As ArrayFire-rb, a GPGPU libray has started taking shape, the next goal is to interface it with NMatrix library, so we can run Linear Mixed Models(mixed_models).

I have also written an LMM(Linear Mixed Models) solver in D for Genome Wide Association studies called faster_lmm_d which has two GPU backends:

  1. CUDA backend which helps it directly interact with CUBLAS libraries and runs only on Nvidia Hardware. For CUDA backend, Faster_LMM_D uses cuda_d(The D bindings I wrote for CUDA libraries).

  2. ArrayFire backend which helps it run on all major GPU vendors(Nvidia, Intel, AMD) by calling CUDA, CuBLAS, OpenCL, clBLAS libraries using the ArrayFire library. For ArrayFire backend, Faster_LMM_D uses arrayfire-d(The D bindings I wrote for ArrayFire library).

So, I found that it would be really great if we could port faster_lmm_d to Ruby by calling D from Ruby. faster_lmm_d uses some cool tricks to efficiently use GPUs for computing like minimizing the warmup time, minimal copying of CPU memory to GPU memory. It logs CPU memory and GPU memory before and after every significant computation. So, it would be an ideal exercise for GPU computing on Ruby by calling D functions under the hood.

Although, this is still a work in progress, I would like to share about my experiences.

Previous Attempts

There has been previous attempts at Calling D from Ruby. In my search for the existing attempts at “Calling D from Ruby”, I stumbled upon these resources.

  1. FFI: Use the Ruby-FFI gem to call a D function from C.
  2. RuDy: An effort / library / gem to enable and ease writing Ruby native extensions in D programming language. It depends on creatind D bindings for the API calls in ruby.h header file.
  3. Ruby-Dlang: Similar approach as Rudy.
  4. Orbit: Similar approach as Rudy.

I have been intereseted in the first two methods, i.e. FFI and Rudy.

Exploring FFI

The idea here is to create a shared object .so and call it with Ruby by loading the shared object using FFI gem.

Dlang has three compilers namely DMD, GDC and LDC. The post on Dlang wiki makes use of DMD, I could easily run the example on my machine using DMD, however I could not run it with LDC. I need to compile the d files with LDC because faster_lmm_d makes use of LDC compiler switches and it would take a lot of effort to be able to run it with DMD.

The error I encountered is:

  1. Error with ld :
    $ ldc2 -shared -m64 -relocation-model=pic i.d
    /usr/bin/ld: /home/prasun/ldclatest/ldc-1.1.0-pk9rkm4zvdp6pglam7s2/lib/libdruntime-ldc.a(errno.c.o): relocation R_X86_64_PC32 against undefined symbol `__errno_location@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
    /usr/bin/ld: final link failed: Bad value
    collect2: error: ld returned 1 exit status
    Error: /usr/lib/nvidia-cuda-toolkit/bin/gcc failed with status: 1
    

I have also tried some hit and trial and yet I was unable to properly compile the file.

Exploring RuDy

I find Rudy as a more suitable way to create Ruby native extensions.

When creating a Ruby native extension in C, we have a set of APIs provided by ruby.h that helps in creating a Module or a Class and the methods are nested to it.

For example, rb_define_module helps in creating a module and rb_define_class_under is used to create a class nested in a module. rb_define_method and rb_define_singleton_method are used to create methods. The variables are used as VALUE which are passed around between Ruby frontend and C backend.

A simple code snippet.

// calculater.c
void Init_extension() {
  Calculator = rb_define_module("Calculator");              // Calculator module
  IO = rb_define_class_under(Calculator, "IO", rb_cObject); // Calculator::IO class
  rb_define_alloc_func(IO, io_alloc);                       // memory allocator for C structs
  rb_define_method(IO, "initialize", io_init, -1);          // Calculator::IO#new constructor
  rb_define_method(IO, "get_stream",io_get_stream,1 );      // Calculator::IO#get_stream method
}

static VALUE io_init(int argc, VALUE* argv, VALUE self){
  // code...
  return self;
}

static VALUE io_get_stream(VALUE self, VALUE some_val){
  return Qtrue;
}

After the C code with the module, classes and methods are in place, we compile it to get a shared object extension.so. Then a Ruby file calculater.rb can just load that extension.so as:

# calculater.rb
require 'calculater.so'

This seems simple but as the size of application grows, the extension becomes tough to manage.

I believe D to be a superior C and provides modern programming paradigm and the LDC compiler is very promising. So, it would be great if we could write the native extension in D and get a shared library. Also, LDC has an incredible garbage collecter that would be very helpful for scientific computing Ruby libraries.

To write the extension in D, the ruby.h bindings could be created in D using dstep or bcd.

RuDy doesn’t have complete support for LDC and I am still getting my head around using RuDy to create Ruby native extensions. Here is a nice blog post about RuDy project.

Conclusion

Calling D from Ruby would for sure prove to be an efficient way of writing Ruby native extensions and use D as a better choice over C. In the meanwhile, porting faster-lmm-d is a work in progress and I will share further updates when it is ready.

The progress of Ruby port of faster-lmm-d can be tracked at Bio-faster_lmm_d and would become a part of BioRuby project. The latest progress can be tracked here.