diff --git a/src/Makefile b/src/Makefile
index f1ee17c..4c2aff4 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -14,14 +14,17 @@
 #   export MATEPLUS_HOME=~/u/sandboxes/mateplus
 MATEPLUS_HOME ?= ~/u/tools/MATE/mateplus-master/src
 
+MATETOOLS_HOME ?= $(MATEPLUS_HOME)
+
 JAVA_HOME ?= /space/group/nrc_ict/pkgs/centos6/gcc-4.9.3/jdk1.8.0_131
 
 MATEPLUS_PATH ?= $(MATEPLUS_HOME)/mateplus.jar
+MATETOOLS_SRL_PATH ?= $(MATETOOLS_HOME)/srl.jar
 
-ifneq ("$(wildcard $(MATEPLUS_PATH))","")
+ifneq ("$(wildcard $(MATEPLUS_PATH))$(wildcard $(MATETOOLS_SRL_PATH))","")
    WITH_SRLMATE ?= True
 else
-   $(info *** mateplus.jar not found)
+   $(info *** mateplus.jar and srl.jar not found)
 endif
 
 ifneq (clean, $(MAKECMDGOALS))
@@ -107,7 +110,10 @@ scripts: | ../bin
 	cd ../obj/java && jar -cvf ../srlmate.jar *
 
 en.mplsconfig de.mplsconfig es.mplsconfig zh.mplsconfig: %: %.template
-	sed -e "s#<YISI_HOME>/#$(dir $(CURDIR))#g; s#<MATEPLUS_HOME>#$(MATEPLUS_HOME)#g;" < $< > $@
+	sed -e "s#<YISI_HOME>#$(dir $(CURDIR))#g; s#//#/#g;" \
+	    -e "s#<MATEPLUS_HOME>#$(MATEPLUS_HOME)#g;" \
+	    -e "s#<MATETOOLS_HOME>#$(MATETOOLS_HOME)#g;" \
+	    < $< > $@
 
 $(SRLMATE_BINS): LDFLAGS += -L${JAVA_HOME}/jre/lib/amd64/server
 $(SRLMATE_BINS): LIBRARIES += -ljvm
diff --git a/src/Mate.java b/src/Mate.java
index 70140aa..fc8342d 100644
--- a/src/Mate.java
+++ b/src/Mate.java
@@ -14,6 +14,7 @@
 package yisi;
 import se.lth.cs.srl.corpus.Sentence;
 import se.lth.cs.srl.options.CompletePipelineCMDLineOptions;
+import se.lth.cs.srl.options.FullPipelineOptions;
 import se.lth.cs.srl.util.FileExistenceVerifier;
 import se.lth.cs.srl.CompletePipeline;
 import se.lth.cs.srl.languages.Language;
@@ -21,11 +22,19 @@
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.ArrayList;
+import java.net.URL;
+import java.net.URLClassLoader;
+import java.lang.Class;
+import java.lang.reflect.Method;
 
 public class Mate {
-   protected CompletePipeline pipeline = null;
+   // protected CompletePipeline pipeline = null;
+   protected Object pipeline = null;
+   protected URLClassLoader classLoader = null;
+   Class<?> class_CompletePipeline = null;
 
