::endl; - exit(0); - } - - ierr = MatSeqAIJRestoreArray(localA, &rawData); CHK; - - return 0; -} - - -int AmgXSolver::getVecScatter(const Mat &A1, const Mat &A2, const IS &devIS) -{ - PetscErrorCode ierr; - - Vec tempV; - - ierr = MatCreateVecs(A1, nullptr, &tempV); CHK; - ierr = MatCreateVecs(A2, nullptr, &redistRhs); CHK; - ierr = MatCreateVecs(A2, nullptr, &redistLhs); CHK; - - ierr = VecScatterCreate(tempV, devIS, redistLhs, devIS, &redistScatter); CHK; - - ierr = VecDestroy(&tempV); CHK; - - return 0; -} diff --git a/external/AmgXWrapper-1.0-beta2/src/solve.inl b/external/AmgXWrapper-1.0-beta2/src/solve.inl deleted file mode 100644 index d59e8a95..00000000 --- a/external/AmgXWrapper-1.0-beta2/src/solve.inl +++ /dev/null @@ -1,106 +0,0 @@ -/** - * @file solve.inl - * @brief Definition of some member functions of the class AmgXSolver - * @author Pi-Yueh Chuang (pychuang@gwu.edu) - * @version alpha - * @date 2016-01-08 - */ -# include "AmgXSolver.hpp" - - -int AmgXSolver::solve(Vec &p, Vec &b) -{ - PetscErrorCode ierr; - - if (redistScatter != nullptr) - { - ierr = VecScatterBegin(redistScatter, - b, redistRhs, INSERT_VALUES, SCATTER_FORWARD); CHK; - ierr = VecScatterEnd(redistScatter, - b, redistRhs, INSERT_VALUES, SCATTER_FORWARD); CHK; - - ierr = VecScatterBegin(redistScatter, - p, redistLhs, INSERT_VALUES, SCATTER_FORWARD); CHK; - ierr = VecScatterEnd(redistScatter, - p, redistLhs, INSERT_VALUES, SCATTER_FORWARD); CHK; - - if (gpuWorld != MPI_COMM_NULL) - { - ierr = solve_real(redistLhs, redistRhs); CHK; - } - MPI_Barrier(globalCpuWorld); - - ierr = VecScatterBegin(redistScatter, - redistLhs, p, INSERT_VALUES, SCATTER_REVERSE); CHK; - ierr = VecScatterEnd(redistScatter, - redistLhs, p, INSERT_VALUES, SCATTER_REVERSE); CHK; - } - else - { - if (gpuWorld != MPI_COMM_NULL) - { - ierr = solve_real(p, b); CHK; - } - MPI_Barrier(globalCpuWorld); - } - - return 0; -} - - -/** - * @brief Solve the linear problem based on given RHS and initial guess - * - * This function solve the linear problem. Users need to set matrix A before - * calling this function. The result will be saved back to the PETSc Vec - * containing initial guess. - * - * It lacks mechanisms to check whether necessary initialization and setting - * matrix A are done first. - * - * @param p Unknowns vector. The values passed in will be an initial guess. - * @param b Right-hand-side vector. - * - * @return Currently meaningless. May be error codes in the future. - */ -int AmgXSolver::solve_real(Vec &p, Vec &b) -{ - PetscErrorCode ierr; - double *unks, - *rhs; - int size; - AMGX_SOLVE_STATUS status; - - // get size of local vector (p and b should have the same local size) - ierr = VecGetLocalSize(p, &size); CHK; - - // get pointers to the raw data of local vectors - ierr = VecGetArray(p, &unks); CHK; - ierr = VecGetArray(b, &rhs); CHK; - - // upload vectors to AmgX - AMGX_vector_upload(AmgXP, size, 1, unks); - AMGX_vector_upload(AmgXRHS, size, 1, rhs); - - // solve - MPI_Barrier(gpuWorld); - AMGX_solver_solve(solver, AmgXRHS, AmgXP); - - // get the status of the solver - AMGX_solver_get_status(solver, &status); - - // check whether the solver successfully solve the problem - if (status != AMGX_SOLVE_SUCCESS) - std::cout << "AmgX solver failed to solve the problem! " - << "Solver status: " << status << std::endl; - - // download data from device - AMGX_vector_download(AmgXP, unks); - - // restore PETSc vectors - ierr = VecRestoreArray(p, &unks); CHK; - ierr = VecRestoreArray(b, &rhs); CHK; - - return 0; -} - diff --git a/external/AmgXWrapper-1.0-beta2/.gitignore b/external/AmgXWrapper-1.4/.gitignore similarity index 93% rename from external/AmgXWrapper-1.0-beta2/.gitignore rename to external/AmgXWrapper-1.4/.gitignore index 953a8a62..8453d622 100644 --- a/external/AmgXWrapper-1.0-beta2/.gitignore +++ b/external/AmgXWrapper-1.4/.gitignore @@ -63,3 +63,7 @@ tests/benchmarks/configs tests/benchmarks/logs tests/benchmarks/results tests/benchmarks/errors + +# Ignore build and install folders +build +install diff --git a/external/AmgXWrapper-1.4/CMakeLists.txt b/external/AmgXWrapper-1.4/CMakeLists.txt new file mode 100644 index 00000000..fcfaf9c0 --- /dev/null +++ b/external/AmgXWrapper-1.4/CMakeLists.txt @@ -0,0 +1,279 @@ +# ===================================================================== +# \file CMakeLists.txt +# \brief for cmake +# \author Pi-Yueh Chuang (pychuang@gwu.edu) +# \date 2017-05-24 +# ===================================================================== + + +CMAKE_MINIMUM_REQUIRED(VERSION 3.0.2) + + +# ===================================================================== +# Cache variables +# ===================================================================== + +# set default c++ compilers +IF (NOT DEFINED ENV{CXX}) + SET(ENV{CXX} mpicxx) +ENDIF() + +# set default c compilers +IF (NOT DEFINED ENV{CC}) + SET(ENV{CC} mpicc) +ENDIF() + +# set default flags for release and debug mode +SET(CMAKE_CXX_FLAGS_DEBUG "-g" CACHE STRING "") +SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "") +SET(CMAKE_C_FLAGS_DEBUG "-g" CACHE STRING "") +SET(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "") +SET(CMAKE_SHARED_LINKER_FLAGS "-Wl,--no-undefined" CACHE STRING "") + +# set default build type +SET(CMAKE_BUILD_TYPE RELEASE CACHE STRING "") + +SET(PETSC_DIR "$ENV{PETSC_DIR}" CACHE PATH "The path to PETSc.") +SET(PETSC_ARCH "$ENV{PETSC_ARCH}" CACHE STRING "The specific build of PETSc under PETSC_DIR.") +SET(CUDA_DIR "$ENV{CUDA_DIR}" CACHE PATH "The path to CUDA.") +SET(AMGX_DIR "$ENV{AMGX_DIR}" CACHE PATH "The path to AmgX.") + + +# ===================================================================== +# Project settings +# ===================================================================== + +MESSAGE("") +MESSAGE("====================================") +MESSAGE("Begin configuration") +MESSAGE("====================================") + +# start generator +PROJECT(AmgxWrapper C CXX) + +# use GNU standard installation folder heirarchy +INCLUDE(GNUInstallDirs) + +# set the sub folders in build folder +SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}) +SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}) + +# Not many vendors are supported by CMAKE_CXX_STANDARD variable before cmake 3.9 +# so we decided to check C++11 flag manually +INCLUDE(CheckCXXCompilerFlag) +CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11) +IF(COMPILER_SUPPORTS_CXX11) + SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +ELSE() + MESSAGE(FATAL_ERROR + "Compiler ${CMAKE_CXX_COMPILER} does not support flag -std=c++11. \ + Please specify C++11 flag manually through CMAKE_CXX_FLAGS.") +ENDIF() + +# other cmake setting +SET(CMAKE_VERBOSE_MAKEFILE ON) +SET(CMAKE_COLOR_MAKEFILE ON) + +# add options +OPTION(BUILD_SHARED_LIBS "Whether to build shared library." ON) + +# add cmake-modules to CMake module searching path +LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules") + + +# ===================================================================== +# PETSc +# ===================================================================== + +MESSAGE("") +MESSAGE("-- Finding PETSc") + +FIND_PACKAGE(PETSc REQUIRED) + +IF(${PETSc_FOUND}) + IF (${PETSC_VERSION} VERSION_LESS "3.8") + MESSAGE(FATAL_ERROR "ERROR: the version of PETSc should >= 3.8") + ENDIF() + MESSAGE("-- Finding PETSc - Success") +ENDIF() + + +# ===================================================================== +# CUDA +# ===================================================================== + +MESSAGE("") +MESSAGE("-- Finding CUDA") + +SET(CUDA_TOOLKIT_ROOT_DIR ${CUDA_DIR} CACHE PATH "" FORCE) + +FIND_PACKAGE(CUDA REQUIRED) + +IF(${CUDA_FOUND}) + SET(CUDA_LIBRARY_DIRS ${CUDA_TOOLKIT_ROOT_DIR}/lib64) + MESSAGE("-- Finding CUDA - Success") +ENDIF() + + +# ===================================================================== +# AmgX +# ===================================================================== + +MESSAGE("") +MESSAGE("-- Finding AmgX") + +MESSAGE("-- Finding amgx_c.h") +FIND_PATH(AMGX_INCLUDE_DIRS + NAMES amgx_c.h + PATHS ${AMGX_DIR} $ENV{AMGX_DIR} + PATH_SUFFIXES "base/include" "examples") + +IF(${AMGX_INCLUDE_DIRS} STREQUAL "AMGX_INCLUDE_DIRS-NOTFOUND") + MESSAGE(FATAL_ERROR "Could not find amgx_c.h!!!") +ELSE() + MESSAGE("-- Finding amgx_c.h - found in " ${AMGX_INCLUDE_DIRS}) +ENDIF() + + +MESSAGE("-- Finding amgx_config.h") +FIND_FILE(AMGX_CONFIG_FOUND + NAMES amgx_config.h + PATHS ${AMGX_INCLUDE_DIRS} + NO_DEFAULT_PATH) + +IF(${AMGX_CONFIG_FOUND} STREQUAL "AMGX_CONFIG_FOUND-NOTFOUND") + MESSAGE(FATAL_ERROR "Could not find amgx_config.h in " ${AMGX_INCLUDE_DIRS}) +ELSE() + MESSAGE("-- Finding amgx_config.h - found") +ENDIF() + + +MESSAGE("-- Finding libamgxsh.so") +FIND_LIBRARY(AMGX_LIBRARIES + NAMES amgxsh + PATHS ${AMGX_DIR} $ENV{AMGX_DIR} + PATH_SUFFIXES "lib") + +IF(${AMGX_LIBRARIES} STREQUAL "AMGX_LIBRARIES-NOTFOUND") + MESSAGE(FATAL_ERROR "libamgxsh.so was not found") +ELSE() + MESSAGE("-- Finding libamgxsh.so - found: " ${AMGX_LIBRARIES}) +ENDIF() + +MESSAGE("-- Finding AmgX - Success") + + +# ===================================================================== +# Doxygen +# ===================================================================== + +MESSAGE("") +MESSAGE("-- Finding Doxygen") + +FIND_PACKAGE(Doxygen) + +IF (DOXYGEN_FOUND) + MESSAGE("-- Finding Doxygen - Success") + + SET(DOXYGEN_INPUT ${CMAKE_SOURCE_DIR}/doc/Doxyfile) + SET(DOXYGEN_OUTPUT ${PROJECT_BINARY_DIR}/doc) + FILE(MAKE_DIRECTORY ${DOXYGEN_OUTPUT}) +ELSE() + MESSAGE("-- Finding Doxygen - Failed.") +ENDIF() + +# ===================================================================== +# Targets +# ===================================================================== + +SET(SRC ${CMAKE_SOURCE_DIR}/src) +SET(SOURCE + ${SRC}/AmgXSolver.cpp + ${SRC}/init.cpp + ${SRC}/misc.cpp + ${SRC}/setA.cpp + ${SRC}/solve.cpp) + +# target AmgXWrapper +ADD_LIBRARY(AmgXWrapper ${SOURCE}) + +TARGET_INCLUDE_DIRECTORIES(AmgXWrapper + PRIVATE ${PETSC_INCLUDES} + PRIVATE ${CUDA_INCLUDE_DIRS} + PRIVATE ${AMGX_INCLUDE_DIRS} + PUBLIC ${SRC}) + + +TARGET_LINK_LIBRARIES(AmgXWrapper + PRIVATE ${PETSC_LIBRARIES} + PRIVATE ${AMGX_LIBRARIES} + PRIVATE ${CUDA_LIBRARIES}) + +ADD_CUSTOM_COMMAND( + TARGET AmgXWrapper + POST_BUILD + COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/include + COMMAND ${CMAKE_COMMAND} -E copy ${SRC}/AmgXSolver.hpp ${PROJECT_BINARY_DIR}/include) + +# target doc +IF (DOXYGEN_FOUND) + ADD_CUSTOM_TARGET(doc + COMMAND ${CMAKE_COMMAND} -E echo "Building API Documentation..." + COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_INPUT} + COMMAND ${CMAKE_COMMAND} -E echo "Done." + WORKING_DIRECTORY ${PROJECT_BINARY_DIR}) +ENDIF() + +# installation +INSTALL(TARGETS AmgXWrapper + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + +INSTALL(FILES ${SRC}/AmgXSolver.hpp DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +INSTALL(DIRECTORY ${PROJECT_BINARY_DIR}/doc DESTINATION ${CMAKE_INSTALL_PREFIX}) + +# ===================================================================== +# Print information +# ===================================================================== + +MESSAGE("") +MESSAGE("====================================") +MESSAGE("Config Information:") +MESSAGE("====================================") +MESSAGE("") + +MESSAGE("Build type: " ${CMAKE_BUILD_TYPE}) +MESSAGE("Build shared library: " ${BUILD_SHARED_LIBS}) +MESSAGE("Doxygen available: " ${DOXYGEN_FOUND}) +MESSAGE("Installation path: " ${CMAKE_INSTALL_PREFIX}) +MESSAGE("") + +MESSAGE("Compilers:") +MESSAGE("\tCXX compiler: " ${CMAKE_CXX_COMPILER}) +MESSAGE("\tC compiler: " ${CMAKE_C_COMPILER}) +MESSAGE("") + +MESSAGE("Flags:") +MESSAGE("\tCXX: " ${CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE}}) +MESSAGE("") + +MESSAGE("PETSc:") +MESSAGE("\tPETSc dir: " ${PETSC_DIR}) +MESSAGE("\tHeader path: " ${PETSC_INCLUDES}) +MESSAGE("\tLibraries: " ${PETSC_LIBRARIES}) +MESSAGE("") + +MESSAGE("CUDA:") +MESSAGE("\tCUDA dir: " ${CUDA_TOOLKIT_ROOT_DIR}) +MESSAGE("\tVersion: " ${CUDA_VERSION_STRING}) +MESSAGE("\tHeader path: " ${CUDA_INCLUDE_DIRS}) +MESSAGE("\tLibrary path: " ${CUDA_LIBRARY_DIRS}) +MESSAGE("\tLibraries: " ${CUDA_LIBRARIES}) +MESSAGE("") + +MESSAGE("AmgX:") +MESSAGE("\tAmgX dir: " ${AMGX_DIR}) +MESSAGE("\tHeader path: " ${AMGX_INCLUDE_DIRS}) +MESSAGE("\tLibraries: " ${AMGX_LIBRARIES}) +MESSAGE("") diff --git a/external/AmgXWrapper-1.4/CONTRIBUTING.md b/external/AmgXWrapper-1.4/CONTRIBUTING.md new file mode 100644 index 00000000..483b94d2 --- /dev/null +++ b/external/AmgXWrapper-1.4/CONTRIBUTING.md @@ -0,0 +1,39 @@ +# Developers' guide + +This is the guideline for who would like to contribute to AmgXWrapper, including +expanding AmgXWrapper, reporting issues or bugs, and seeking help. + +## Contribute to AmgXWrapper + +AmgXWrapper lives on GitHub, so we follow what most GitHub projects do. In other +words, follow these general steps: + +1. Fork AmgXWrapper. +2. Create a new branch with any name you like. +3. Make modification. +4. Test and make sure your modification is not breaking AmgXWrapper. +5. Make a pull request from your new branch to our master branch. Remember to + specify what changed in your branch and why these changes should be made. +6. Give us time to test and discuss your changes. +7. Merge if everything's all set. + +AmgXWrapper is a small piece of code, so we currently don't maintain a separate +development branch. You can make pull requests directly to the `master` branch. + +The coding style: + +1. Use four spaces for an indent, i.e., no tab (`\t`). +2. Try to make each line not exceed 79 characters (a little bit longer is + acceptable). +3. Use Doxygen style for API documentation +4. Put comments for API users (in Doxygen style) above the prototypes of + functions, and put comments for AmgXWrapper developers above and in the + definitions of functions. + +## Report issues and seek support + +Please use [GitHub repo](https://github.com/barbagroup/AmgXWrapper)'s issue page +to submit bug reports, issues, or any questions. + +If you want to contact us in private, please email pychuang@gwu.edu + diff --git a/external/AmgXWrapper-1.0-beta2/LICENSE b/external/AmgXWrapper-1.4/LICENSE similarity index 94% rename from external/AmgXWrapper-1.0-beta2/LICENSE rename to external/AmgXWrapper-1.4/LICENSE index b8357497..5802ddb2 100644 --- a/external/AmgXWrapper-1.0-beta2/LICENSE +++ b/external/AmgXWrapper-1.4/LICENSE @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2015 Barba group +Copyright (c) 2015-2017 Pi-Yueh Chuang, Lorena A. Barba Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/external/AmgXWrapper-1.4/Makefile.am b/external/AmgXWrapper-1.4/Makefile.am new file mode 100644 index 00000000..a000aa86 --- /dev/null +++ b/external/AmgXWrapper-1.4/Makefile.am @@ -0,0 +1,13 @@ +if WITH_AMGXWRAPPER +noinst_LIBRARIES = libamgxwrapper.a +endif + +libamgxwrapper_a_SOURCES = src/AmgXSolver.cpp \ + src/init.cpp \ + src/misc.cpp \ + src/setA.cpp \ + src/solve.cpp + +libamgxwrapper_a_CPPFLAGS = -I$(srcdir)/src \ + -I$(AMGX_DIR)/examples \ + -I$(CUDA_DIR)/include diff --git a/external/AmgXWrapper-1.0-beta2/Makefile.in b/external/AmgXWrapper-1.4/Makefile.in similarity index 66% rename from external/AmgXWrapper-1.0-beta2/Makefile.in rename to external/AmgXWrapper-1.4/Makefile.in index 2f30c008..e442491b 100644 --- a/external/AmgXWrapper-1.0-beta2/Makefile.in +++ b/external/AmgXWrapper-1.4/Makefile.in @@ -86,12 +86,10 @@ POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : -subdir = external/AmgXWrapper-1.0-beta2 +subdir = external/AmgXWrapper-1.4 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -am__aclocal_m4_deps = $(top_srcdir)/m4/check_version_openmpi.m4 \ - $(top_srcdir)/m4/configure_amgx.m4 \ +am__aclocal_m4_deps = $(top_srcdir)/m4/configure_amgx.m4 \ $(top_srcdir)/m4/configure_cuda.m4 \ - $(top_srcdir)/m4/configure_doxygen.m4 \ $(top_srcdir)/m4/configure_petsc.m4 \ $(top_srcdir)/m4/package_utilities.m4 \ $(top_srcdir)/configure.ac @@ -112,7 +110,11 @@ libamgxwrapper_a_AR = $(AR) $(ARFLAGS) libamgxwrapper_a_LIBADD = am__dirstamp = $(am__leading_dot)dirstamp am_libamgxwrapper_a_OBJECTS = \ - src/libamgxwrapper_a-AmgXSolver.$(OBJEXT) + src/libamgxwrapper_a-AmgXSolver.$(OBJEXT) \ + src/libamgxwrapper_a-init.$(OBJEXT) \ + src/libamgxwrapper_a-misc.$(OBJEXT) \ + src/libamgxwrapper_a-setA.$(OBJEXT) \ + src/libamgxwrapper_a-solve.$(OBJEXT) libamgxwrapper_a_OBJECTS = $(am_libamgxwrapper_a_OBJECTS) AM_V_P = $(am__v_P_@AM_V@) am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) @@ -197,15 +199,12 @@ CXXFLAGS = @CXXFLAGS@ CYGPATH_W = @CYGPATH_W@ DEFS = @DEFS@ DEPDIR = @DEPDIR@ -DOXYGEN = @DOXYGEN@ -DOXYGEN_DIR = @DOXYGEN_DIR@ ECHO_C = @ECHO_C@ ECHO_N = @ECHO_N@ ECHO_T = @ECHO_T@ EGREP = @EGREP@ EXEEXT = @EXEEXT@ GREP = @GREP@ -HAVE_DOXYGEN = @HAVE_DOXYGEN@ INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ @@ -284,7 +283,12 @@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ @WITH_AMGXWRAPPER_TRUE@noinst_LIBRARIES = libamgxwrapper.a -libamgxwrapper_a_SOURCES = src/AmgXSolver.cpp +libamgxwrapper_a_SOURCES = src/AmgXSolver.cpp \ + src/init.cpp \ + src/misc.cpp \ + src/setA.cpp \ + src/solve.cpp + libamgxwrapper_a_CPPFLAGS = -I$(srcdir)/src \ -I$(AMGX_DIR)/examples \ -I$(CUDA_DIR)/include @@ -302,9 +306,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi exit 1;; \ esac; \ done; \ - echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign external/AmgXWrapper-1.0-beta2/Makefile'; \ + echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign external/AmgXWrapper-1.4/Makefile'; \ $(am__cd) $(top_srcdir) && \ - $(AUTOMAKE) --foreign external/AmgXWrapper-1.0-beta2/Makefile + $(AUTOMAKE) --foreign external/AmgXWrapper-1.4/Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status @case '$?' in \ *config.status*) \ @@ -333,6 +337,14 @@ src/$(DEPDIR)/$(am__dirstamp): @: > src/$(DEPDIR)/$(am__dirstamp) src/libamgxwrapper_a-AmgXSolver.$(OBJEXT): src/$(am__dirstamp) \ src/$(DEPDIR)/$(am__dirstamp) +src/libamgxwrapper_a-init.$(OBJEXT): src/$(am__dirstamp) \ + src/$(DEPDIR)/$(am__dirstamp) +src/libamgxwrapper_a-misc.$(OBJEXT): src/$(am__dirstamp) \ + src/$(DEPDIR)/$(am__dirstamp) +src/libamgxwrapper_a-setA.$(OBJEXT): src/$(am__dirstamp) \ + src/$(DEPDIR)/$(am__dirstamp) +src/libamgxwrapper_a-solve.$(OBJEXT): src/$(am__dirstamp) \ + src/$(DEPDIR)/$(am__dirstamp) libamgxwrapper.a: $(libamgxwrapper_a_OBJECTS) $(libamgxwrapper_a_DEPENDENCIES) $(EXTRA_libamgxwrapper_a_DEPENDENCIES) $(AM_V_at)-rm -f libamgxwrapper.a @@ -347,6 +359,10 @@ distclean-compile: -rm -f *.tab.c @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/libamgxwrapper_a-AmgXSolver.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/libamgxwrapper_a-init.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/libamgxwrapper_a-misc.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/libamgxwrapper_a-setA.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/libamgxwrapper_a-solve.Po@am__quote@ .cpp.o: @am__fastdepCXX_TRUE@ $(AM_V_CXX)depbase=`echo $@ | sed 's|[^/]*$$|$(DEPDIR)/&|;s|\.o$$||'`;\ @@ -378,6 +394,62 @@ src/libamgxwrapper_a-AmgXSolver.obj: src/AmgXSolver.cpp @AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ @am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o src/libamgxwrapper_a-AmgXSolver.obj `if test -f 'src/AmgXSolver.cpp'; then $(CYGPATH_W) 'src/AmgXSolver.cpp'; else $(CYGPATH_W) '$(srcdir)/src/AmgXSolver.cpp'; fi` +src/libamgxwrapper_a-init.o: src/init.cpp +@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT src/libamgxwrapper_a-init.o -MD -MP -MF src/$(DEPDIR)/libamgxwrapper_a-init.Tpo -c -o src/libamgxwrapper_a-init.o `test -f 'src/init.cpp' || echo '$(srcdir)/'`src/init.cpp +@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) src/$(DEPDIR)/libamgxwrapper_a-init.Tpo src/$(DEPDIR)/libamgxwrapper_a-init.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='src/init.cpp' object='src/libamgxwrapper_a-init.o' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o src/libamgxwrapper_a-init.o `test -f 'src/init.cpp' || echo '$(srcdir)/'`src/init.cpp + +src/libamgxwrapper_a-init.obj: src/init.cpp +@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT src/libamgxwrapper_a-init.obj -MD -MP -MF src/$(DEPDIR)/libamgxwrapper_a-init.Tpo -c -o src/libamgxwrapper_a-init.obj `if test -f 'src/init.cpp'; then $(CYGPATH_W) 'src/init.cpp'; else $(CYGPATH_W) '$(srcdir)/src/init.cpp'; fi` +@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) src/$(DEPDIR)/libamgxwrapper_a-init.Tpo src/$(DEPDIR)/libamgxwrapper_a-init.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='src/init.cpp' object='src/libamgxwrapper_a-init.obj' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o src/libamgxwrapper_a-init.obj `if test -f 'src/init.cpp'; then $(CYGPATH_W) 'src/init.cpp'; else $(CYGPATH_W) '$(srcdir)/src/init.cpp'; fi` + +src/libamgxwrapper_a-misc.o: src/misc.cpp +@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT src/libamgxwrapper_a-misc.o -MD -MP -MF src/$(DEPDIR)/libamgxwrapper_a-misc.Tpo -c -o src/libamgxwrapper_a-misc.o `test -f 'src/misc.cpp' || echo '$(srcdir)/'`src/misc.cpp +@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) src/$(DEPDIR)/libamgxwrapper_a-misc.Tpo src/$(DEPDIR)/libamgxwrapper_a-misc.Po +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='src/misc.cpp' object='src/libamgxwrapper_a-misc.o' libtool=no @AMDEPBACKSLASH@ +@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@ +@am__fastdepCXX_FALSE@ $(AM_V_CXX@am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o src/libamgxwrapper_a-misc.o `test -f 'src/misc.cpp' || echo '$(srcdir)/'`src/misc.cpp + +src/libamgxwrapper_a-misc.obj: src/misc.cpp +@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(libamgxwrapper_a_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT src/libamgxwrapper_a-misc.obj -MD -MP -MF src/$(DEPDIR)/libamgxwrapper_a-misc.Tpo -c -o src/libamgxwrapper_a-misc.obj `if test -f 'src/misc.cpp'; 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+ // initialize the instance with communicator, executation mode, and config file + solver.initialize(comm, mode, file); + // set matrix A. Currently it only accept PETSc AIJ matrix + solver.setA(A); + // solve. x and rhs are PETSc vectors. unkns will be the final result in the end + solver.solve(unks, rhs); + // get number of iterations + int iters; + solver.getIters(iters); + // get residual at the last iteration + double res; + solver.getResidual(iters, res); + // finalization + solver.finalize(); + + // other codes + .... + + return 0; +} +``` + + +Note, this wrapper was originally designed for our CFD solver -- **[PetIBM](https://github.com/barbagroup/PetIBM)**, +so it may lack some features for other kinds of PETSc-based applications. +We are trying to make it more general. + +## Document + + +1. [Dependencies](doc/dependencies.md) +2. [Build and install](doc/install.md) +3. [Usage](doc/usage.md) +4. [Test](doc/test.md) +5. [Examples](example) + +## Update + + +### 01/08/2016 + +Now the wrapper has better performance when there are more MPI processes than the number of GPUs. + +For old version, +it had poor performance when we have multiple MPI processes calling AmgX on a single GPU. +These MPI processes would compete for GPU resource, which is not good. +The solution is to always allow only one MPI process to call AmgX on each GPU. +So, in order to do this, +this wrapper will now only call AmgX at some of MPI processes when there are more MPI processes than the number of GPUs. +Data on other processes will be gathered to those calling AmgX before solving, and then scattered back after. + +For example, +if there are totally 18 MPI processes and 6 GPUs (12 MPI processes and 2 GPUs on node 1, and 6 MPI ranks and 4 GPUs on node 2), +only the rank 0, 6, 12, 14, 16, 17 will call AmgX solvers. +Data on rank 1-5 will be gathered to rank 0; +data on rank 7-11 will go to rank 6; +data on rank 13 and 15 go to rank 12 and 14, respectively; +and both rank 16 and 17 enjoys a single GPU by itself. +This causes some penalties on computing time because of communications between processes. +However, the overall performance is much better comparing to calling AmgX solvers at ALL processes directly. + +The redistribution method may be naive, but it's working. +And we have been satisfied with the performance so far. + +## Limitation + + +* CPU version of AmgX solver (i.e., `hDDI` mode in AmgX or `AmgX_CPU` option + in our Poisson example) is not supported in this wrapper. Some APIs in current + AmgX version don't work on CPU, and we are not interested in AmgX's CPU + capability, so we left out the support AmgX's CPU solvers. Using PETSc's (or + third-party's, like Hypre) solvers and preconditioners may be a better choice + for CPU capability. +* Due to our PETSc applications only use AIJ format for sparse matrices, AmgXWrapper + currently only support AIJ format. + +## Future work + + +* Add support of updating entry values of the matrix A that is already on CUDA device. +* Support other matrix format other than AIJ. +* Add mechanisms for debugging and error handling. + +## Contributing + +To contribute to AmgXWrapper, see [CONTRIBUTING](CONTRIBUTING.md). + +## How to cite + +To cite this code, please use the citation or the BibTeX entry below. + +> Pi-Yueh Chuang, & Lorena A. Barba (2017). AmgXWrapper: An interface between PETSc and the NVIDIA AmgX library. _J. Open Source Software_, **2**(16):280, [doi:10.21105/joss.00280](http://dx.doi.org/10.21105/joss.00280) + + +```console +@article{Chuang2017, + doi = {10.21105/joss.00280}, + url = {https://doi.org/10.21105/joss.00280}, + year = {2017}, + month = {aug}, + publisher = {The Open Journal}, + volume = {2}, + number = {16}, + author = {Pi-Yueh Chuang and Lorena A. Barba}, + title = {{AmgXWrapper}: An interface between {PETSc} and the {NVIDIA} {AmgX} library}, + journal = {The Journal of Open Source Software} +} +``` + +## Reference + +[1] Chuang, Pi-Yueh; Barba, Lorena A. (2017): Using AmgX to Accelerate PETSc-Based +CFD Codes. figshare. +[https://doi.org/10.6084/m9.figshare.5018774.v1](https://doi.org/10.6084/m9.figshare.5018774.v1) diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/cmake-modules/LICENSE b/external/AmgXWrapper-1.4/cmake-modules/LICENSE similarity index 100% rename from external/AmgXWrapper-1.0-beta2/example/Poisson/cmake-modules/LICENSE rename to external/AmgXWrapper-1.4/cmake-modules/LICENSE diff --git a/external/AmgXWrapper-1.0-beta2/example/Poisson/cmake-modules/README b/external/AmgXWrapper-1.4/cmake-modules/README similarity index 100% rename from external/AmgXWrapper-1.0-beta2/example/Poisson/cmake-modules/README rename to external/AmgXWrapper-1.4/cmake-modules/README diff --git a/external/AmgXWrapper-1.4/codemeta.json b/external/AmgXWrapper-1.4/codemeta.json new file mode 100644 index 00000000..f4d9e126 --- /dev/null +++ b/external/AmgXWrapper-1.4/codemeta.json @@ -0,0 +1,30 @@ +{ + "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld", + "@type": "Code", + "author": [ + { + "@id": "0000-0001-6330-2709", + "@type": "Person", + "email": "pychuang@gwu.edu", + "name": "Pi-Yueh Chuang", + "affiliation": "The George Washington University" + }, + { + "@id": "0000-0001-5812-2711", + "@type": "Person", + "email": "labarba@gwu.edu", + "name": "Lorena A. Barba", + "affiliation": "The George Washington University" + } + ], + "identifier": "https://doi.org/10.6084/m9.figshare.5018774.v1", + "codeRepository": "https://github.com/barbagroup/AmgXWrapper", + "datePublished": "2017-06-02", + "dateModified": "2017-06-02", + "dateCreated": "2017-06-02", + "description": "A wrapper for using AmgX in PETSc applications", + "keywords": "PETSc, AmgX, multigrid, multi-GPU computing", + "license": "MIT", + "title": "AmgXWrapper", + "version": "" +} diff --git a/external/AmgXWrapper-1.4/doc/Doxyfile b/external/AmgXWrapper-1.4/doc/Doxyfile new file mode 100644 index 00000000..a388fd78 --- /dev/null +++ b/external/AmgXWrapper-1.4/doc/Doxyfile @@ -0,0 +1,2474 @@ +# Doxyfile 1.8.13 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. 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Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = /home/pychuang/Cloud/MyGit/AmgXWrapper/src \ + ../README.md + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, +# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.idl \ + *.ddl \ + *.odl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.cs \ + *.d \ + *.php \ + *.php4 \ + *.php5 \ + *.phtml \ + *.inc \ + *.m \ + *.markdown \ + *.md \ + *.mm \ + *.dox \ + *.py \ + *.pyw \ + *.f90 \ + *.f95 \ + *.f03 \ + *.f08 \ + *.f \ + *.for \ + *.tcl \ + *.vhd \ + *.vhdl \ + *.ucf \ + *.qsf + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = README.md + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /