I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a & .so), libcblas (.a & .so), libf77blas (.a & .so), liblapack (.a & .so), libptcblas (.a & .so), libptf77blas (.a & .so) and libstatatlas.a. When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? Thanks.
This is explained in detail in the manual "R Installation and Administration". Best, Uwe Ligges On 03.05.2010 06:02, Chuck White wrote:> I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a& .so), libcblas (.a& .so), libf77blas (.a& .so), liblapack (.a& .so), libptcblas (.a& .so), libptf77blas (.a& .so) and libstatatlas.a. > > When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? > > Thanks. > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
Thank you for your response. I did look in the suggested manual under A.3.1.5 Shared BLAS. Here are my steps: compiled R using --with-readline=yes --enable-R-shlib=yes --enable-BLAS-shlib=yes --with-x=yes --prefix=/usr/local/R-2.11.0 Compiled LAPACK first and then ATLAS using http://www.scipy.org/Installing_SciPy/Linux#head-89e1f6afaa3314d98a22c79b063cceee2cc6313c All the .so files have been copied to /usr/lib64 In /usr/local/R-2.11.0/lib64/R/lib, I renamed the .so files for blas and lapack and linked as libRblas.so -> /usr/local/lib64/libf77blas.so libRlapack.so -> /usr/local/lib64/liblapack.so R does startup OK but when I do the following: require(nlme) fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc), data = Loblolly, fixed = Asym + R0 + lrc ~ 1, random = Asym ~ 1, start = c(Asym = 103, R0 = -8.5, lrc = -3.3)) I get /usr/local/R-2.11.0/lib64/R/bin/exec/R: symbol lookup error: /usr/local/R-2.11.0/lib64/R/lib/libRblas.so: undefined symbol: ATL_dgemm This runs just fine without using the .so files which were built with R. Can you please help? Thanks. ---- Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:> This is explained in detail in the manual "R Installation and > Administration". > > Best, > Uwe Ligges > > > On 03.05.2010 06:02, Chuck White wrote: > > I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a& .so), libcblas (.a& .so), libf77blas (.a& .so), liblapack (.a& .so), libptcblas (.a& .so), libptf77blas (.a& .so) and libstatatlas.a. > > > > When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? > > > > Thanks. > > > > ______________________________________________ > > R-devel at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel
On 05.05.2010 04:52, Chuck White wrote:> Thank you for your response. I did look in the suggested manual under A.3.1.5 Shared BLAS. > > Here are my steps: compiled R using > --with-readline=yes --enable-R-shlib=yes --enable-BLAS-shlib=yes --with-x=yes --prefix=/usr/local/R-2.11.0Why do you want shlib support, do you really need it? For the static case, A.3.1.1 ATLAS described the way to go.> Compiled LAPACK first and then ATLAS using http://www.scipy.org/Installing_SciPy/Linux#head-89e1f6afaa3314d98a22c79b063cceee2cc6313c All the .so files have been copied to /usr/lib64 > > In /usr/local/R-2.11.0/lib64/R/lib, I renamed the .so files for blas and lapack and linked as > libRblas.so -> /usr/local/lib64/libf77blas.so > libRlapack.so -> /usr/local/lib64/liblapack.so > > R does startup OK but when I do the following: > require(nlme) > fm1<- nlme(height ~ SSasymp(age, Asym, R0, lrc), data = Loblolly, fixed = Asym + R0 + lrc ~ 1, random = Asym ~ 1, start = c(Asym = 103, R0 = -8.5, lrc = -3.3)) > > I get > /usr/local/R-2.11.0/lib64/R/bin/exec/R: symbol lookup error: /usr/local/R-2.11.0/lib64/R/lib/libRblas.so: undefined symbol: ATL_dgemm > This runs just fine without using the .so files which were built with R.I have never before linked dynamically to ATLAS versions. ATL_dgemm is probably defined in one of the other libraries. I have not looked since I currently do not have any ATLAS left on my machines which I was more used to roughly 3 years ago. Uwe Ligges> Can you please help? Thanks. > > ---- Uwe Ligges<ligges at statistik.tu-dortmund.de> wrote: >> This is explained in detail in the manual "R Installation and >> Administration". >> >> Best, >> Uwe Ligges >> >> >> On 03.05.2010 06:02, Chuck White wrote: >>> I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a& .so), libcblas (.a& .so), libf77blas (.a& .so), liblapack (.a& .so), libptcblas (.a& .so), libptf77blas (.a& .so) and libstatatlas.a. >>> >>> When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? >>> >>> Thanks. >>> >>> ______________________________________________ >>> R-devel at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >