[GR-23958] Use dummy libR.so and actually implement R API in libRnative.so and libRllvm.so.

PullRequest: fastr/2476

Author: steve-s

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/common/LibPaths.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015, 2019, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2015, 2020, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -30,14 +30,6 @@
 
 public class LibPaths {
 
-    /**
-     * Returns the absolute path to the directory containing the builtin libraries.
-     */
-    @TruffleBoundary
-    public static String getBuiltinLibPath(RContext context) {
-        return REnvVars.getRHomeTruffleFile(context).resolve("lib").toString();
-    }
-
     /**
      * Returns the absolute path to the builtin library {@code libName} for use with
      * {@link System#load}.
@@ -48,12 +40,7 @@ public static String getBuiltinLibPath(RContext context, String libName) {
         return REnvVars.getRHomeTruffleFile(context).resolve("lib").resolve("lib" + libName + "." + osInfo.libExt).toString();
     }
 
-    /**
-     * Returns the absolute path to the shared library associated with package {@code name}. (Does
-     * not check for existence).
-     */
-    @TruffleBoundary
-    public static String getPackageLibPath(RContext context, String name) {
-        return REnvVars.getRHomeTruffleFile(context).resolve("library").resolve(name).resolve("libs").resolve(name + ".so").toString();
+    public static String normalizeLibRPath(String path, String backend) {
+        return path.replace(".so", backend + ".so").replace(".dylib", backend + ".dylib");
     }
 }

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/llvm/TruffleLLVM_DLL.java

@@ -35,6 +35,7 @@
 import com.oracle.truffle.api.interop.UnsupportedMessageException;
 import com.oracle.truffle.api.nodes.Node;
 import com.oracle.truffle.api.source.Source;
+import com.oracle.truffle.r.ffi.impl.common.LibPaths;
 import com.oracle.truffle.r.runtime.DSLConfig;
 import com.oracle.truffle.r.runtime.REnvVars;
 import com.oracle.truffle.r.runtime.RError;
@@ -71,7 +72,7 @@ static LibHandle dlOpen(RContext context, String path) {
         boolean isLibR = libName.equals("libR");
         if (isLibR) {
             // TODO: make it generic, if +"l" file exists, use that instead
-            file = context.getSafeTruffleFile(path + "l");
+            file = context.getSafeTruffleFile(LibPaths.normalizeLibRPath(path, "llvm"));
         }
         boolean isInitialization = isLibR;
         Object before = null;

com.oracle.truffle.r.ffi.impl/src/com/oracle/truffle/r/ffi/impl/nfi/TruffleNFI_DLL.java

@@ -65,11 +65,21 @@ public LibHandle execute(String path, boolean local, boolean now) {
         }
     }
 
-    public static LibHandle dlOpen(RContext ctx, String path, boolean local, boolean now) {
+    public static LibHandle dlOpen(RContext ctx, String pathIn, boolean local, boolean now) {
         String librffiPath = LibPaths.getBuiltinLibPath(ctx, "R");
         // Do not call before/afterDowncall when loading libR to prevent the pushing/popping of
         // the callback array, which requires that the libR have already been loaded
-        boolean notifyStateRFFI = !librffiPath.equals(path);
+        String path = pathIn;
+        boolean isLibR = librffiPath.equals(path);
+        if (isLibR) {
+            // In case of libR.so we are actually going to load libR.son, the libR.so is an empty
+            // dummy library,
+            // which is there so that packages can be linked against it, but we load the R API
+            // (implemented in libR.son)
+            // here explicitly before loading any package
+            path = LibPaths.normalizeLibRPath(path, "native");
+        }
+        boolean notifyStateRFFI = !isLibR;
         Object before = notifyStateRFFI ? ctx.getStateRFFI().beforeDowncall(null, Type.NFI) : 0;
         try {
             String libName = DLL.libName(ctx, path);

com.oracle.truffle.r.native/fficall/Makefile

@@ -24,9 +24,14 @@
 # Builds libR
 #
 # We build all the source files with the given compiler (CC), which may be the Labs LLVM clang that produces embedded bitcode.
-# When building the final artifact, we either build only libR.so from the source files in common and NFI specific directories,
-# and if FASTR_RFFI is "LLVM", we build also libR.sol, which is a regular so file with embedded bitcode, but that one is built
-# from the source files in common and LLVM specific directories.
+#
+# In order to support running both backend (NFI and Sulong) in one process, we produce three artifacts here:
+#  * libR.so - dummy library, which standard name in standard location that most of the packages will link with
+#    - when the native loader/Sulong is loading a package (e.g., stats.so), it loads this dummy libR.so
+#  * libRnative.so - library with actual implementation of the R API for NFI
+#    - dlopen'ed by FastR into the global space (RTLD_GLOBAL)
+#  * libRllvm.so - library with actual implementation of the R API for Sulong
+#    - FastR explicitly loads this via Sulong
 #
 # This is the only situation, where we produce different artifacts for NFI/LLVM. When building pacakges,
 # we produce only one so file with embedded bitcode that is supposed to be used for both NFI and LLVM execution
@@ -52,11 +57,12 @@ endif
 .PHONY: all clean
 
