Changes from nauty 2.4 to nauty 2.5
-----------------------------------
* Add Traces. The main files are traces.h and traces.c, but
many changes were made to dreadnaut.c and nausparse.c also.
* Allow thread-safe storage if requested by configure --enable-tls
and available. This allows parallel running of nauty and Traces
in separate threads.
* The makefile now creates static libraries like nauty.a in
addition to object files like nauty.o.
* Remove all uses of types permutation, nvector, np2vector, shortish.
These are now int.
* Add schreier.h, schreier.c and the optional use of the random
Schreier method in nauty. These are also used in Traces, but
are not optional there.
* Add large-file support to all programs, assuming it is available.
Now there is no longer a 4GB limit on files read or written on
32-bit systems.
* Use gcc extensions like __builtin_clz() if available and not
disabled by configure --disable-clz.
Use FIRSTBITNZ instead of FIRSTBIT if the argument is certain
to be nonzero.
* New macros defined in nauty.h:
COUNTER_FMT
PRINT_COUNTER
SETWORDSNEEDED
ADDONEARC
ADDONEEDGE
EMPTYGRAPH
* The options structure has a new boolean field schreier.
* New procedures:
densenauty() in naugraph.c - simplified dense graph interface
sparsenauty() in nausparse.c - simplified sparse graph interface
writegroupsize() in nautil.c - write two part group size
copy_sg() in nausparse.c - make a copy of a sparse graph
densenauty() and sparsenauty() are now the recommended ways to
call nauty from a program. See the sample programs in the package.
* Use quicksort in place of shell sort in many places. This is
implemented in the file sorttemplates.c that can be used in any
applications.
* Apply the const attribute more liberally across the code.
* The sparsegraph fields nde and *v changed type from int to size_t.
This is to allow more than 2^31 edges on 64-bit hardware.
* sparsegraph.h and sparsegraph.c:
Corrected definition of SG_DECL in sparsegraph.h. (The erroneous
definition would have worked but generated warnings.)
Added DEFAULTOPTIONS_SPARSEDIGRAPH.
Added comparelab_tr(), testcanlab_tr(), updatecan_tr() for Traces.
* gtools.h and gtools.c:
Now gtools.h is made from gtools-h.in by configure.
Updated G6LEN() to work for larger graphs.
Use large-file functions fseeko(), ftello() if possible.
* Most tools now use the random number generator in naurng.c rather
than that in rng.c.
* gutils.h, gutil1.c and gutil2.c:
New procedures maxcliques(), indpathcount1(), indcyclecount1(),
indcyclecount().
* Invariants:
Corrected getbigcells(), making a small change to invariants
celltrips, cellquins and refinvar.
* dreadnaut:
Sparse nauty and Traces now incorported.
New commands: A, G, F, FF, sr, O, OO, P, PP, S, V
w command is now in units of 2*m.
Command-line can run commands using -o.
M command is extended; now applies to i as well as x.
Implement ANSI controls if requested.
File names for > and < can be given in "..." to allow spaces.
* Updates to utilities:
listg: add -b (Bliss format), -G (GRAPE format) and
-y/-Y (dotty format), -H (HCP format)
labelg: add -t (Traces) and -i16 (refinvar)
countg/pickg: add -m (vertices of min degree),
-M (vertices of max degree), -H (induced cycles),
-K (number of maximal independent sets)
genrang: add -t (tree)
genbg: add -A (antichain)
The makefile can also make genbgL which makes larger sizes
directg: add PROCESS feature
shortg: -S (use sparse nauty), -t (use traces), i16 (refinvar)
* New utilities:
ranlabg: randomly relabel graphs
linegraphg: compute linegraphs
subdivideg: compute subdivision graphs
watercluster2: orient edges of graphs (by Gunnar Brinkmann)
* Version 25r2 fixed a rare bug in Traces
* Version 25r3 fixed some problems in the configure script (thanks to Daniel Grayson)
Changes from nauty 2.5 to nauty 2.6
-----------------------------------
Changes to dreadnaut:
* dreadnaut now catches control-C when nauty or Traces is running.
This uses the global variable nauty_kill_request.
* new command "vv" to display sorted degree sequence.
* new command "r&" to relabel according to the partition.
* new command "->>" to flush the output.
* new command "B" to turn on output flushing at the end of every
command. Command "-B" turns it off. Default off.
* Command with short arguments now have to be all on one line.
Most errors cause the rest of the input line to be skipped.
* The "R" command now preserves the colouring.
Changes to nauty:
* nauty has an extra hook usercanonproc().
* The maximum number of vertices is now 2 billion.
* Many modern processors have instructions POPCNT and CLZ* that can
help nauty. The configuration script now looks for them and
attempts to use them if possible.
New file formats (see formats.txt for definitions):
* sparse6 format is now extended with "incremental sparse6"
format. Graphs in incremental sparse6 format specify only the
differences from the previous graph.
As yet, incremental sparse6 is only supported by copyg (which
has new options -i/-I to write this format), listg, pickg and
countg. For listg, pickg and countg, the -p switch might not work
if the input is incremental.
* The new format digraph6 is for directed graphs. There are
procedures for reading and writing it in gtools.c.
The following programs can handle digraph6 so far:
labelg, shortg, ranlabg, directg, gentourng, amtog, complg,
copyg, dretog, catg, listg, showg, converse, converseg, delptg,
deledgeg, countg/pickg (partially), genrang (partially), genspecialg
New utilities:
* converseg : take converse of a digraph
* cubhamg : hamiltonian cycles in subcubic graphs
* hamheuristic : heuristic for hamiltonian cycles
* twohamg : partition quartic graphs into two hamiltonian cycles
* genspecialg : generate special graphs like paths and cycles
* gentreeg : generateg trees, based on a program of Li and Ruskey.
* genquarticg : generate quartic graphs, written with Narjess Afzaly.
* dretodot : reads one graph in dreadnaut format and writes a picture
of it in dot format. You can use tools in the graphviz library
to deal with it.
* vcolg : colours the vertices of graphs in all distinct ways.
If you choose the number of colours to be 2, this the same as
adding loops in all distinct ways.
* delptg : delete vertices.
As always, run the command with argument "-help" to get instructions.
Extra options in existing utilities:
* amtog now properly handles loops. (Recall that loops are ok
in sparse6 format but not in graph6 format.)
amtog has a switch -o that allows selecting one colour class of
a coloured graph, and -w to suppress the warning about loops.
* copyg has -z for writing digraph6 format. An undirected graph
can be written as a digraph, but not vice-versa.
* directg default output format is directg6.
directg has a new option -s for splitting into cases.
* dretog allows "d" command for digraph input.
* Option -B added to countg and pickg.
* complg has new option -R.
* genrang has new option -d that makes random regular graphs of
any degree but does not guarantee uniform distribution.
Also option -T for random tournaments.
Some options now work for bipartite graphs; specify the number
of vertices on each side like n1,n2.
* labelg has extra options -C and -W. These can help to determine
what is different between two different programs that generate
almost the same output.
* linegraphg has -t for making the total graph.
* Most utilities can take a single argument --version, which will
print a message stating which nauty&traces package they belong to.
Other changes:
* Traces has substantial improvements.
* Extra argument macros SWDOUBLE, SWREALRANGE, SWSEQUENCE in gtools.h.
* girth() in gutil1.c got the wrong answer for K2. Thanks to
Sean Irvine for reporting it.
* gtools.c defines checkgline() to check if a graph input
line looks ok.
* The procedures in gtnauty.c, used by labelg and other utilities,
had an old limit of 2^22 (4 million+) vertices. This limit is
now removed. Also a new procedure setlabptn() was added to set
lab/ptn according to an integer weight.
* planarg -p had a bug causing wrong output for n >= 65536. Fixed.
* The structured type bigint has disappeared in favour of integer type
nauty_counter, which is "unsigned long long" if that exists and
"unsigned long" is only 32 bits, or "unsigned long" otherwise.
This means that some plugins for geng/genbg/gentourng may need
to be revised.
Changes from nauty 2.6 to nauty 2.7
-----------------------------------
* -h and -k options for independent set size and clique size were added
to countg and pickg. For some graphs these use the program cliquer,
kindly provided by Sampo Nisjkanen and Patric Ostergard.
* Macros SWHIBIT, REMOVEHIBIT and ATMOSTONEBIT added to nauty.h.
* Added option -a to complg.
* Program copyg can now be used to make a simple filter. See the
instructions inside the source file and the example numleaves.c.
* Programs countg and pickg can now display some parameter values
as ranges instead of writing a separate line for each value. For
example, countg --ne:T will write a separate line for each number
of vertices and edges, with that line showing the range of the
number of triangles. Everything after the ':' is shown as a range.
