Displaying 20 results from an estimated 1000 matches similar to: "2.9.0 and make check errors | mystery deepens"
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
2009 Jun 26
0
ready to toss the towel | lapack and 2.9.0
Well, I've now tried just about every permutation I can think of -
including using the ATLAS lapack (instead of generic), in various
combinations with ACML, or generic BLAS, or ATLAS blas. No matter what I
do, so long as I have lapack of any flavour, I get the 'stats error'
with make check. And, it always seems to throw the error at the same
point in the stats test file (an svd in
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
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,
2009 Jun 25
1
check stats fail | part III
For grins, tried rebuilding R 2.9.0 without using ACML 4.3.0. Config
goes fine, make runs without any errors.
make check - and - ta-dah! - no errors for stats. Everything seems to
check out just fine.
So, it seems as if R 2.9.0, ACML 4.3.0, and perhaps one/more things
under CentOS don't play nice.
Will trying unloading 4.3.0, installing 4.2.0 (which worked before on
the Fedora box), and
2008 Jun 13
2
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,
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
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 Nov 30
1
about cancor.R
Hello,
I'm a beginning user of R, now I have a question about canonical correlation analysis (cca).
In R,there is a function "cancor.R" used for cca; For example X(n*p1) and Y(n*p2)are the two matrix to be analyzed. In the example given by R, when n> max(p1,n2), cancor(X,Y) works; but when n<p1 or n<p2, cancor(X,Y) doesn't work well because cancor$cor == 1; how to cope
2013 Jan 29
3
how to suppress the intercept in an lm()-like formula method?
I'm trying to write a formula method for canonical correlation analysis,
that could be called similarly to lm() for
a multivariate response:
cancor(cbind(y1,y2,y3) ~ x1+x2+x3+x4, data=, ...)
or perhaps more naturally,
cancor(cbind(y1,y2,y3) ~ cbind(x1,x2,x3,x4), data=, ...)
I've adapted the code from lm() to my case, but in this situation, it
doesn't make sense to
include an
2005 Dec 01
0
tuned BLAS
I've been updating the information on tuned BLAS for R-admin in R-patched
and R-devel. We have
ATLAS (widely available, including for Windows)
MKL (licensed on ix86 and x86_64 Linux and Windows)
ACML (by AMD, but for all ix86 and x86_64 chips, Linux and Windows.
Now available for gfortran.)
Goto (academic use only, only some chips, only Linux)
MKL and ACML provide full LAPACK,
2003 Apr 22
4
"LAPACK routine DGESDD gave error code -12" with Debian (PR#2822)
Dear All,
Under Debian GNU/Linux La.svd (with method = "dgesdd") sometimes gives the
error
"Error in La.svd(data, nu = 0, nv = min(nrow, ncol), method = "dgesdd") :
LAPACK routine DGESDD gave error code -12"
It seems not to depend on the data per se, but on the relationship between
numbers of rows and columns.
For example, if the number of columns is 100,
2007 Mar 29
1
Using functions in LAPACK in a C program
Hi,
I wonder where I can find an example of using a function in LAPACK library in a user's own C code. I wrote a C program which will be compiled and linked to produce a DLL file and then loaded into R. I hope to use a function from LAPACK library, for example, dgesdd, in the program. Following R manual, I call the function by F77_CALL(dgesdd) in the program. The program can be compiled
2012 May 03
0
error in La.svd Lapack routine 'dgesdd'
Dear Philipp,
this is just a tentative answer because debugging is really not possible
without a reproducible example (or, at a very bare minimum, the output
from traceback()).
Anyway, thank you for reporting this interesting numerical issue; I'll
try to replicate some similar behaviour on a similarly dimensioned
artificial dataset when I have some time (which might not be soon). As
for now,
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
2004 Sep 11
4
Cancor
Dear R's!
I am strugling with cancor procedure in R. I cannot figure out the
meaning of xcoef and of yxcoef.
Are these:
1. standardized coefficients
2. structural coefficients
3. something else?
I have tried to simulate canonical correlation analysis by checking the
eigenstructure of the expression:
Sigma_xx %*% Sigma_xy %*% Sigma_yy %*% t(Sigma_xy).
The resulting eigenvalues were the same
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
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
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
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