-   public String init(String lang,
+   public String init(String mate_jars,
+                      String lang,
                       boolean rerank,
                       boolean hybrid,
                       String token,
@@ -37,6 +46,16 @@ public String init(String lang,
       String result= new String();
       try {
          System.setOut(System.err);
+
+         // Each Mate object has it's own class loader with it's own "classpath".
+         String[] mateJars = mate_jars.split(":");
+         URL[] urls = new URL[mateJars.length];
+         for (int i = 0; i < mateJars.length; ++i) {
+            urls[i] = new File(mateJars[i]).toURI().toURL();
+//            System.err.println("URL: " + urls[i]);
+         }
+         classLoader = new URLClassLoader(urls, Thread.currentThread().getContextClassLoader());
+
          ArrayList<String> argsBuilder = new ArrayList<String>();
          argsBuilder.add(lang);
          argsBuilder.add("-tokenize");
@@ -73,13 +92,31 @@ public String init(String lang,
          String[] args = new String[argsBuilder.size()];
          argsBuilder.toArray(args);
          System.err.println(java.util.Arrays.toString(args));
-         CompletePipelineCMDLineOptions options = new CompletePipelineCMDLineOptions();
-         options.parseCmdLineArgs(args);
-         String error = FileExistenceVerifier.verifyCompletePipelineAllNecessaryModelFiles(options);
+
+         Class<?> class_FullPipelineOptions = classLoader.loadClass("se.lth.cs.srl.options.FullPipelineOptions");
+         // CompletePipelineCMDLineOptions options = new CompletePipelineCMDLineOptions();
+         Class<?> class_CompletePipelineCMDLineOptions = classLoader.loadClass("se.lth.cs.srl.options.CompletePipelineCMDLineOptions");
+         Object options = class_CompletePipelineCMDLineOptions.newInstance();
+         // options.parseCmdLineArgs(args);
+         Method method_parseCmdLineArgs = class_CompletePipelineCMDLineOptions.getMethod("parseCmdLineArgs", String[].class);
+//         System.err.println("Got Method " + method_parseCmdLineArgs);
+         method_parseCmdLineArgs.invoke(options, (Object)args);
+
+         // String error = FileExistenceVerifier.verifyCompletePipelineAllNecessaryModelFiles(options);
+         Class<?> class_FileExistenceVerifier = classLoader.loadClass("se.lth.cs.srl.util.FileExistenceVerifier");
+         Method method_verifyCompletePipelineAllNecessaryModelFiles = 
+               class_FileExistenceVerifier.getMethod("verifyCompletePipelineAllNecessaryModelFiles", class_FullPipelineOptions);
+//         System.err.println("Got Method " + method_verifyCompletePipelineAllNecessaryModelFiles);
+         String error = (String) method_verifyCompletePipelineAllNecessaryModelFiles.invoke(null, options);
+
          if (error != null){
             result += error + "\n";
          } else {
-            pipeline = CompletePipeline.getCompletePipeline(options);
+            // pipeline = CompletePipeline.getCompletePipeline(options);
+            class_CompletePipeline = classLoader.loadClass("se.lth.cs.srl.CompletePipeline");
+            Method method_getCompletePipeline = class_CompletePipeline.getMethod("getCompletePipeline", class_FullPipelineOptions);
+//            System.err.println("Got Method " + method_getCompletePipeline);
+            pipeline = method_getCompletePipeline.invoke(null, options);
          }
       } catch (Exception e){
          result += e.getMessage();
@@ -90,7 +127,10 @@ public String init(String lang,
    public String parse(String sentence) {
       String result = null;
       try {
-         result = pipeline.parse(sentence).toString();
+         // result = pipeline.parse(sentence).toString();
+         Method method_parse = class_CompletePipeline.getMethod("parse", String.class);
+//         System.err.println("Got Method " + method_parse);
+         result = method_parse.invoke(pipeline, sentence).toString();
       } catch (Exception e) {
          e.printStackTrace();
          System.err.println(sentence);
diff --git a/src/de.mplsconfig.template b/src/de.mplsconfig.template
index a0d91a5..d7fc3c2 100644
--- a/src/de.mplsconfig.template
+++ b/src/de.mplsconfig.template
@@ -1,4 +1,8 @@
-matejar=<YISI_HOME>/obj/srlmate.jar:<MATEPLUS_HOME>/mateplus.jar:<MATEPLUS_HOME>/lib/anna-3.3.jar:<MATEPLUS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATEPLUS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATEPLUS_HOME>/lib/liblinear-1.92.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar:<MATEPLUS_HOME>/lib/transition-1.30.jar
+# yisi_home is needed to locate srlmate.jar within YiSi.
+yisi_home=<YISI_HOME>
+# mate_jars is a colon (:) separated list of all jar files needed to run
+# mateplus or mate-tools for this language.
+mate_jars=<MATEPLUS_HOME>/mateplus.jar:<MATEPLUS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATEPLUS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATEPLUS_HOME>/lib/transition-1.30.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar
 lang=ger
 rerank=1
 hybrid=1
diff --git a/src/en.mplsconfig.template b/src/en.mplsconfig.template
index ac73f51..be98d14 100644
--- a/src/en.mplsconfig.template
+++ b/src/en.mplsconfig.template
@@ -1,4 +1,8 @@
-matejar=<YISI_HOME>/obj/srlmate.jar:<MATEPLUS_HOME>/mateplus.jar:<MATEPLUS_HOME>/lib/anna-3.3.jar:<MATEPLUS_HOME>/lib/liblinear-1.92.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar
+# yisi_home is needed to locate srlmate.jar within YiSi.
+yisi_home=<YISI_HOME>
+# mate_jars is a colon (:) separated list of all jar files needed to run
+# mateplus or mate-tools for this language.
+mate_jars=<MATEPLUS_HOME>/mateplus.jar:<MATEPLUS_HOME>/lib/anna-3.3.jar:<MATEPLUS_HOME>/lib/liblinear-1.92.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar
 lang=eng
 rerank=1
 hybrid=0
diff --git a/src/es.mplsconfig.template b/src/es.mplsconfig.template
index 07e029b..491b2d3 100644
--- a/src/es.mplsconfig.template
+++ b/src/es.mplsconfig.template
@@ -1,10 +1,15 @@
-matejar=<YISI_HOME>/obj/srlmate.jar:<MATEPLUS_HOME>/lib/srl.jar:<MATEPLUS_HOME>/lib/anna-3.3.jar:<MATEPLUS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATEPLUS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATEPLUS_HOME>/lib/liblinear-1.92.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar:<MATEPLUS_HOME>/lib/transition-1.30.jar:<MATEPLUS_HOME>/lib/whatswrong-0.2.3.jar:<MATEPLUS_HOME>/lib/seg.jar:<MATEPLUS_HOME>/lib/slf4j-api-1.7.25.jar:<MATEPLUS_HOME>/lib/slf4j-jdk14-1.7.25.jar
+# yisi_home is needed to locate srlmate.jar within YiSi.
+yisi_home=<YISI_HOME>
+# mate_jars is a colon (:) separated list of all jar files needed to run
+# mateplus or mate-tools for this language.
+mate_jars=<MATETOOLS_HOME>/lib/srl.jar:<MATETOOLS_HOME>/lib/anna-3.3.jar:<MATETOOLS_HOME>/lib/opennlp-maxent-3.0.2-incubating.jar:<MATETOOLS_HOME>/lib/opennlp-tools-1.5.2-incubating.jar:<MATETOOLS_HOME>/lib/liblinear-1.51-with-deps.jar:<MATETOOLS_HOME>/lib/whatswrong-0.2.3.jar
+#mate_jars=<MATETOOLS_HOME>/lib/srl.jar:<MATETOOLS_HOME>/lib/anna-3.3.jar:<MATETOOLS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATETOOLS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATETOOLS_HOME>/lib/liblinear-1.92.jar:<MATETOOLS_HOME>/lib/stanford-corenlp-3.9.1.jar:<MATETOOLS_HOME>/lib/whatswrong-0.2.3.jar:/<MATETOOLS_HOME>/lib/slf4j-api-1.7.25.jar:<MATETOOLS_HOME>/lib/slf4j-jdk14-1.7.25.jar
 lang=spa
 rerank=0
 hybrid=0
 token=
-morph=MATEPLUS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.morphtagger.model
-lemma=MATEPLUS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.lemmatizer.model
-tagger=MATEPLUS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.postagger.model
-parser=MATEPLUS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.parser.model
-srl=MATEPLUS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.srl-4.21.srl-rr.model
+morph=<MATETOOLS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.morphtagger.model
+lemma=<MATETOOLS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.lemmatizer.model
+tagger=<MATETOOLS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.postagger.model
+parser=<MATETOOLS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.parser.model
+srl=<MATETOOLS_HOME>/models/CoNLL2009-ST-Spanish-ALL.anna-3.3.srl-4.21.srl-rr.model
diff --git a/src/srlmate.cpp b/src/srlmate.cpp
index 025c39e..8bc9bf7 100644
--- a/src/srlmate.cpp
+++ b/src/srlmate.cpp
@@ -39,6 +39,10 @@ auto name = jni_env_ptr->expr;                              \
    }                                                        \
 }                                                           \
 
+JavaVM* srlmate_t::jvm_m = NULL;
+JNIEnv* srlmate_t::jen_m = NULL;
+int srlmate_t::obj_cnt_m = 0;
+
 srlmate_t::srlmate_t(string path) {
    cerr << "Setting up MATE ...";
 
@@ -48,7 +52,8 @@ srlmate_t::srlmate_t(string path) {
       exit(1);
    }
 
-   string matejar = "";
+   string yisi_home = "";
+   string mate_jars = "";
    string lang = "";
    string token = "";
    string morph = "";
@@ -66,76 +71,83 @@ srlmate_t::srlmate_t(string path) {
       string cfgn, cfgv;
       getline(iss, cfgn, '=');
       getline(iss, cfgv);
-      if (cfgn == "matejar") {
-         matejar = cfgv;
+      if (cfgn == "yisi_home") {
+         yisi_home = cfgv;
+      }
+      else if (cfgn == "mate_jars") {
+         mate_jars = cfgv;
       }
-      if (cfgn == "lang") {
+      else if (cfgn == "lang") {
          lang = cfgv;
       }
-      if (cfgn == "rerank") {
+      else if (cfgn == "rerank") {
          if ((cfgv.compare("0") == 0) || (cfgv.compare("false") == 0)) {
             rerank = false;
          } else {
             rerank = true;
          }
       }
-      if (cfgn == "hybrid") {
+      else if (cfgn == "hybrid") {
          if ((cfgv.compare("0") == 0) || (cfgv.compare("false") == 0)) {
             hybrid = false;
          } else {
             hybrid = true;
          }
       }
-      if (cfgn == "token") {
+      else if (cfgn == "token") {
          token = cfgv;
       }
-      if (cfgn == "morph") {
+      else if (cfgn == "morph") {
          morph = cfgv;
       }
-      if (cfgn == "lemma") {
+      else if (cfgn == "lemma") {
          lemma = cfgv;
       }
-      if (cfgn == "tagger") {
+      else if (cfgn == "tagger") {
          tagger = cfgv;
       }
-      if (cfgn == "parser") {
+      else if (cfgn == "parser") {
          parser = cfgv;
       }
-      if (cfgn == "srl") {
+      else if (cfgn == "srl") {
          srl = cfgv;
       }
    }
 
