[R-sig-hpc] Installing gputools fails on Ubuntu 14.04LTS

[gartim]

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>*
>>>
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>>>
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>>
>>
>
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