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

Charles Determan cdetermanjr at gmail.com
Thu Jul 2 14:08:19 CEST 2015 

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
> > >*
> > >>>
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> > >>>
> > >>> _______________________________________________
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> > >>
> > >>
> > >>
> > >
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