Fix runcluster.pl

Makefile

@@ -84,7 +84,6 @@ DAIKON_RESOURCE_FILES := daikon/config/example-settings.txt \
 	daikon/test/InvariantFormatTest.commands \
 	daikon/test/SampleTester.commands \
 	daikon/test/SampleTester.decls \
-	daikon/test/SampleTesterGlobal.decls \
 	daikon/test/SampleTester.commands_linear_ternary \
 	daikon/test/varInfoNameTest.testEscForall \
 	daikon/test/varInfoNameTest.testEscForall.goal \

doc/CHANGELOG.md

@@ -28,10 +28,27 @@ Further documentation can be found in:
    with status 0.
 * `daikon.diff.Diff` no longer accepts the `-u` and `-z` options, which had
    no effect.
+* In a splitter info (`.spinfo`) file, a `PPT_NAME` that contains `:::` is a
+  complete program point name, and it matches only the program point of that
+  name.  A name ending with `:::EXIT` also matches the numbered exit points.
+  This affects where Daikon uses a condition only if indiscriminate splitting
+  is disabled via `--config_option daikon.split.SplitterList.all_splitters=false`.
+* ExtractConsequent writes splitting conditions that Daikon can use.
 * `daikon.bashrc` sets only `DAIKONDIR` and `PATH`.  It no longer sets
    `JAVA_HOME`, `DAIKON_CLASSPATH`, `DAIKONSCRIPTS`, `PLUME_SCRIPTS`, `PERLLIB`,
    or `PERL5LIB`.
 * Removed the Perl front end, dfepl.
+* Daikon and its tools no longer read `.decls` and `.dtrace` files in the
+  obsolete version 1 format (files that contain `decl-version 1.0`,
+  `VarComparability`, or `DECLARE` records).  Daikon also cannot read
+  `.inv` files written by earlier versions of Daikon.
+  * Removed configuration option `daikon.PrintInvariants.remove_post_vars`, which
+    had an effect only for version 1 files.
+  * Removed scripts that processed only version 1 files:  `auxinfo.pl`,
+    `clean-decls.php`, `copy_comparable.pl`, `decls2comp-1.0.py`,
+    `decls-lackwit-disjoint.pl`, `dfec-to-kvasir.py`, `dfec-to-kvasir-dtrace.py`,
+    `dtrace-rm-decls.php`, `find_comparable.pl`, `find_globals.pl`,
+    `generate-dec-types.py`, `lwpp.pl`, `lwpp-init.pl`, and `set_decl_type.pl`.
 
 Scripts:
 

doc/daikon.texinfo

@@ -2415,6 +2415,16 @@ that are prefixes of other method names.  For instance, if the class
 which was encountered first.  Instead writing @samp{PPT_NAME
 List.add(} will match only the @code{add} method.
 
+If @var{pptname} contains @samp{:::}, then it is a complete program
+point name, such as @samp{pkg.List.add(Object):::EXIT12}, and it
+matches only the program point of that name.  As a special case, a
+name that ends with @samp{:::EXIT} also matches the method's numbered
+exit points, such as @samp{:::EXIT12}.  By default, Daikon uses every
+condition at every program point, regardless of @var{pptname}; to use
+each condition only at the program points that its @var{pptname}
+matches, disable indiscriminate splitting (@pxref{Indiscriminate
+splitting}).
+
 Each condition is a Java expression of boolean type.  All variables
 that appear in the condition must also appear in the declaration of
 the program point in the @file{.decls} file.  (In other words, all the
@@ -2723,9 +2733,16 @@ To find splitting conditions using cluster analysis, run the
 @command{runcluster.pl} program (found in the @file{$@{DAIKONDIR@}/scripts}
 directory) in the following way:
 @example
-runcluster.pl [@var{options}] @var{dtrace_file ...} @var{decls_files ...}
+runcluster.pl [@var{options}] @var{dtrace_file ...} [@var{decls_files ...}]
 @end example
 
+@noindent
+If no decls files are given, @command{runcluster.pl} uses the
+declarations in the dtrace files, as written by Chicory.  The input files
+are not modified.  The result is written to file
+@file{cluster-@var{ALG}-@var{k}.spinfo} (or @file{cluster-xm.spinfo})
+in the current directory.
+
 @noindent
 The @var{options} are:
 @table @option
@@ -2753,7 +2770,10 @@ programs.  They are implementations of the kmeans algorithm,
 hierarchical clustering, and the xmeans algorithm (kmeans algorithm
 with efficient discovery of the number of clusters).  The kmeans and
 hierarchical clustering tools are provided in the Daikon
-distribution.  The xmeans code and executable are publicly available at
+distribution, in directories @file{$@{DAIKONDIR@}/tools/kmeans} and
+@file{$@{DAIKONDIR@}/tools/hierarchical}; run @command{make} in each
+directory, and put each directory on your path.
+The xmeans code and executable are publicly available at
 @uref{http://www.cs.cmu.edu/~dpelleg/kmeans.html} (fill in the license
 form and mail it in).
 
