Re: [R] linux compile options (64-bit)
We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Quite a few packages have been written in ways that stop them building on 64-bit platforms (and the maintainers have been informed but not fixed them). On Mon, 1 Aug 2005, Jacob Michaelson wrote: Sorry--sent this before I added a subject line... Begin forwarded message: From: Jacob Michaelson [EMAIL PROTECTED] Date: August 1, 2005 8:51:58 PM MDT To: r-help@stat.math.ethz.ch I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation on some configure flags/options for compiling a 64-bit version of R on Linux. I thought this was very strange, considering Linux is apparently the R developer's platform of choice. Can anyone point me to some good build instructions for 64-bit R under Linux? Should I compile it against any additional libraries for better performance? [[alternative HTML version deleted]] PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 07:34:39AM +0100, Prof Brian Ripley wrote: We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after - R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:/usr/bin/gcc-4.0 -g -O2 C++ compiler: /usr/bin/g++-4.0 -g -O2 Fortran compiler: /usr/bin/gfortran-4.0 -g -O2 Interfaces supported: X11, tcltk External libraries:readline, BLAS(ATLAS) Additional capabilities: PNG, JPEG, iconv, MBCS, NLS Options enabled: R profiling Recommended packages: yes --- amilo:/usr/local/src/R/R-2.1.1# make check make[1]: Entering directory `/usr/local/src/R/R-2.1.1/tests' make[2]: Entering directory `/usr/local/src/R/R-2.1.1/tests' make[3]: Enteri|ng directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Entering directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Entering directory `/usr/local/src/R/R-2.1.1/tests/Examples' collecting examples for package 'base' ... make[5]: Entering directory `/usr/local/src/R/R-2.1.1/src/library' Building/Updating help pages for package 'base' Formats: text html latex example make[5]: Leaving directory `/usr/local/src/R/R-2.1.1/src/library' running code in 'base-Ex.R' .../bin/sh: line 1: 9010 Segmentation fault ../../bin/R --vanilla base-Ex.R base-Ex.Rout 21 make[4]: *** [base-Ex.Rout] Error 1 make[4]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/usr/local/src/R/R-2.1.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/usr/local/src/R/R-2.1.1/tests' make: *** [check] Error 2 eigen(print(cbind(c(0,1i), c(-1i,0# Hermite == real Eigen values [,1] [,2] [1,] 0+0i 0-1i [2,] 0+1i 0+0i Running it under 'R -d gdb': R hangs; after C-c: Program received signal SIGINT, Interrupt. zhetd2_ ([EMAIL PROTECTED], [EMAIL PROTECTED], a=0x10900f0, [EMAIL PROTECTED], d=0x13b06e8, e=0xb6add8, tau=0x1bb6448, [EMAIL PROTECTED], _uplo=1) at cmplx.f:8330 8330 CALL ZAXPY( N-I, ALPHA, A( I+1, I ), 1, TAU( I ), 1 ) Current language: auto; currently fortran --- [...] Göran -- Göran Broströmtel: +46 90 786 5223 Department of Statistics fax: +46 90 786 6614 Umeå University http://www.stat.umu.se/~goran.brostrom/ SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linux compile options (64-bit)
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 07:34:39AM +0100, Prof Brian Ripley wrote: We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. ... eigen(print(cbind(c(0,1i), c(-1i,0# Hermite == real Eigen values [,1] [,2] [1,] 0+0i 0-1i [2,] 0+1i 0+0i Running it under 'R -d gdb': R hangs; after C-c: Program received signal SIGINT, Interrupt. zhetd2_ ([EMAIL PROTECTED], [EMAIL PROTECTED], a=0x10900f0, [EMAIL PROTECTED], d=0x13b06e8, e=0xb6add8, tau=0x1bb6448, [EMAIL PROTECTED], _uplo=1) at cmplx.f:8330 8330 CALL ZAXPY( N-I, ALPHA, A( I+1, I ), 1, TAU( I ), 1 ) Current language: auto; currently fortran -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote: On Tue, 2 Aug 2005, Göran Broström wrote: [...] Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. I apologize for the incomplete description; gcc -v gives: gcc version 3.4.5 20050706 (prerelease) (Debian 3.4.4-5) but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? Probably not; I just 'apt-get install'ed atlas3-base etc. I'll build atlas from source and try again. On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. OK. An additional advantage with gfortran(-4.x) will be the possibility to use fortan95 code, n'est ce pas? Göran __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linux compile options (64-bit)
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote: On Tue, 2 Aug 2005, Göran Broström wrote: [...] Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. I apologize for the incomplete description; gcc -v gives: gcc version 3.4.5 20050706 (prerelease) (Debian 3.4.4-5) but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? Probably not; I just 'apt-get install'ed atlas3-base etc. I'll build atlas from source and try again. On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. OK. An additional advantage with gfortran(-4.x) will be the possibility to use fortan95 code, n'est ce pas? Some Fortran95 code, anyway. (It is not yet a complete implementation.) The problems we are seeing with gcc4 are mainly (but not entirely) with gfortran: it seems not quite ready for production use. -4.0.1 is already a considerable improvement over -4.0.0. There is another project (www.g95.org) that is using a slightly different version of these sources, and either g95 or gfortran can be used with gcc3 if you want to use F95 sources. However, F95 is unlikely to be suitable for use in distributed R packages for a long time to come. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 10:58:31AM +0100, Prof Brian Ripley wrote: The problems we are seeing with gcc4 are mainly (but not entirely) with gfortran: it seems not quite ready for production use. -4.0.1 is already a considerable improvement over -4.0.0. There is another project (www.g95.org) that is using a slightly different version of these sources, and either g95 or gfortran can be used with gcc3 if you want to use F95 sources. However, F95 is unlikely to be suitable for use in distributed R packages for a long time to come. Thanks; I'll stick to 3.4.4(!) and f77 for the time being. Göran __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
