Building with MKL on Ubuntu
And how does that help you? At some future point on a real problem you will get incorrect answers/segfault. That test was put there as a result of such incorrect results found the hard way.
On Wed, 5 Nov 2008, Anand Patil wrote:
Scratch that- finally got it working! The steps were:
- Change configure to 'break the thermometer' as suggested:
===================================================================
--- configure ? (revision 46843)
+++ configure ? (working copy)
@@ -37473,6 +37473,8 @@
?
?fi
?
+r_cv_zdotu_is_usable=yes
+
?? rm -rf conftest conftest.* conftestf.* core
?? if test -n "${r_cv_zdotu_is_usable}"; then
?? ? { echo "$as_me:$LINENO: result: yes" >&5
- Set environment variables:
CFLAGS=-pthread -O3
FC=gfortran -pthread
FFLAGS=-pthread
CXXFLAGS=-O3 -pthread
FCLAGS=-pthread
LDFLAGS=-lpthread
- Configure command:
./configure --with-blas='-L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl -lguide
-lpthread' --enable-R-shlib
I owe you all a beer!
Anand
On Wed, Nov 5, 2008 at 9:10 PM, Anand Patil
<anand.prabhakar.patil at gmail.com> wrote:
Thanks for your help, everyone. I was using gcc previously, but
building with the Intel compilers causes its own problems:
/opt/intel/cce/10.1.018/lib/libguide.so: undefined reference to
`pthread_atfork'
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/working_copies/R/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/working_copies/R/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/working_copies/R/src'
make: *** [R] Error 1
If your experience with MKL has been negative, I've definitely had
enough; I'll try my luck with gcc and GotoBLAS.?
Cheers,
Anand
On Wed, Nov 5, 2008 at 9:02 PM, <plummer at iarc.fr> wrote:
Quoting Peter Dalgaard <P.Dalgaard at biostat.ku.dk>:
> Anand Patil wrote:
> > On Wed, Nov 5, 2008 at 5:59 PM, Martyn Plummer
<plummer at iarc.fr> wrote:
> >
> >> It looks like the em64t version of MKL fails the test
for the accuracy
> >> of zdotu ("checking whether double complex BLAS can
be used") and is
> >> therefore dropped in favour of R's built-in BLAS. ?I
have just tested
> >> this on Fedora and get the same result.
> >>
> >> The 32-bit MKL does work for me.
> >>
> >> Martyn
> >>
> >
> > Many thanks, Martyn. The 64-bit index space is
important to me, will I lose
> > it if I link against the 32-bit MKL? Also, should I
file a bug report with
> > Intel?
> > Anand
>
> There's also the option of "breaking the thermometer".
You might examine
> that check and decide whether the loss of accuracy is
enough for you to
> worry about and if not, take out the test from
configure.
>
> Apparently, this check was put in place in R-2.2.0
>
> ? ? o Any external BLAS found is now tested to see if
the complex
> ? ? ? ? routine zdotu works correctly: this provides a
compatibility
> ? ? ? ? test of compiler return conventions.
>
> which suggests that the expected failure is
catastrophic, and looking at
> the code, there's a fuzz of 1e-10 which would seem to be
about 1e5 times
> larger than required.
My apologies. I skimmed the code of the test program, but as
Brian says
it is not a question of accuracy. The test program does in fact
segfault,
although you won't see this in your config.log.
Anyway, Anand, I would just carry on with libRblas.
Martyn
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