[Rd] question about Makeconf and nvcc/CUDA

Hodgess, Erin HodgessE at uhd.edu
Thu Jul 18 20:01:31 CEST 2013

Hi again:

Here is another problem that I am having.  Hope this will be the last one.  I really want to see if I can put it together.  Sorry for belaboring the issue.

Well, here is my story:

c:\Program Files\R\R-3.0.1\bin\i386>R CMD build cudasize
R CMD build cudasize
* checking for file 'cudasize/DESCRIPTION' ... OK
* preparing 'cudasize':
* checking DESCRIPTION meta-information ... OK
* cleaning src
Warning: C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:33: unexpected '{'
Warning: C:/Users/erin/AppData/Local/Temp/RtmpOKsfga/Rbuild22e066bf13fb/cudasize/man/f1.Rd:37: unexpected '}'
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'cudasize_1.0.tar.gz'

c:\Program Files\R\R-3.0.1\bin\i386>R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz 
R CMD INSTALL --no-multiarch cudasize_1.0.tar.gz 
* installing to library 'c:/myRlib'
* installing *source* package 'cudasize' ...
** libs
nvcc -m32 --shared -o cuda4.dll cuda4.cu
installing to c:/myRlib/cudasize/libs/i386
** R
** preparing package for lazy loading
** help
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:33: unexpected '{'
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:37: unexpected '}'
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:31: All text must be in a section
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:32: All text must be in a section
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:34: All text must be in a section
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:35: All text must be in a section
Warning: C:/Users/erin/AppData/Local/Temp/RtmpKSm696/R.INSTALL7fc517f4e58/cudasize/man/f1.Rd:36: All text must be in a section
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (cudasize)

c:\Program Files\R\R-3.0.1\bin\i386>R --vanilla
R --vanilla

R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cudasize)
> f1
function (x) 
    y <- .Call("cuda4", as.character(x))
<environment: namespace:cudasize>
> f1(2)
Error in .Call("cuda4", as.character(x)) : 
  "cuda4" not resolved from current namespace (cudasize)
Calls: f1 -> .Call
Execution halted

Here is the Makevars.win file

	nvcc -m32 --shared -o cuda4.dll cuda4.cu

And finally, the program itself:

#include <stdio.h>
#include <cuda.h>
// Kernel that executes on the CUDA device
__global__ void square_array(float *a, int N)
  int idx = blockIdx.x * blockDim.x + threadIdx.x;
  if (idx<N) a[idx] = a[idx] * a[idx];
// main routine that executes on the host
void  stuff(int argc, char **argv)
  float *a_h, *a_d;  // Pointer to host & device arrays
  int N = atoi(argv[1]);
//  const int N = 10;   Number of elements in arrays
  size_t size = N * sizeof(float);
  a_h = (float *)malloc(size);        // Allocate array on host
  cudaMalloc((void **) &a_d, size);   // Allocate array on device
  // Initialize host array and copy it to CUDA device
  for (int i=0; i<N; i++) a_h[i] = (float)i;
  cudaMemcpy(a_d, a_h, size, cudaMemcpyHostToDevice);
  // Do calculation on device:
  int block_size = 4;
  int n_blocks = N/block_size + (N%block_size == 0 ? 0:1);
  square_array <<< n_blocks, block_size >>> (a_d, N);
  // Retrieve result from device and store it in host array
  cudaMemcpy(a_h, a_d, sizeof(float)*N, cudaMemcpyDeviceToHost);
  // Print results
  for (int i=0; i<N; i++) printf("%d %f\n", i, a_h[i]);
  // Cleanup
  free(a_h); cudaFree(a_d);

Any suggestions would be appreciated.


From: r-devel-bounces at r-project.org [r-devel-bounces at r-project.org] on behalf of Duncan Temple Lang [dtemplelang at ucdavis.edu]
Sent: Thursday, July 18, 2013 9:16 AM
To: r-devel at r-project.org
Subject: Re: [Rd] question about Makeconf and nvcc/CUDA

Hi Erin

 Glad you are making progress on this with Brian's help.

 I thought I would mention a different approach that might save you some
programming time and actually make the code more flexible at the same time.
Basically, in a high-level language like R, it is nice to keep the code
calling a GPU kernel also high-level rather than writing code in C/C++
to do the transfer of data to and from the CPU and GPU.

Simon's OpenCL package (on CRAN) and the new RCUDA package (www.omegahat.org/RCUDA)
allow us to load and invoke kernels directly from R.
These provide more flexibility for invoking GPU kernels from R than fixed C/C++ code.

RCUDA provides an interface to almost all of the CUDA API and so allows us to transfer
values from R to the GPU and back (in different ways), invoke kernels asynchronously, etc.
I haven't built the package on Windows yet, but may be able to get to that in the next
few days.

With a Windows binary of RCUDA (or OpenCL), you would be able to skip nvcc in your
package by  compiling the kernel code generically so that it contains code for GPUs
with different  capabilities (e.g. sm_20, sm_30, sm_35).

In the last few days, I have also managed to compile very simple R code
directly in R to PTX code that we can load and invoke using RCUDA.
The compilation uses the Rllvm and RLLVMCompile packages. So in the
future, I expect we will be able to compile simple R functions
to native and PTX code.


On 7/17/13 11:45 PM, Hodgess, Erin wrote:
> Dear R development:
> I'm not sure if this is the appropriate list, but it's a start.
> I would like to put together a package which contains a CUDA program on Windows 7.  I believe that it has to do with the Makeconf file in the etc directory.
> But when I just use the nvcc with the shared option, I can use the dyn.load command, but when I use the is.loaded function, it shows FALSE.
> Here are the results of the check command:
> c:\PROGRA~1\R\R-3.0.1\bin\i386>R CMD check cudasize
> R CMD check cudasize
> * using log directory 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck'
> * using R version 3.0.1 (2013-05-16)
> * using platform: i386-w64-mingw32 (32-bit)
> * using session charset: ISO8859-1
> * checking for file 'cudasize/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'cudasize' version '1.0'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking whether package 'cudasize' can be installed ... ERROR
> Installation failed.
> See 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/00install.out' for details.
> And the 00install.out file:
> * installing *source* package 'cudasize' ...
> ** libs
> *** arch - i386
> cygwin warning:
>   MS-DOS style path detected: c:/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
>   Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
>   CYGWIN environment variable option "nodosfilewarning" turns off this warning.
>   Consult the user's guide for more details about POSIX paths:
>     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
> cygwin warning:
>   MS-DOS style path detected: c:/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
>   Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-30~1.1/etc/i386/Makeconf
>   CYGWIN environment variable option "nodosfilewarning" turns off this warning.
>   Consult the user's guide for more details about POSIX paths:
>     http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
> make: `symbols.rds' is up to date.
> ERROR: compilation failed for package 'cudasize'
> * removing 'c:/PROGRA~1/R/R-3.0.1/bin/i386/cudasize.Rcheck/cudasize'
> I've been experimenting with the Makeconf file, but to no avail.
> Does anyone have any suggestions, please?
> Thanks,
> Erin
>       [[alternative HTML version deleted]]
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