Update fplll (and lots of other programs/libraries)

.github/workflows/test_build.yml

@@ -66,7 +66,7 @@ jobs:
           brew config
           brew tap macaulay2/tap
           brew install --overwrite python
-          brew install automake boost tbb ccache ctags texinfo llvm make ninja yasm libffi msolve
+          brew install automake boost tbb ccache ctags texinfo llvm make ninja yasm libffi msolve fplll
           brew install --only-dependencies macaulay2/tap/M2
           brew link factory --force
 
@@ -85,7 +85,8 @@ jobs:
                   libgc-dev libgdbm-dev libglpk-dev libgmp3-dev libgtest-dev libmpfr-dev libmpfi-dev libntl-dev gfan \
                   libgivaro-dev libboost-regex-dev fflas-ffpack libflint-dev libmps-dev libfrobby-dev \
                   libsingular-dev singular-data libcdd-dev cohomcalg topcom 4ti2 libnormaliz-dev normaliz coinor-csdp \
-                  libnauty-dev nauty lrslib polymake pipx phcpack w3c-markup-validator libtbb-dev qepcad libomp-16-dev msolve
+                  libnauty-dev nauty lrslib polymake pipx phcpack w3c-markup-validator libtbb-dev qepcad libomp-16-dev \
+                  msolve libfplll-dev
 
 # ----------------------
 #   Steps common to all build variants
@@ -165,7 +166,8 @@ jobs:
             -L`brew --prefix readline`/lib       \
             -L/Library/Frameworks/Python.framework/Versions/${PYVERSION}/lib"
           export F77=gfortran-14
-          ../../configure --enable-download --with-system-gc
+          export FC=gfortran-14
+          ../../configure --enable-download --with-system-gc --with-fplll
 
       - name: Build Macaulay2 using Make
         if: matrix.build-system == 'autotools'

.gitmodules

@@ -9,7 +9,7 @@
 	url = https://github.com/Macaulay2/mathicgb
 [submodule "M2/submodules/bdwgc"]
 	path = M2/submodules/bdwgc
-	url = https://github.com/Macaulay2/bdwgc.git
+	url = https://github.com/ivmai/bdwgc.git
 [submodule "M2/submodules/flint"]
 	path = M2/submodules/flint
 	url = https://github.com/Macaulay2/flint2.git

M2/Macaulay2/d/actors5.d

@@ -2111,7 +2111,8 @@ toExternalString(e:Expr):Expr := (
 setupfun("toExternalString0",toExternalString);
 
 header "
-#ifndef GC_get_full_gc_total_time /* added in bdwgc 8 */
+/* added in bdwgc 8 */
+#if GC_VERSION_MAJOR < 8
 unsigned long GC_get_full_gc_total_time(void) {return 0;}
 #endif
 #define DEF_GC_FN0(s)	static void * s##_0(void *client_data) { (void) client_data; return (void *) (long) s(); }

M2/Macaulay2/d/ffi.d

@@ -679,3 +679,19 @@ ffiFunctionPointerAddress(e:Expr):Expr := (
 	else WrongArg(1, "a function"))
     else WrongNumArgs(2));
 setupfun("ffiFunctionPointerAddress", ffiFunctionPointerAddress);
+
+getMemory0(e:Expr):Expr := (
+    when e
+    is a:Sequence
+    do (
+	when a.0
+	is n:ZZcell do (
+	    if !isInt(n) then WrongArgSmallInteger(1)
+	    else when a.1
+	    is atomic:Boolean do (
+		if atomic.v then toExpr(getMemAtomic(toInt(n.v)))
+		else toExpr(getMem(toInt(n.v))))
+	    else WrongArgBoolean(2))
+	else WrongArgZZ(1))
+    else WrongNumArgs(2));
+setupfun("getMemory0", getMemory0);

M2/Macaulay2/d/version.dd

@@ -65,6 +65,10 @@ header "
    #include <Eigen/Core>
 
    #include <libnormaliz/version.h>
+
+   #ifdef HAVE_FPLLL
+   #include <fplll.h>
+   #endif
    ";
 
 header "
@@ -162,6 +166,13 @@ setupconst("version", Expr(toHashTable(Sequence(
 	  #endif
 	  "),
    "fflas_ffpack version" => ffpackVersion(),
+   "fplll version" => Ccode(constcharstar, "
+       #ifdef HAVE_FPLLL
+	   stringize(FPLLL_VERSION)
+       #else
+	   \"not present\"
+       #endif
+       "),
    "mpsolve version" => Ccode(constcharstar, "stringize(MPS_MAJOR_VERSION) \".\" stringize(MPS_MINOR_VERSION) \".\" stringize(MPS_PATCH_VERSION)" ),
    "python version" => Ccode(constcharstar,"
 	#ifdef WITH_PYTHON

M2/Macaulay2/e/fplll-interface.cpp

@@ -15,37 +15,37 @@ bool fp_LLL(MutableMatrix *M, MutableMatrix *U, int strategy)
   assert(U == NULL);
   double delta = 0.99;
   double eta = 0.51;
-  LLLMethod method = LM_WRAPPER;
-  FloatType floatType = FT_DEFAULT;
+  fplll::LLLMethod method = fplll::LM_WRAPPER;
+  fplll::FloatType floatType = fplll::FT_DEFAULT;
   int precision = 0;
-  int flags = LLL_DEFAULT;
+  int flags = fplll::LLL_DEFAULT;
 
   int ncols = static_cast<int>(M->n_rows());
   int nrows = static_cast<int>(M->n_cols());
 
-  ZZ_mat<mpz_t> mat(nrows, ncols);
+  fplll::ZZ_mat<mpz_t> mat(nrows, ncols);
 
   for (int i = 0; i < nrows; i++)
     for (int j = 0; j < ncols; j++)
       {
         ring_elem a;
         if (M->get_entry(j, i, a))
           {
-            mpz_set(mat[i][j].getData(), a.get_mpz());
+            mpz_set(mat[i][j].get_data(), a.get_mpz());
           }
       }
 
   int result =
-      lllReduction(mat, delta, eta, method, floatType, precision, flags);
+      lll_reduction(mat, delta, eta, method, floatType, precision, flags);
 
   switch (result)
     {
-      case RED_SUCCESS:
+      case fplll::RED_SUCCESS:
         break;
-      case RED_BABAI_FAILURE:
+      case fplll::RED_BABAI_FAILURE:
         ERROR("Error in fpLLL");
         return 0;
-      case RED_LLL_FAILURE:
+      case fplll::RED_LLL_FAILURE:
         ERROR("infinite loop in LLL");
         return 0;
       default:
@@ -60,7 +60,7 @@ bool fp_LLL(MutableMatrix *M, MutableMatrix *U, int strategy)
   for (int j = 0; j < ncols; j++)
     for (int i = 0; i < nrows; i++)
       {
-        mpz_set(a, mat[i][j].getData());
+        mpz_set(a, mat[i][j].get_data());
         ring_elem b = globalZZ->from_int(a);
         M->set_entry(j, i, b);
       }

M2/Macaulay2/packages/ForeignFunctions.m2

@@ -18,8 +18,8 @@
 
 newPackage("ForeignFunctions",
     Headline => "foreign function interface",
-    Version => "0.4",
-    Date => "October 1, 2024",
+    Version => "0.5",
+    Date => "March 8, 2025",
     Authors => {{
 	    Name => "Doug Torrance",
 	    Email => "[email protected]",
@@ -33,6 +33,10 @@ newPackage("ForeignFunctions",
 
 -*
 
+0.5 (2025-03-08, M2 1.25.05)
+* make LAPACK example canned since it may be a static library
+* move getMemory implementation to ffi.d so we can link bdwgc statically
+
 0.4 (2024-10-01, M2 1.24.11)
 * remove redundant Constant methods now that it's a subclass of Number
 * further tweak macOS dlopen hack (not just ARM machines)
@@ -150,6 +154,7 @@ importFrom_Core {
     "ffiStructAddress",
     "ffiUnionType",
     "ffiFunctionPointerAddress",
+    "getMemory0",
     "registerFinalizerForPointer",
     "toExternalFormat"
     }
@@ -668,13 +673,10 @@ foreignSymbol(String, ForeignType) := (symb, T) -> dereference_T dlsym symb
 -- working with pointers --
 ---------------------------
 
