[gmx-users] Intel compiling failed

[Carsten Kutzner]

On Apr 5, 2013, at 12:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 4/5/13 6:38 AM, Carsten Kutzner wrote:
>> Hi Albert,
>> 
>> one reason for the error you see could be that you are using a non-Intel
>> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
>> 
> 
> Is there any point in compiling FFTW in parallel?  I have never once done it nor found it necessary.
Hi,

you are absolutely right, sorry I did not express that clearly. The thing is, if you
compile the FFTW using the Intel compiler and then compile Gromacs using Intels
mpicc or mpigcc compiler wrapper, you will get these undefined references to _intel*
at link time. To make it work, you need to use the mpiicc (two i's here) compiler wrapper
for Gromacs.

Carsten

> 
> -Justin
> 
>> On Apr 5, 2013, at 12:25 PM, Albert <mailmd2011 at gmail.com> wrote:
>> 
>>> Hello:
>>> 
>>> I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command:
>>> 
>>> 
>>> ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort
>>> 
>>> here is the log file:
>>> 
>>> mp.c:(.text+0x3148): undefined reference to `_intel_fast_memset'
>>> ../libbench2/libbench2.a(mp.o):mp.c:(.text+0x3488): more undefined references to `_intel_fast_memset' follow
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [mpi-bench] Error 1
>>> make[3]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
>>> make[2]: *** [all] Error 2
>>> make[2]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3/mpi'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory `/home/albert/install/00-source/fftw-3.3.3'
>>> 
>>> 
>>> make: *** [all] Error 2
>>> 
>>> thank you very much
>>> best
>>> Albert
>>> --
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>> 
>> 
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>> 
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa