Fix #448: Transform global variables in stats package

.gitignore

@@ -16,3 +16,4 @@ atlassian-ide-plugin.xml
 *.o
 *.gimple
 .Rproj.user
+.gradle

packages/stats/pom.xml

@@ -65,6 +65,9 @@
               <goal>gnur-sources-compile</goal>
             </goals>
             <phase>compile</phase>
+            <configuration>
+              <transformGlobalVariables>true</transformGlobalVariables>
+            </configuration>
           </execution>
           <execution>
             <id>build</id>

packages/stats/src/main/c/apply_optim.c

@@ -641,7 +641,9 @@ void cgmin(int n, double *Bvec, double *X, double *Fmin,
 }
 
 /* include setulb() */
-#include "lbfgsb.c"
+void setulb(int n, int m, double *x, double *l, double *u, int *nbd,
+	    double *f, double *g, double factr, double *pgtol,
+	    double *wa, int * iwa, char *task, int iprint, int *isave);
 
 void lbfgsb(int n, int m, double *x, double *l, double *u, int *nbd,
 	    double *Fmin, optimfn fminfn, optimgr fmingr, int *fail,

packages/stats/src/main/c/lbfgsb.c

@@ -123,7 +123,6 @@ static void prn3lb(int n, double *x, double *f, char *task, int iprint,
 
 
 /* ================    L-BFGS-B (version 2.3)	========================== */
-static
 void setulb(int n, int m, double *x, double *l, double *u, int *nbd,
 	    double *f, double *g, double factr, double *pgtol,
 	    double *wa, int * iwa, char *task, int iprint, int *isave)

packages/stats/src/main/c/lbfgsb.h

@@ -0,0 +1,69 @@
+
+static void active(int, double *, double *, int *, double *, int *,
+		   int, int *, int *, int *);
+static void bmv(int, double *, double *, int *, double *, double *, int *);
+static void cauchy(int, double *, double *,
+		   double *, int *, double *, int *, int *,
+		   double *, double *, double *, int, double *,
+		   double *, double *, double *, double *, int * ,
+		   int *, double *, double *, double *, double *,
+		   int *, int, double *, int *, double *);
+static void cmprlb(int, int, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, double *, double *, int *,
+		   double *, int *, int *, int *, int *,
+		   int *);
+static void dcsrch(double *, double *, double *,
+		   double, double, double,
+		   double, double, char *);
+static void dcstep(double *, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, double *, int *, double *,
+		   double *);
+static void errclb(int, int, double,
+		   double *, double *, int *, char *, int *, int *);
+static void formk(int, int *, int *, int *, int *, int *, int *,
+		  int *, double *, double *, int, double *,
+		  double *, double *, double *, int *, int *, int *);
+static void formt(int, double *, double *,
+		  double *, int *, double *, int *);
+static void freev(int, int *, int *,
+		  int *, int *, int *, int *, int *, int *,
+		  int *, int, int *);
+static void hpsolb(int, double *, int *, int);
+static void lnsrlb(int, double *, double *,
+		   int *, double *, double *, double *, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, double *, int *, int *,
+		   int *, int *, int *, char *, int *, int *,
+		   char *);
+static void mainlb(int, int, double *,
+		   double *, double *, int *, double *, double *,
+		   double, double *, double *, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, double *, double *,
+		   double *, double *, int *, int *, int *, char *,
+		   int, char *, int *);
+static void matupd(int, int, double *, double *, double *,
+		   double *, double *, double *, int *, int *,
+		   int *, int *, double *, double *, double *,
+		   double *, double *);
+static void projgr(int, double *, double *,
+		   int *, double *, double *, double *);
+static void subsm(int, int, int *, int *, double *, double *,
+		  int *, double *, double *, double *, double *,
+		  double *, int *, int *, int *, double *,
+		  double *, int, int *);
+
+static void prn1lb(int n, int m, double *l, double *u, double *x,
+		   int iprint, double epsmch);
+static void prn2lb(int n, double *x, double *f, double *g, int iprint,
+		   int iter, int nfgv, int nact, double sbgnrm,
+		   int nint, char *word, int iword, int iback,
+		   double stp, double xstep);
+static void prn3lb(int n, double *x, double *f, char *task, int iprint,
+		   int info, int iter, int nfgv, int nintol, int nskip,
+		   int nact, double sbgnrm, int nint,
+		   char *word, int iback, double stp, double xstep,
+		   int k);

script-engine/src/test/java/org/renjin/script/OptimMultiThreadTest.java

@@ -0,0 +1,90 @@
+/*
+ * Renjin : JVM-based interpreter for the R language for the statistical analysis
+ * Copyright © 2010-${$file.lastModified.year} BeDataDriven Groep B.V. and contributors
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, a copy is available at
+ *  https://www.gnu.org/licenses/gpl-2.0.txt
+ *
+ */
+
+package org.renjin.script;
+
+import org.junit.Test;
+import org.renjin.sexp.DoubleVector;
+import org.renjin.sexp.ListVector;
+
+import javax.script.ScriptEngine;
+
+public class OptimMultiThreadTest {
+  private static final ThreadLocal<ScriptEngine> engines = new ThreadLocal<>();
+  private static final int RUNS = 20;
+  private static final int THREADS_NUMBER = 2;
+
+
+  @Test
+  public void testMultithread() throws InterruptedException {
+    Thread[] threads = new Thread[THREADS_NUMBER];
+    for (int i = 0; i < THREADS_NUMBER; i++) {
+      threads[i] = new Thread(this::task);
+      threads[i].start();
+    }
+    for (int i = 0; i < THREADS_NUMBER; i++) {
+      threads[i].join();
+
+    }
+  }
+
+  private void task() {
+    ScriptEngine engine = getEngine();
+    try {
+      // Rosenbrock Banana function
+      engine.eval("fr <- function(x) { " +
+          " x1 <- x[1]\n" +
+          " x2 <- x[2]\n" +
+          " 100 * (x2 - x1 * x1) ^ 2 + (1 - x1) ^ 2\n" +
+          "}");
+    } catch (Exception e) {
+      System.err.println(e.getMessage());
+    }
+    for (int i = 0; i < RUNS; i++) {
+      try {
+        ListVector result = (ListVector) engine.eval("optim(c(-1.2,1), fr, method = \"L-BFGS\")");
+        System.out.println(result);
+
+        DoubleVector parameters = (DoubleVector) result.get("par");
+        double p0 = parameters.getElementAsDouble(0);
+        double p1 = parameters.getElementAsDouble(1);
+        if(Math.abs(p0 - 0.9998000) > 0.00001) {
+          throw new AssertionError("Incorrect result: p0 = " + String.format("%f", p0));
+        }
+        if(Math.abs(p1 - 0.9996001) > 0.00001) {
+          throw new AssertionError("Incorrect result: p1 = " + String.format("%f", p1));
+        }
+      } catch (Exception e) {
+        System.err.println(e.getMessage());
+      }
+    }
+  }
+
+  private ScriptEngine getEngine() {
+    ScriptEngine engine = engines.get();
+    if (engine == null) {
+      RenjinScriptEngineFactory factory = new RenjinScriptEngineFactory();
+      engine = factory.getScriptEngine();
+      engines.set(engine);
+    }
+    return engine;
+  }
+
+}

tests/src/test/R/test.format.R

@@ -0,0 +1,23 @@
+#
+# Renjin : JVM-based interpreter for the R language for the statistical analysis
+# Copyright © 2010-2019 BeDataDriven Groep B.V. and contributors
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, a copy is available at
+# https://www.gnu.org/licenses/gpl-2.0.txt
+#
+library(hamcrest)
+
+test.format.double <- function() {
+    assertThat(format(1/3), equalTo("0.3333333"))
+}

tools/gcc-bridge/compiler/src/main/java/org/renjin/gcc/codegen/FunctionGenerator.java

@@ -73,6 +73,7 @@ public class FunctionGenerator implements InvocationStrategy {
   private TypeOracle typeOracle;
   private FunctionOracle functionOracle;
   private ExprFactory exprFactory;
+  private List<GlobalVarTransformer> globalVarTransformers;
   private LocalStaticVarAllocator staticVarAllocator;
   private LocalVariableTable localSymbolTable;
   private LocalVariableTable localStaticSymbolTable;
@@ -85,7 +86,9 @@ public class FunctionGenerator implements InvocationStrategy {
   private boolean compilationFailed = false;
 
   public FunctionGenerator(String className, GimpleFunction function, TypeOracle typeOracle,
-                           GlobalVarAllocator globalVarAllocator, UnitSymbolTable symbolTable) {
+                           GlobalVarAllocator globalVarAllocator,
+                           List<GlobalVarTransformer> globalVarTransformers,
+                           UnitSymbolTable symbolTable) {
     this.className = className;
     this.function = function;
     this.typeOracle = typeOracle;
@@ -103,6 +106,7 @@ public FunctionGenerator(String className, GimpleFunction function, TypeOracle t
     this.staticVarAllocator = new LocalStaticVarAllocator("$" + function.getSafeMangledName() + "$", globalVarAllocator);
     this.localSymbolTable = new LocalVariableTable(symbolTable);
     this.localStaticSymbolTable = new LocalVariableTable(symbolTable);
+    this.globalVarTransformers = globalVarTransformers;
 
   }
 
@@ -375,15 +379,14 @@ private void scheduleLocalVariables() {
       }
 
       try {
-        GExpr generator = functionOracle.variable(varDecl,
-            varDecl.isStatic() ?
-                staticVarAllocator :
-                mv.getLocalVarAllocator());
-
-        localSymbolTable.addVariable(varDecl.getId(), generator);
-
         if(varDecl.isStatic()) {
+          GExpr generator = localStaticGenerator(varDecl);
+          localSymbolTable.addVariable(varDecl.getId(), generator);
           localStaticSymbolTable.addVariable(varDecl.getId(), generator);
+
+        } else {
+          localSymbolTable.addVariable(varDecl.getId(),
+              functionOracle.variable(varDecl, mv.getLocalVarAllocator()));
         }
 
