On Monday 12 July 2010 23:51:55 Simon Urbanek wrote: > On Jul 12, 2010, at 5:59 PM, lI wrote: > > On Monday 12 July 2010 20:52:15 Simon Urbanek wrote: > >> On Jul 12, 2010, at 2:50 PM, lI wrote: > >>> On Monday 12 July 2010 11:07:23 lI wrote: > >>>> On Monday 12 July 2010 10:29:30 lI wrote: > >>>>> Greetings, > >>>>> > >>>>> I have a computer with the following setup: > >>>>> 1)cblfs (pure 64-bit (amd64) linux), kernel2.6.34 gcc4.4.2 > >>>>> 2)R-2.11.1 > >>>>> > >>>>> I compiled R with BLAS and lapack using the switched ( > >>>>> --with-blas="- lpthread -latlas -lfptf77blas" > >>>>> --with-lapack="-llapack -lcblas" ). > >>>>> (( http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra) > >>>>> ) > >>>>> > >>>>> Prior to compiling R-2.11.1 > >>>>> sh conigure --help gave options including the following > >>>>> SHLIB_LD command for linking shared libraries > >>>>> which contain object files from a C or Fortran > >>>>> compiler only SHLIB_LDFLAGS special flags used by SHLIB_LD > >>>>> SHLIB_CXXLDFLAGS special flags used by SHLIB_CXXLD > >>>>> SHLIB_FCD command for linking shared libraries which contain object > >>>>> files from the Fortran 95 compiler > >>>>> SHLIB_FCLDFLAGS special flags used by SHLIB_FCLD > >>>>> > >>>>> > >>>>> I did not know what to set for these and accepted whatever the > >>>>> defaults were. I ended up with shared-libraries which are as > >>>>> follows:- > >>>>> > >>>>> $R_HOME/lib/{libRblas.so,libRlapack.so } i.e. with the prefix > >>>>> 'lib' and the following shared-libraries without the 'lib' prefix. > >>>>> > >>>>> $R_HOME/modules/{R_X11.so,internet.so,lapack.so,vfonts.so } > >>>>> $R_HOME/library/cluster/libs/cluster.so > >>>>> $R_HOME/library/foreign/libs/foreign.so > >>>>> $R_HOME/library/grDevices/libs/grDevices.so > >>>>> $R_HOME/library/grid/libs/grid.so > >>>>> $R_HOME/library/KernSmooth/libs/KernSmooth.so > >>>>> $R_HOME/library/lattice/libs/lattice.so > >>>>> $R_HOME/library/MASS/libs/MASS.so > >>>>> $R_HOME/library/Matrix/libs/Matrix.so > >>>>> $R_HOME/library/methods/libs/methods.so > >>>>> $R_HOME/library/mgcv/libs/mgcv.so > >>>>> $R_HOME/library/nlme/libs/nlme.so > >>>>> $R_HOME/library/nnet/libs/nnet.so > >>>>> $R_HOME/library/rpart/libs/rpart.so > >>>>> $R_HOME/library/spatial/libs/spatial.so > >>>>> $R_HOME/library/splines/libs/splines.so > >>>>> $R_HOME/library/stats/libs/stats.so > >>>>> $R_HOME/library/survival/libs/survival.so > >>>>> $R_HOME/library/tools/libs/tools.so > >>>>> > >>>>> > >>>>> In linux builds the linker usually looks for libs with the 'lib' > >>>>> prefix. In this installation all the libraries > >>>>> ---in $R_HOME/modules > >>>>> ---in $R_HOME/library/patha/to/whatevr > >>>>> > >>>>> do not have the 'lib' prefix. > >>>>> > >>>>> QUESTION: > >>>>> A) does any on list know SHLIB_LD SHLIB_LDFLAGS SHLIB_CXXLDFLAGS > >>>>> SHLIB_FCD SHLIB_FCLDFLAGS settings for compiling R and do these > >>>>> result in so libs with the 'lib' prefix? > >>>>> B) If all of A) is negative what is there to be done to to enable > >>>>> generation libraries in $R_HOME/modules $R_HOME/library/~ with the > >>>>> 'lib' prefix? > >>>> > >>>> I forgot to add my configure/make options. These were:- > >>>> ######################## > >>>> export BUILD64="-m64" > >>>> sh configure \ > >>>> CC="gcc $BUILD64" \ > >>>> CXX="g++ $BUILD64" \ > >>>> F77="gfortran $BUILD64" \ > >>>> FC="gfortran $BUILD64" \ > >>>> JAVA_HOME=$JAVA_HOME \ > >>>> LIBnn=lib64 \ > >>>> CPPFLAGS="-I$ATLAS_HOME/include -I/opt/acml4.4.0/gfortran64_mp/include > >>>> - I/opt/acml4.4.0/gfortran64/include -I/usr/local/numerics/include" \ > >>>> LDFLAGS="-L$ATLAS_HOME/lib -L/opt/acml4.4.0/gfortran64_mp/lib - > >>>> L/usr/local/numerics/lib -L/usr/lib" \ > >>>> --prefix=/opt/TEST/R-2.11.1 \ > >>>> --x-includes=$XORG_PREFIX/include \ > >>>> --x-libraries=$XORG_PREFIX/lib \ > >>>> --with-tcl-config=/usr/lib \ > >>>> --with-tk-config=/usr/lib \ > >>>> --with-system-zlib=/usr \ > >>>> --with-system-bzlib=/usr \ > >>>> --with-system-pcre=/usr \ > >>>> --with-x \ > >>>> --with-libpth-prefix=/usr \ > >>>> --with-libintl-prefix=/usr \ > >>>> --with-blas="-lpthread -latlas -lfptf77blas" \ > >>>> --with-lapack="-llapack -lcblas" \ > >>>> --enable-R-shlib \ > >>>> --enable-BLAS-shlib > >>>> ################ > >>>> > >>>> The sources compiled trouble-free. with 'make' as normal user. > >>>> I then ran 'make install' as super-user and int installed in the > >>>> prefix as set.. > >>>> > >>>> A reply to the following questions would be much appreciateed:- > >>>> QUESTION: > >>>> A) does any on list know SHLIB_LD SHLIB_LDFLAGS SHLIB_CXXLDFLAGS > >>>> SHLIB_FCD SHLIB_FCLDFLAGS settings for compiling R and do these > >>>> result in so libs with the 'lib' prefix? > >>>> B) If all of A) is negative what is there to be done to enable > >>>> generation of shared-libraries in $R_HOME/modules/ and > >>>> $R_HOME/library/~ directories/sub-directories with the 'lib' > >>>> prefix? > >>> > >>> thanks everyone for the help in clarifying what were share-libraries > >>> and otherwise. > >>> > >>> As stated above I used two switches > >>> --enable-R-shlib \ > >>> --enable-BLAS-shlib > >>> in the configure options of the downloaded R-2.11.1 source prior to > >>> compilation. > >>> > >>> I am compiling R-2.11.1 as an optional dependency of kdeedu-4.4.5. > >>> This asks for R-shlib )which I noticed it is disable by the default > >>> in the configure script.) > >>> > >>> After compile and install of R-2.11.1, I am only able to start R from > >>> the command line > >> > >> How are you starting it? The R start script does setup everything so > >> that you should never touch anything inside. > >> > >>> when I move the generated libRblas.so to libRblas.soDUFF and > >>> symlink libacml.so to libRblas.so and update $R_HOME/etc/ldpaths > >>> accordingly. I am unable to start R with the compiled-in > >>> $R_HOME/libR.so and $R_HOME/libRblas.so. > >>> > >>> QUESTIONS: > >>> A) How does one start R with the the generated libR.so and > >>> libRblas.so? > >> > >> bin/R > >> > >>> B) is the generated libR.so interchangable with libRblas.so (i.e. R > >>> library without blas enhanced algebra capabilities?) > >> > >> No - those are two entirely different libraries. The libRblas can be > >> interchanged with a suitably complete BLAS implementation, but please do > >> read the manuals for details. > >> > >> Cheers, > >> Simon > > > > Thanks to you for your help. Following your guidance, kdeedu-4.4.5 now > > builds successfully against R-2.11.1. However when I edit > > ~/etc/ldpaths with the line > > > > export LD_LIBRARY_PATH=path/to/acml/lib:$LD_LIBRARY_PATH > > > > R fails to start. > > Of course as you should expect. Why would you edit? It has nothing to do > with BLAS ... I hope I did mention there was a symbolic link of libRblas.so to libacml.so (as recommended by the manual) > Also did you read the manual? It explicitly covers your case ... yes I did here http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra) > Cheers, > Simon > > > it only starts when the above point to $R_HOME/lib. (nb I > > have a symbolic link of libacml.so to libRblas.so > > any ideas? >
______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