@@ -2789,6 +2809,10 @@ The @var{daikon_options} are the same options that can be provided to the
 The @var{options} for @command{TraceSelect} are:
 @table @option
 
+@item -SEED @var{n}
+Use the integer @var{n} as the seed for random selection, so that repeated
+runs select the same samples.
+
 @item -NOCLEAN
 Don't delete the temporary trace samples created by the random
 selection process.  This can help for debugging or for using the tool
@@ -7118,25 +7142,18 @@ should indicate where the problem is occurring.
 
 If Daikon terminates with an error such as
 @smallexample
-decl format '2.0' does not match previous setting at line 4 in file test.dtrace
+Error at line 1 in file test.decls: File is in the version 1 format, which is no longer supported. ...
 @end smallexample
 
 @noindent
-it means you are using multiple @file{.dtrace} and/or @file{.decls} files
-and they are not all in the same format.
+it means that the file was produced by an old front end (or an old version
+of Chicory or DynComp) that wrote the obsolete version 1 file format.
 (See @ref{Declaration version,,,developer,Daikon Developer Manual}
 for information about how to determine a data file's format.)
-
-The most probable cause is you are using at least one
-version 1 @file{.decls} file or @file{.dtrace} file generated by an older version of
-Chicory/DynComp and at least one current @file{.decls} file or @file{.dtrace} file (which
-defaults to version 2) as input to Daikon.
-(Note that the C/C++ front end Kvasir generates a version 2 file @file{.decls}.)
-The way to
-avoid this problem is to use your Java-DynComp-generated @file{.decls} files
-as input to Chicory. The resulting @file{.dtrace} file will contain the
-comparability values from the @file{.decls} file(s) and can then be used
-as input to Daikon.
+Daikon reads only version 2 files.  Re-generate the file with a current front
+end.  For example, if the file is a @file{.decls} file produced by an old
+version of DynComp, re-run DynComp, and then pass the resulting
+@file{.decls} file to Chicory.
 Passing a @file{.decls} file to Chicory is
 described in @ref{Detecting invariants in Java programs}, for example:
 
@@ -8649,14 +8666,14 @@ of, or in addition to, referencing this manual and the Daikon website
 @c  LocalWords:  fd Linux's GNUC mkdir tmp gunzip xf li dkconfig CreateSpinfo
 @c  LocalWords:  ParameterDoclet CreateSpinfoC un biconditional addAll isFull
 @c  LocalWords:  smallexample simpleStack currentSize jtb ParseException kmeans
-@c  LocalWords:  runcluster xm ALG xmeans TraceSelect NOCLEAN DIFFS MergeESC pp
+@c  LocalWords:  runcluster xm ALG xmeans TraceSelect NOCLEAN DIFFS SEED MergeESC pp
 @c  LocalWords:  escannotated jmlannotated dbcannotated Annnotate xml INVINFO
 @c  LocalWords:  ubs Throwable throwable rethrown WriteViolationFile MyProg
 @c  LocalWords:  callMethod isInstrumented getInvariants INVS ijmp exin wp
 @c  LocalWords:  bBoOmjpi de iconv undefine DHAVE Xie Ast rt MyPackage jre
 @c  LocalWords:  superdirectory SOURCEPATH InvalidClassDataError strace lstat
 @c  LocalWords:  RuntimeException IFLNK interconvert interconvertible strdup ld
-@c  LocalWords:  lwpp ine runtime's malloced MaxPermSize JVM's MyVector perc vv
+@c  LocalWords:  ine runtime's malloced MaxPermSize JVM's MyVector perc vv
 @c  LocalWords:  falsetime trueinvs testsuite MergeInvariants fns untruncate mx
 @c  LocalWords:  subsubheading bzip fontspecific sublicense NONINFRINGEMENT Cok
 @c  LocalWords:  getopt Renn Nethercote MemCheck readelf Binutils Yuriy Brun ps