Using R's GPU packages on Amazon

Walkthrough:

Step 1: Lookup the AMI-ID ami-87377cee (the one Erik Hazzard built at http://vasir.net/blog/opencl/installing-cuda-opencl-pyopencl-on-aws-ec2) in AWS in the Community AMIs and start up a cg1.4xlarge machine.

Step 2: From command line run: sudo apt-get update then sudo apt-get install r-base-core

** this will install R2.14.1. If you want to use the latest R version, I would use the guide here: How to install R version 3

Step 3: run R, then use install.packages('OpenCL') to install OpenCL

Step 4: Have fun learning OpenCL!!

It is really that easy to get it working. Writing the code in a way that OpenCL can use is a bit tricky, but once you get the hang of it utilizing the GPU can be a very powerful tool.

See http://cran.r-project.org/web/packages/OpenCL/OpenCL.pdf for some code snippets to get you started.

With this machine you can also easily use Python with OpenCL, where I would recommend: http://enja.org/category/tutorial/advcl/ if you want to go that route.

My solution may apply on your case. I installed successfully by resolving two errors messages. First error message I resolved comes from the source file, rpudist.cu (in src folder), as the error message suggests it is in line 159. You can use a text editor to read the source file and find this code, (dev = 1.).

rpudist.cu(159): warning: use of "=" where "==" may have been intended

So I changed it to (dev == 1.), the error message was then gone.

The second error message, indeed as you have found out, is about -Wl. I think this may be more critical. It seems to conflict with another linker option -Xlinker, which is used in the file, Makefile.in in the src folder of the rpud folder (if you extract the tarball rpud_0.0.2.tar.gz).

LD_PARAMS := -Xlinker "@R_LIB@ @RPATHFLAG@"    

As explained in the gcc doc and I replicate here, both "Pass option as an option to the linker". So I think they passed options after them to ld to link with the files nvcc has compiled. In the following code, nvcc calls both -Xlinker, and -Wl

/usr/local/cuda/bin/nvcc -shared -Xlinker "-Wl,--export-dynamic-fopenmp  -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lrt -ldl -lm -Wl,-rpath,/usr/local/cuda/lib64" -L/usr/local/cuda/lib64 -lcublas -lcuda rpud.o rpudist.o -o rpud.so

Thus, the not-very-elegant workaround is to make nvcc only use -Xlinker. To sum up, except changing the (maybe not critical) file, rpudist.cu, the solution is to alter the contents in the files (1) Makefile.in (in src folder) and (2) configure (in top-level folder).

Changing the line 10 in original Makefile.in from

LD_PARAMS := -Xlinker "@R_LIB@ @RPATHFLAG@"

to:

LD_PARAMS := -Xlinker @R_LIB@ -Xlinker @RPATHFLAG@

Then change the line 1786 in the original configure from,

R_LIB=`"${R_HOME}/bin/R" CMD config --ldflags`

to

R_LIB="-E -fopenmp  -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm"

and line 1797 from,

RPATHFLAG="-Wl,-rpath,${CUDA_HOME}${CUDA_LIB_DIR}"

to

RPATHFLAG="-rpath=${CUDA_HOME}${CUDA_LIB_DIR}"

Finally, just follow Chi Yau's installation instruction

3) Expand the package in a temporary folder:

tar xf rpud_<version>.tar.gz

4) Run configure in rpud:

cd rpud./configurecd ..

5) Then enter the following:

R CMD INSTALL rpud

HTH