gfan 0.7

Macaulay2 · Oct 4, 2024 · f9df6a5 · f9df6a5
1 parent 48a482b
commit f9df6a5
Showing 1 changed file with 322 additions and 27 deletions.
diff --git a/Formula/gfan.rb b/Formula/gfan.rb
@@ -1,10 +1,9 @@
 class Gfan < Formula
   desc "Grobner fans and tropical varieties"
   homepage "https://users-math.au.dk/~jensen/software/gfan/gfan.html"
-  url "https://users-math.au.dk/~jensen/software/gfan/gfan0.6.2.tar.gz"
-  sha256 "a674d5e5dc43634397de0d55dd5da3c32bd358d05f72b73a50e62c1a1686f10a"
+  url "https://users-math.au.dk/~jensen/software/gfan/gfan0.7.tar.gz"
+  sha256 "ab833757e1e4d4a98662f4aa691394013ea9a226f6416b8f8565356d6fcc989e"
   license "GPL-2.0-or-later"
-  revision 11
 
   bottle do
     root_url "https://ghcr.io/v2/macaulay2/tap"
@@ -25,11 +24,6 @@ class Gfan < Formula
   depends_on "cddlib"
   depends_on "gmp"
 
-  patch do
-    url "https://raw.githubusercontent.com/Macaulay2/M2/d51564127d757a3132684e9730f4085cb89297bb/M2/libraries/gfan/patch-0.6.2"
-    sha256 "9ebbf25e6de16baec877050bef69c85504e7bfa81e79407c2ab00ea4433e838c"
-  end
-
   patch :DATA
 
   def install
@@ -55,31 +49,332 @@ def install
 
 __END__
 
-diff --git a/Makefile-orig b/Makefile
-index 737208abfb..52e010e0b3 100644
+diff --git a/Makefile b/Makefile
+index 67c8164..0c9bbf2 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -110,15 +110,15 @@ MKDIR=mkdir -p
- PREFIX =
+@@ -117,11 +117,6 @@ PREFIX =
  SHELL       = /bin/sh
  #ARCH        = LINUX
+
 -CC          = $(PREFIX)gcc
 -CLINKER     = $(CC)
 -CXX         = $(PREFIX)g++
 -CCLINKER    = $(CXX)
-+#CC          = $(PREFIX)gcc
-+#CLINKER     = $(CC)
-+#CXX         = $(PREFIX)g++
-+#CCLINKER    = $(CXX)
- #OPTFLAGS    = -O2 -DGMPRATIONAL -DNDEBUG
- # Note that gcc produces wrong code with -O3
--OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -fno-guess-branch-probability #-DNDEBUG
-+#OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2	 #-O3 -fno-guess-branch-probability #-DNDEBUG
- #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2  -finline-limit=1000 -ffast-math -Wuninitialized # -fno-guess-branch-probability #-DNDEBUG -ftree-vectorizer-verbose=2
--#OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O1             -fno-guess-branch-probability
-+OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O1             -fno-guess-branch-probability
-  #-DNDEBUG
- #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2 -ftree-vectorizer-verbose=2 -finline-limit=1000 -ffast-math #-DNDEBUG
- #OPTFLAGS    =  -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O3 -mavx -msse2 -ftree-vectorizer-verbose=2 -march=native -unroll-loops --param max-unroll-times=4 -ffast-math #-DNDEBUG
+-
+ #CC          = $(PREFIX)gcc-8.1
+ #CLINKER     = $(CC)
+ #CXX         = $(PREFIX)g++-8.1
+@@ -420,9 +415,9 @@ EXECS	  = $(MAIN)
+ # (compiling with gcc version 4.7.2 and running gfan _tropicaltraverse on a starting cone for Grassmann3_7)
+ # Either this is a bug in the code or in the compiler. The bug disappears by compiling with -fno-guess-branch-probability
+ src/symmetrictraversal.o: src/symmetrictraversal.cpp
+-	$(CXX) $(CFLAGS) -fno-guess-branch-probability  -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
