* [gentoo-commits] proj/sci:master commit in: sci-libs/bliss/, sci-libs/bliss/files/
@ 2013-04-28 21:04 Christoph Junghans
0 siblings, 0 replies; 2+ messages in thread
From: Christoph Junghans @ 2013-04-28 21:04 UTC (permalink / raw
To: gentoo-commits
commit: 108f84103f49751cf0363ff2359c9590281f0c6e
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 28 21:00:37 2013 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Apr 28 21:00:37 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=108f8410
initial commit
Package-Manager: portage-2.2.0_alpha173
---
sci-libs/bliss/ChangeLog | 7 +
sci-libs/bliss/bliss-0.72.ebuild | 42 ++
sci-libs/bliss/files/bliss-0.72-autotools.patch | 159 ++++++
sci-libs/bliss/files/bliss-0.72-fedora.patch | 648 +++++++++++++++++++++++
sci-libs/bliss/metadata.xml | 9 +
5 files changed, 865 insertions(+), 0 deletions(-)
diff --git a/sci-libs/bliss/ChangeLog b/sci-libs/bliss/ChangeLog
new file mode 100644
index 0000000..880e42f
--- /dev/null
+++ b/sci-libs/bliss/ChangeLog
@@ -0,0 +1,7 @@
+
+*bliss-0.72 (28 Apr 2013)
+
+ 28 Apr 2013; Christoph Junghans <ottxor@gentoo.org> +bliss-0.72.ebuild,
+ +files/bliss-0.72-autotools.patch, +files/bliss-0.72-fedora.patch,
+ +metadata.xml:
+ initial commit
diff --git a/sci-libs/bliss/bliss-0.72.ebuild b/sci-libs/bliss/bliss-0.72.ebuild
new file mode 100644
index 0000000..1aa7a16
--- /dev/null
+++ b/sci-libs/bliss/bliss-0.72.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit autotools-utils
+
+SRC_URI="http://www.tcs.hut.fi/Software/${PN}/${P}.zip"
+DESCRIPTION="A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs"
+HOMEPAGE="http://www.tcs.hut.fi/Software/bliss/index.shtml"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc gmp"
+
+RDEPEND="gmp? ( dev-libs/gmp )"
+
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+AUTOTOOLS_AUTORECONF=1
+
+PATCHES=(
+ "${FILESDIR}/${P}-fedora.patch"
+ "${FILESDIR}/${P}-autotools.patch"
+)
+
+src_configure() {
+ local myeconfargs=( $(use_with gmp) )
+ autotools-utils_src_configure
+}
+
+src_install() {
+ autotools-utils_src_install
+ if use doc; then
+ cd "${BUILD_DIR}"
+ emake html
+ dohtml -r html
+ fi
+}
diff --git a/sci-libs/bliss/files/bliss-0.72-autotools.patch b/sci-libs/bliss/files/bliss-0.72-autotools.patch
new file mode 100644
index 0000000..264d21e
--- /dev/null
+++ b/sci-libs/bliss/files/bliss-0.72-autotools.patch
@@ -0,0 +1,159 @@
+Replace simple Makefile by autotools
+- allow shared library
+- parallel build
+- added pkg-config support
+
+Author: Christoph Junghans <ottxor@gentoo.org>
+
+diff -Naur bliss-0.72-fedora/config/.dummy bliss-0.72/config/.dummy
+--- bliss-0.72-fedora/config/.dummy 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/config/.dummy 2013-04-28 14:43:06.143760368 -0600
+@@ -0,0 +1 @@
++Dummy file to make patch create config dir, which is needed for autotools
+diff -Naur bliss-0.72-fedora/configure.ac bliss-0.72/configure.ac
+--- bliss-0.72-fedora/configure.ac 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/configure.ac 2013-04-28 14:40:42.283242722 -0600
+@@ -0,0 +1,31 @@
++AC_PREREQ([2.65])
++AC_INIT([bliss], [0.72], [Tommi.Junttil@kk.fi])
++
++AC_CONFIG_AUX_DIR(config)
++AC_CONFIG_MACRO_DIR(config)
++
++AM_INIT_AUTOMAKE([1.8 foreign])
++
++SHARED_VERSION_INFO="1:0:0"
++AC_SUBST(SHARED_VERSION_INFO)
++
++# Checks for programs.
++AC_PROG_CXX
++
++LT_INIT
++# Checks for libraries.
++AC_ARG_WITH([gmp],
++ [AS_HELP_STRING([--with-gmp], [enable support for GNU Multiple Precision Arithmetic Library @<:@default=check@:>@])],
++ [], [with_readline=no])
++AS_IF([test "x$with_readline" != xno],
++ [AC_CHECK_HEADERS([gmp.h],,AC_MSG_ERROR([Cannot find gmp.h header]))
++ AC_CHECK_LIB([gmp],_init,,AC_MSG_ERROR([Cannot find gmp library]))
++ AC_SUBST([GMP],[-lgmp])
++ [CPPFLAGS="$CPPFLAGS -DBLISS_USE_GMP"]])
++
++AC_CHECK_PROG(DOXYGEN,doxygen,doxygen,no)
++AM_CONDITIONAL(HAVE_DOXYGEN,[test .$DOXYGEN != .no])
++
++AC_CONFIG_FILES([Makefile])
++AC_CONFIG_FILES([bliss.pc])
++AC_OUTPUT
+diff -Naur bliss-0.72-fedora/bliss.pc.in bliss-0.72/bliss.pc.in
+--- bliss-0.72-fedora/bliss.pc.in 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/bliss.pc.in 2013-04-28 14:40:54.223285686 -0600
+@@ -0,0 +1,13 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: bliss
++Description: Library for Computing Automorphism Groups and Canonical Labelings of Graphs
++URL: http://www.tcs.hut.fi/Software/bliss/index.shtml
++Version: @VERSION@
++Requires:
++Libs: -L${libdir} -lbliss @GMP@
++Libs.private: -lm
++Cflags: -I${includedir}
+diff -Naur bliss-0.72-fedora/Makefile bliss-0.72/Makefile
+--- bliss-0.72-fedora/Makefile 2013-04-28 14:40:10.543128514 -0600
++++ bliss-0.72/Makefile 1969-12-31 17:00:00.000000000 -0700
+@@ -1,57 +0,0 @@
+-CFLAGS = -I.
+-CFLAGS += -g
+-#CFLAGS += -pg
+-CFLAGS += -Wall
+-CFLAGS += --pedantic
+-CFLAGS += -O9
+-#CFLAGS += -DBLISS_DEBUG
+-CFLAGS += -fPIC
+-
+-SRCS = defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc
+-SRCS += timer.cc utils.cc bliss_C.cc
+-
+-OBJS = $(addsuffix .o, $(basename $(SRCS)))
+-
+-GMPOBJS = $(addsuffix g, $(OBJS))
+-
+-LIB =
+-#LIB += /usr/lib/ccmalloc.o -ldl
+-
+-CC = g++
+-RANLIB = ranlib
+-AR = ar
+-BLISSLIB = libbliss.a
+-
+-gmp: LIB += -lgmp
+-gmp: CFLAGS += -DBLISS_USE_GMP
+-
+-normal: bliss
+-gmp: bliss_gmp
+-
+-
+-all:: lib bliss
+-
+-%.o %.og: %.cc
+- $(CC) $(CFLAGS) -c -o $@ $<
+-
+-lib: $(OBJS)
+- rm -f $(BLISSLIB)
+- $(AR) cr $(BLISSLIB) $(OBJS)
+- $(RANLIB) $(BLISSLIB)
+-
+-lib_gmp: $(GMPOBJS)
+- rm -f $(BLISSLIB)
+- $(AR) cr $(BLISSLIB) $(GMPOBJS)
+- $(RANLIB) $(BLISSLIB)
+-
+-bliss: bliss.o lib $(OBJS)
+- $(CC) $(CFLAGS) -o bliss bliss.o $(OBJS) $(LIB)
+-
+-bliss_gmp: bliss.og lib_gmp $(GMPOBJS)
+- $(CC) $(CFLAGS) -o bliss bliss.og $(GMPOBJS) $(LIB)
+-
+-
+-clean:
+- rm -f bliss $(BLISSLIB) $(OBJS) bliss.o $(GMPOBJS) bliss.og
+-
+-# DO NOT DELETE
+diff -Naur bliss-0.72-fedora/Makefile.am bliss-0.72/Makefile.am
+--- bliss-0.72-fedora/Makefile.am 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/Makefile.am 2013-04-28 14:47:26.944698789 -0600
+@@ -0,0 +1,30 @@
++ACLOCAL_AMFLAGS = -I config
++
++lib_LTLIBRARIES = libbliss.la
++
++libbliss_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@
++libbliss_la_SOURCES = \
++ defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc \
++ timer.cc utils.cc bliss_C.cc
++
++include_HEADERS = \
++ bignum.hh bliss_C.h defs.hh graph.hh heap.hh kqueue.hh kstack.hh \
++ orbit.hh partition.hh timer.hh uintseqhash.hh utils.hh
++
++bin_PROGRAMS = bliss
++bliss_SOURCES = bliss.cc
++bliss_LDADD = libbliss.la
++dist_man1_MANS = bliss.1
++
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = bliss.pc
++
++html-local: Doxyfile
++if HAVE_DOXYGEN
++ $(DOXYGEN) $(srcdir)/Doxyfile
++else
++ @echo "doxygen was not found, please re-run configure"
++endif
++
++clean-local:
++ -rm -rf html
diff --git a/sci-libs/bliss/files/bliss-0.72-fedora.patch b/sci-libs/bliss/files/bliss-0.72-fedora.patch
new file mode 100644
index 0000000..e1f8b66
--- /dev/null
+++ b/sci-libs/bliss/files/bliss-0.72-fedora.patch
@@ -0,0 +1,648 @@
+Pulled on 28-04-13 from
+http://pkgs.fedoraproject.org/cgit/bliss.git/tree/
+
+- Man page written by Jerry James using text borrowed from the sources.
+ The man page therefore has the same copyright and license as the sources.
+- Don't call exit() in library code.
+- Patch from Thomas Rehn, also sent upstream. Fix one bug and add one
+ performance enhancement.
+
+diff -Naur bliss-0.72.orig/bliss.1 bliss-0.72/bliss.1
+--- bliss-0.72.orig/bliss.1 1969-12-31 17:00:00.000000000 -0700
++++ bliss-0.72/bliss.1 2013-04-28 14:35:37.000000000 -0600
+@@ -0,0 +1,55 @@
++.TH "BLISS" "1" "@VERSION@" "Tommi Junttila & Petteri Kaski" "User Commands"
++.SH "NAME"
++bliss \- Compute automorphism groups and canonical labelings of graphs
++.SH "SYNOPSIS"
++.B bliss
++[\fIOPTIONS\fR] [<\fIGRAPH FILE\fR>]
++.SH "DESCRIPTION"
++.PP
++Bliss is an open source tool for computing automorphism groups and
++canonical forms of graphs. The graphs are specified in DIMACS format.
++.TP
++\fB\-directed\fR
++the input graph is directed
++.TP
++\fB\-can\fR
++compute canonical form
++.TP
++\fB\-ocan\fR=\fIf\fR
++compute canonical form and output it in file \fIf\fR
++.TP
++\fB\-v\fR=\fIN\fR
++set verbosity level to N [N >= 0, default: 1]
++.TP
++\fB\-sh\fR=\fIX\fR
++select splitting heuristics, where X is:
++.TS
++tab(;);
++R L.
++f;first non-singleton cell
++fl;first largest non-singleton cell
++fs;first smallest non-singleton cell
++fm;first maximally non-trivially connected non-singleton cell
++flm;first largest maximally non-trivially connected
++;non-singleton cell
++fsm;first smallest maximally non-trivially connected
++;non-singleton cell (default)
++.TE
++.TP
++\fB\-fr\fR=\fIX\fR
++use failure recording? [X=y/n, default: y]
++.TP
++\fB\-cr\fR=\fIX\fR
++use component recursion? [X=y/n, default: y]
++.TP
++\fB\-version\fR
++print the version number and exit
++.TP
++\fB\-help\fR
++print this help and exit
++.SH "AUTHORS"
++Bliss was written by Tommi Junttila <Tommi.Junttila@tkk.fi> and
++Petteri Kaski <petteri.kaski@aalto.fi>.
++.PP
++This man page was written by Jerry James <loganjerry@gmail.com>.
++It is distributed under the same terms as bliss.
+diff -Naur bliss-0.72.orig/bliss.cc bliss-0.72/bliss.cc
+--- bliss-0.72.orig/bliss.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -276,13 +276,16 @@
+ if(opt_canonize == false)
+ {
+ /* No canonical labeling, only automorphism group */
+- g->find_automorphisms(stats, &report_aut, stdout);
++ if (!g->find_automorphisms(stats, &report_aut, stdout))
++ exit(1);
+ }
+ else
+ {
+ /* Canonical labeling and automorphism group */
+ const unsigned int* cl = g->canonical_form(stats, &report_aut, stdout);
+
++ if (!cl)
++ exit(1);
+ fprintf(stdout, "Canonical labeling: ");
+ bliss::print_permutation(stdout, g->get_nof_vertices(), cl, 1);
+ fprintf(stdout, "\n");
+@@ -290,6 +293,8 @@
+ if(opt_output_can_file)
+ {
+ bliss::AbstractGraph* cf = g->permute(cl);
++ if (!cf)
++ exit(1);
+ FILE* const fp = fopen(opt_output_can_file, "w");
+ if(!fp)
+ _fatal("Cannot open '%s' for outputting the canonical form, aborting", opt_output_can_file);
+diff -Naur bliss-0.72.orig/bliss_C.cc bliss-0.72/bliss_C.cc
+--- bliss-0.72.orig/bliss_C.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss_C.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -131,7 +131,7 @@
+ }
+
+ extern "C"
+-void
++int
+ bliss_find_automorphisms(BlissGraph *graph,
+ void (*hook)(void *user_param,
+ unsigned int n,
+@@ -142,7 +142,8 @@
+ bliss::Stats s;
+ assert(graph);
+ assert(graph->g);
+- graph->g->find_automorphisms(s, hook, hook_user_param);
++ if (!graph->g->find_automorphisms(s, hook, hook_user_param))
++ return 0;
+
+ if(stats)
+ {
+@@ -154,6 +155,7 @@
+ stats->nof_generators = s.get_nof_generators();
+ stats->max_level = s.get_max_level();
+ }
++ return 1;
+ }
+
+
+@@ -173,7 +175,7 @@
+
+ canonical_labeling = graph->g->canonical_form(s, hook, hook_user_param);
+
+- if(stats)
++ if(canonical_labeling && stats)
+ {
+ stats->group_size_approx = s.get_group_size_approx();
+ stats->nof_nodes = s.get_nof_nodes();
+diff -Naur bliss-0.72.orig/bliss_C.h bliss-0.72/bliss_C.h
+--- bliss-0.72.orig/bliss_C.h 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/bliss_C.h 2013-04-28 14:36:28.792330603 -0600
+@@ -156,6 +156,7 @@
+ * The argument \a perm should be an array of
+ * N=bliss::bliss_get_nof_vertices(\a graph) elements describing
+ * a bijection on {0,...,N-1}.
++ * Returns NULL if insufficient memory or internal error.
+ */
+ BlissGraph *bliss_permute(BlissGraph *graph, const unsigned int *perm);
+
+@@ -174,8 +175,9 @@
+ * if you want to use the automorphism later, you have to take a copy of it.
+ * Do not call bliss_* functions in the hook.
+ * If \a stats is non-null, then some search statistics are copied there.
++ * \return nonzero if successful, zero if insufficient memory or internal error
+ */
+-void
++int
+ bliss_find_automorphisms(BlissGraph *graph,
+ void (*hook)(void *user_param,
+ unsigned int N,
+@@ -194,6 +196,7 @@
+ * then bliss_permute() with the returned canonical labeling.
+ * Note that the computed canonical version may depend on the applied version
+ * of bliss.
++ * Returns NULL if insufficient memory or internal error.
+ */
+ const unsigned int *
+ bliss_find_canonical_labeling(BlissGraph *graph,
+diff -Naur bliss-0.72.orig/defs.cc bliss-0.72/defs.cc
+--- bliss-0.72.orig/defs.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/defs.cc 2013-04-28 14:36:28.792330603 -0600
+@@ -33,7 +33,6 @@
+ vfprintf(stderr, fmt, ap);
+ fprintf(stderr, "\nAborting!\n");
+ va_end(ap);
+- exit(1);
+ }
+
+ }
+diff -Naur bliss-0.72.orig/graph.cc bliss-0.72/graph.cc
+--- bliss-0.72.orig/graph.cc 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/graph.cc 2013-04-28 14:37:16.162501050 -0600
+@@ -34,7 +34,10 @@
+ namespace bliss {
+
+ #define _INTERNAL_ERROR() fatal_error("%s:%d: internal error",__FILE__,__LINE__)
+-#define _OUT_OF_MEMORY() fatal_error("%s:%d: out of memory",__FILE__,__LINE__)
++#define _OUT_OF_MEMORY(label) do { \
++ fatal_error("%s:%d: out of memory",__FILE__,__LINE__); \
++ goto label; \
++ } while (0)
+
+ /*-------------------------------------------------------------------------
+ *
+@@ -279,20 +282,6 @@
+ *perm = i;
+ }
+
+-bool
+-AbstractGraph::is_automorphism(unsigned int* const perm)
+-{
+- _INTERNAL_ERROR();
+- return false;
+-}
+-
+-bool
+-AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const
+-{
+- _INTERNAL_ERROR();
+- return false;
+-}
+-
+
+
+
+@@ -608,17 +597,7 @@
+ };
+
+
+-
+-
+-typedef struct {
+- unsigned int splitting_element;
+- unsigned int certificate_index;
+- unsigned int subcertificate_length;
+- UintSeqHash eqref_hash;
+-} PathInfo;
+-
+-
+-void
++bool
+ AbstractGraph::search(const bool canonical, Stats& stats)
+ {
+ const unsigned int N = get_nof_vertices();
+@@ -658,7 +637,7 @@
+ if(N == 0)
+ {
+ /* Nothing to do, return... */
+- return;
++ return true;
+ }
+
+ /* Initialize the partition ... */
+@@ -696,10 +675,10 @@
+ */
+ if(first_path_labeling) free(first_path_labeling);
+ first_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!first_path_labeling) _OUT_OF_MEMORY();
++ if(!first_path_labeling) _OUT_OF_MEMORY(oom1);
+ if(best_path_labeling) free(best_path_labeling);
+ best_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!best_path_labeling) _OUT_OF_MEMORY();
++ if(!best_path_labeling) _OUT_OF_MEMORY(oom2);
+
+ /*
+ * Is the initial partition discrete?
+@@ -710,7 +689,7 @@
+ update_labeling(best_path_labeling);
+ /* Update statistics */
+ stats.nof_leaf_nodes = 1;
+- return;
++ return true;
+ }
+
+ /*
+@@ -718,20 +697,39 @@
+ */
+ if(first_path_labeling_inv) free(first_path_labeling_inv);
+ first_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!first_path_labeling_inv) _OUT_OF_MEMORY();
++ if(!first_path_labeling_inv) _OUT_OF_MEMORY(oom3);
+ if(best_path_labeling_inv) free(best_path_labeling_inv);
+ best_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int));
+- if(!best_path_labeling_inv) _OUT_OF_MEMORY();
++ if(!best_path_labeling_inv) _OUT_OF_MEMORY(oom4);
+
+ /*
+ * Allocate space for the automorphisms
+ */
+ if(first_path_automorphism) free(first_path_automorphism);
+ first_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
+- if(!first_path_automorphism) _OUT_OF_MEMORY();
++ if(!first_path_automorphism) _OUT_OF_MEMORY(oom5);
+ if(best_path_automorphism) free(best_path_automorphism);
+ best_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int));
+- if(!best_path_automorphism) _OUT_OF_MEMORY();
++ if(!best_path_automorphism) {
++ _OUT_OF_MEMORY(oom6);
++ oom6:
++ free(first_path_automorphism);
++ first_path_automorphism = NULL;
++ oom5:
++ free(best_path_labeling_inv);
++ best_path_labeling_inv = NULL;
++ oom4:
++ free(first_path_labeling_inv);
++ first_path_labeling_inv = NULL;
++ oom3:
++ free(best_path_labeling);
++ best_path_labeling = NULL;
++ oom2:
++ free(first_path_labeling);
++ first_path_labeling = NULL;
++ oom1:
++ return false;
++ }
+
+ /*
+ * Initialize orbit information so that all vertices are in their own orbits
+@@ -745,7 +743,6 @@
+ initialize_certificate();
+
+ std::vector<TreeNode> search_stack;
+- std::vector<PathInfo> first_path_info;
+ std::vector<PathInfo> best_path_info;
+
+ search_stack.clear();
+@@ -974,7 +971,6 @@
+ */
+ {
+ unsigned int next_split_element = UINT_MAX;
+- unsigned int* next_split_element_pos = 0;
+ unsigned int* ep = p.elements + cell->first;
+ if(current_node.fp_on)
+ {
+@@ -985,7 +981,6 @@
+ *ep < next_split_element and
+ first_path_orbits.is_minimal_representative(*ep)) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1001,7 +996,6 @@
+ current_node.long_prune_redundant.find(*ep) ==
+ current_node.long_prune_redundant.end())) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1015,7 +1009,6 @@
+ current_node.long_prune_redundant.find(*ep) ==
+ current_node.long_prune_redundant.end())) {
+ next_split_element = *ep;
+- next_split_element_pos = ep;
+ }
+ }
+ }
+@@ -1203,8 +1196,10 @@
+
+ #if defined(BLISS_VERIFY_EQUITABLEDNESS)
+ /* The new partition should be equitable */
+- if(!is_equitable())
++ if(!is_equitable()) {
+ fatal_error("consistency check failed - partition after refinement is not equitable");
++ return false;
++ }
+ #endif
+
+ /*
+@@ -1366,6 +1361,7 @@
+ goto handle_first_path_automorphism;
+ /* Should never get here because of CR:FP */
+ _INTERNAL_ERROR();
++ return false;
+ }
+ }
+
+@@ -1598,8 +1594,10 @@
+
+ #if defined(BLISS_VERIFY_AUTOMORPHISMS)
+ /* Verify that it really is an automorphism */
+- if(!is_automorphism(best_path_automorphism))
++ if(!is_automorphism(best_path_automorphism)) {
+ fatal_error("Best path automorhism validation check failed");
++ return false;
++ }
+ #endif
+
+ unsigned int gca_level_with_first = 0;
+@@ -1666,6 +1664,7 @@
+
+
+ _INTERNAL_ERROR();
++ return false;
+
+
+ handle_first_path_automorphism:
+@@ -1701,8 +1700,10 @@
+
+ #if defined(BLISS_VERIFY_AUTOMORPHISMS)
+ /* Verify that it really is an automorphism */
+- if(!is_automorphism(first_path_automorphism))
++ if(!is_automorphism(first_path_automorphism)) {
+ fatal_error("First path automorphism validation check failed");
++ return false;
++ }
+ #endif
+
+ if(opt_use_long_prune)
+@@ -1749,12 +1750,13 @@
+ /* Release component recursion data in partition */
+ if(opt_use_comprec)
+ p.cr_free();
++ return true;
+ }
+
+
+
+
+-void
++bool
+ AbstractGraph::find_automorphisms(Stats& stats,
+ void (*hook)(void *user_param,
+ unsigned int n,
+@@ -1764,7 +1766,8 @@
+ report_hook = hook;
+ report_user_param = user_param;
+
+- search(false, stats);
++ if (!search(false, stats))
++ return false;
+
+ if(first_path_labeling)
+ {
+@@ -1776,6 +1779,7 @@
+ free(best_path_labeling);
+ best_path_labeling = 0;
+ }
++ return true;
+ }
+
+
+@@ -1790,7 +1794,8 @@
+ report_hook = hook;
+ report_user_param = user_param;
+
+- search(true, stats);
++ if (!search(true, stats))
++ return NULL;
+
+ return best_path_labeling;
+ }
+@@ -3480,15 +3485,17 @@
+ * Check whether perm is an automorphism.
+ * Slow, mainly for debugging and validation purposes.
+ */
+-bool
++int
+ Digraph::is_automorphism(unsigned int* const perm)
+ {
+ std::set<unsigned int, std::less<unsigned int> > edges1;
+ std::set<unsigned int, std::less<unsigned int> > edges2;
+
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return -1;
++ }
+ #endif
+
+ for(unsigned int i = 0; i < get_nof_vertices(); i++)
+@@ -3507,7 +3514,7 @@
+ ei++)
+ edges2.insert(*ei);
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+
+ edges1.clear();
+ for(std::vector<unsigned int>::iterator ei = v1.edges_out.begin();
+@@ -3520,10 +3527,10 @@
+ ei++)
+ edges2.insert(*ei);
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+ }
+
+- return true;
++ return 1;
+ }
+
+ bool
+@@ -4330,8 +4337,10 @@
+ Graph::permute(const unsigned int* perm) const
+ {
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return NULL;
++ }
+ #endif
+
+ Graph* const g = new Graph(get_nof_vertices());
+@@ -5270,15 +5279,17 @@
+ *
+ *-------------------------------------------------------------------------*/
+
+-bool
++int
+ Graph::is_automorphism(unsigned int* const perm)
+ {
+ std::set<unsigned int, std::less<unsigned int> > edges1;
+ std::set<unsigned int, std::less<unsigned int> > edges2;
+
+ #if defined(BLISS_CONSISTENCY_CHECKS)
+- if(!is_permutation(get_nof_vertices(), perm))
++ if(!is_permutation(get_nof_vertices(), perm)) {
+ _INTERNAL_ERROR();
++ return -1;
++ }
+ #endif
+
+ for(unsigned int i = 0; i < get_nof_vertices(); i++)
+@@ -5298,10 +5309,10 @@
+ edges2.insert(*ei);
+
+ if(!(edges1 == edges2))
+- return false;
++ return 0;
+ }
+
+- return true;
++ return 1;
+ }
+
+
+@@ -5444,7 +5455,7 @@
+ component.clear();
+ component_elements = 0;
+ sh_return = 0;
+- unsigned int sh_first = 0;
++ unsigned int sh_first = 1 << 31;
+ unsigned int sh_size = 0;
+ unsigned int sh_nuconn = 0;
+
+diff -Naur bliss-0.72.orig/graph.hh bliss-0.72/graph.hh
+--- bliss-0.72.orig/graph.hh 2013-04-28 14:35:20.582085167 -0600
++++ bliss-0.72/graph.hh 2013-04-28 14:37:16.162501050 -0600
+@@ -109,9 +109,12 @@
+ unsigned long int get_max_level() const {return max_level;}
+ };
+
+-
+-
+-
++typedef struct {
++ unsigned int splitting_element;
++ unsigned int certificate_index;
++ unsigned int subcertificate_length;
++ UintSeqHash eqref_hash;
++} PathInfo;
+
+
+ /**
+@@ -270,7 +273,7 @@
+ void reset_permutation(unsigned int *perm);
+
+ /* Mainly for debugging purposes */
+- virtual bool is_automorphism(unsigned int* const perm);
++ virtual int is_automorphism(unsigned int* const perm) = 0;
+
+ std::vector<unsigned int> certificate_current_path;
+ std::vector<unsigned int> certificate_first_path;
+@@ -284,7 +287,11 @@
+ virtual Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell) = 0;
+
+
+- void search(const bool canonical, Stats &stats);
++ /**
++ * \return true if successful, false if insufficient memory to complete or
++ * other internal error
++ */
++ bool search(const bool canonical, Stats &stats);
+
+
+ void (*report_hook)(void *user_param,
+@@ -351,7 +358,7 @@
+ */
+ unsigned int cr_component_elements;
+
+-
++ std::vector<PathInfo> first_path_info;
+
+
+ public:
+@@ -362,7 +369,7 @@
+ * Check whether \a perm is an automorphism of this graph.
+ * Unoptimized, mainly for debugging purposes.
+ */
+- virtual bool is_automorphism(const std::vector<unsigned int>& perm) const;
++ virtual bool is_automorphism(const std::vector<unsigned int>& perm) const = 0;
+
+
+
+@@ -427,8 +434,10 @@
+ * if you want to use the automorphism later, you have to take a copy of it.
+ * Do not call any member functions in the hook.
+ * The search statistics are copied in \a stats.
++ * \return true if successful, false if insufficient memory to search or
++ * other internal error.
+ */
+- void find_automorphisms(Stats& stats,
++ bool find_automorphisms(Stats& stats,
+ void (*hook)(void* user_param,
+ unsigned int n,
+ const unsigned int* aut),
+@@ -448,6 +457,8 @@
+ * Note that the computed canonical version may depend on the applied version
+ * of bliss as well as on some other options (for instance, the splitting
+ * heuristic selected with bliss::Graph::set_splitting_heuristic()).
++ * This function returns NULL if there is insufficient memory, or another
++ * internal error occurs.
+ */
+ const unsigned int* canonical_form(Stats& stats,
+ void (*hook)(void* user_param,
+@@ -500,6 +511,10 @@
+ opt_use_long_prune = active;
+ }
+
++ /**
++ * Get an information vector about the first path.
++ */
++ std::vector<PathInfo> get_first_path_info() { return first_path_info; }
+ };
+
+
+@@ -615,7 +630,7 @@
+
+ void initialize_certificate();
+
+- bool is_automorphism(unsigned int* const perm);
++ int is_automorphism(unsigned int* const perm);
+
+
+ bool nucr_find_first_component(const unsigned int level);
+@@ -856,7 +871,7 @@
+
+ void initialize_certificate();
+
+- bool is_automorphism(unsigned int* const perm);
++ int is_automorphism(unsigned int* const perm);
+
+ void sort_edges();
+
diff --git a/sci-libs/bliss/metadata.xml b/sci-libs/bliss/metadata.xml
new file mode 100644
index 0000000..119d0fd
--- /dev/null
+++ b/sci-libs/bliss/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci</herd>
+ <maintainer>
+ <email>ottxor@gentoo.org</email>
+ <name>Christoph Junghans</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/bliss/, sci-libs/bliss/files/
@ 2013-07-11 15:40 Christoph Junghans
0 siblings, 0 replies; 2+ messages in thread
From: Christoph Junghans @ 2013-07-11 15:40 UTC (permalink / raw
To: gentoo-commits
commit: 34524742ae07906352746c8ea906af8b9f1f8b87
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 11 15:39:58 2013 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jul 11 15:40:12 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34524742
install heads into a bliss subdir
Package-Manager: portage-2.2.0_alpha188
---
sci-libs/bliss/ChangeLog | 4 ++++
sci-libs/bliss/files/bliss-0.72-autotools.patch | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-libs/bliss/ChangeLog b/sci-libs/bliss/ChangeLog
index b5ab8e5..7041e05 100644
--- a/sci-libs/bliss/ChangeLog
+++ b/sci-libs/bliss/ChangeLog
@@ -1,4 +1,8 @@
+ 11 Jul 2013; Christoph Junghans <ottxor@gentoo.org>
+ files/bliss-0.72-autotools.patch:
+ install heads into a bliss subdir
+
28 Apr 2013; Christoph Junghans <ottxor@gentoo.org> bliss-0.72.ebuild:
remove la files, added static-libs use flag
diff --git a/sci-libs/bliss/files/bliss-0.72-autotools.patch b/sci-libs/bliss/files/bliss-0.72-autotools.patch
index 264d21e..d30c516 100644
--- a/sci-libs/bliss/files/bliss-0.72-autotools.patch
+++ b/sci-libs/bliss/files/bliss-0.72-autotools.patch
@@ -136,7 +136,7 @@ diff -Naur bliss-0.72-fedora/Makefile.am bliss-0.72/Makefile.am
+ defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc \
+ timer.cc utils.cc bliss_C.cc
+
-+include_HEADERS = \
++pkginclude_HEADERS = \
+ bignum.hh bliss_C.h defs.hh graph.hh heap.hh kqueue.hh kstack.hh \
+ orbit.hh partition.hh timer.hh uintseqhash.hh utils.hh
+
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