From ligges at statistik.tu-dortmund.de  Wed May  5 11:29:21 2010
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Wed, 05 May 2010 11:29:21 +0200
Subject: [Rd] R 2.11.0 on RHEL5
In-Reply-To: <20100504225227.56GSE.5692750.root@mp17>
References: <20100504225227.56GSE.5692750.root@mp17>
Message-ID: <4BE13A71.4070406@statistik.tu-dortmund.de>



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-2.11.0


Why 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
>



[Rd] R 2.11.0 on RHEL5
Uwe Ligges