JAL-2662 Updated README

diff --git a/benchmarking/README b/benchmarking/README
index 63381ce..4011e5a 100644 (file)
--- a/benchmarking/README
+++ b/benchmarking/README
@@ -1,18 +1,40 @@
 To set up benchmarking:
 
+
 1. In the jalview directory run 
   ant makedist
 
 This builds a jalview.jar file and puts it into dist/
 
+
 2. Make a lib directory in benchmarking/ if not already present.
 
-3. Run
-  mvn install:install-file -Dfile=../dist/jalview.jar -DgroupId=jalview.org -DartifactId=jalview -Dversion=1.0 -Dpackaging=jar -DlocalRepositoryPath=lib
+
+3. In the benchmarking directory run:
+       mvn install:install-file -Dfile=../dist/jalview.jar -DgroupId=jalview.org -DartifactId=jalview -Dversion=1.0 -Dpackaging=jar -DlocalRepositoryPath=lib
 
 to install the jalview.jar file in the local maven repository. The pom.xml in the benchmarking references this installation, so if you change the names the pom.xml file will also need to be updated.
 
+
 4. Build and run jmh benchmarking. In the benchmarking directory:
-  mvn clean install
-  java -jar target/benchmarks.jar
+       mvn clean install
+       java -jar target/benchmarks.jar
+  
+  To get output as a json file use instead:
+       java -jar target/benchmarks.jar -rf json
+  
+  JSON files can be visualised using the viewer at http://jmh.morethan.io/
+  
+  To get help use the standard -h option:
+       java -jar target/benchmarks.jar -h
+       
+  More information here:
+       http://openjdk.java.net/projects/code-tools/jmh/
+       http://java-performance.info/jmh/
+  
+  
+ 5. If you make changes to the jalview code everything will need to be refreshed, by calling:
+       mvn dependency:purge-local-repository -DactTransitively=false -DreResolve=false
+  
+  followed by steps 3 and 4 again.
   
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