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. 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