       } catch (Exception e) {
@@ -392,6 +395,15 @@ private void scheduleLocalVariables() {
     }
   }
 
+  private GExpr localStaticGenerator(GimpleVarDecl varDecl) {
+    for (GlobalVarTransformer globalVarTransformer : globalVarTransformers) {
+      if(globalVarTransformer.acceptLocalStaticVar(varDecl)) {
+        return globalVarTransformer.generator(typeOracle, function, varDecl);
+      }
+    }
+    return functionOracle.variable(varDecl, staticVarAllocator);
+  }
+
   private void emitBasicBlock(GimpleBasicBlock basicBlock) {
     mv.visitLabel(labels.of(basicBlock));
 

tools/gcc-bridge/compiler/src/main/java/org/renjin/gcc/codegen/GlobalVarTransformer.java

@@ -21,10 +21,17 @@
 import org.renjin.gcc.codegen.expr.GExpr;
 import org.renjin.gcc.codegen.type.TypeOracle;
 import org.renjin.gcc.gimple.GimpleCompilationUnit;
+import org.renjin.gcc.gimple.GimpleFunction;
 import org.renjin.gcc.gimple.GimpleVarDecl;
 
 public interface GlobalVarTransformer {
-  boolean accept(GimpleVarDecl decl);
+
+  boolean acceptGlobalVar(GimpleVarDecl decl);
+
+  boolean acceptLocalStaticVar(GimpleVarDecl decl);
 
   GExpr generator(TypeOracle typeOracle, GimpleCompilationUnit unit, GimpleVarDecl decl);
+
+  GExpr generator(TypeOracle typeOracle, GimpleFunction function, GimpleVarDecl decl);
+
 }

tools/gcc-bridge/compiler/src/main/java/org/renjin/gcc/codegen/ProvidedVarTransformer.java

@@ -22,6 +22,7 @@
 import org.renjin.gcc.codegen.expr.GExpr;
 import org.renjin.gcc.codegen.type.TypeOracle;
 import org.renjin.gcc.gimple.GimpleCompilationUnit;
+import org.renjin.gcc.gimple.GimpleFunction;
 import org.renjin.gcc.gimple.GimpleVarDecl;
 
 import java.util.Map;
@@ -37,12 +38,22 @@ public ProvidedVarTransformer(TypeOracle typeOracle, Map<String, ProvidedGlobalV
   }
 
   @Override
-  public boolean accept(GimpleVarDecl decl) {
+  public boolean acceptGlobalVar(GimpleVarDecl decl) {
     return decl.isPublic() && providedVariables.containsKey(decl.getName());
   }
 
+  @Override
+  public boolean acceptLocalStaticVar(GimpleVarDecl decl) {
+    return false;
+  }
+
   @Override
   public GExpr generator(TypeOracle typeOracle, GimpleCompilationUnit unit, GimpleVarDecl decl) {
     return providedVariables.get(decl.getName()).createExpr(decl, this.typeOracle);
   }
+
+  @Override
+  public GExpr generator(TypeOracle typeOracle, GimpleFunction function, GimpleVarDecl decl) {
+    throw new UnsupportedOperationException();
+  }
 }

tools/gcc-bridge/compiler/src/main/java/org/renjin/gcc/codegen/UnitClassGenerator.java

@@ -107,7 +107,7 @@ public UnitClassGenerator(TypeOracle typeOracle,
       if (!isExcluded(function)) {
         try {
           symbolTable.addFunction(function,
-              new FunctionGenerator(className, function, typeOracle, globalVarAllocator, symbolTable));
+              new FunctionGenerator(className, function, typeOracle, globalVarAllocator, globalVarTransformers, symbolTable));
         } catch (Exception e) {
           throw new InternalCompilerException(String.format("Exception creating %s for %s in %s: %s",
               FunctionGenerator.class.getSimpleName(),
@@ -135,7 +135,7 @@ private GExpr generatorForGlobalVar(List<GlobalVarTransformer> globalVarTransfor
                                       GimpleVarDecl decl) {
 
     for (GlobalVarTransformer transformer : globalVarTransformers) {
-      if(transformer.accept(decl)) {
+      if(transformer.acceptGlobalVar(decl)) {
         return transformer.generator(typeOracle, this.unit, decl);
       }
     }

tools/gcc-bridge/runtime/src/main/java/org/renjin/gcc/runtime/PointerPtr.java

@@ -25,7 +25,7 @@
  */
 public class PointerPtr extends AbstractPtr {
 
-  private static final int BYTES = 4;
+  public static final int BYTES = 4;
 
   public static final PointerPtr NULL = new PointerPtr(null, 0);