++#	$(CXX) $(CFLAGS) -fno-guess-branch-probability  -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+ # If compiling with clang, use the line below instead:
+-#	$(CXX) $(CFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
++	$(CXX) $(CFLAGS) -c src/symmetrictraversal.cpp -o src/symmetrictraversal.o
+
+ # Define suffixes to make the program compile on legolas.imf.au.dk :
+ .SUFFIXES: .o .cpp .c
+diff --git a/src/application.cpp b/src/application.cpp
+index 77f830b..baf3589 100644
+--- a/src/application.cpp
++++ b/src/application.cpp
+@@ -567,7 +567,7 @@ void Application::makeSymbolicLinks(const char *name, bool all, const char *path
+ 	if(strlen(p->name())>0)
+ 	  {
+ 	    char c[1024];
+-	    sprintf(c,"ln -s %s%s %s%s%s\n",path,name,path,name,p->name());
++	    sprintf(c,"ln -sf %s%s %s%s%s\n",path,name,path,name,p->name());
+ 	    fprintf(stderr,"%s",c);
+ 	    int err=system(c);
+ 	    assert(err==0);
+diff --git a/src/enumeration.cpp b/src/enumeration.cpp
+index 44d0a4f..6d3870e 100644
+--- a/src/enumeration.cpp
++++ b/src/enumeration.cpp
+@@ -14,7 +14,7 @@ EnumerationFilePrinter::EnumerationFilePrinter():
+
+ EnumerationFilePrinter::~EnumerationFilePrinter()
+ {
+-  assert(file==0);
++  // assert(file==0);
+ }
+
+
+diff --git a/src/enumeration.h b/src/enumeration.h
+index b0bd187..d91c9ff 100644
+--- a/src/enumeration.h
++++ b/src/enumeration.h
+@@ -36,7 +36,7 @@ class EnumerationFilePrinter: public EnumerationPrinter
+   FILE *file;
+  public:
+   EnumerationFilePrinter();
+-  ~EnumerationFilePrinter();
++  virtual ~EnumerationFilePrinter();
+
+   void open(std::string filename);
+   void open(FILE *file);
+diff --git a/src/field.h b/src/field.h
+index 866be22..7df1600 100644
+--- a/src/field.h
++++ b/src/field.h
+@@ -208,6 +208,7 @@ class FieldElementImplementation
+   {
+ 	  fprintf(stderr,"*this is not in Z/pZ.\n");
+ 	  assert(0);
++	  exit(0);
+   }
+   virtual bool isInteger()const
+   {
+@@ -223,6 +224,7 @@ class FieldElementImplementation
+   Field& operator=(const Field& a)
+     {
+       assert(0);
++      exit(1);
+     }//assignment
+ };
+
+@@ -271,7 +273,8 @@ class FieldImplementation
+   virtual FieldElement random()
+   {
+ 	  assert(0);
+-  }
++	  exit(1);
++       }
+     virtual int getCharacteristic()const=0;
+     virtual const char *name()=0;
+   virtual std::string toString()const=0;
+diff --git a/src/field_rationalfunctions2.cpp b/src/field_rationalfunctions2.cpp
+index 4e80c5a..ccc6ae9 100644
+--- a/src/field_rationalfunctions2.cpp
++++ b/src/field_rationalfunctions2.cpp
+@@ -524,6 +524,7 @@ class FieldElementRationalFunction2 : public FieldElementImplementation
+
+     return sign+string("{").append(s,startIndex,slashIndex-startIndex)+string("\\over ").append(s,slashIndex+1,s.length()-slashIndex-1)+string("}");
+ */
++	  exit(1);
+ 	  }
+
+   std::string toString(bool writeIfOne=true, bool alwaysWriteSign=false, bool latexMode=false /*, bool mathMode=true*/) const
+diff --git a/src/field_rationals.cpp b/src/field_rationals.cpp
+index 30a92f6..06c95c9 100644
+--- a/src/field_rationals.cpp
++++ b/src/field_rationals.cpp
+@@ -398,7 +398,7 @@ const char *FieldRationalsImplementation::name()
+ /*FieldRationals::FieldRationals():
