R help - Jun 2005 - linking R to goto blas

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"

I did read the R-Admin doc and therefore I am aware of the fact that
passing "-lgoto" is supposed to be sufficient, but as a matter of fact
configuring with --with-blas="-lgoto" only ends up in a libR.so being
linked to the standard libblas.so. config.log reports in this settings
that libgoto.xxx.so is missing links to libpthread etc. Therefore, I
added the two flags "-lpthread -lm" as indicated at GOTO's website
and I
got a clean configure run. (Am I concluding correctly that I am using a
threaded version of goto blas?)

3: Running make, however, freezed when trying to build "grDevices",
without throwing any warning or error messages:

[...]
../../../../library/grDevices/libs/grDevices.so is unchanged
make[5]: Leaving directory
`/home/ssoberni/R-2.1.0/src/library/grDevices/src'
make[4]: Leaving directory
`/home/ssoberni/R-2.1.0/src/library/grDevices/src'
[freeze]

4: I then rummaged the R mailing list archives and stumbled over a
thread dating from May this year pointing to a similar issue, concerning
gcc-3.4 and broken lapack libraries provided by FC3 (see
https://stat.ethz.ch/pipermail/r-devel/2005-May/033117.html).

Following these opinions/ findings, I did the following (though I knew
that -- in principle -- R is supposed to handle this issue by passing a
--ffloat-store flag to the fortran compiler, doesn't it?):

* I wanted to remove the FC3 native lapack libraries, and to my
surprise, they were not installed at all (no liblapack.so.xxx in /usr/lib).
* I set up an older gcc environment, i.e. the last release from the
3.3.x family (3.3.6) and tried to recompile R ending up with the same
hang-up.

As a last step, I tried to exclude R's internal package explicitly by
setting --wihtout-lapack, which did not hava a visible effect on the
building process and did not provide a workaround for the hang-up.

Please, I highly appreciate any thoughts or hints as my colleagues and I
are eager to get into GOTO's universe.

//stefan

-- 

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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On Sun, 12 Jun 2005, Stefan Sobernig wrote:
> 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"
>
> I did read the R-Admin doc and therefore I am aware of the fact that
> passing "-lgoto" is supposed to be sufficient, but as a matter of
fact
Only for single-threaded versions.  For others you need 
--with-blas="-lgoto -lpthread".
> configuring with --with-blas="-lgoto" only ends up in a libR.so
being
> linked to the standard libblas.so. config.log reports in this settings
> that libgoto.xxx.so is missing links to libpthread etc. Therefore, I
> added the two flags "-lpthread -lm" as indicated at GOTO's
website and I
> got a clean configure run. (Am I concluding correctly that I am using a
> threaded version of goto blas?)
Dunno: the organization of the Goto site has changed since that section 
was written.  Looks like only multi-threaded (2 threads) versions are 
currently available.
> 3: Running make, however, freezed when trying to build
"grDevices",
> without throwing any warning or error messages:
>
> [...]
> ../../../../library/grDevices/libs/grDevices.so is unchanged
> make[5]: Leaving directory
> `/home/ssoberni/R-2.1.0/src/library/grDevices/src'
> make[4]: Leaving directory
> `/home/ssoberni/R-2.1.0/src/library/grDevices/src'
> [freeze]
>
> 4: I then rummaged the R mailing list archives and stumbled over a
> thread dating from May this year pointing to a similar issue, concerning
> gcc-3.4 and broken lapack libraries provided by FC3 (see
> https://stat.ethz.ch/pipermail/r-devel/2005-May/033117.html).
>
> Following these opinions/ findings, I did the following (though I knew
> that -- in principle -- R is supposed to handle this issue by passing a
> --ffloat-store flag to the fortran compiler, doesn't it?):
It does.  For me this works with the internal BLAS and with Goto's 
blas versions 0.96-2 and 0.99-3, on an Opteron.  (It also works on i686 
with several other BLASes.)
> * I wanted to remove the FC3 native lapack libraries, and to my
> surprise, they were not installed at all (no liblapack.so.xxx in /usr/lib).
> * I set up an older gcc environment, i.e. the last release from the
> 3.3.x family (3.3.6) and tried to recompile R ending up with the same
> hang-up.
They are not used unless you explicitly asked for them.
> As a last step, I tried to exclude R's internal package explicitly by
> setting --wihtout-lapack, which did not hava a visible effect on the
> building process and did not provide a workaround for the hang-up.
Assuming that is a typo for --without-lapack, it does nothing (it is the 
default and excludes an external LAPACK).
> Please, I highly appreciate any thoughts or hints as my colleagues and I
> are eager to get into GOTO's universe.
First get a version with the internal BLAS working.  That will rule out
any issues about LAPACK.  Then change the BLAS: it looks as if this might 
be a problem with the particular Goto BLAS.

Please note: the R-devel list would be a much better choice for such 
issues -- see the posting guide.

-- 
Brian D. Ripley,                  ripley at 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

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...

-- 
   O__  ---- Peter Dalgaard             ??ster Farimagsgade 5, Entr.B
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