Recently I posted to this list with a question about using the Intel 10.1 compilers in building R and one response was basically, "why in the heck would you want to do that?" The answer is that my sysadmin believes that there will be a performance boost with the Intel vs. Gnu compilers on our Linux cluster, of which I am one of many users. Wanting to be a good citizen and use my machine time wisely, I'd of course like to use right tool to build the most efficient installation of R and associated packages. BTW, we got R to compile nicely using the settings at the end of this post. Looking back on previous posts, however, it seems that there is no consensus as to how to benchmark R. I realize such a task is not trivial, nor controversial, but does anyone have a set of time-consuming tasks that can be used to compare R installations? It would seem logical that such a benchmark would include sub-benchmarks on file access, interpreted intensive tasks, C intensive tasks, BLAS intensive tasks, etc. You developers know more about this than I do, but I know enough to realize that there won't be one simple answer. Nevertheless, I'd like to make my usage decisions on something rather than anedotal claims. So, does anyone know of a good benchmarking script or would be willing to contribute one? And here are the settings we used to compile R with Intel 10.1 compilers: ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk \ --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh \ --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ --without-x --without-readline --without-iconv \ CC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ CFLAGS="-O3 -no-prec-div -unroll" \ F77="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ FFLAGS="-O3 -no-prec-div -unroll" \ CXX="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icpc" \ CXXFLAGS="-O3 -no-prec-div -unroll" \ FC="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ FCFLAGS="-O3 -no-prec-div -unroll" \ OBJC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ OBJCFLAGS="-O3 -no-prec-div -unroll" \ --disable-R-profiling --disable-memory-profiling ## make all make install Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** [[alternative HTML version deleted]]
recently there was a post on R-help/Rd ?? with this link on benchmarking different 'number crunching packages'. They used a series of tests, although I didn't check they used all the types you mentioned. I couldn't find test code at first glance but myyebe it is available on request??? http://www.sciviews.org/benchmark/ Ludo On Mon, 2 Jun 2008, Mark Kimpel wrote:> Recently I posted to this list with a question about using the Intel 10.1 > compilers in building R and one response was basically, "why in the heck > would you want to do that?" The answer is that my sysadmin believes that > there will be a performance boost with the Intel vs. Gnu compilers on our > Linux cluster, of which I am one of many users. Wanting to be a good citizen > and use my machine time wisely, I'd of course like to use right tool to > build the most efficient installation of R and associated packages. BTW, we > got R to compile nicely using the settings at the end of this post. > > Looking back on previous posts, however, it seems that there is no consensus > as to how to benchmark R. I realize such a task is not trivial, nor > controversial, but does anyone have a set of time-consuming tasks that can > be used to compare R installations? It would seem logical that such a > benchmark would include sub-benchmarks on file access, interpreted intensive > tasks, C intensive tasks, BLAS intensive tasks, etc. You developers know > more about this than I do, but I know enough to realize that there won't be > one simple answer. Nevertheless, I'd like to make my usage decisions on > something rather than anedotal claims. > > So, does anyone know of a good benchmarking script or would be willing to > contribute one? > > And here are the settings we used to compile R with Intel 10.1 compilers: > > ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ > --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ > --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk \ > --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh \ > --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ > --without-x --without-readline --without-iconv \ > CC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ > CFLAGS="-O3 -no-prec-div -unroll" \ > F77="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ > FFLAGS="-O3 -no-prec-div -unroll" \ > CXX="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icpc" \ > CXXFLAGS="-O3 -no-prec-div -unroll" \ > FC="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ > FCFLAGS="-O3 -no-prec-div -unroll" \ > OBJC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ > OBJCFLAGS="-O3 -no-prec-div -unroll" \ > --disable-R-profiling --disable-memory-profiling > ## > make all > make install > > Mark > > -- > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Dirk, At the moment, our emphasis is getting an installation that will run Rmpi in batch mode. I imagine my sysadmin put that line in to minimize potential problems. To be honest, I didn't catch it, I was just glad to get a compile :) As to the line that doesn't apply to the R install, I think you are referring to the "with mpi", which I think he also slipped in not realizing it should more properly go with the Rmpi install. Mark On Tue, Jun 3, 2008 at 12:18 AM, Dirk Eddelbuettel <edd@debian.org> wrote:> On Mon, Jun 02, 2008 at 11:56:16PM -0400, Mark Kimpel wrote: > > ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ > > --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ > > --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk > \ > > There is no such option for R's configure. > > > --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh > \ > > --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ > > --without-x --without-readline --without-iconv \ > > So you never want your compute cluster to be able to do an interactive > plot under x11 ? > > Dirk > > -- > Three out of two people have difficulties with fractions. >-- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** [[alternative HTML version deleted]]