+   Field(new FieldRationalsImplementation())
+ {
+-  /*  fprintf(Stderr,"Adding field rationals\n");
++  fprintf(Stderr,"Adding field rationals\n");
+   next=list;
+   list=this;
+   */
+diff --git a/src/gfanlib_circuittableint.h b/src/gfanlib_circuittableint.h
+index 2b5ced4..609d2d2 100644
+--- a/src/gfanlib_circuittableint.h
++++ b/src/gfanlib_circuittableint.h
+@@ -25,6 +25,7 @@ namespace gfan{
+   template<typename> struct MyMakeUnsigned;
+   template <> struct MyMakeUnsigned<int>{typedef unsigned int type;};
+   template <> struct MyMakeUnsigned<long int>{typedef unsigned long int type;};
++  template <> struct MyMakeUnsigned<long long int>{typedef unsigned long long int type;};
+   template <> struct MyMakeUnsigned<__int128>{typedef unsigned __int128 type;};
+
+   class MVMachineIntegerOverflow: public std::exception
+@@ -239,6 +240,17 @@ static my256s extMul(__int128_t a, __int128_t b)
+ 	return my256s(r);
+ }
+
++static my256s extMul(long long int a, long long int b)
++{
++//	std::cerr<<"mul"<<toStr(a)<<"*"<<toStr(b)<<"\n";
++	auto temp=unsignedProd128(a,b);
++	my256s r(temp.lo,temp.hi);
++	if(a<0)r=r+my256s(0,-b);
++	if(b<0)r=r+my256s(0,-a);
++//	std::cerr<<"result"<<toStr(r)<<"\n";
++	return my256s(r);
++}
++
+ /*
+  * The philosophy here is that if this class overflows, then the computation needs to be restarted. Therefore
+  * all overflows must be caught.
+@@ -530,7 +542,7 @@ public:
+ 		   */
+ 		  else
+ 		  {
+-			  if(0){
++#if 0
+ 				  std::cerr<<toStr(positiveResultBoundTimesD)<<"\n"<<toStr(denominatorDivisor.v)<<"\n";
+ 				  std::cerr<<"---\n";
+ 				  std::cerr<<toStr(negabs(t).v)<<"\n";
+@@ -542,7 +554,7 @@ public:
+ 				  std::cerr<<"---\n";
+
+ //				  std::cerr<<this->)
+-			  }
++#endif
+ 			  int D=std::numeric_limits<word>::digits;
+ 			  if(D==0){D=127;}//fixes bug in gcc-8.1
+ 			  bool doesOverflow=(((word)t.v)==(word{1}<<(D-1)));// What is the purpose of this line. Do we really want to subtract 1? That seems wrong since word is signed. Look at comment below
+diff --git a/src/gfanlib_z.h b/src/gfanlib_z.h
+index f56597c..5a62076 100644
+--- a/src/gfanlib_z.h
++++ b/src/gfanlib_z.h
+@@ -8,6 +8,7 @@
+ #ifndef LIB_Z_H_
+ #define LIB_Z_H_
+
++#include <cstdint>
+ #include <string.h>
+ #include <ostream>
+ #include <iostream>
+diff --git a/src/gmpallocator.cpp b/src/gmpallocator.cpp
+index e308412..07c6b74 100644
+--- a/src/gmpallocator.cpp
++++ b/src/gmpallocator.cpp
+@@ -29,7 +29,7 @@ static inline int bufNum(int size)
+     {
+       ret++;
+       if(ret>=(NBUCKETSGMP))return -1;
+-      size>>1;
++      size>>=1;
+     }
+   return ret;
+ }
+diff --git a/src/lp.cpp b/src/lp.cpp
+index 744e2a9..420b853 100644
+--- a/src/lp.cpp
++++ b/src/lp.cpp
+@@ -59,6 +59,7 @@ bool LpSolver::hasInteriorPoint(const IntegerVectorList &g, bool strictlyPositiv
+ {
+   fprintf(stderr,"hasInteriorPoint method not supported in \"%s\" LP class\n",name());
+   assert(0);
++  exit(1);
+ }
+
+
+@@ -119,6 +120,7 @@ bool LpSolver::hasHomogeneousSolution(int n, const IntegerVectorList &inequaliti
+ {
+   fprintf(stderr,"hasHomogeneousSolution method not supported in \"%s\" LP class\n",name());
+   assert(0);
++  exit(1);
+ }