There is also a switch -1 that causes output to be in a simple
numerical table easy to read from a program and a similar switch
-2 that omits counts.
* Program vcolg now handles digraphs and graphs with loops.
* genrang can now make random spanning trees of K(n1,n2)
* amtog has an "s" command for reading tournaments
* gentreeg made the same tree twice for n=2; thanks to Kevin Ryde
for reporting it.
* The configure script (compiled from configure.ac) was modified to
update some tests and remove some old code that is useless. The
time-critical parts of nauty are now compiled with
-march=native
if the compiler allows those switches. Since this may result in
a binary which does not run on older machines in the same family,
there is a configuration option --enable-generic to disable
these switches. To work around a bug with -march-native for
gcc version 7 on MacOSX computers (due to the linker not knowing
some of the instructions), the extra switch -mno-avx is also added
if it appears necessary.
* genspecialg can now make multiple special graphs at once.
The -b option has been extended to allow removing a matching from
a complete bipartite graph.
* watercluster2 has an option Z to write in digraph6 format.
* Problems for input of graphs with 0 vertices were fixed with help
from Kevin Ryde. However, note that many utilities in the package
will not work with such graphs. It is NOT TRUE that graphs of
order 0 are now supported. However, the primary function nauty()
(but not traces()) should work for both dense and sparse versions.
* Stronger measures are taken to ensure that the sort order used by
shortg is plain byte order. This corresponds to the C collation
order, also known as POSIX, but it may be different from the
collation order used by default on your command line. This means
that utilities like sort, uniq, comm and join might consider the
output of shortg to be out of order. To avoid this, define the
environment variable LC_ALL to equal the string "C".
bash: export LC_ALL=C
tcsh: setenv LC_ALL C
If LC_ALL is undefined, it will also be sufficient to define
LC_COLLATE to equal "C". The POSIX standard says that LC_ALL
takes precedence over LC_COLLATE if both are defined, but this
might not be true for older systems. If you really don't want
to change environment variables, you can compile shortg with
-DKEEP_SORT_LOCALE but beware that some collation orders are
are not even deterministic (i.e. different characters might
compare equal).
* The bipartite graph generator genbg now has a -Y switch to
specify the minimum number of common neighbours for two
vertices on the second side.
* A new version of Traces (including some bug fixes) is included.
See traces.c for more.
* New utilities: underlyingg takes the undirected graph underlying
a graph or digraph. assembleg combines a file of graphs (usually
connected graphs) as components to make disconnected graphs
of a specified size.
* geng has been modified to allow more than 32 vertices. The
makefile knows "geng" for up to 32 vertices, and "gengL" for
up to 64 vertices.
* pickg and countg now have -X to reverse the selection.
A change was made to allow these utilities to work on Windows
computers with sizeof(long) < sizeof(void*). Also, pickg
now writes a header if there is one in the input file.
* listg has -L that can be used in conjunction with -W or -M to
write the Laplacian matrix instead of the adjacency matrix.
* Fixed a possible bug in the combination "shortg -kt".
* You can change the archive manager (default "ar") by defining
the environment variable AR at configure time.
* Some portability issues in nautycliquer.c were fixed (thanks
to Isuru Fernando).
* The -B/--B switch of listg/countg is now isomomorphism-invariant.
It equals 0 for non-bipartite graph, and the smallest possible
side of a 2-colouring otherwise. This change reflects rewriting
of function bipartiteside() in gutil1.c. The values can differ
from those for nauty version <= 2.7rc1 when there are three or
more components.
* Fixed the type of the 4th parameter of options.usercanonproc.
* Check kill requests more often. If the global int variable
nauty_kill_request becomes nonzero, nauty and Traces will
exit at certain key points. In dreadnaut nauty_kill_request
is set if the user types control-C (if the operating system
provides this facility).
* nauty.h loads <limits.h> and <stdint.h> if they exist.
* Some features were added to assist installation on non-POSIX
systems or where 'configure' can't be easily run, such as
Microsoft Visual Studio. These changes are mostly in nauty.h.
1. The predefined names _MSC_VER, _WIN32 and _WIN64 are examined.
2. HAVE_HWLZCNT and HAVE_HWPOPCNT can be defined at compile time
(to 0 or 1) to indicate the presence of hardware lzcnt and
popcnt instructions.
3. The FIRSTBITNZ, FIRSTBIT and POPCOUNT macros can be defined
at compile time (though it is unlikely you will be able to do
much better than the default versions). FIRSTBIT is defined
in terms of FIRSTBITNZ if it isn't defined separately.
4. Loading of unavailable header files can be disabled by
predefining macros: AVOID_SYS_TYPES_H, AVOID_UNISTD_H,
AVOID_STRINGS_H and AVOID_SYS_WAIT_H.
There is more to do here; there are lots of variations in
different software versions and documentation is inconsistent.
Thanks to Andy Mercier for discussions so far.
* Bug fixed in directg that caused crash when digraphg6 output
was selected for more than WORDSIZE vertices.
* The external variables labelorg and nauty_kill_request were
moved into the "C" block of nauty.h for C++ compatibility.
* Identical BUGS in naugraph.c and sparsegraph.c.
The static sizes of dnwork[] and snwork[] were too small.
This bug first crept into version 2.6 beta 10. To meet this
bug, all of the following must be true:
(a) called densenauty() or sparsenauty() rather than calling
nauty() directly.
(b) processed graphs with 20 or more vertices.
(c) compiled naugraph.c or sparsegraph.c with an explicit
value of MAXN, rather than the default MAXN=0.
This includes using the libraries nauty1.a, nautyW1.a
or nautyL1.a. However nauty.a, nautyW.a and nautyL.a
were safe. Likewise, the utilities distributed with
nauty were also safe.
Thanks to James Trimble and Chris Jefferson for uncovering this.
Versions 2.6r12 and 2.7rc5 were fixed.
* A bug in nauty.h caused compilation failure on some hardware
without popcnt instructions. You didn't encounter this if you
didn't get compile-time error messages about POPCOUNT. Thanks
to Anthony Matos for reporting this error.
* Tweak the configure script to more reliably detect standard
function declarations and to improve the test for the POPCNT
instruction.
* Don't define INFINITY even if it isn't defined in math.h.
Note that nauty's infinity is NAUTY_INFINITY and plain
INFINITY is a required macro in the C standard.
* A bug prevented a filtering version of copyg (needs special
compilation, see copyg.c) from playing nice with incremental
sparse6 input. You didn't meet this bug unless you saw an
error message like "readg_inc: missing prior". Another
bug in the same facility caused the number of outputs to
be reported as the same as the number of inputs even if some
of them had been filtered out. The outputs themselves were
correct.
* -march=native is not added to compiles if the user has
provided an architecture via CC or CFLAGS.
* traces.h has extern "C" { } for function declarations to
assist calling from C++.
* nauty.h defines FLEX_ARRAY_OK to 1 if flexible array
members of structures are allowed, and 0 otherwise.
* Compiling with preprocessor variable USE_TLS defined will
have the same effect as configuring with --enable-tls.
(a) If either --enable-tls or USE_TLS is defined then:
USE_TLS is defined, HAVE_TLS is defined as 1, and
TLS_ATTR is defined to be the attribute for thread-local
memory (either thread_local, _Thread_local, __thread or
__declspec(thread)).
If the compiler doesn't support thread-local memory at
all, an error is issued.
(b) If --enable-tls is not used and USE_TLS is not defined,
then USE_TLS is not defined, HAVE_TLS is defined as 0,
and TLS_ATTR is defined as empty.
(1) The line "AR?=ar" in the makefile violated the Posix standard, see
https://pubs.opengroup.org/onlinepubs/9699919799/utilities/make.html
It is now gone. This shouldn't be a problem since the variable AR
is used instead and its default value is "ar" unless a different
value is specified on the make command line.
(2) There is an install target. It puts executables into ${bindir},
include files into ${includedir}, static libraries into ${libdir},
and pkg-config configuration files into ${pkgconfigexecdir}.
Configure with --prefix=PATH to specify a parent directory for these.
There is still no target for dynamic libraries.
(3) Several rearrangements that most users won't notice.
* New utility nbrhoodg can extract neighbourhoods of vertices
Changes from nauty 2.7 to nauty 2.8
-----------------------------------
* New utilities: (as always, use --help to get help)
- addptg : add additional vertices in various ways
- ancestorg : removes a specified number of final vertices
- productg : product of two graphs (such as Cartesian product)
- genposetg : generate posets (mostly written by Gunnar Brinkmann)
- dimacs2g : read files of graphs in DIMACS format
* Changes to existing utilities:
- geng got sigificantly faster for connected graphs with a
small number of edges. However, if you want trees the program
gentreeg is still much faster. There are also new options:
-k generate graphs without K4
-T generate chordal graphs
-S generate split graphs
-P generate perfect graphs
-F generate claw-free graphs
All the options can be used in combination unless the program
complains.
