R devel - Jun 2008 - compiling 2.7.0 GNU/Linux | BLAS & Lapack query

Greetings -

For a host of reasons I chose (was forced) to upgrade my multi-Opteron box
from Fedora 7 -> Fedora 8. In the process, I also updated the ACML I had
installed from 4.0.0 to 4.1.0.

While I get no errors (that I can find) in the config -> make -> make
install sequence, I'm pretty sure (based on some benchmarks) that I'm
not
getting BLAS and/or Lapack to compile in. So, either something has changed
from 2.6.2 -> 2.7.0, or something has changed from Fedora 7 -> Fedora 8,
or
both.

Here is the sequence I follow to do the config (which seemed to work
perfectly before - note: using bash shell):

1. LD_LIBRARY_PATH=/opt/acml4.1.0/gfortran64/lib

2. export LD_LIBRARY_PATH

3. ./configure --with-lapack="-L/usr/lib64"
--with-blas="L/opt/acml4.1.0/gfortran64/lib -lacml"


However, when I try this, at the end of the config script I'm told

Interfaces supported:      X11
External libraries:           readline
Additional capabilites:   PNG, JPEG, iconv, MBCS, NLS, cairo
Options enabled:           shared BLAS, R profiling, Java


I'm pretty sure that readline being the only external library being reported
is diagnostic of some sort of issue - normally, I'm given information about
lapack, and generic BLAS being linked. But, no more.

Suggestions? Points to the obvious? Both ACML and Lapack are where they
should be, so I'm quite frankly puzzled as to what is going on.


Thanks very much in advance.

	[[alternative HTML version deleted]]

Evan,

It might depend on the way ACML has been compiled by the AMD people. Your
version of gcc/gfortran might be incompatible with ACML 4.1.0.
This is known to users and is causing  problems. You can see it reported in
the ACML forum here (it applies to 4.0.1 but I think the problems have not
been solved)

http://forums.amd.com/devforum/messageview.cfm?catid=217&threadid=90399&enterthread=y

Here I report a part of a post of that thread

Begin quote:

"The gfortran ACML libraries are currently built with two different
GCC/GFORTRAN compilers.

The SINGLE THREADED libraries found in /opt/gfortran64 and
/opt/gfortran64_int64 are built with 4.1.2. This compiler version is used
because it is the most widely supported compiler with most new linux
distributions (or was in 2007).

The OpenMP MULTI THREADED libraries found in /opt/gfortran64_mp and
/opt/gfortran64_mp_int64 are built with 4.2.0. This compiler is used because
it was finally released in 2007 and 4.1.2 does not natively support OpenMP.

This is mentioned in the release notes, but it's obvious not very clear.

When using GCC/GFORTRAN 4.3, you will likely need to use the mp versions of
the library. This has not been tested by AMD. When 4.3 releases, AMD may
provide a 4.3 build.

This issue happens because of the incompatibility between GCC 4.1.2 and 4.2.
Now that more distributions are supplying GCC 4.2 AMD may only support GCC
4.2 for 2008 releases. In other words, no more 4.1.2 builds. Both single-
and multi-threaded libraries would be built with 4.2. "
end quote

Se also subsequent replies.
Maybe you should try first to see  whether the ACML work at all on your
system apart from R.
Hope this helps

Ciao

Simone


On Fri, Jun 13, 2008 at 5:03 PM, evan cooch <forum.query@gmail.com> wrote:
> Greetings -
>
> For a host of reasons I chose (was forced) to upgrade my multi-Opteron box
> from Fedora 7 -> Fedora 8. In the process, I also updated the ACML I had
> installed from 4.0.0 to 4.1.0.
>
> While I get no errors (that I can find) in the config -> make -> make
> install sequence, I'm pretty sure (based on some benchmarks) that
I'm not
> getting BLAS and/or Lapack to compile in. So, either something has changed
> from 2.6.2 -> 2.7.0, or something has changed from Fedora 7 -> Fedora
8, or
> both.
>
> Here is the sequence I follow to do the config (which seemed to work
> perfectly before - note: using bash shell):
>
> 1. LD_LIBRARY_PATH=/opt/acml4.1.0/gfortran64/lib
>
> 2. export LD_LIBRARY_PATH
>
> 3. ./configure --with-lapack="-L/usr/lib64"
> --with-blas="L/opt/acml4.1.0/gfortran64/lib -lacml"
>
>
> However, when I try this, at the end of the config script I'm told
>
> Interfaces supported:      X11
> External libraries:           readline
> Additional capabilites:   PNG, JPEG, iconv, MBCS, NLS, cairo
> Options enabled:           shared BLAS, R profiling, Java
>
>
> I'm pretty sure that readline being the only external library being
> reported
> is diagnostic of some sort of issue - normally, I'm given information
about
> lapack, and generic BLAS being linked. But, no more.
>
> Suggestions? Points to the obvious? Both ACML and Lapack are where they
> should be, so I'm quite frankly puzzled as to what is going on.
>
>
> Thanks very much in advance.
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
______________________________________________________

Simone Giannerini
Dipartimento di Scienze Statistiche "Paolo Fortunati"
Universita' di Bologna
Via delle belle arti 41 - 40126 Bologna, ITALY
Tel: +39 051 2098262 Fax: +39 051 232153
http://www2.stat.unibo.it/giannerini/
______________________________________________________

	[[alternative HTML version deleted]]

You need to look in config.log to see what happened.

But note what 'R Installation and Administration' says about

   See @pxref{Shared BLAS} for an alternative (and in many ways preferable)
   way to use ACML.


On Fri, 13 Jun 2008, evan cooch wrote:
> Greetings -
>
> For a host of reasons I chose (was forced) to upgrade my multi-Opteron box
> from Fedora 7 -> Fedora 8. In the process, I also updated the ACML I had
> installed from 4.0.0 to 4.1.0.
>
> While I get no errors (that I can find) in the config -> make -> make
> install sequence, I'm pretty sure (based on some benchmarks) that
I'm not
> getting BLAS and/or Lapack to compile in. So, either something has changed
> from 2.6.2 -> 2.7.0, or something has changed from Fedora 7 -> Fedora
8, or
> both.
>
> Here is the sequence I follow to do the config (which seemed to work
> perfectly before - note: using bash shell):
>
> 1. LD_LIBRARY_PATH=/opt/acml4.1.0/gfortran64/lib
>
> 2. export LD_LIBRARY_PATH
>
> 3. ./configure --with-lapack="-L/usr/lib64"
> --with-blas="L/opt/acml4.1.0/gfortran64/lib -lacml"
>
>
> However, when I try this, at the end of the config script I'm told
>
> Interfaces supported:      X11
> External libraries:           readline
> Additional capabilites:   PNG, JPEG, iconv, MBCS, NLS, cairo
> Options enabled:           shared BLAS, R profiling, Java
>
>
> I'm pretty sure that readline being the only external library being
reported
> is diagnostic of some sort of issue - normally, I'm given information
about
> lapack, and generic BLAS being linked. But, no more.
>
> Suggestions? Points to the obvious? Both ACML and Lapack are where they
> should be, so I'm quite frankly puzzled as to what is going on.
>
>
> Thanks very much in advance.
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
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