[gmx-users] Compile-time errors with MKL

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 14 03:52:52 CEST 2010

On 13/07/2010 11:28 PM, Elton Carvalho wrote:
> On Mon, Jul 12, 2010 at 9:29 PM, Mark Abraham<mark.abraham at anu.edu.au>  wrote:
>> On 13/07/10 08:20, Elton Carvalho wrote:
>>> and edit line 26576 of ./config to read
>>> LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core $LIBS"
>>> instead of
>>> LIBS="-lmkl $LIBS",
>> That seems like asking for trouble. Why not set the LIBS environment
>> variable properly before calling configure?
> Because using "-lmkl" returns an error like "-lmkl not found", so, to
> remove "-lmkl" from the configure I need to edit the line. That is
> what earlier posts in this list (which the FAQ points to) recommends.
I would object to the form of that solution too.

./configure --with-fft=mkl LIBS="-L${MKL}/lib/em64t -lmkl_lapack 
-lmkl_core -lmkl_em64t -lguide -lpthread" works for me, but you need the 
right libs in the right order for your system. Clearly this kind of 
solution works, is much less error-prone than editing configure output 
by hand (which you'll never remember you did!), and gets documented in 
the top of config.log.
>> You need to provide the support libraries in the right order. The MKL docs
>> for your platform should make the correct order clear.
>> Otherwise, since there's a nearly insignificant advantage to icc+mkl over
>> gcc+FFTW3, use the latter.
> Thanks, I'll check the MKL docs, then (i have no idea why I haven't
> done this yet). If all else fails, I'll go through icc + FFTW3.
> Are there still problems with gcc 4.x?

gcc 4.1.x is still thought to have problems in some cases. Other gcc4 
are generally fine.


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