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@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@iarc.fr> wrote:
>
>> Quoting Peter Dalgaard <P.Dalgaard@biostat.ku.dk>:
>>
>> > Anand Patil wrote:
>> > > On Wed, Nov 5, 2008 at 5:59 PM, Martyn Plummer <plummer@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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