MKL seems to beat ATLAS, but some problems... (was RE: [R] li nkin g R against MKL)

[Liaw, Andy]

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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