Displaying 20 results from an estimated 11000 matches similar to: "compiling 2.7.0 GNU/Linux | BLAS & Lapack query"
2009 Jun 26
1
can't use ATLAS or ACML | 2.9.0
So, tried again from scratch. Again, CentOS 5.3, which is essentially
RHEL 5.3.
./configure --with-blas="-L/opt/acml4.3.0/gfortran64/lib -lacml"
In config.log, get things like
configure:37199: checking for dgemm_ in -L/opt/acml4.3.0/gfortran64/lib
-lacml
configure:37230: gcc -std=gnu99 -o conftest -g -O2
-I/usr/local/include -L/usr/local/lib64 conftest.c
2009 Jun 26
1
problems compiling for RHEL 5.3 x86_64
Well, CentOS 5.3, which amounts to the same thing.
I recently decided to upgrade my main research machine from Fedora Core
8 -> CentOS 5.3. Basically, I was looking to move to a distro with
longer 'term-of-life' than the release schedule for Fedora currently
allows. The machine is a multi-Opteron box, so both 32- and 64-bit apps
natively supported. Since I do a lot of 'linear
2006 Oct 16
3
x86_64, acml-3.5.0-gfortran64 and lme4
I am encountering segfaults when checking the lme4 package on an
Athlon64 system if I use the acml blas. R was built as a 64-bit
application using the GCC 4.0.3 compiler suite including gfortran.
The version of acml is 3.5.0 gfortran64.
I do not encounter the segfaults when I compile R with R's built-in
BLAS. The errors occur in the first example in lme4 in a call to
lmer. It looks like
2005 Dec 14
1
Building R-devel with ACML
I'm trying to build R-devel with AMD's ACML. I downloaded version 3.0.0
64bit for gfortran (acml-3-0-0-gfortran-64bit.tgz) and copied the
libraries to /usr/local/lib. When I configure R to build against the
ACML library, how do I know if the library has been detected and will be
used?
I run 'configure' with the '--with-blas=-lacml' flag and am using gcc
4.0.2 (with
2007 Aug 24
2
config error during 2.5.1 compile
Have been running 2.5.1 on my multi-pro Opteron box running Fedora Core
5 with no problems. Had compiled previously with no problems. However,
for a variety of reasons (mostly due to ACML upgrade), I tried a
recompile using the following sequence of commands (note I'm compiling
in ACML support for blas):
LD_LIBRARY_PATH=/opt/acml3.6.1/gfortran64/lib
export LD_LIBRARY_PATH
./configure
2009 Jun 26
0
proper link to ACML blas | compiling 2.9.0
Normally, I do the following to configure R for compilation on my
Opteron box with ACML installed:
./configure --with-tcltk --with-blas="-L/opt/acml4.3.0/gfortran64/lib
-lacml"
However, when I do so, and look at Makeconf, I see
BLAS_LIBS = -lblas
I thought I would see
BLAS_LIBS = -L/opt/acml4.3.0/gfortran64/lib -lacml
Why isn't Makeconf picking up the right BLAS_LIBS (or is
2004 Mar 25
1
yet another fast BLAS (from AMD this time)
Dear R-devel,
Has anyone played with this?
http://www.amd.com/us-en/Processors/DevelopWithAMD/0,,30_2252_2282,00.html
<http://www.amd.com/us-en/Processors/DevelopWithAMD/0,,30_2252_2282,00.html>
.
I'll probably give it a shot...
Best,
Andy
Andy Liaw, PhD
Biometrics Research PO Box 2000, RY33-300
Merck Research Labs Rahway, NJ 07065
mailto:andy_liaw@merck.com
2004 Oct 19
1
lapack test failed (PR#7294)
Hallo,
I've just installed R on our Opteron System (AMD Opteron 246). Running make check-all
results in a failure during the lapack test:
> ## ------- tests of random real and complex matrices ------
>
> ## 100 may cause failures here.
> eigenok <- function(A, E, Eps=1000*.Machine$double.eps)
+ {
+ V <- E$vect; lam <- E$values
+
2010 May 28
2
Compiling R-2.11.0 with ATLAS-tuned BLAS and LAPACK
Hello. I am a Linux neophyte and know almost nothing ?about compiling,
so I would appreciate any help and advice y'all would care to offer.
I am trying to compile the 64 bit version of R using a tuned ATLAS and
LAPACK (ATLAS 3.9.24). I am running Ubunto 10.04 LTS (through wubi,
FWIW). The ATLAS and LAPACK files (atlas.so, f77blas.so, lapack.so,
and cblas.so) are sitting in the folder
2006 Jul 22
1
compile R with ACML support | RHEL 4
Greetings -
I'm trying to compile R under GNU/Linux (RHEL 4) on a multi-Opteron box,
with ACML support.