+
+ static LpSolver *soplex,*soplexCddGmp,*huber,*cdd,*cddgmp,*default_;
+diff --git a/src/nbody.cpp b/src/nbody.cpp
+index e6d2e6e..3384bb0 100644
+--- a/src/nbody.cpp
++++ b/src/nbody.cpp
+@@ -17,6 +17,7 @@ static int rIndex(int i, int j, int N, bool withMasses)
+ 	r++;
+       }
+   assert(0);
++  exit(1);
+ }
+
+ static int sIndex(int i, int j, int N, bool withMasses)
+diff --git a/src/packedmonomial.cpp b/src/packedmonomial.cpp
+index 65a9242..37404e6 100644
+--- a/src/packedmonomial.cpp
++++ b/src/packedmonomial.cpp
+@@ -39,6 +39,7 @@ vector<MonomialType> minimized(vector<MonomialType> const &generators)
+
+ 	  *g=ret;
+ */
++	exit(1);
+ }
+
+
+diff --git a/src/parser.cpp b/src/parser.cpp
+index 8c09b1a..ed807f8 100644
+--- a/src/parser.cpp
++++ b/src/parser.cpp
+@@ -638,6 +638,7 @@ Field CharacterBasedParser::parseField()
+
+   parserError("field",c);
+   assert(0);
++  exit(1);
+ }
+
+
+diff --git a/src/polyhedralfan.cpp b/src/polyhedralfan.cpp
+index e62cae4..90eae40 100644
+--- a/src/polyhedralfan.cpp
++++ b/src/polyhedralfan.cpp
+@@ -1672,6 +1672,7 @@ PolyhedralCone PolyhedralFan::coneContaining(IntegerVector const &v)const
+     if(i->contains(v))return i->faceContaining(v);
+   debug<<"Vector "<<v<<" not contained in support of fan\n";
+   assert(0);
++  exit(1);
+ }
+
+
+diff --git a/src/polymakefile.cpp b/src/polymakefile.cpp
+index a7ea692..55d3d39 100644
+--- a/src/polymakefile.cpp
++++ b/src/polymakefile.cpp
+@@ -329,6 +329,7 @@ void PolymakeFile::writeMatrixProperty(const char *p, const IntegerMatrix &m, bo
+ IntegerMatrix PolymakeFile::readArrayArrayIntProperty(const char *p, int width)
+ {
+   assert(0);//Not implemented yet.
++  exit(1);
+ }
+
+
+@@ -371,7 +372,7 @@ static list<int> readIntList(istream &s)
+ {
+   list<int> ret;
+   int c=s.peek();
+-  while((c>='0') && (c<='9')|| (c==' '))
++  while(((c>='0') && (c<='9'))|| (c==' '))
+     {
+       //      fprintf(Stderr,"?\n");
+       int r;
+diff --git a/src/polynomialgcd.cpp b/src/polynomialgcd.cpp
+index 82aea06..14cb528 100644
+--- a/src/polynomialgcd.cpp
++++ b/src/polynomialgcd.cpp
+@@ -618,7 +618,7 @@ Polynomial NonMonomialPolynomialGCDForZ(PolynomialSet p)
+ if(1)	{
+ 		static int i;
+ 		i++;
+-		if((i==1000))
++		if(i==1000)
+ 		{
+ //			debug<<simplifyPolysViaHomogeneitySpace(p);
+ //			debug<<"NonMon on:"<<p.getRing()<<p<<"\n";
+diff --git a/src/timer.cpp b/src/timer.cpp
+index 7421c41..b5d8741 100644
+--- a/src/timer.cpp
++++ b/src/timer.cpp
+@@ -1,10 +1,10 @@
+ #include "timer.h"
+-#include "log.h"
+-
+ #include "iostream"
+ #include <time.h>
+ #include <assert.h>
+
++#include "log.h" // include last, because it defines a macro "log2" also defined as a function in math.h
++
+ using namespace std;
+
+ Timer* Timer::timers;
+diff --git a/src/vektor.cpp b/src/vektor.cpp
+index d17579a..63e39f0 100644
+--- a/src/vektor.cpp
++++ b/src/vektor.cpp
+@@ -96,7 +96,7 @@ int gcdGFAN(int r, int s)
+ int gcdOfVector(IntegerVector const &v)
+ {
+   int ret=0;
+-  for(int i=0;i<v.size();i++)if(ret=v[i])break;
++  for(int i=0;i<v.size();i++)if((ret=v[i]))break;
+   if(ret<0)ret=-ret;
+   assert(ret!=0);
+   for(int i=0;i<v.size();i++)ret=gcdGFAN(ret,v[i]);
 -- 
-2.31.1
+2.46.0