R help - Jan 2002 - MKL seems to beat ATLAS, but some problems... (was RE: li nkin g R against MKL)

Prof. Ripley,
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
[snipped...]
> R cannot currently make use of anyone else's LAPACK routines (because
> we've found too many problems with them).
> 
> If you are getting no useful diagnostics, try
> dyn.load("RHOME/modules/lapack.so").  That ought to tell you 
> why you can't
> load it.  My guess would be to do with libraries, so do an ldd on
> lapack.so and check that all the dependencies are resolved as 
> you expect.
I wonder if the problem is the clash between the Lapack routines in MKL and
those packaged with R.

Sorry, but seems like I need a bit more spoon-feeding:
I did the dyn.load, and got:
        unable to load shared library
"/home/andy/R-patched-mkl/modules/lapack.so":
  /home/andy/R-patched-mkl/modules/lapack.so: undefined symbol: lsame_

I then did ldd -r lapack.so, and got:
        libm.so.6 => /lib/libm.so.6 (0x401ef000)
        libz.so.1 => /usr/lib/libz.so.1 (0x4020d000)
        libreadline.so.4.1 => /usr/lib/libreadline.so.4.1 (0x4021b000)
        libdl.so.2 => /lib/libdl.so.2 (0x40243000)
        libncurses.so.5 => /usr/lib/libncurses.so.5 (0x40248000)
        libpthread.so.0 => /lib/libpthread.so.0 (0x4028f000)
        libc.so.6 => /lib/libc.so.6 (0x402a2000)
        /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x2aaaa000)
        libgpm.so.1 => /usr/lib/libgpm.so.1 (0x40389000)
undefined symbol: R_NamesSymbol (./lapack.so)
undefined symbol: R_NilValue    (./lapack.so)
undefined symbol: R_DimSymbol   (./lapack.so)
undefined symbol: R_NaInt       (./lapack.so)
undefined symbol: Rf_isString   (./lapack.so)
undefined symbol: STRING_ELT    (./lapack.so)
undefined symbol: Rf_isComplex  (./lapack.so)
undefined symbol: Rf_duplicate  (./lapack.so)
undefined symbol: LENGTH        (./lapack.so)
undefined symbol: Rf_allocMatrix        (./lapack.so)
undefined symbol: Rf_coerceVector       (./lapack.so)
undefined symbol: Rf_mkChar     (./lapack.so)
undefined symbol: R_alloc       (./lapack.so)
undefined symbol: SET_STRING_ELT        (./lapack.so)
undefined symbol: Rf_allocVector        (./lapack.so)
undefined symbol: R_CHAR        (./lapack.so)
undefined symbol: Rf_unprotect_ptr      (./lapack.so)
undefined symbol: SET_VECTOR_ELT        (./lapack.so)
undefined symbol: Rf_isMatrix   (./lapack.so)
undefined symbol: R_setLapackRoutines   (./lapack.so)
undefined symbol: Rf_protect    (./lapack.so)
undefined symbol: VECTOR_ELT    (./lapack.so)
undefined symbol: Rf_asLogical  (./lapack.so)
undefined symbol: COMPLEX       (./lapack.so)
undefined symbol: Rf_unprotect  (./lapack.so)
undefined symbol: REAL  (./lapack.so)
undefined symbol: INTEGER       (./lapack.so)
undefined symbol: Rf_error      (./lapack.so)
undefined symbol: Rf_setAttrib  (./lapack.so)
undefined symbol: Rf_getAttrib  (./lapack.so)
undefined symbol: lsame_        (./lapack.so)

Looks like all the libraries it needs are there, but why can't it find those
undefined symbols?

Any help is greatly appreciated!

Regards,
Andy

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On Thu, 17 Jan 2002, Liaw, Andy wrote:
> Prof. Ripley,
>
> > From: Prof Brian Ripley [mailto:ripley@stats.ox.ac.uk]
>
> [snipped...]
>
> > R cannot currently make use of anyone else's LAPACK routines
(because
> > we've found too many problems with them).
> >
> > If you are getting no useful diagnostics, try
> > dyn.load("RHOME/modules/lapack.so").  That ought to tell you
> > why you can't
> > load it.  My guess would be to do with libraries, so do an ldd on
> > lapack.so and check that all the dependencies are resolved as
> > you expect.
>
> I wonder if the problem is the clash between the Lapack routines in MKL and
> those packaged with R.
> Sorry, but seems like I need a bit more spoon-feeding:
> I did the dyn.load, and got:
>         unable to load shared library
> "/home/andy/R-patched-mkl/modules/lapack.so":
>   /home/andy/R-patched-mkl/modules/lapack.so: undefined symbol: lsame_
Right, that's it.  LSAME is a BLAS routine, and your BLAS doesn't have
it.  There is a version in src/appl/blas.f, but you don't seem to
have a complete BLAS to link against.

If you really have a complete LAPACK3 (which I would not bet on)
you can try building in src/modules/lapack omitting double.f and
complex.f: you will need to rename a few entry points in Lapack.h
as they have already been changed to avoid conflicts with sunperf
(I think).  See also the comments in the README there.

[....]
> Looks like all the libraries it needs are there, but why can't it find
those
> undefined symbols?
They are in R.bin itself.


-- 
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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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