Wouldn't it be great to be able to compile code written in languages like FORTRAN, C, and C++ to Java bytecode? NestedVM - almost magically - can do just that. This article documents a failed first attempt to compile the popular cheminformatics toolkit Open Babel, which is written in C and C++, to pure Java bytecode with NestedVM.
A previous article described the successful compilation of the InChI toolkit, a C library, to a platform-independent executable jarfile.
Open Babel is one of cheminformatics' most widely-used open source packages. It interconverts dozens of molecular languages, performs a host of cheminformatics analyses, and serves as a platform for many programs and Web services.
As useful as Open Babel is, it doesn't run directly on a Java Virtual Machine (JVM). Although an Open Babel JNI interface does exist, using it introduces a platform dependency, which in many cases is not acceptable. JNI is a great solution in some cases, but when maintaining a single version of a program is important, or when applets need to be used, or when code needs to work with unusual system configurations, it's a poor choice.
Our goal is to compile Open Babel's "babel" command-line utility into pure Java bytecode that can be run on any recent JVM without using JNI.
Overview of NestedVM
In a nutshell, NestedVM converts MIPS binaries to Java class files. In theory, this allows software written in any language that can be compiled to a MIPS binary to be run on a JVM.
To do this, NestedVM distributes two categories of tools: (1) a complete MIPS cross-compiler toolchain; and (2) a MIPS binary to Java bytecode compiler and accessories.
The preferred method to install NestedVM is to compile it from source found in the project repository. There are a number of prerequisites your system must meet in order to be able to do so. For now, this article assumes your system has all of them. Some of the following steps can be found in these instructions as well.
To obtain the source code from the NestedVM darcs repository:
darcs get --repo-name=nestedvm http://nestedvm.ibex.org
Then change into the nestedvm directory and build the main code:
cd nestedvm make
On my machine, this step takes 10-15 minutes.
To make sure your build works, run the tests:
make test ... 1.574000e+00 -4.315000e+01l -43 -4.315000e+01 4.315000e+01 Hello, World 7F fabs(-2.24) = 2.34 Destructor!
NestedVM doesn't build the g++ compiler by default - it's something that needs to be done manually. Fortunately, it's not difficult to do:
make cxxtest ... java -cp build tests.CXXTest Test's constructor Name: 0x50b40 Name: PKc Is pointer: 1 Name: 0x50b3c Name: i Is pointer: 0 Hello, World from Test Now throwing an exception sayhi threw: const char *:Hello, Exception Handling! Test's destructor
Finally, with all tools built, we need to set up our environment:
make env.sh source env.sh
We're now ready to cross-compile Open Babel.
Cross-Compiling Open Babel
For this tutorial, we'll use the Open Babel 2.1.1 source distribution. Unpack the tarball and change into the directory.
Next, we'll need to set up our cross-compiler environment. Fortunately, NestedVM has made this easy. If you check your environment variables, you'll find that
CC have both been set. All that remains is to notify the configure script that we'll be cross-compiling:
Then we build the MIPS binaries:
Peeking into the
tools directory, we can see all of the Open Babel command line tools have been built, including
Unless you're running a MIPS machine, though, this binary won't be executable.
So far, it looks like everything worked. Although it didn't work the first time I tried it, the NestedVM team were most helpful.
Building the Java Class File
We're now ready for the final stage in the process, converting the MIPS binary to a Java class file. Again, NestedVM makes this simple:
cd tools java org.ibex.nestedvm.Compiler -outfile Babel.class Babel babel Exception in thread "main" java.lang.IllegalStateException: unresolved phantom target at org.ibex.classgen.MethodGen.resolveTarget(MethodGen.java:555) at org.ibex.classgen.MethodGen._generateCode(MethodGen.java:664) at org.ibex.classgen.MethodGen.generateCode(MethodGen.java:618) at org.ibex.classgen.MethodGen.dump(MethodGen.java:888) at org.ibex.classgen.ClassFile._dump(ClassFile.java:193) at org.ibex.classgen.ClassFile.dump(ClassFile.java:160) at org.ibex.nestedvm.ClassFileCompiler.__go(ClassFileCompiler.java:380) at org.ibex.nestedvm.ClassFileCompiler._go(ClassFileCompiler.java:72) at org.ibex.nestedvm.Compiler.go(Compiler.java:259)
Unfortunately, NestedVM has blown up with an exception. Although our target class file, Babel.class is now in our working directory, it is not complete and won't run.
What Went Wrong?
However, the way
babel works is to load its various language modules dynamically. It may be possible to fix the problem by producing a version of
babel containing all of its modules in a single binary.
Although there is a major issue to be resolved, this tutorial illustrates the full process of compiling C++ code to Java bytecode using NestedVM.