First, I downloaded and installed ACML 3.5 - GNU version, although I'm
not entirely sure what the differences are - from the AMD website. The
ACML libraries were installed to /opt/acml3.5.0/
Second, I ran ./configure --with-blas='-lacml'
The configure went fine,
2006 Sep 28
1
unable to load lapack.so
Hi,
I'm having problems using ACML with R. I made two changes in
config.site by setting
LDFLAGS="-L/opt/acml3.1.0/gnu64/lib"
BLAS_LIBS="-lacml"
./config and make go through but when I try to use the lm() function,
I get the error message
Error in chol2inv(Qr$qr[p1, p1, drop = FALSE]) :
lapack routines cannot be loaded
In addition: Warning message:
unable to load
2018 Jan 04
2
Fixed BLAS tests for external BLAS library
Hi Tomas,
Thanks for your reply.
I find your response curious, however. Surely the identical() test is
simply incorrect when catering for possibly different BLAS
implementations? Or is it the case that conformant BLAS implementations
all produce bit-identical results, which seems unlikely? (Sorry, I am
unfamiliar with the BLAS spec.) Although whatever the answer to this
theoretical question,
2006 Jul 24
1
R and ACML
While I recently received some very helpful files and email from Kevin
Hendricks for compiling with ATLAS, thought I'd first have a stab at
ACML. Having problems, which I suspect are trivial to solve:
1. machine is running RHEL 4, meaning, it uses gcc 3.4.5 out of the box,
and g77. In my experience, over-riding RHEL's choice, and manually
upgrading to gcc 4.x.x (and, as a consequence
2009 Apr 30
1
[Fwd: problems installing rjags | tcltk]
Quick followup. Confirmed that TCl/Tk are both installed on the machine
(they are, in both 32- and 64-bit flavours), as are all tcl and
tk-related libs, devel packages, and about everything else I could find.
It occurred to me that perhaps the R I compiled isn't 'tcltk' aware. I
checked the config.log, and there is some hint that this might be the
case. Just before ## File
2006 Jul 23
1
compiling R | multi-Opteron | BLAS source
Greetings -
A quick perusal of some of the posts to this maillist suggest the level
of the questions is probably beyond someone working at my level, but at
the risk of looking foolish publicly (something I find I get
increasingly comfortable with as I get older), here goes:
My research group recently purchased a multi-Opteron system (bunch of
880 chips), running 64-bit RHEL 4 (which we have
2005 Sep 06
1
Build R with AMD pgi compiled ACML library
Hi,
Has anyone had any luck in using portland group compiler to build
R(-devel) with AMD's pgi compiled ACML library? I've downloaded the
packages and set LD_LIBRARY_PATH, and run configuration script as follow:
% ./configure --prefix=/usr/local/R.pgcc --with-blas='-lacml'
However, it failed to pick up double complex BLAS,
checking for sgemm_ in -lacml... yes
checking
2018 Jan 05
1
Fixed BLAS tests for external BLAS library
>>>>> Tomas Kalibera <tomas.kalibera at gmail.com>
>>>>> on Fri, 5 Jan 2018 00:41:47 +0100 writes:
> In practical terms, failing tests are not preventing anyone from using
> an optimized BLAS/LAPACK implementation they trust. Building R with
> dynamically linked BLAS on Unix is supported, documented and easy for
> anyone who
2010 Aug 24
1
Trouble configuring R to use ACML
I am trying to get R to use the ACML BLAS, specifically the 'mp' version for
multithreading.
I have installed acml-4-4-0-gfortran-64bit
I added /opt/acml4.4.0/gfortran64_mp/lib to $LD_LIBRARY_PATH.
I ran: sudo ./configure --with-blas="-L/opt/acml4.4.0/gfortran64_mp/lib
-lacml_mp"
At the end of the configuration, the only external library listed is
readline, and at the end
2002 Dec 26
3
BLAS/Lapack on OS X
R-devel has the --with-lapack flag for configure. If you build R with
--with-blas="-framework vecLib" --with-lapack="--framework vecLib"
then the build goes through, using the native optimized BLAS and
Lapack in /System/Library/Frameworks/vecLib.framework. Also, it
works, in the sense that it does eigenvalue problems correctly.
I don't have any timings yet, because I
2007 Sep 11
2
building with atlas version of blas and lapack
I'd like to build R using my optimized blas and lapack libraries. It seems
know matter what I do, the configure script uses the blas supplied with the
source. My blas and lapack libraries are in /usr/local/atlas/lib. How can I
get configure to use these?
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