-gcMalloc = foreignFunction("GC_malloc", voidstar, ulong)
-gcMallocAtomic = foreignFunction("GC_malloc_atomic", voidstar, ulong)
-
 getMemory = method(Options => {Atomic => false}, TypicalValue => voidstar)
 getMemory ZZ := o -> n -> (
-    if n <= 0 then error "expected positive number";
-    (if o.Atomic then gcMallocAtomic else gcMalloc) n)
+    if n <= 0 then error "expected positive number"
+    else voidstar getMemory0(n, o.Atomic))
 getMemory ForeignType := o -> T -> getMemory(size T, Atomic => isAtomic T)
 getMemory ForeignVoidType := o -> T -> error "can't allocate a void"
 
@@ -2208,8 +2210,12 @@ doc ///
       so we use @TO voidstar@ to represent them in our call to
       @TO foreignFunction@.  Since Macaulay2 is already linked against LAPACK,
       we don't need to worry about calling @TO openSharedLibrary@.
-    Example
-      dggglm = foreignFunction("dggglm_", void, toList(13:voidstar))
+    CannedExample
+      i1 : dggglm = foreignFunction("dggglm_", void, toList(13:voidstar))
+
+      o1 = dggglm_
+
+      o1 : ForeignFunction
     Text
       The parameters @CODE "n"@, @CODE "m"@ and @CODE "p"@ are exactly the
       numbers $n$, $m$, and $p$ above.  The parameters @CODE "A"@, @CODE "B"@,
@@ -2219,12 +2225,14 @@ doc ///
       helper methods to take care of this conversion.  The local variable
       @CODE "T"@ is a @TO ForeignArrayType@ created by
       @TO (symbol *, ZZ, ForeignType)@.
-    Example
-      toLAPACK = method();
-      toLAPACK Matrix := A -> (
-          T := (numRows A * numColumns A) * double;
-          T flatten entries transpose A);
-      toLAPACK Vector := toLAPACK @@ matrix;
+    CannedExample
+      i2 : toLAPACK = method();
+
+      i3 : toLAPACK Matrix := A -> (
+              T := (numRows A * numColumns A) * double;
+              T flatten entries transpose A);
+
+      i4 : toLAPACK Vector := toLAPACK @@ matrix;
     Text
       The parameters @CODE "ldA"@ and @CODE "ldB"@ are the "leading dimensions"
       of the arrays @CODE "A"@ and @CODE "B"@.  We will use $n$ for both.  The
@@ -2241,35 +2249,56 @@ doc ///
       with @TO info@) and @TO address@ to get pointers to the other integer
       arguments.  We also use @TO (symbol *, ForeignType, voidstar)@ to
       dereference @CODE "i"@ and determine whether the call was successful.
-    Example
-      generalLinearModel= method();
-      generalLinearModel(Matrix, Matrix, Vector) := (A, B, d) -> (
-          if numRows A != numRows B
-          then error "expected first two arguments to have the same number of rows";
-          n := numRows A;
-          m := numColumns A;
-          p := numColumns B;
-          x := getMemory(m * size double);
-          y := getMemory(p * size double);
-          lwork := n + m + p;
-          work := getMemory(lwork * size double);
-          i := getMemory int;
-          dggglm(address int n, address int m, address int p, toLAPACK A,
-              address int n, toLAPACK B, address int n, toLAPACK d, x, y, work,
-              address int lwork, i);
-          if value(int * i) != 0 then error("call to dggglm failed");
-          (vector value (m * double) x, vector value (p * double) y));
+    CannedExample
+      i5 : generalLinearModel= method();
+
+      i6 : generalLinearModel(Matrix, Matrix, Vector) := (A, B, d) -> (
+               if numRows A != numRows B
+               then error "expected first two arguments to have the same number of rows";
+               n := numRows A;
+               m := numColumns A;
+               p := numColumns B;
+               x := getMemory(m * size double);
+               y := getMemory(p * size double);
+               lwork := n + m + p;
+               work := getMemory(lwork * size double);
+               i := getMemory int;
+               dggglm(address int n, address int m, address int p, toLAPACK A,
+                   address int n, toLAPACK B, address int n, toLAPACK d, x, y, work,
+                   address int lwork, i);
+               if value(int * i) != 0 then error("call to dggglm failed");
+               (vector value (m * double) x, vector value (p * double) y));
     Text
       Finally, let's call this method and solve a constrained least squares
       problem.  This example is from
       @HREF{"https://doi.org/10.1080/01621459.1981.10477694",
 	  "Kourouklis, S., & Paige, \"A Constrained Least Squares Approach to
 	  the General Gauss-Markov Linear Model\""}@.
-    Example
-      A = matrix {{1, 2, 3}, {4, 1, 2}, {5, 6, 7}, {3, 4, 6}};
-      B = matrix {{1, 0, 0, 0}, {2, 3, 0, 0}, {4, 5, 1e-5, 0}, {7, 8, 9, 10}};
-      d = vector {1, 2, 3, 4};
-      generalLinearModel(A, B, d)
+    CannedExample
+      i7 : A = matrix {{1, 2, 3}, {4, 1, 2}, {5, 6, 7}, {3, 4, 6}};
+
+                    4       3
+      o7 : Matrix ZZ  <-- ZZ
+
+      i8 : B = matrix {{1, 0, 0, 0}, {2, 3, 0, 0}, {4, 5, 1e-5, 0}, {7, 8, 9, 10}};
+
+                      4         4
+      o8 : Matrix RR    <-- RR
+                    53        53
+
+      i9 : d = vector {1, 2, 3, 4};
+
+             4
+      o9 : ZZ
+
+      i10 : generalLinearModel(A, B, d)
+
+      o10 = (|   .3141  |, | .0296627 |)
+             | -.334417 |  | .0451036 |
+             |  .441691 |  | .0585128 |
+                           | .0650142 |
+
+      o10 : Sequence
 ///
 
 doc ///

M2/Macaulay2/packages/LLLBases.m2

@@ -1244,6 +1244,10 @@ TEST ///
 
     time (mz,ch) = LLL(m, ChangeMatrix=>true)
     time (mz5,ch5) = LLL(m, Strategy=>CohenTopLevel, ChangeMatrix=>true)
+
+    if version#"fplll version" != "not present" then (
+	time mz6 = LLL(m, Strategy => fpLLL);
+	assert isLLL mz6)
 ///
 
 TEST 

M2/Macaulay2/packages/Licenses.m2

@@ -73,8 +73,6 @@ licenseInfo = hashTable {
         },
     "gmp version" => hashTable {
         },
-    "linbox version" => hashTable {
-        },
     "mathic version" => hashTable {
 	 "1.0" => VerticalList {
 	      "LGPL 2 or later",

M2/Macaulay2/util/Makefile.in

@@ -20,7 +20,15 @@ all: gc_tested
 gc_test : gc_test.c
 gc_test : LDLIBS += @LIBS@ @BUILTLIBS@
 
-gc_tested: gc_test; LD_LIBRARY_PATH="$(BUILTLIBPATH)/lib:$(LD_LIBRARY_PATH)" ./$< && touch $@
+gc_tested: gc_test
+ifeq (@OS@,Darwin)
+	DYLD_LIBRARY_PATH="$(BUILTLIBPATH)/lib:$(DYLD_LIBRARY_PATH)" \
+		./$< && touch $@
+else
+	LD_LIBRARY_PATH="$(BUILTLIBPATH)/lib:$(LD_LIBRARY_PATH)" \
+		./$< && touch $@
+endif
+
 # Local Variables:
 # compile-command: "make -C $M2BUILDDIR/Macaulay2/util "
 # End: