CUDA + OCTAVE

I’ve been experimenting with CUDA and OCTAVE; there is at least one company who have produced GPU enabled MEX functions. The big difficulty is of course that there is no support for internal floats within OCTAVE (afaik) and similarly with Matlab. However if one can leave the data and work with it on the device for some time, then there are only two explicit conversions btwn float <-> double needed. Or you could sacrifice some performance in CUDA in return for using doubles. At any rate here’s an example Makefile, happy experimenting. For this example I gutted the matrix Mul example from the CUDA sdk; the wrapper *oct source code (*cc, really C++ with octave extensions) contains an extern C section which references the cuda kernel (*cu). Don’t forget to indent instructions under ‘all’ with a single tab for make.

---

#! /usr/bin/env make
#make file for octfile/cuda
#Mac OSX 10.5.8 intel core 2 duo
#cuda include/lib
CUDA_INC_PATH=/usr/local/cuda/include
CUDA_LIB_PATH=/usr/local/cuda/lib
#octfile compiler
CC=mkoctfile
#basic flags
CFLAGS= -I$(CUDA_INC_PATH)
LDFLAGS= -L$(CUDA_LIB_PATH) -lcudart -lcuda

all:
$(CC) $(CFLAGS) -c cudaMatrixMul.cc -o cudaMatrixMul.o
nvcc  -c matMul_kernel.cu -o matMul_kernel.o -Wall
$(CC) $(LDFLAGS) cudaMatrixMul.o matMul_kernel.o -o cudaMatrixMul.oct

#clean:
rm -f  cudaMatrixMul.o matMul_kernel.o

MCMC paper finished

Abstract:

Many nuclei probed by NMR are relatively insensitive to detection, requiring methods such as the Carr-Purcell Meiboom-Gill (CPMG) pulse sequence. Experiments which follow this general approach are composed of pulse trains, giving rise to characteristic spikelet patterns in the frequency domain. In the presence of multiple underlying chemical sites, each spikelet intensity is a sum of some unknown proportion of contributions from each site. This work outlines a modeling approach based around Markov Chain Monte Carlo (MCMC), which negates the need for intensive simulations using density matrix formalism. In support of this technique, a spikelet pattern is produced using the density matrix formalism for an ensemble of spin 1/2 nuclei, and the underlying chemical shifts and intensities reproduced using the method outlined. Finally, MCMC is used to model the CPMG spectrum of a (3,3,3-trifluoropropyl)dimethylchlorosilane (TFS) treated aluminosilicate, providing evidence in support of a particular model of silanol group surface attachment to the bulk.