    // init JVM
-   size_t opt_count = 2;
-   JavaVMOption* vm_opts = new JavaVMOption[opt_count];
-   string opt0 = "-Djava.class.path=" + matejar;
-   string opt1 = "-Xmx6g";
-   vm_opts[0].optionString = const_cast<char*>(opt0.c_str());
-   vm_opts[1].optionString = const_cast<char*>(opt1.c_str());
-
-   JavaVMInitArgs vm_args;
-   vm_args.version = JNI_VERSION_1_6;
-   vm_args.options = vm_opts;
-   vm_args.nOptions = opt_count;
-
-   jint result = JNI_CreateJavaVM(&jvm_m, (void**)&jen_m, &vm_args);
-   delete vm_opts;
-   if (result != JNI_OK) {
-      cerr << "ERROR: Failed to create Java VM. (error code = " << result << "). Exiting..." << endl;
-      exit(1);
-      jvm_m = NULL;
+   if (jvm_m == NULL) {
+      size_t opt_count = 2;
+      JavaVMOption* vm_opts = new JavaVMOption[opt_count];
+      string opt0 = "-Djava.class.path=" + yisi_home + "/obj/srlmate.jar";
+      string opt1 = "-Xmx12g";
+      vm_opts[0].optionString = const_cast<char*>(opt0.c_str());
+      vm_opts[1].optionString = const_cast<char*>(opt1.c_str());
+
+      JavaVMInitArgs vm_args;
+      vm_args.version = JNI_VERSION_1_6;
+      vm_args.options = vm_opts;
+      vm_args.nOptions = opt_count;
+
+      jint result = JNI_CreateJavaVM(&jvm_m, (void**)&jen_m, &vm_args);
+      delete vm_opts;
+      if (result != JNI_OK) {
+         cerr << "ERROR: Failed to create Java VM. (error code = " << result << "). Exiting..." << endl;
+         exit(1);
+         jvm_m = NULL;
+      }
    }
+   ++obj_cnt_m;
 
    JNI_SAFE_CALL(mcls, jen_m, FindClass("yisi/Mate"));
    JNI_SAFE_CALL(ctor, jen_m, GetMethodID(mcls, "<init>", "()V"));
    JNI_SAFE_CALL(mobj, jen_m, NewObject(mcls, ctor));
    JNI_SAFE_CALL(init, jen_m, GetMethodID(mcls, "init",
-      "(Ljava/lang/String;ZZLjava/lang/String;Ljava/lang/String;Ljava/lang/String;"
+      "(Ljava/lang/String;Ljava/lang/String;ZZLjava/lang/String;Ljava/lang/String;Ljava/lang/String;"
       "Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;"));
    JNI_SAFE_CALL(jerr, jen_m,
                  CallObjectMethod(mobj,
                                   init,
+                                  jen_m->NewStringUTF(mate_jars.c_str()),
                                   jen_m->NewStringUTF(lang.c_str()),
                                   rerank ? JNI_TRUE : JNI_FALSE,
                                   hybrid ? JNI_TRUE : JNI_FALSE,
@@ -157,8 +169,11 @@ srlmate_t::srlmate_t(string path) {
 }  // srlmate_t
 
 srlmate_t::~srlmate_t() {
-   if (jvm_m != NULL) {
+   --obj_cnt_m;
+   if (obj_cnt_m == 0 && jvm_m != NULL) {
       jvm_m->DestroyJavaVM();
+      jvm_m = NULL;
+      jen_m = NULL;
    }
 }
 
diff --git a/src/srlmate.h b/src/srlmate.h
index 206b736..0201287 100644
--- a/src/srlmate.h
+++ b/src/srlmate.h
@@ -40,8 +40,9 @@ namespace yisi {
       virtual std::vector<srlgraph_t> parse(std::vector<std::string> sents);
    private:
       std::string noparse(std::vector<std::string> tokens);
-      JavaVM* jvm_m;
-      JNIEnv* jen_m;
+      static JavaVM* jvm_m;
+      static JNIEnv* jen_m;
+      static int obj_cnt_m;
       jclass mate_class_m;
       jobject mate_object_m;
    };
diff --git a/src/zh.mplsconfig.template b/src/zh.mplsconfig.template
index 0ec1562..6309669 100644
--- a/src/zh.mplsconfig.template
+++ b/src/zh.mplsconfig.template
@@ -1,10 +1,15 @@
-matejar=<YISI_HOME>/obj/srlmate.jar:<MATEPLUS_HOME>/lib/srl.jar:<MATEPLUS_HOME>/lib/anna-3.3.jar:<MATEPLUS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATEPLUS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATEPLUS_HOME>/lib/liblinear-1.92.jar:<MATEPLUS_HOME>/lib/stanford-corenlp-3.9.1.jar:<MATEPLUS_HOME>/lib/transition-1.30.jar:<MATEPLUS_HOME>/lib/whatswrong-0.2.3.jar:<MATEPLUS_HOME>/lib/seg.jar:<MATEPLUS_HOME>/lib/slf4j-api-1.7.25.jar:<MATEPLUS_HOME>/lib/slf4j-jdk14-1.7.25.jar
+# yisi_home is needed to locate srlmate.jar within YiSi.
+yisi_home=<YISI_HOME>
+# mate_jars is a colon (:) separated list of all jar files needed to run
+# mateplus or mate-tools for this language.
+mate_jars=<MATETOOLS_HOME>/lib/srl.jar:<MATETOOLS_HOME>/lib/anna-3.3.jar:<MATETOOLS_HOME>/lib/opennlp-maxent-3.0.2-incubating.jar:<MATETOOLS_HOME>/lib/opennlp-tools-1.5.2-incubating.jar:<MATETOOLS_HOME>/lib/liblinear-1.51-with-deps.jar:<MATETOOLS_HOME>/lib/whatswrong-0.2.3.jar:<MATETOOLS_HOME>/lib/seg.jar
+#mate_jars=<MATETOOLS_HOME>/lib/srl.jar:<MATETOOLS_HOME>/lib/anna-3.3.jar:<MATETOOLS_HOME>/lib/opennlp-maxent-3.0.3.jar:<MATETOOLS_HOME>/lib/opennlp-tools-1.5.3.jar:<MATETOOLS_HOME>/lib/liblinear-1.92.jar:<MATETOOLS_HOME>/lib/whatswrong-0.2.3.jar:<MATETOOLS_HOME>/lib/stanford-segmenter-3.6.0.jar:/<MATETOOLS_HOME>/lib/slf4j-api-1.7.25.jar:<MATETOOLS_HOME>/lib/slf4j-jdk14-1.7.25.jar
 lang=chi
 rerank=0
 hybrid=0
-token=<MATEPLUS_HOME>/models/stanford-segmenter-2015-12-09/data
+token=<MATETOOLS_HOME>/models/stanford-segmenter-2015-12-09/data
 morph=
 lemma=
-tagger=<MATEPLUS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.postagger.model
-parser=<MATEPLUS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.parser.model
-srl=<MATEPLUS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.srl-4.1.srl.model
+tagger=<MATETOOLS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.postagger.model
+parser=<MATETOOLS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.parser.model
+srl=<MATETOOLS_HOME>/models/CoNLL2009-ST-Chinese-ALL.anna-3.3.srl-4.1.srl.model
diff --git a/test/Makefile b/test/Makefile
index c303606..66eb343 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -49,11 +49,11 @@ SIMPLE_TEST_PROGS += srlgraph_test
 SIMPLE_TEST_PROGS += yisiscorer_test
 
 ifdef WITH_SRLMATE
-   SIMPLE2_TEST_PROGS += srl_test
-   SIMPLE2_TEST_PROGS += srlmate_test
+   SIMPLE_SRL_TEST_PROGS += srl_test
+   SIMPLE_SRL_TEST_PROGS += srlmate_test
 endif
 
-ALL_SIMPLE_TEST_PROGS := $(CMDLP_TEST_PROGS) $(SIMPLE_TEST_PROGS) $(SIMPLE2_TEST_PROGS)
+ALL_SIMPLE_TEST_PROGS := $(CMDLP_TEST_PROGS) $(SIMPLE_TEST_PROGS) $(SIMPLE_SRL_TEST_PROGS)
 
 all: $(ALL_SIMPLE_TEST_PROGS)
 all: test_yisi
@@ -67,13 +67,18 @@ compare.%: %
 
 SUB:="s/^[0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*  */00.00.000 /"
 
-compare2.%: %
+compare_w_java_log.%: %
 	diff <(cat $< | sed -e $(SUB)) <(cat ref/$< | sed -e $(SUB)) -q
 
+compare_w_alt.%: %
+	diff $< ref/$< -q || diff -s $< ref/$<.alt -q
+
+# Simple tests
+
 .PHONY: $(ALL_SIMPLE_TEST_PROGS)
 $(CMDLP_TEST_PROGS): %: compare.%.out
 $(SIMPLE_TEST_PROGS): %: compare.%.out
-$(SIMPLE2_TEST_PROGS): %: compare2.%.out
+$(SIMPLE_SRL_TEST_PROGS): %: compare_w_java_log.%.out
 
 cmdlp_test.1.out: ARGS = --beta 0 --settings <(echo hello) --refs test_ref.en --help
 cmdlp_test.2.out: ARGS = --beta 0 --settings <(echo hello) --refs /etc/timezone
@@ -93,18 +98,19 @@ srl_test.out: ARGS = mate ../src/en.mplsconfig test_ref.en test_ref.en.srl
 srlmate_test.out: ARGS = ../src/en.mplsconfig <<<'Hello there'
 
 $(CMDLP_TEST_PROGS): BIN = ../src/cmdlp/build/bin
-$(SIMPLE_TEST_PROGS) $(SIMPLE2_TEST_PROGS): BIN = ../bin
+$(SIMPLE_TEST_PROGS) $(SIMPLE_SRL_TEST_PROGS): BIN = ../bin
 
-compare2.srl_test.out: compare.test_ref.en.srl
+compare_w_java_log.srl_test.out: compare_w_alt.test_ref.en.srl
 
 test_ref.en.srl: srl_test.out ;
 
 $(addsuffix .out, $(ALL_SIMPLE_TEST_PROGS)): %.out:
 	$(BIN)/$(firstword $(subst ., ,$*)) $(ARGS) &> $@
 
+# YiSi tests
+
 YSFX_NOSRL := 0 1 2
-#YSFX_SRL := 1_srl 2_srl
-YSFX_SRL := 1_srl
+YSFX_SRL := 1_srl 2_srl
 
 .PHONY: test_yisi
 .PHONY: $(foreach n,$(YSFX_NOSRL),test_yisi_$n)
@@ -118,8 +124,11 @@ ifdef WITH_SRLMATE
 test_yisi: $(foreach n,$(YSFX_SRL),test_yisi_$n)
 endif
 
-$(foreach n,$(YSFX_SRL),test_yisi_$n): test_yisi_%: compare2.test_yisi_%.out
-$(foreach n,$(YSFX_SRL),compare2.test_yisi_$n.out): compare2.test_yisi_%.out: compare.test_hyp.docyisi% compare.test_hyp.sntyisi%
+# YiSi SRL tests have alternate reference files too because mateplus may return
+# an alternate parse.
+
+$(foreach n,$(YSFX_SRL),test_yisi_$n): test_yisi_%: compare_w_java_log.test_yisi_%.out
+$(foreach n,$(YSFX_SRL),compare_w_java_log.test_yisi_$n.out): compare_w_java_log.test_yisi_%.out: compare_w_alt.test_hyp.docyisi% compare_w_alt.test_hyp.sntyisi%
 
 test_yisi_%.out: yisi-%.config
 	../bin/yisi --config $< &> $@
diff --git a/test/ref/test_hyp.docyisi1_srl.alt b/test/ref/test_hyp.docyisi1_srl.alt
new file mode 100644
index 0000000..a9768df
--- /dev/null
+++ b/test/ref/test_hyp.docyisi1_srl.alt
@@ -0,0 +1 @@
+0.639393
diff --git a/test/ref/test_hyp.docyisi2_srl b/test/ref/test_hyp.docyisi2_srl
new file mode 100644
index 0000000..1ffef82
--- /dev/null
+++ b/test/ref/test_hyp.docyisi2_srl
@@ -0,0 +1 @@
+0.0652749
diff --git a/test/ref/test_hyp.docyisi2_srl.alt b/test/ref/test_hyp.docyisi2_srl.alt
new file mode 100644
index 0000000..462088b
--- /dev/null
+++ b/test/ref/test_hyp.docyisi2_srl.alt
@@ -0,0 +1 @@
+0.0641709
diff --git a/test/ref/test_hyp.sntyisi1_srl.alt b/test/ref/test_hyp.sntyisi1_srl.alt
new file mode 100644
index 0000000..f9eeee9
--- /dev/null
+++ b/test/ref/test_hyp.sntyisi1_srl.alt
@@ -0,0 +1,10 @@
+0.859824
+0.691795
+0.645973
+0.633111
+0.455921
+0.59255
+0.557174
+0.54644
+0.546505
+0.864636
diff --git a/test/ref/test_hyp.sntyisi2_srl b/test/ref/test_hyp.sntyisi2_srl
new file mode 100644
index 0000000..ecaa858
--- /dev/null
+++ b/test/ref/test_hyp.sntyisi2_srl
@@ -0,0 +1,10 @@
+0.0464296
+0.0116361
+0.0696774
+0.0665215
+0.0274319
+0.0927175
+0.00336682
+0.0519643
+0.141262
+0.141742
diff --git a/test/ref/test_hyp.sntyisi2_srl.alt b/test/ref/test_hyp.sntyisi2_srl.alt
new file mode 100644
index 0000000..ccab905
--- /dev/null
+++ b/test/ref/test_hyp.sntyisi2_srl.alt
@@ -0,0 +1,10 @@
+0.0354018
+0.0116361
+0.0696774
+0.0665215
+0.0274319
+0.0927175
+0.00336682
+0.0519643
+0.141262
+0.14173
diff --git a/test/ref/test_ref.en.srl.alt b/test/ref/test_ref.en.srl.alt
new file mode 100644
index 0000000..445d76e
--- /dev/null
+++ b/test/ref/test_ref.en.srl.alt
@@ -0,0 +1,45 @@
+0: A [A0 Republican] [V strategy] [A1 to counter the re - election of Obama] 
+0: A Republican strategy to [V counter] [A1 the re - election of Obama] 
+0: A Republican strategy to counter the re - [V election] [A1 of Obama] 
+1: [A0 [A2 Republican] [V leaders]] justified their policy by the need to combat electoral fraud . 
+1: [A0 Republican leaders] [V justified] [A1 their policy] [A2 by the need to combat electoral fraud] . 
+1: Republican leaders justified [A0 their] [V policy] by the need to combat electoral fraud . 
+1: Republican leaders justified their policy by the [V need] [A1 to combat electoral fraud] . 
+1: [A0 Republican leaders] justified their policy by the need to [V combat] [A1 electoral fraud] . 
+1: Republican leaders justified their policy by the need to combat [A1 electoral] [V fraud] . 
+2: [AM-DIS However] , [A0 the Brennan Centre] [V considers] [A1 this] [A2 a myth] , [AM-ADV stating that electoral fraud is rarer in the United States than the number of people killed by lightning] . 
+2: However , [A0 the Brennan Centre] considers this a myth , [V stating] [A1 that electoral fraud is rarer in the United States than the number of people killed by lightning] . 
+2: However , the Brennan Centre considers this a myth , stating that [A1 electoral] [V fraud] is rarer in the United States than the number of people killed by lightning . 
+2: However , the Brennan Centre considers this a myth , stating that electoral fraud is rarer in the United States than the [V number] [A1 of people killed by lightning] . 
+2: However , the Brennan Centre considers this a myth , stating that electoral fraud is rarer in the United States than the number of [A1 people] [V killed] [A0 by lightning] . 
+3: Indeed , [A0 [A2 Republican] [V lawyers]] identified only 300 cases of electoral fraud in the United States in a decade . 
+3: [AM-DIS Indeed] , [A0 Republican lawyers] [V identified] [A1 only 300 cases of electoral fraud in the United States] [AM-TMP in a decade] . 
+3: Indeed , Republican lawyers identified only 300 [V cases] [A1 of electoral fraud] in the United States in a decade . 
+3: Indeed , Republican lawyers identified only 300 cases of [A1 electoral] [V fraud] in the United States in a decade . 
+4: One thing is certain : [A0 these new provisions] [AM-MOD will] [V have] [A1 a negative impact on voter turn - out] . 
+4: One thing is certain : these new provisions will have a [AM-MNR negative] [V impact] [A1 on voter turn - out] . 
+4: One thing is certain : these new provisions will have a negative impact on [A1 voter] [A1 turn -] [V out] . 
+5: [AM-ADV In this sense] , [A0 the measures] [AM-MOD will] [AM-MNR partially] [V undermine] [A1 the American democratic system] . 
+5: In this sense , the measures will partially undermine the American [A1 democratic] [V system] . 
+6: Unlike in Canada , the American States are responsible for the [V organisation] [A1 of federal elections in the United States] . 
+6: Unlike in Canada , the American States are responsible for the organisation of [A2 federal] [V elections] [AM-LOC in the United States] . 
+7: It is in this spirit that a [V majority] [A1 of American governments] have passed new laws since 2009 making the registration or voting process more difficult . 
+7: It is in this spirit that a majority of [A0 [A2 American] [V governments]] have passed new laws since 2009 making the registration or voting process more difficult . 
+7: It is in this spirit that [A0 a majority of American governments] have [V passed] [A1 new laws] [AM-TMP since 2009] making the registration or voting process more difficult . 
+7: It is in this spirit that [A0 a majority of American governments] have passed [A1 new [V laws]] since 2009 making the registration or voting process more difficult . 
+7: It is in this spirit that [A0 a majority of American governments] have passed new laws since 2009 [V making] [A1 the registration or voting process] [A2 more difficult] . 
+7: It is in this spirit that a majority of American governments have passed new laws since 2009 making the [V registration] or voting process more difficult . 
+7: It is in this spirit that a majority of American governments have passed new laws since 2009 making the registration or [V voting] process more difficult . 
+7: It is in this spirit that a majority of American governments have passed new laws since 2009 making the registration or [A1 voting] [V process] more difficult . 
+8: [A1 This phenomenon] [V gained] [A2 momentum] [AM-TMP following the November 2010 elections , which saw 675 new Republican representatives added in 26 States] . 
+8: [A1 This phenomenon] gained [A2 [V momentum]] following the November 2010 elections , which saw 675 new Republican representatives added in 26 States . 
+8: This phenomenon gained momentum [V following] [A2 the November 2010 elections , which saw 675 new Republican representatives added in 26 States] . 
+8: This phenomenon gained momentum following the November 2010 [A0 elections] , [R-A0 which] [V saw] [A1 675 new Republican representatives] [C-A1 added in 26 States] . 
+8: This phenomenon gained momentum following the November 2010 elections , which saw [A0 675 new [A4 Republican] [V representatives]] added in 26 States . 
+8: This phenomenon gained momentum following the November 2010 elections , which saw [A1 675 new Republican representatives] [V added] [AM-LOC in 26 States] . 
+9: [A2 As a [V result] , 180 bills restricting the exercise of the right to vote in 41 States were introduced in 2011 alone .] 
+9: As a result , 180 [A0 bills] [V restricting] [A1 the exercise of the right to vote in 41 States] were introduced in 2011 alone . 
+9: As a result , 180 bills restricting the [V exercise] [A1 of the right to vote in 41 States] were introduced in 2011 alone . 
+9: As a result , 180 bills restricting the exercise of the [V right] [A1 to vote in 41 States] were introduced in 2011 alone . 
+9: As a result , 180 bills restricting the exercise of the right to [V vote] [AM-LOC in 41 States] were introduced in 2011 alone . 
+9: [AM-DIS As a result] , [A1 180 bills restricting the exercise of the right to vote in 41 States] were [V introduced] [AM-TMP in 2011 alone] . 
diff --git a/test/ref/test_yisi_2_srl.out b/test/ref/test_yisi_2_srl.out
new file mode 100644
index 0000000..c45f324
--- /dev/null
+++ b/test/ref/test_yisi_2_srl.out
@@ -0,0 +1,71 @@
+Reading labelconfig from ../src/yisi_srl.labelconfig ... Done.
+Reading w2v text model from mini.d300.en
+Size of voc: 500 Dimension: 300
+Finished reading w2v model.
+Reading w2v text model from mini.d300.de
+Size of voc: 500 Dimension: 300
+Finished reading w2v model.
+Setting up MATE ...[eng, -tokenize, -reranker, -lemma, /home/das011/u/sandboxes/mateplus/models/CoNLL2009-ST-English-ALL.anna-3.3.lemmatizer.model, -tagger, /home/das011/u/sandboxes/mateplus/models/CoNLL2009-ST-English-ALL.anna-3.3.postagger.model, -parser, /home/das011/u/sandboxes/mateplus/models/CoNLL2009-ST-English-ALL.anna-3.3.parser.model, -srl, /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-eng.model]
+34.12.536  is2.data.ParametersFloat 121:read ->        read parameters 134217727 not zero 296071
+34.12.541  is2.data.Cluster 113:<init> ->              Read cluster with 0 words 
+34.12.541  is2.lemmatizer.Lemmatizer 192:readModel ->  Loading data finished. 
+34.12.542  is2.lemmatizer.Lemmatizer 194:readModel ->  number of params  134217727
+34.12.542  is2.lemmatizer.Lemmatizer 195:readModel ->  number of classes 92
+34.18.323  is2.data.ParametersFloat 121:read ->        read parameters 134217727 not zero 1613201
+34.18.324  is2.data.Cluster 113:<init> ->              Read cluster with 0 words 
+34.18.325  is2.tag.Lexicon 103:<init> ->               Read lexicon with 0 words 
+34.18.326  is2.tag.Tagger 141:readModel ->             Loading data finished. 
+34.18.336  is2.parser.Parser 188:readModel ->          Reading data started
+34.18.364  is2.data.Cluster 113:<init> ->              Read cluster with 0 words 
+34.25.37   is2.parser.ParametersFloat 101:read ->      read parameters 134217727 not zero 19957525
+34.25.37   is2.parser.Parser 201:readModel ->          parsing -- li size 134217727
+34.25.44   is2.parser.Parser 211:readModel ->          Stacking false
+34.25.44   is2.parser.Extractor 56:initStat ->         mult  (d4) 
+Used parser   class is2.parser.Parser
+Creation date 2012.11.02 14:33:53
+Training data CoNLL2009-ST-English-ALL.txt.crossannotated
+Iterations    10 Used sentences 10000000
+Cluster       null
+34.25.46   is2.parser.Parser 240:readModel ->          Reading data finnished
+34.25.47   is2.parser.Extractor 56:initStat ->         mult  (d4) 
+Loading pipeline from /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-eng.model
+Loading reranker from /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-eng.model
+Done.
+Setting up MATE ...[ger, -tokenize, -reranker, -hybrid, -token, /home/das011/u/sandboxes/mateplus/models/de-token.bin, -lemma, /home/das011/u/sandboxes/mateplus/models/lemma-ger-3.6.model, -tagger, /home/das011/u/sandboxes/mateplus/models/tag-ger-3.6.model, -parser, /home/das011/u/sandboxes/mateplus/models/pet-ger-S2a-40-0.25-0.1-2-2-ht4-hm4-kk0, -srl, /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-ger.model]
+34.47.11   is2.data.ParametersFloat 142:read ->        read parameters 50000000 not zero 840044
+34.47.16   is2.data.Cluster 111:<init> ->              Read cluster with 0 words 
+34.47.17   is2.lemmatizer.Lemmatizer 185:readModel ->  Loading data finished. 
+34.47.17   is2.lemmatizer.Lemmatizer 187:readModel ->  number of params  50000000
+34.47.17   is2.lemmatizer.Lemmatizer 188:readModel ->  number of classes 336
+34.47.25   is2.transitionS2a.Parser 720:readModel ->   Reading data started
+34.47.196  is2.data.Cluster 111:<init> ->              Read cluster with 0 words 
+34.47.196  is2.transitionS2a.Lexicon 296:read ->       read 0 lexicon entries.
+35.2.492   is2.transitionS2a.ParametersFloat 197:read -> read parameters 300000001 not zero 64569303
+35.2.493   is2.transitionS2a.Parser 734:readModel ->   parsing -- li size 300000001
+35.2.499   is2.transitionS2a.ExtractorR 82:initStat -> values 1824
+35.5.298   is2.transitionS2a.ParametersFloat 197:read -> read parameters 70000001 not zero 1456038
+35.8.436   is2.transitionS2a.ParametersFloat 197:read -> read parameters 70000001 not zero 5355132
+35.8.437   is2.transitionS2a.Parser 776:readModel ->   projective	false
+config {tags-considered=2.0, threshold-tag=0.25, beam=40.0, tagger-iterations=2.0, mthreshold-tag=0.1, morph-tags-considered=2.0, beam-tag=4.0, beam-morph=4.0}
+1st  2nd abcd 3rd ab
+Used parser   class is2.transitionS2apply.Parser
+Creation date 2014.02.23 18:43:23
+Training data corpora/Tiger2Dep//tiger2dep.standard.train.ltm
+Iterations    25 Used sentences 10000000
+Cluster       null
+35.8.444   is2.transitionS2a.Parser 813:readModel ->   Reading data finnished
+Loading pipeline from /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-ger.model
+Loading reranker from /home/das011/u/sandboxes/mateplus/models/srl-EMNLP14+fs-ger.model
+Done.
+Tokenizing/SRL-ing hyp ... Done.
+Tokenizing/SRL-ing inp ... Done.
+Evaluating line 1
+Evaluating line 2
+Evaluating line 3
+Evaluating line 4
+Evaluating line 5
+Evaluating line 6
+Evaluating line 7
+Evaluating line 8
+Evaluating line 9
+Evaluating line 10