 C_LIBNAME := libR$(DYLIB_EXT)
-LLVM_LIBNAME := libR$(DYLIB_EXT)l
-C_LIB := $(FASTR_LIB_DIR)/$(C_LIBNAME)
+NFI_LIBNAME := libRnative$(DYLIB_EXT)
+LLVM_LIBNAME := libRllvm$(DYLIB_EXT)
+
+R_LIB := $(FASTR_LIB_DIR)/$(C_LIBNAME)
+NFI_LIB := $(FASTR_LIB_DIR)/$(NFI_LIBNAME)
 LLVM_LIB := $(FASTR_LIB_DIR)/$(LLVM_LIBNAME)
-R_LIBNAME := libR$(DYLIB_EXT)
-R_LIB := $(FASTR_LIB_DIR)/$(R_LIBNAME)
 
 ifeq ($(OS_NAME), Darwin)
 VERSION_FLAGS := -current_version $(R_VERSION) -compatibility_version $(R_VERSION)
@@ -75,34 +81,31 @@ ifeq ($(FASTR_RFFI),managed)
 	# nop
 else
 ifeq ($(OS_NAME),Darwin)
-	$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -o $(R_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lRblas -lRlapack -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
-	$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -L$(LLVM_LIBS_DIR) -lpolyglot-mock -ldl -lRblas -lRlapack -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -o $(R_LIB) -L$(FASTR_LIB_DIR) -lRblas -lRlapack $(VERSION_FLAGS)
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lR -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) -Wl,-rpath,@loader_path/ -Wl,-undefined,dynamic_lookup -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -L$(LLVM_LIBS_DIR) -lpolyglot-mock -ldl -lR -lpcre -lz $(F2C) -liconv $(VERSION_FLAGS)
 
 	install_name_tool -add_rpath @loader_path/ $(FASTR_LIB_DIR)/libRblas.dylib
 	install_name_tool -add_rpath @loader_path/ $(FASTR_LIB_DIR)/libRlapack.dylib
-	
-	# The following commands will be changed to use @loader_path (or @rpath) instead of the absolute paths $(LLVM_LIBS_DIR) and $(FASTR_LIB_DIR)
-	# when Sulong supports @loader_path (resp. @rpath) substitution.
+
 	install_name_tool -change bin/libpolyglot-mock.dylib $(LLVM_LIBS_DIR)/libpolyglot-mock.dylib $(LLVM_LIB)
-	#install_name_tool -change @rpath/libRblas.dylib $(FASTR_LIB_DIR)/libRblas.dylib $(LLVM_LIB)
-	#install_name_tool -change @rpath/libRlapack.dylib $(FASTR_LIB_DIR)/libRlapack.dylib $(LLVM_LIB)
-	#install_name_tool -change @rpath/libpcre.dylib $(FASTR_LIB_DIR)/libpcre.dylib $(LLVM_LIB)
-	#install_name_tool -change @rpath/libz.dylib $(FASTR_LIB_DIR)/libz.dylib $(LLVM_LIB)
-	#install_name_tool -change @rpath/libf2c.so $(FASTR_LIB_DIR)/libf2c$(DYLIB_EXT) $(LLVM_LIB)
 
-	install_name_tool -change libRblas.dylib @rpath/libRblas.dylib $(R_LIB)
-	install_name_tool -change libRlapack.dylib @rpath/libRlapack.dylib $(R_LIB)
-	install_name_tool -change libf2c.so @rpath/libf2c$(DYLIB_EXT) $(R_LIB)
+	install_name_tool -change libRblas.dylib @rpath/libRblas.dylib $(NFI_LIB)
+	install_name_tool -change libRlapack.dylib @rpath/libRlapack.dylib $(NFI_LIB)
+	install_name_tool -change libf2c.so @rpath/libf2c$(DYLIB_EXT) $(NFI_LIB)
+
 	install_name_tool -id @rpath/libR.dylib $(R_LIB)
-	install_name_tool -id @rpath/libR.dylibl $(LLVM_LIB)
-# check if we captured libpcre/libz, rpath those in libR
+	install_name_tool -id @rpath/$(NFI_LIBNAME) $(NFI_LIB)
+	install_name_tool -id @rpath/$(LLVM_LIBNAME) $(LLVM_LIB)
+    # check if we captured libpcre/libz, rpath those in libR
 	python $(FASTR_R_HOME)/mx.fastr/copylib.py updatelib $(FASTR_LIB_DIR) $(FASTR_R_HOME)
 else
 	# not Darwin:
-	$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(R_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -lRblas -lRlapack -ldl -lpcre -lz $(F2C)
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(R_LIB) -L$(FASTR_LIB_DIR) -lRblas -lRlapack
+	$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(NFI_LIB) $(wildcard lib/nfi/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -lRblas -lRlapack -ldl -lpcre -lz $(F2C)
     # We do not link with Rlapack and Rblas so that we can load those libraries manually later after loading libR
     # Otherwise Sulong would attempt to load Rlapack and Rblas and fail, because there is a dependency cycle:
-    #     libR provides xerbla_, but Rlapack/Rblas depend on it, it seems that Sulong is not able to resolve this unlike the native loader
+    # libR provides xerbla_, but Rlapack/Rblas depend on it, it seems that Sulong is not able to resolve this unlike the native loader
 	$(DYLIB_LD) $(DYLIB_LDFLAGS) $(shell echo $(PKG_LDFLAGS_OVERRIDE)) -Wl,-rpath,'$$ORIGIN' -o $(LLVM_LIB) $(wildcard lib/llvm/*.o) $(wildcard lib/common/*.o) $(wildcard lib/JavaGD/*.o) -L$(FASTR_LIB_DIR) -ldl -lpcre -lz $(F2C)
 endif # Darwin
 endif # managed
@@ -131,13 +134,13 @@ common.done:
 
