[R] linking R to goto blas

[Peter Dalgaard]

Peter Dalgaard <p.dalgaard at biostat.ku.dk> writes:

> Stefan Sobernig <stefan.sobernig at 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...

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907