Define gc counted allocator functions with libc API and use them in

CHOLMOD wrappers
JuliaLang · Jul 10, 2015 · 7f74c23 · 7f74c23
1 parent e3dfa56
commit 7f74c23
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Showing 3 changed files with 61 additions and 5 deletions.
diff --git a/base/sparse/cholmod.jl b/base/sparse/cholmod.jl
@@ -65,6 +65,7 @@ const version = VersionNumber(version_array...)
 function __init__()
     ### Check if the linked library is compatible with the Julia code
     if Libdl.dlsym(Libdl.dlopen("libcholmod"), :cholmod_version) == C_NULL
+        hasversion = false
         warn("""
 
             CHOLMOD version incompatibility
@@ -81,6 +82,7 @@ function __init__()
             versions of all dependencies.
         """)
     else
+        hasversion = true
         tmp = Array(Cint, 3)
         ccall((:cholmod_version, :libcholmod), Cint, (Ptr{Cint},), version_array)
         ccall((:jl_cholmod_version, :libsuitesparse_wrapper), Cint, (Ptr{Cint},), tmp)
@@ -140,6 +142,15 @@ function __init__()
     start(commonStruct)              # initializes CHOLMOD
     set_print_level(commonStruct, 0) # no printing from CHOLMOD by default
 
+    # Register gc tracked allocator if CHOLMOD is new enough
+    if hasversion && version >= v"3.0.0"
+        cnfg = cglobal((:SuiteSparse_config, :libsuitesparseconfig), Ptr{Void})
+        unsafe_store!(cnfg, cglobal(:jl_malloc, Ptr{Void}), 1)
+        unsafe_store!(cnfg, cglobal(:jl_calloc, Ptr{Void}), 2)
+        unsafe_store!(cnfg, cglobal(:jl_realloc, Ptr{Void}), 3)
+        unsafe_store!(cnfg, cglobal(:jl_free, Ptr{Void}), 4)
+    end
+
 end
 
 function set_print_level(cm::Array{UInt8}, lev::Integer)

diff --git a/contrib/repackage_system_suitesparse4.make b/contrib/repackage_system_suitesparse4.make
@@ -25,14 +25,16 @@ default:
 	mkdir -p $(JULIAHOME)/deps/SuiteSparse-SYSTEM/lib
 	cd $(JULIAHOME)/deps/SuiteSparse-SYSTEM/lib && \
 	rm -f $(build_libdir)/lib{amd,cholmod,colamd,spqr,umfpack}.$(SHLIB_EXT)
-	$(CC) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libamd.a $(SS_LIB)/libsuitesparseconfig.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libamd.$(SHLIB_EXT)
+	$(CC) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libsuitesparseconfig.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libsuitesparseconfig.$(SHLIB_EXT)
+	$(INSTALL_NAME_CMD)libsuitesparseconfig.$(SHLIB_EXT) $(build_libdir)/libsuitesparseconfig.$(SHLIB_EXT)
+	$(CC) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libamd.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libamd.$(SHLIB_EXT) $(LDFLAGS) -L$(build_libdir) -lsuitesparseconfig $(RPATH_ORIGIN)
 	$(INSTALL_NAME_CMD)libamd.$(SHLIB_EXT) $(build_libdir)/libamd.$(SHLIB_EXT)
-	$(CC) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libcolamd.a $(SS_LIB)/libsuitesparseconfig.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libcolamd.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS)
+	$(CC) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libcolamd.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libcolamd.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lsuitesparseconfig $(RPATH_ORIGIN)
 	$(INSTALL_NAME_CMD)libcolamd.$(SHLIB_EXT) $(build_libdir)/libcolamd.$(SHLIB_EXT)
-	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libcholmod.a $(SS_LIB)/libsuitesparseconfig.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libcholmod.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lcolamd -lccolamd -lcamd -lamd $(RPATH_ORIGIN)
+	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libcholmod.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libcholmod.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lsuitesparseconfig -lcolamd -lccolamd -lcamd -lamd $(RPATH_ORIGIN)
 	$(INSTALL_NAME_CMD)libcholmod.$(SHLIB_EXT) $(build_libdir)/libcholmod.$(SHLIB_EXT)
-	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libsuitesparseconfig.a $(SS_LIB)/libumfpack.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libumfpack.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lcolamd -lccolamd -lcamd -lamd -lcholmod $(RPATH_ORIGIN)
+	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libumfpack.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libumfpack.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lsuitesparseconfig -lcolamd -lccolamd -lcamd -lamd -lcholmod $(RPATH_ORIGIN)
 	$(INSTALL_NAME_CMD)libumfpack.$(SHLIB_EXT) $(build_libdir)/libumfpack.$(SHLIB_EXT)
-	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libsuitesparseconfig.a $(SS_LIB)/libspqr.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libspqr.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lcolamd -lccolamd -lcamd -lamd -lcholmod $(RPATH_ORIGIN)
+	$(CXX) -shared $(WHOLE_ARCHIVE) $(SS_LIB)/libspqr.a $(NO_WHOLE_ARCHIVE) -o $(build_libdir)/libspqr.$(SHLIB_EXT) $(LDFLAGS) $(LIBBLAS) -L$(build_libdir) -lsuitesparseconfig -lcolamd -lccolamd -lcamd -lamd -lcholmod $(RPATH_ORIGIN)
 	$(INSTALL_NAME_CMD)libspqr.$(SHLIB_EXT) $(build_libdir)/libspqr.$(SHLIB_EXT)
 
diff --git a/src/gc.c b/src/gc.c
@@ -2690,6 +2690,17 @@ DLLEXPORT void *jl_gc_counted_malloc(size_t sz)
     return b;
 }
 
+DLLEXPORT void *jl_gc_counted_calloc(size_t nm, size_t sz)
+{
+    maybe_collect();
+    allocd_bytes += nm*sz;
+    gc_num.malloc++;
+    void *b = calloc(nm, sz);
+    if (b == NULL)
+        jl_throw(jl_memory_exception);
+    return b;
+}
+
 DLLEXPORT void jl_gc_counted_free(void *p, size_t sz)
 {
     free(p);
@@ -2712,6 +2723,38 @@ DLLEXPORT void *jl_gc_counted_realloc_with_old_size(void *p, size_t old, size_t
     return b;
 }
 
+DLLEXPORT void *jl_malloc(size_t sz)
+{
+    int64_t *p = (int64_t *)jl_gc_counted_malloc(sz + 16);
+    p[0] = sz;
+    return (void *)(p + 2);
+}
+
+DLLEXPORT void *jl_calloc(size_t nm, size_t sz)
+{
+    int64_t *p;
+    size_t nmsz = nm*sz;
+    p = (int64_t *)jl_gc_counted_calloc(nmsz + 16, 1);
+    p[0] = nmsz;
+    return (void *)(p + 2);
+}
+
+DLLEXPORT void jl_free(void *p)
+{
+    int64_t *pp = (int64_t *)p - 2;
+    size_t sz = pp[0];
+    jl_gc_counted_free(pp, sz + 16);
+}
+
+DLLEXPORT void *jl_realloc(void *p, size_t sz)
+{
+    int64_t *pp = (int64_t *)p - 2;
+    size_t szold = pp[0];
+    int64_t *pnew = (int64_t *)jl_gc_counted_realloc_with_old_size(pp, szold + 16, sz + 16);
+    pnew[0] = sz;
+    return (void *)(pnew + 2);
+}
+
 DLLEXPORT void *jl_gc_managed_malloc(size_t sz)
 {
     maybe_collect();