[R-sig-hpc] Installing gputools fails on Ubuntu 14.04LTS
Erol Biceroglu
erol.biceroglu at alumni.utoronto.ca
Mon Jul 6 18:30:43 CEST 2015
Hi Charles,
Thanks for providing feedback on the output, and for sharing your projects,
I'll definitely check them out.
Regards,
Erol Biceroglu
*erol.biceroglu at alumni.utoronto.ca <erol.biceroglu at alumni.utoronto.ca>*
On Mon, Jul 6, 2015 at 8:18 AM, Charles Determan <cdetermanjr at gmail.com>
wrote:
> Erol,
>
> Glad to here you got it working. The errors, I believe, are a consequence
> of how the code was written not a consequence of anything you have done.
> These warnings mean that various variables that live on the device are
> trying to be accessed on the host. I believe most of the functions should
> still work but it is something that shouldn't be ignored either. There has
> been some recent development on the github repo for the package (
> https://github.com/nullsatz/gputools) so perhaps the code is being
> updated to fit CUDA's standards. I would submit issues there if you have
> any further problems with the functions themselves.
>
> A quick self-plug, if you are just exploring some GPU related applications
> within R you may wish to check out my gpuR (
> https://github.com/cdeterman/gpuR) and gpuRcuda (
> https://github.com/cdeterman/gpuRcuda) packages for OpenCL and CUDA
> backend code. My intention with these packages is to make GPU computing as
> simple as possible for the R user. They are still in development and I
> need to add some more functions before I release them but I would love to
> have these packages get some exposure so people can submit what they would
> like to see implemented and contribute ideas to make them better.
>
> Regards,
> Charles
>
>
> On Thu, Jul 2, 2015 at 7:13 PM, Erol Biceroglu <
> erol.biceroglu at alumni.utoronto.ca> wrote:
>
>> Hello Charles,
>>
>> Great news, it worked, this is wonderful. I opened R Studio, loaded the
>> library, and ran gpuCor, so looks like it worked.
>>
>> There were a lot of warnings in the output (I apologize in advance for
>> the large block of text), I'm hoping they're harmless as it appears to be
>> working.
>>
>> Thank you very much for your help.
>>
>>
>>
>> * installing to library ‘/home/erol/R/library’
>> * installing *source* package ‘gputools’ ...
>> checking "CUDA compiler"... "environment variable NVCC not set"
>> checking for nvcc... /usr/local/cuda/bin/nvcc
>> "using NVCC=/usr/local/cuda/bin/nvcc"
>> checking "root of the CUDA install directory"... "environment variable
>> CUDA_HOME not set"
>> "using CUDA_HOME=/usr/local/cuda"
>> checking "location of CUDA libraries"... checking for
>> "/usr/local/cuda/lib/libcublas.so"... no
>> checking for "/usr/local/cuda/lib64/libcublas.so"... yes
>> checking "R"... "using /usr/lib/R for the root of the R install directory"
>> "using /usr/lib/R/include for R header files"
>> checking for rpath flag style... checking for cc... cc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether cc accepts -g... yes
>> checking for cc option to accept ISO C89... none needed
>> rpath flag style... gnu
>> 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
>> ** libs
>> ** arch -
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" rinterface.cu -o rinterface.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" mi.cu -o mi.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" sort.cu -o sort.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" granger.cu -o granger.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" qrdecomp.cu -o qrdecomp.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" correlation.cu -o correlation.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" hcluster.cu -o hcluster.o
>> hcluster.cu(449): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(457): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(468): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(516): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(517): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(518): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(518): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(522): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(523): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(523): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(523): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(524): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(524): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(530): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(531): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(532): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(532): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(532): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(539): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(541): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(543): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(548): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(549): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(550): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(551): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(552): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(553): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(554): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(561): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly written in a host function
>>
>> hcluster.cu(579): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(589): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(636): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(637): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(638): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(638): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(642): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(643): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(643): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(643): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(644): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(644): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(650): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(651): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(652): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(652): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(652): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(659): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(661): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(663): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(668): warning: a __device__ variable "hcluster_dist_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(669): warning: a __device__ variable "hcluster_count_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(670): warning: a __device__ variable "hcluster_min_val_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(671): warning: a __device__ variable "hcluster_min_col_d"
>> cannot be directly read in a host function
>>
>> hcluster.cu(672): warning: a __device__ variable "hcluster_sub_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(673): warning: a __device__ variable "hcluster_sup_d" cannot
>> be directly read in a host function
>>
>> hcluster.cu(674): warning: a __device__ variable "hcluster_merge_val_d"
>> cannot be directly read in a host function
>>
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" distance.cu -o distance.o
>> distance.cu(829): warning: a __constant__ variable "distance_vg_a_d"
>> cannot be directly read in a host function
>>
>> distance.cu(837): warning: a __constant__ variable "distance_vg_a_d"
>> cannot be directly read in a host function
>>
>> distance.cu(838): warning: a __constant__ variable "distance_vg_a_d"
>> cannot be directly read in a host function
>>
>> distance.cu(838): warning: a __device__ variable "distance_d_d" cannot
>> be directly read in a host function
>>
>> distance.cu(843): warning: a __constant__ variable "distance_vg_b_d"
>> cannot be directly read in a host function
>>
>> distance.cu(848): warning: a __constant__ variable "distance_vg_a_d"
>> cannot be directly read in a host function
>>
>> distance.cu(848): warning: a __constant__ variable "distance_vg_b_d"
>> cannot be directly read in a host function
>>
>> distance.cu(849): warning: a __device__ variable "distance_d_d" cannot
>> be directly read in a host function
>>
>> distance.cu(853): warning: a __device__ variable "distance_d_d" cannot
>> be directly read in a host function
>>
>> distance.cu(858): warning: a __constant__ variable "distance_vg_a_d"
>> cannot be directly read in a host function
>>
>> distance.cu(859): warning: a __constant__ variable "distance_vg_b_d"
>> cannot be directly read in a host function
>>
>> distance.cu(860): warning: a __device__ variable "distance_d_d" cannot
>> be directly read in a host function
>>
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" matmult.cu -o matmult.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" lsfit.cu -o lsfit.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" kendall.cu -o kendall.o
>> /usr/local/cuda/bin/nvcc -c -Xcompiler "-fpic -g -O2 -fstack-protector
>> --param=ssp-buffer-size=4 -Wformat -Werror=format-security
>> -D_FORTIFY_SOURCE=2 -g" -I. -I"/usr/local/cuda/include"
>> -I"/usr/lib/R/include" cuseful.cu -o cuseful.o
>> cuseful.cu(55): warning: result of call is not used
>>
>> cuseful.cu(55): warning: result of call is not used
>>
>> cuseful.cu: In function ‘float* getMatFromFile(int, int, const char*)’:
>> cuseful.cu:55:24: warning: ignoring return value of ‘int fscanf(FILE*,
>> const char*, ...)’, declared with attribute warn_unused_result
>> [-Wunused-result]
>> fscanf(matFile, " \n ");
>> ^
>> /usr/local/cuda/bin/nvcc -shared -Xlinker -rpath="/usr/local/cuda/lib64"
>> -L"/usr/local/cuda/lib64" -lcublas rinterface.o mi.o sort.o granger.o
>> qrdecomp.o correlation.o hcluster.o distance.o matmult.o lsfit.o kendall.o
>> cuseful.o -o gputools.so
>> installing to /home/erol/R/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)
>>
>>
>>
>> Erol Biceroglu
>>
>>
>> *erol.biceroglu at alumni.utoronto.ca <erol.biceroglu at alumni.utoronto.ca>*
>>
>> On Thu, Jul 2, 2015 at 8:08 AM, Charles Determan <cdetermanjr at gmail.com>
>> wrote:
>>
>>> Are you zipping the extracted package back up? It doesn't look like it
>>> as your output doesn't show any compilation by the nvcc compiler. You
>>> don't need to run the configure script yourself, R will run it for you if
>>> you just have it there. Try the following:
>>>
>>> 1. Move gputools_0.5.tar.gz to some backup directory (you don't want it)
>>> 2. Switch to the directory with the gputools directory and run `tar czf
>>> gputools.tar.gz gputools` to compress it (assuming that is where you
>>> created the 'configure' file)
>>> 3. Then try to install the newly zipped source file `R CMD INSTALL
>>> gputools.tar.gz`
>>>
>>> Charles
>>>
>>> On Wed, Jul 1, 2015 at 7:29 PM, Erol Biceroglu <
>>> erol.biceroglu at alumni.utoronto.ca> wrote:
>>>
>>>> Hi Gary,
>>>>
>>>> I've ran the lines of code
>>>>
>>>> *sudo aptitude install r-base-dev*
>>>> *cd /usr/lib/R*
>>>> *sudo ln -s /usr/share/R/include .*
>>>>
>>>> which upgraded my R to 3.2.1
>>>>
>>>> I then attempted to install with command:
>>>>
>>>> *R CMD INSTALL gputools_0.5.tar.gz*
>>>>
>>>> which yields the same error.
>>>>
>>>> ....[I omitted many lines of output since it's the same as before]
>>>> *Error in library.dynam(lib, package, package.lib) : *
>>>> * shared object ‘gputools.so’ not found*
>>>>
>>>> Thanks for your time and effort on this, very much appreciate it.
>>>>
>>>>
>>>> Erol Biceroglu
>>>>
>>>>
>>>> *erol.biceroglu at alumni.utoronto.ca <erol.biceroglu at alumni.utoronto.ca>*
>>>>
>>>> On Wed, Jul 1, 2015 at 6:05 PM, gartim <gartim at genepi.berkeley.edu>
>>>> wrote:
>>>>
>>>> > check this also
>>>> > http://superuser.com/questions/568349/how-to-install-gputools-in-r
>>>> > -- gary
>>>> >
>>>> > On Wed, Jul 01, 2015 at 04:31:15PM -0400, Erol Biceroglu wrote:
>>>> > >Hello,
>>>> > >
>>>> > >Thank you both for the help.
>>>> > >
>>>> > >The short answer is it's still not working, with the same error
>>>> message.
>>>> > >Here are the actions I took.
>>>> > >
>>>> > >1) So in my /gputools folder I see a 'configure.ac' file.
>>>> > >
>>>> > >I opened it in a text editor, and changed all the AC_HELP_STRING
>>>> lines
>>>> > with
>>>> > >the appropriate paths (lines 6, 18, 42, 55, 64, respectively):
>>>> > >
>>>> > > AC_HELP_STRING([--with-nvcc=/usr/local/cuda/bin/nvcc],
>>>> > > AC_HELP_STRING([--with-cuda=/usr/local/cuda],
>>>> > > AC_HELP_STRING([--with-r=/usr/lib/R],
>>>> > > AC_HELP_STRING([--with-r-include=/usr/share/R/include],
>>>> > > AC_HELP_STRING([--with-r-lib=/usr/lib/R/lib],
>>>> > >
>>>> > >saved the file...
>>>> > >
>>>> > >2)
>>>> > >So then I ran
>>>> > >*autoconf configure.ac <http://configure.ac> > configure *
>>>> > >and then
>>>> > >*chmod +x configure*
>>>> > >
>>>> > >I get a "configure" file in my /gputools folder.
>>>> > >
>>>> > >3)
>>>> > >I then ran the executable by typing:
>>>> > >*./configure*
>>>> > >
>>>> > >and then got the following output:
>>>> > >
>>>> > >*checking "CUDA compiler"... "environment variable NVCC not set"*
>>>> > >*checking for nvcc... /usr/local/cuda/bin/nvcc*
>>>> > >*"using NVCC=/usr/local/cuda/bin/nvcc"*
>>>> > >*checking "root of the CUDA install directory"... "environment
>>>> variable
>>>> > >CUDA_HOME not set"*
>>>> > >*"using CUDA_HOME=/usr/local/cuda"*
>>>> > >*checking "location of CUDA libraries"... checking for
>>>> > >"/usr/local/cuda/lib/libcublas.so"... no*
>>>> > >*checking for "/usr/local/cuda/lib64/libcublas.so"... yes*
>>>> > >*checking "R"... "using /usr/lib/R for the root of the R install
>>>> > directory"*
>>>> > >*"using /usr/lib/R/include for R header files"*
>>>> > >*checking for rpath flag style... checking for cc... cc*
>>>> > >*checking whether the C compiler works... yes*
>>>> > >*checking for C compiler default output file name... a.out*
>>>> > >*checking for suffix of executables... *
>>>> > >*checking whether we are cross compiling... no*
>>>> > >*checking for suffix of object files... o*
>>>> > >*checking whether we are using the GNU C compiler... yes*
>>>> > >*checking whether cc accepts -g... yes*
>>>> > >*checking for cc option to accept ISO C89... none needed*
>>>> > >*rpath flag style... gnu*
>>>> > >*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*
>>>> > >
>>>> > >4)
>>>> > >so then, I go back to my home directory and run:
>>>> > >* R CMD INSTALL gputools_0.5.tar.gz*
>>>> > >
>>>> > >and then I get:
>>>> > >
>>>> > >* installing to library ‘/home/erol/R/library’
>>>> > >* installing *source* package ‘gputools’ ...
>>>> > >** libs
>>>> > >Warning: no source files found
>>>> > >** R
>>>> > >** preparing package for lazy loading
>>>> > >** help
>>>> > >*** installing help indices
>>>> > >** building package indices
>>>> > >** testing if installed package can be loaded
>>>> > >Error in library.dynam(lib, package, package.lib) :
>>>> > > shared object ‘gputools.so’ not found
>>>> > >Error: loading failed
>>>> > >Execution halted
>>>> > >ERROR: loading failed
>>>> > >* removing ‘/home/erol/R/library/gputools’
>>>> > >
>>>> > >My apologies if I've missed something or misinterpreted anything.
>>>> > >
>>>> > >I do want to add that I re-ran *deviceQuery* and it passed, as well
>>>> as
>>>> > >*bandwidthTest*, which also passed. Let me know if the output of
>>>> the two
>>>> > >tests would be helpful.
>>>> > >
>>>> > >Thanks very much for your advice and help.
>>>> > >
>>>> > >Regards,
>>>> > >
>>>> > >
>>>> > >Erol Biceroglu
>>>> > >
>>>> > >
>>>> > >*erol.biceroglu at alumni.utoronto.ca <
>>>> erol.biceroglu at alumni.utoronto.ca>*
>>>> > >
>>>> > >On Wed, Jul 1, 2015 at 2:37 PM, Charles Determan <
>>>> cdetermanjr at gmail.com>
>>>> > >wrote:
>>>> > >
>>>> > >> If you download directory from the github repo you aren't provided
>>>> with
>>>> > a
>>>> > >> 'configure' file but the 'configure.ac' file (which is in the src/
>>>> > >> directory of your gputools directory). As such none of compilation
>>>> > >> instructions, which are rather complex for CUDA, are being passed
>>>> to
>>>> > your
>>>> > >> compiler which will create the gputools.so file you are looking
>>>> for.
>>>> > You
>>>> > >> first need use the 'autoconf' program to create the 'configure'
>>>> file.
>>>> > >>
>>>> > >> autoconf configure.ac > configure
>>>> > >> # make executable
>>>> > >> chmod +x configure
>>>> > >>
>>>> > >> Then try it again, report back if you have further problems.
>>>> > >>
>>>> > >> Regards,
>>>> > >>
>>>> > >> Charles
>>>> > >>
>>>> > >> On Wed, Jul 1, 2015 at 12:25 PM, Erol Biceroglu <
>>>> > >> erol.biceroglu at alumni.utoronto.ca> wrote:
>>>> > >>
>>>> > >>> Hello,
>>>> > >>>
>>>> > >>> I'm trying to install gputools on Ubuntu 14.04LTS and I'm not
>>>> having
>>>> > much
>>>> > >>> luck. I'm not sure if it helps, but here's the R info that's
>>>> output
>>>> > when
>>>> > >>> I
>>>> > >>> run it:
>>>> > >>>
>>>> > >>>
>>>> > >>> R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
>>>> > >>> Copyright (C) 2015 The R Foundation for Statistical Computing
>>>> > >>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>> > >>>
>>>> > >>>
>>>> > >>> Here are the steps I've taken so far:
>>>> > >>> *1) Run the following in the terminal:*
>>>> > >>>
>>>> > >>> *git clone https://github.com/nullsatz/gputools.git
>>>> > >>> <https://github.com/nullsatz/gputools.git>*
>>>> > >>>
>>>> > >>> -This creates a "gputools" folder in my /home directory
>>>> > >>>
>>>> > >>> *2) Then run the following in the terminal:*
>>>> > >>>
>>>> > >>> *R CMD build gputools*
>>>> > >>>
>>>> > >>> -This creates the gputools_0.5.tar.gz in my home folder
>>>> > >>>
>>>> > >>> *3) Then I run the following command (which is causing issues)*
>>>> > >>>
>>>> > >>> *R CMD INSTALL
>>>> --configure-args="--with-nvcc=/usr/local/cuda/bin/nvcc
>>>> > >>> --with-r-lib=/usr/lib/R/lib --with-r=/usr/lib/R/ "
>>>> gputools_0.5.tar.gz*
>>>> > >>>
>>>> > >>> and I get the following output:
>>>> > >>>
>>>> > >>> ** installing to library ‘/home/erol/R/library’*
>>>> > >>> ** installing *source* package ‘gputools’ ...*
>>>> > >>> *** libs*
>>>> > >>> *Warning: no source files found*
>>>> > >>> *** R*
>>>> > >>> *** preparing package for lazy loading*
>>>> > >>> *** help*
>>>> > >>> **** installing help indices*
>>>> > >>> *** building package indices*
>>>> > >>> *** testing if installed package can be loaded*
>>>> > >>> *Error in library.dynam(lib, package, package.lib) : *
>>>> > >>> * shared object ‘gputools.so’ not found*
>>>> > >>> *Error: loading failed*
>>>> > >>> *Execution halted*
>>>> > >>> *ERROR: loading failed*
>>>> > >>> ** removing ‘/home/erol/R/library/gputools’*
>>>> > >>> ** restoring previous ‘/home/erol/R/library/gputools’*
>>>> > >>>
>>>> > >>> I've checked the paths, and found my '*libR.so*' tucked away all
>>>> alone
>>>> > in
>>>> > >>> */usr/lib/R/lib*, but I don't know where *gputools.so* is and I
>>>> can't
>>>> > find
>>>> > >>> it by searching.
>>>> > >>>
>>>> > >>> Any feedback on how to proceed would be greatly appreciated.
>>>> > >>>
>>>> > >>> Thanks for your help.
>>>> > >>>
>>>> > >>> Regards,
>>>> > >>>
>>>> > >>> Erol Biceroglu
>>>> > >>>
>>>> > >>>
>>>> > >>> *erol.biceroglu at alumni.utoronto.ca <
>>>> erol.biceroglu at alumni.utoronto.ca
>>>> > >*
>>>> > >>>
>>>> > >>> [[alternative HTML version deleted]]
>>>> > >>>
>>>> > >>> _______________________________________________
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>>>> > >>> R-sig-hpc at r-project.org
>>>> > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>> > >>
>>>> > >>
>>>> > >>
>>>> > >
>>>> > > [[alternative HTML version deleted]]
>>>> > >
>>>> > >_______________________________________________
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>>>> > >R-sig-hpc at r-project.org
>>>> > >https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>> >
>>>>
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>>>>
>>>> _______________________________________________
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>>
>
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