[R-sig-hpc] question about install gputools

[Hodgess, Erin]

Hi again!

I installed R-2.14.1 via apt-get install.

I'll get the complete set in a moment.

Thanks,
Erin


-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org] 
Sent: Wednesday, February 22, 2012 8:54 PM
To: Hodgess, Erin
Cc: r-sig-hpc at 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 at 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 at max:/tmp$ 


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