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

Erol Biceroglu erol.biceroglu at alumni.utoronto.ca
Thu Jul 2 02:29:05 CEST 2015


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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