There is a program callgeng2.c that shows how geng can be
called in multiple threads. Read the instructions at the
start of the source file. It has a target in the makefile but
it might not work with all operating systems and compilers.
- countg/pickg now have an expanded set of available properties,
using double letters. Because --eee and similar are ambiguous,
options can be separated by commas: --e,ee or --ee,e.
Here are all the options added since version 2.7:
-LL 2-cycles (of digraphs)
-ee non-edges (including non-loops for digraphs)
-TT independent sets of size 3
-x sources
-xx sinks
-W 4-cycles (undirected only so far)
-WW diamonds (4-cycles with diagonal), only undirected
- gentreeg now allows a range of number of vertices.
Example: forests on 15 vertices with no isolated vertices:
gentreeg 2:15 | assembleg -n15cL
Also new option -i for no vertices of degree 2.
Fixed output for n=1, diameter > 0.
- genrang has an option -M# can be used in conjunction with
-d (pseudo-random regular graphs). It runs a Markov chain
for #*n steps. The chain has a uniform distribution as
its limit and, although the precise rate of convergence
is unknown, running it with a decent number of iterations
will produce a more uniform distribution than -d alone.
- listg has a new option -S for use with -M or -W to write
the signless Laplacian.
- subdivideg now works for digraphs.
- delptg has several new options:
-v select which vertices to delete
-m lower bound on minimum degree of output graphs
-a delete a clique
-b delete an independent set
-i leave vertices as isolates rather than removing them
-r delete a random set of vertices
- multig has a new option -V that lets it read the -T outout of
vcolg. Also, the output code has been made faster.
- vcolg has new options bounding the number of vertices of each
colour and bounding the vertex degrees for each colour. Also
the output code has been made faster.
- directg has a new option -a for acyclic orientations
* New functions
- gutil1.c has new procedures:
numcomponents(g,m,n) for counting the components of an
undirected graph, and
sources_sinks(g,m,n,*sources,*sinks) for counting sources
and sinks in digraphs.
- gutil2.c has new procedures:
digoncount(g,m,n) that counts how many cycles of length 2
a digraph has.
numind3sets1(g,n) for counting independent sets of size 3,
so far only for n <= WORDSIZE.
numsquares(g,m,n) counts 4-cycles in undirected graphs.
- gtnauty.c has a new procedure
breakcellwt() to split a cell according to weights on the
vertices
- naututil.c has new procedures
settolist() for converting a set into a list of integers
listtoset() for converting a list of integers into a set
Functions nextelement(), permset(), setsize(), setinter(),
settolist() and listtoset() now work for multi-word sets
even if nauty is compiled with MAXN=WORDSIZE.
* Miscellaneous
- The default "make" now creates the 16-bit libraries nautyS.a
and nautyS1.a. There are new targets for making thread-enabled
libraries nautyT.a, nautyT1.a, nautyTW.a, nautyTW1.a,
nautyTL.a and nautyTL1.a; these are not built by "make all".
- The compiler switch -march=native is omitted if the build is
for Alpine Linux. This is due to a problem with the compiler
issuing illegal instructions. Thanks to Gordon Royle for
helping with this.
- Changes were made to the configure script and nauty.h to
support ARM64 (aarch64) architecture. So far this is only
tested on the Apple M1 architecture.
- Bugs were fixed in multig (if multiple edges were present,
also combination of -V and the INPUTGRAPH hook),
genspecialg (argument parsing for -T), pickg/countg (help
text for -s,-S), and watercluster2 (shifting right by the
wordsize is undefined! This only effected clang.), assembleg
found by Szabolcs Horvát.
- Programs that use randomisation now initialise the random
generator from the high-resolution realtime clock if possible.
Specifically, it uses the first available of gettimeofday(),
clock_gettime() and time(). This makes it much less likely
that processes started close together will use the same seed.
- The proceedure gtools_getline() in gtools.c, which is used by
most utilities for reading graphs, is now faster except for
for very small graphs.
* A new version of Traces is included, that fixes a bug reported
by Aleksandr Krotov and makes other improvements. A side-effect
is that the canonical labelling made by Traces has changed.
* Nauty now uses a more standard version numbering system such as
2.8.6. Corrections will be made to the most recent version only.
----- Now 2.8.6
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