Re: [R] linking R to goto blas

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue 14 Jun 2005 - 07:03:52 EST

R already contains a xerbla: you should not be adding one.

On Mon, 13 Jun 2005, Stefan Sobernig wrote:

> 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 ###################################
>
> * Therefore, we got the auxiliary lapack routine xerbla offered at
> http://www.cs.utexas.edu/users/kgoto/libraries/xerbla.c
> and compiled it by calling: "gcc -c xerbla.c -o xerbla.o" (please note,
> that I am not that expierenced in C programming as such,
> my knowledge is limited to deploying and fixing c-coded apps). Am I
> right to say that this xerbla extension changes the entry
> point of the goto library?
>
> * Then, we re-configured R using: ./configure --prefix=/usr
> --with-blas="-L/usr/lib/ -lgoto_prescott-32-r0.99-3
> /home/ssoberni/xerbla.o -lpthread"
>
> * Unfortunately, this resulted in another error affecting the configure
> process so that BLAS_LIBS is set to "-lblas" (pointing to standard blas
> libs):
>
> ########### 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>
>
>
>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595

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Received on Tue Jun 14 07:09:04 2005

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