 clean:
 	$(MAKE) -C src/common clean
-	rm -rf src/truffle_*/*.o
-	rm -rf $(R_LIB)
-	rm -rf fficall.done
-	rm -rf common.done
-	rm -rf fficallllvm.done
+	rm -f src/truffle_*/*.o
+	rm -f $(R_LIB) $(NFI_LIB) $(LLVM_LIB)
+	rm -f fficall.done
+	rm -f common.done
+	rm -f fficallllvm.done
 	$(MAKE) -C src/JavaGD clean
-	rm -rf JavaGD.done
+	rm -f JavaGD.done
 ifneq ($(FASTR_RFFI),managed)
 	$(MAKE) -C src/truffle_nfi clean
 	$(MAKE) -C src/truffle_llvm clean

com.oracle.truffle.r.native/gnur/patch/src/library/lib.mk

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2014, 2019, Oracle and/or its affiliates. All rights reserved.
+# Copyright (c) 2014, 2020, Oracle and/or its affiliates. All rights reserved.
 # DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
 #
 # This code is free software; you can redistribute it and/or modify it
@@ -99,7 +99,7 @@ $(OBJ):
 	mkdir -p $(OBJ)
 
 ifeq ($(OS_NAME),Darwin)
-  RPATH_OPT =
+  RPATH_OPT = -Wl,-undefined,dynamic_lookup
 else
   RPATH = $$ORIGIN/../../../lib/
   RPATH_OPT = -Wl,-rpath='$(RPATH)'

com.oracle.truffle.r.native/run/fastr_etc/Darwin/Makeconf.llvm

@@ -70,7 +70,7 @@ CXX17STD = -std=gnu++17
 CXX_VISIBILITY = 
 DYLIB_EXT = .dylib
 DYLIB_LD = $(CC)
-DYLIB_LDFLAGS = "-Wl,-headerpad_max_install_names,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS)
+DYLIB_LDFLAGS = "-Wl,-headerpad_max_install_names,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS)
 DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
 ECHO = echo
 ECHO_C = \c
@@ -110,7 +110,7 @@ JAR = $(JAVA_HOME)/bin/jar
 ## JAVA_HOME might be used in the next three.
 ## They are for packages 'JavaGD' and 'rJava'
 LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
-LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -L"$(R_HOME)/../llvm/native/lib" -lf2c $(PKG_LDFLAGS_OVERRIDE)
+LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -L"$(R_HOME)/../llvm/native/lib" -lf2c $(PKG_LDFLAGS_OVERRIDE)
 ## we only need this is if it is external, as otherwise link to R
 LIBM = -lm
 LIBR0 = -lR 
@@ -122,7 +122,7 @@ LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
 LTO = 
 ## needed to build applications linking to static libR
 MAIN_LD = $(CC)
-MAIN_LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -L"$(R_HOME)/../llvm/native/lib" -lf2c
+MAIN_LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -L"$(R_HOME)/../llvm/native/lib" -lf2c
 MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
 MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
 OBJC = $(CC)
@@ -137,19 +137,19 @@ SHELL = /bin/sh
 SHLIB_CFLAGS = 
 SHLIB_CXXFLAGS = 
 SHLIB_CXXLD = $(CXX)
-SHLIB_CXXLDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
+SHLIB_CXXLDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
 SHLIB_CXX98LD = $(CXX98) $(CXX98STD)
-SHLIB_CXX98LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
+SHLIB_CXX98LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
 SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
-SHLIB_CXX11LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
+SHLIB_CXX11LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
 SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
-SHLIB_CXX14LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
+SHLIB_CXX14LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
 SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
-SHLIB_CXX17LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
+SHLIB_CXX17LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress
 SHLIB_EXT = .so
 SHLIB_FFLAGS = 
 SHLIB_LD = $(CC)
-SHLIB_LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS)
+SHLIB_LDFLAGS = "-Wl,-rpath,$(R_HOME)/lib/,-rpath,$(R_HOME)/../llvm/native/lib,-undefined,dynamic_lookup" -L"$(R_HOME)/lib" -undefined dynamic_lookup -L"$(R_HOME)/../llvm/native/lib" -lf2c -dynamiclib -Wl,-headerpad_max_install_names  -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS)
 SHLIB_LIBADD = 
 ## We want to ensure libR is picked up from $(R_HOME)/lib
 ## before e.g. /usr/local/lib if a version is already installed.