Here we go:


R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

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[Previously saved workspace restored]

> install.packages("gputools_0.26.tar.gz",repos=NULL,configure.args=c("--with-cuda-home=/bccd/software/cuda-3.2.16"))
Installing package(s) into '/bccd/home/bccd/R/x86_64-pc-linux-gnu-library/2.14'
(as 'lib' is unspecified)
* installing *source* package 'gputools' ...
** package 'gputools' successfully unpacked and MD5 sums checked
configure: checking for critical tools used by configure
checking "environment variable COMPILER_BINDIR"... "COMPILER_BINDIR not set; using user's default path"
checking "environment variable CUDA_HOME"... "using CUDA_HOME=/bccd/software/cuda-3.2.16"
checking "environment variable CULA_HOME"... "CULA_HOME not set; using default /usr/local/cula"
checking for /bccd/software/cuda-3.2.16/bin/nvcc... yes
"nvcc found"
checking "whether this is the 64 bit linux version of CUDA"... checking for /bccd/software/cuda-3.2.16/lib64/libcublas.so... no
"no -- using /bccd/software/cuda-3.2.16/lib for CUDA libs"
"using -I/usr/share/R/include for R header files"
"using -L/usr/lib/R/lib -lR for R shared libraries"
checking "whether this is the 64 bit version of CULA"... checking for /usr/local/cula/lib64/libcula.so... no
checking for /usr/local/cula/lib64/libcula.dylib... no
"no"
checking "checking whether cula is present at all"... checking for /usr/local/cula/lib/libcula.so... no
checking for /usr/local/cula/lib/libcula.dylib... no
"cula is not installed; gpuFastICA is disabled"
configure: determining host platform
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating R/gpuSvm.R
config.status: creating R/gpuFastICA.R
config.status: creating R/gpuSvd.R
** libs
** arch - 
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic kendall.cu -o kendall.o
ptxas /tmp/tmpxft_000018cd_00000000-9_kendall.compute_12.ptx, line 299; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_000018cd_00000000-7_kendall.compute_11.ptx, line 299; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_000018cd_00000000-5_kendall.compute_10.ptx, line 299; warning : Double is not supported. Demoting to float
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic classification.cu -o classification.o
ptxas /tmp/tmpxft_00001a5e_00000000-9_classification.compute_12.ptx, line 370; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00001a5e_00000000-7_classification.compute_11.ptx, line 370; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00001a5e_00000000-5_classification.compute_10.ptx, line 370; warning : Double is not supported. Demoting to float
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic rinterface.cu -o rinterface.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic mi.cu -o mi.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic sort.cu -o sort.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic granger.cu -o granger.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic qrdecomp.cu -o qrdecomp.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic correlation.cu -o correlation.o
ptxas /tmp/tmpxft_00001fbf_00000000-9_correlation.compute_12.ptx, line 1212; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00001fbf_00000000-7_correlation.compute_11.ptx, line 1212; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00001fbf_00000000-5_correlation.compute_10.ptx, line 1212; warning : Double is not supported. Demoting to float
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic hcluster.cu -o hcluster.o
ptxas /tmp/tmpxft_000020a6_00000000-9_hcluster.compute_12.ptx, line 708; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_000020a6_00000000-7_hcluster.compute_11.ptx, line 708; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_000020a6_00000000-5_hcluster.compute_10.ptx, line 708; warning : Double is not supported. Demoting to float
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic distance.cu -o distance.o
ptxas /tmp/tmpxft_00002179_00000000-9_distance.compute_12.ptx, line 934; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00002179_00000000-7_distance.compute_11.ptx, line 934; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00002179_00000000-5_distance.compute_10.ptx, line 934; warning : Double is not supported. Demoting to float
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic matmult.cu -o matmult.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic lsfit.cu -o lsfit.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/bccd/software/cuda-3.2.16/include -I/usr/share/R/include -Xcompiler -fpic cuseful.cu -o cuseful.o
/bccd/software/cuda-3.2.16/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -shared -Xlinker  -L/usr/lib/R/lib -lR -L/bccd/software/cuda-3.2.16/lib -lcublas kendall.o classification.o   rinterface.o mi.o sort.o granger.o qrdecomp.o correlation.o hcluster.o distance.o matmult.o lsfit.o cuseful.o -o gputools.so
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../libR.so when searching for -lR
/usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when searching for -lR
/usr/bin/ld: skipping incompatible /usr/lib/libR.so when searching for -lR
/usr/bin/ld: cannot find -lR
collect2: ld returned 1 exit status
make: *** [gputools.so] Error 1
ERROR: compilation failed for package 'gputools'
* removing '/bccd/home/bccd/R/x86_64-pc-linux-gnu-library/2.14/gputools'
* restoring previous '/bccd/home/bccd/R/x86_64-pc-linux-gnu-library/2.14/gputools'
Warning message:
In install.packages("gputools_0.26.tar.gz", repos = NULL, configure.args = c("--with-cuda-home=/bccd/software/cuda-3.2.16")) :
  installation of package 'gputools_0.26.tar.gz' had non-zero exit status
> 
[1] "Please use mpi.quit() to quit R"




Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodgesse@uhd.edu



-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd@debian.org]
Sent: Wed 2/22/2012 8:53 PM
To: Hodgess, Erin
Cc: r-sig-hpc@r-project.org
Subject: Re: [R-sig-hpc] question about install gputools
 

On 22 February 2012 at 20:40, Hodgess, Erin wrote:
| Dear HPC People:
| 
| I'm not sure if R GPU has its own sig, so I thought I'd start here.
| 
| I'm trying to install gputools on a Debian (squeeze) and I keep getting the error:
| 
| /usr/bin/ld cannot find -lR

A *complete* and *reproduceable* example, please!
 
| Has anyone run into this, please?

