Re: [R] linking R to goto blas

From: Stefan Sobernig <stefan.sobernig_at_wu-wien.ac.at>
Date: Tue 14 Jun 2005 - 05:01:05 EST

Prof. Ritley, Mr. Dalgaard, thank you very much for the immediate reply and your efforts!
We investigated a littlle further, though not directly following Mr. Dalgaard's findings
on dynamic linking. We got aware of another short notice published on the R-devel list,
providing some hints for installing R and goto (see
http://maths.newcastle.edu.au/~rking/R/devel/03b/1267.html):

############ snip ###################################
[What I did to link R against Goto's BLAS (mostly following Prof. Bates' instruction):
- Install libgoto*.so and symlink to libgoto.so.
- Download xerbla.f and compile to xerbla.o.
- Run the R configure script with --with-blas="-lgoto /path/to/xerbla.o".
- Edit Makeconf and delete the path to xerbla.o in BLAS_LIB.
- make; make check

]
############ snip ###################################

########### config.log ################################
configure:32429: gcc -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib conftest.c -L/usr/lib/ -lgoto_prescott-32-r0.99-3
/home/ssoberni/xerbla.o -lpthread -lg2c -lm -lgcc_s -ldl -lm >&5
/home/ssoberni/xerbla.o(.text+0x0): In function `xerbla_':
: multiple definition of `xerbla_'
/tmp/ccMxAKbu.o(.text+0x0):/home/ssoberni/R-2.1.0/conftest.c:143: first
defined here
/usr/bin/ld: Warning: size of symbol `xerbla_' changed from 5 in
/tmp/ccMxAKbu.o to 43 in /home/ssoberni/xerbla.o
collect2: ld returned 1 exit status
########### config.log ################################

We keep on trying ...
Thanks for your thoughts ...

//stefan

Peter Dalgaard wrote:

>Peter Dalgaard <p.dalgaard@biostat.ku.dk> writes:
>
>  
>
>>Stefan Sobernig <stefan.sobernig@wu-wien.ac.at> writes:
>>
>>    
>>
>>>Dear all,
>>>
>>>I am currently trying to link R 2.1.0 to the GOTO BLAS 0.99.3 library on
>>>a box running Fedora Core 3 , basically following the steps indicated in
>>>the R-Admin document:
>>>
>>>1: I downloaded the current libgoto.xxx.so from
>>>http://www.cs.utexas.edu/users/kgoto/libraries/libgoto_prescott-32-r0.99-3.so.gz,
>>>a version suitable for our XEON machine (Nocona core), unpacked it to
>>>/usr/lib and created a symlink libgoto.so pointing to the library.
>>>
>>>2: Then, I got ready to re-configure and re-compile R (2.1.0) using the
>>>following configure flags: ./configure --prefix=/usr --enable-R-shlib
>>>--enable-shared --with-tcltk --with-blas="-lgoto -lpthread -lm"
>>>      
>>>
>>... 
>>    
>>
>>>Please, I highly appreciate any thoughts or hints as my colleagues and I
>>>are eager to get into GOTO's universe.
>>>      
>>>
>>Hmm. Looks over-complicated to me. What works for me on AMD64 is to
>>have a config.site file in my BUILD-GOTO directory, containing
>>
>>    
>>
>>>cat config.site
>>>      
>>>
>>BLAS_LIBS="-L/home/pd/GOTO -lgoto_opt64p-r0.96 -lpthread"
>>CFLAGS="-O3 -g"
>>#CFLAGS="-g"
>>FFLAGS=$CFLAGS
>>CXXFLAGS=$CFLAGS
>>
>>(the .*FLAGS business is optional, of course). With this in place, a
>>simple ../R/configure followed by make seems to do the trick.
>>
>>I'll give it a try on my FC3 system, but it's a 500 MHz PIII, so it
>>takes a while...
>>    
>>
>
>Hmm... That gives me the grDevices issue, which boils down to an R
>that segfaults immediately upon startup, in
>
>#0  0x05c0aea7 in tilde_expand () from /usr/lib/libreadline.so.4
>#1  0x08170254 in R_ExpandFileName_readline (
>    s=0x8bb4020
>#"/home/pd/r-patched/BUILD-GOTO/library/grDevices/R/sysdata.rdb",
>#buff=0x8295300
>#"/home/pd/r-patched/BUILD-GOTO/library/grDevices/R/grDevices")
>    at ../../../R/src/unix/sys-std.c:406
>#2  0x0816f5da in R_ExpandFileName (
>    s=0x8bb4020
>#"/home/pd/r-patched/BUILD-GOTO/library/grDevices/R/sysdata.rdb") at
>#../../../R/src/unix/sys-unix.c:129
>#3  0x08167352 in R_FileExists (
>    path=0x8bb4020
>#"/home/pd/r-patched/BUILD-GOTO/library/grDevices/R/sysdata.rdb") at
>#stat.h:365
>#4  0x08105da3 in do_fileexists (call=0x84fd544, op=0x82c5f78,
>#args=0x0,
>    rho=0x8c514a4) at ../../../R/src/main/platform.c:857
>#5  0x080edc85 in do_internal (call=0x0, op=0x82ba5d4, args=0x3920,
>    env=0x8c514a4) at ../../../R/src/main/names.c:1078
>#6  0x080c0daa in Rf_eval (e=0x84fd57c, rho=0x8c514a4)
>    at ../../../R/src/main/eval.c:382
>#7  0x080c3695 in Rf_applyClosure (call=0x8668c28, op=0x84fd5b4,
>    arglist=0x8c50564, rho=0x8ad5cc4, suppliedenv=0x82aa5f0)
>
>running --no-readline gives me another crash
>
>(gdb) bt
>#0  0x003fb0da in strcmp () from /lib/ld-linux.so.2
>#1  0x003f009a in _dl_map_object () from /lib/ld-linux.so.2
>#2  0x004fdb58 in dl_open_worker () from /lib/tls/libc.so.6
>#3  0x00000000 in ?? ()
>
>...which suggests that something is up with dynamic linking. 
>
>I'll give it another spin...
>
>  
>



-- 

Stefan Sobernig
Department of Information Systems and New Media
Vienna University of Economics	
Augasse 2-6
A - 1090 Vienna
     
Phone: +43 - 1 - 31336 - 4878
Fax: +43 - 1 - 31336 - 746     
Email: stefan.sobernig@wu-wien.ac.at <mailto:stefan.sobernig@wu-wien.ac.at>
PubKey: http://julia.wu-wien.ac.at/~ssoberni/0x5FC2D3FA.asc <http://julia.wu-wien.ac.at/%7Essoberni/0x5FC2D3FA.asc>
 


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Received on Tue Jun 14 07:06:28 2005

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