As shown below, "it just works for me" (provided I make sure CC is the
gcc-4.4 as I use the CUDA 4.0 APU) on Ubuntu 11.10; it would the same on
Debian as CRAN tests are done on Debian too.

How did you install R? Did you install it yourself by chance and forget to
build as a shared library?  I have to guess as you did not supply the
required information.

Dirk

install log below

edd@max:/tmp$ R CMD INSTALL gputools_0.26.tar.gz 
* installing to library '/usr/local/lib/R/site-library'
* installing *source* package 'gputools' ...
** package 'gputools' successfully unpacked and MD5 sums checked
configure: checking for critical tools used by configure
checking "environment variable COMPILER_BINDIR"... "COMPILER_BINDIR not set; using user's default path"
checking "environment variable CUDA_HOME"... "using CUDA_HOME=/usr/local/cuda"
checking "environment variable CULA_HOME"... "using CULA_HOME=/usr/local/cula"
checking for /usr/local/cuda/bin/nvcc... yes
"nvcc found"
checking "whether this is the 64 bit linux version of CUDA"... checking for /usr/local/cuda/lib64/libcublas.so... yes
"yes -- using /usr/local/cuda/lib64 for CUDA libs"
"using -I/usr/share/R/include for R header files"
"using -L/usr/lib/R/lib -lR for R shared libraries"
checking "whether this is the 64 bit version of CULA"... checking for /usr/local/cula/lib64/libcula.so... no
checking for /usr/local/cula/lib64/libcula.dylib... no
"no"
checking "checking whether cula is present at all"... checking for /usr/local/cula/lib/libcula.so... no
checking for /usr/local/cula/lib/libcula.dylib... no
"cula is not installed; gpuFastICA is disabled"
configure: determining host platform
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating R/gpuSvm.R
config.status: creating R/gpuFastICA.R
config.status: creating R/gpuSvd.R
** libs
** arch - 
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic kendall.cu -o kendall.o
ptxas /tmp/tmpxft_00003a13_00000000-11_kendall.compute_12.ptx, line 282; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003a13_00000000-7_kendall.compute_11.ptx, line 282; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003a13_00000000-5_kendall.compute_10.ptx, line 282; warning : Double is not supported. Demoting to float
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic classification.cu -o classification.o
ptxas /tmp/tmpxft_00003ae0_00000000-11_classification.compute_12.ptx, line 384; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003ae0_00000000-7_classification.compute_11.ptx, line 384; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003ae0_00000000-5_classification.compute_10.ptx, line 384; warning : Double is not supported. Demoting to float
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic rinterface.cu -o rinterface.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic mi.cu -o mi.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic sort.cu -o sort.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic granger.cu -o granger.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic qrdecomp.cu -o qrdecomp.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic correlation.cu -o correlation.o
ptxas /tmp/tmpxft_00003fc1_00000000-11_correlation.compute_12.ptx, line 1195; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003fc1_00000000-7_correlation.compute_11.ptx, line 1195; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_00003fc1_00000000-5_correlation.compute_10.ptx, line 1195; warning : Double is not supported. Demoting to float
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic hcluster.cu -o hcluster.o
ptxas /tmp/tmpxft_0000408f_00000000-11_hcluster.compute_12.ptx, line 730; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_0000408f_00000000-7_hcluster.compute_11.ptx, line 730; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_0000408f_00000000-5_hcluster.compute_10.ptx, line 730; warning : Double is not supported. Demoting to float
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic distance.cu -o distance.o
ptxas /tmp/tmpxft_0000415c_00000000-11_distance.compute_12.ptx, line 942; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_0000415c_00000000-7_distance.compute_11.ptx, line 942; warning : Double is not supported. Demoting to float
ptxas /tmp/tmpxft_0000415c_00000000-5_distance.compute_10.ptx, line 942; warning : Double is not supported. Demoting to float
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic matmult.cu -o matmult.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic lsfit.cu -o lsfit.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -c -I. -I/usr/local/cuda/include -I/usr/share/R/include -Xcompiler -fpic cuseful.cu -o cuseful.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_10,code=sm_10 -gencode arch=compute_11,code=sm_11 -gencode arch=compute_12,code=sm_12 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -shared -Xlinker  -L/usr/lib/R/lib -lR -L/usr/local/cuda/lib64 -lcublas kendall.o classification.o   rinterface.o mi.o sort.o granger.o qrdecomp.o correlation.o hcluster.o distance.o matmult.o lsfit.o cuseful.o -o gputools.so
installing to /usr/local/lib/R/site-library/gputools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (gputools)
edd@max:/tmp$ 


-- 
"Outside of a dog, a book is a man's best friend. Inside of a dog, it is too
dark to read." -- Groucho Marx


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